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tmpdir not reassigning in fastqc in rule_fastqc #424

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benyoung93 opened this issue Nov 8, 2023 · 8 comments
Closed

tmpdir not reassigning in fastqc in rule_fastqc #424

benyoung93 opened this issue Nov 8, 2023 · 8 comments
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@Ulthran
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bug

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@benyoung93
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Describe the bug
The /tmp ion our cluster is only 2Gb (8Gb if on a login node). As such I have export TMPDIR=/rc_scratch/beyo2625/temp_space (10Tb space on my scratch) which has fixed the majority of crashes from no space being avaliable on the /tmp. Unfortunately, when running rule_fastqc I can successfully get the main submission script to route to my scratch space, but then within the fastqc it is still routing to the /tmp and thus crashing (see the log below). Is there anyway to get fastqc in the rule to redirect to the scratch space as well?

I know there is probably a simple way to do this, but I am coming up blank at the moment.

I also get I could keep the snakemake running as the fastqc is not really required for anything else, only the reports, but it would be nice to have them all for my files :).

Output/logs/screenshots

Found extension sbx_annotation in folder sbx_assembly
Found extension sbx_assembly in folder sbx_assembly
Found extension sbx_coverage in folder sbx_assembly
Found extension sbx_kraken in folder sbx_kraken
Collecting host/contaminant genomes... done.
Building DAG of jobs...
Your conda installation is not configured to use strict channel priorities. This is however crucial for having robust and correct environments (for details, see https://conda-forge.org/docs/user/tipsandtricks.html). Please consider to configure strict priorities by executing 'conda config --set channel_priority strict'.
Using shell: /bin/bash
Provided cores: 40
Rules claiming more threads will be scaled down.
Provided resources: mem_mb=50000, mem_mib=47684, disk_mb=50000, disk_mib=47684, nodes=1, ntasks=10
Select jobs to execute...

[Wed Nov  8 08:02:21 2023]
rule fastqc:
    input: /rc_scratch/beyo2625/sunbeam/sunbeam_output/qc/02_trimmomatic/P25_1.fastq.gz, /rc_scratch/beyo2625/sunbeam/sunbeam_output/qc/02_trimmomatic/P25_2.fastq.gz
    output: /rc_scratch/beyo2625/sunbeam/sunbeam_output/qc/reports/P25_1_fastqc/fastqc_data.txt, /rc_scratch/beyo2625/sunbeam/sunbeam_output/qc/reports/P25_2_fastqc/fastqc_data.txt
    log: /rc_scratch/beyo2625/sunbeam/sunbeam_output/logs/fastqc_P25.log
    jobid: 0
    benchmark: /rc_scratch/beyo2625/sunbeam/sunbeam_output/benchmarks/fastqc_P25.tsv
    reason: Forced execution
    wildcards: sample=P25
    resources: mem_mb=50000, mem_mib=47684, disk_mb=50000, disk_mib=47684, tmpdir=/rc_scratch/beyo2625/temp_space, runtime=200, nodes=1, ntasks=10

Activating conda environment: ../../../projects/beyo2625/programs/sunbeam4.0.0/.snakemake/e972c15c96b9e03c5f212c45f1887dc5_
application/gzip
application/gzip
Started analysis of P25_1.fastq.gz
Approx 5% complete for P25_1.fastq.gz
Approx 10% complete for P25_1.fastq.gz
Approx 15% complete for P25_1.fastq.gz
Approx 20% complete for P25_1.fastq.gz
Approx 25% complete for P25_1.fastq.gz
Approx 30% complete for P25_1.fastq.gz
Approx 35% complete for P25_1.fastq.gz
Approx 40% complete for P25_1.fastq.gz
Approx 45% complete for P25_1.fastq.gz
Approx 50% complete for P25_1.fastq.gz
Approx 55% complete for P25_1.fastq.gz
Approx 60% complete for P25_1.fastq.gz
Approx 65% complete for P25_1.fastq.gz
Approx 70% complete for P25_1.fastq.gz
Approx 75% complete for P25_1.fastq.gz
Approx 80% complete for P25_1.fastq.gz
Approx 85% complete for P25_1.fastq.gz
Approx 90% complete for P25_1.fastq.gz
Approx 95% complete for P25_1.fastq.gz
Analysis complete for P25_1.fastq.gz
javax.imageio.IIOException: Can't create cache file!
	at java.desktop/javax.imageio.ImageIO.createImageInputStream(ImageIO.java:363)
	at java.desktop/javax.imageio.ImageIO.read(ImageIO.java:1411)
	at uk.ac.babraham.FastQC.Report.HTMLReportArchive.base64ForIcon(HTMLReportArchive.java:383)
	at uk.ac.babraham.FastQC.Report.HTMLReportArchive.startDocument(HTMLReportArchive.java:307)
	at uk.ac.babraham.FastQC.Report.HTMLReportArchive.<init>(HTMLReportArchive.java:84)
	at uk.ac.babraham.FastQC.Analysis.OfflineRunner.analysisComplete(OfflineRunner.java:189)
	at uk.ac.babraham.FastQC.Analysis.AnalysisRunner.run(AnalysisRunner.java:123)
	at java.base/java.lang.Thread.run(Thread.java:833)
Caused by: java.nio.file.FileSystemException: /tmp/imageio16494143062226574812.tmp: No space left on device
	at java.base/sun.nio.fs.UnixException.translateToIOException(UnixException.java:100)
	at java.base/sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:106)
	at java.base/sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:111)
	at java.base/sun.nio.fs.UnixFileSystemProvider.newByteChannel(UnixFileSystemProvider.java:218)
	at java.base/java.nio.file.Files.newByteChannel(Files.java:380)
	at java.base/java.nio.file.Files.createFile(Files.java:658)
	at java.base/java.nio.file.TempFileHelper.create(TempFileHelper.java:136)
	at java.base/java.nio.file.TempFileHelper.createTempFile(TempFileHelper.java:159)
	at java.base/java.nio.file.Files.createTempFile(Files.java:923)
	at java.desktop/javax.imageio.stream.FileCacheImageInputStream.<init>(FileCacheImageInputStream.java:102)
	at java.desktop/com.sun.imageio.spi.InputStreamImageInputStreamSpi.createInputStreamInstance(InputStreamImageInputStreamSpi.java:69)
	at java.desktop/javax.imageio.ImageIO.createImageInputStream(ImageIO.java:359)
	... 7 more
javax.imageio.IIOException: Can't create cache file!
	at java.desktop/javax.imageio.ImageIO.createImageInputStream(ImageIO.java:363)
	at java.desktop/javax.imageio.ImageIO.read(ImageIO.java:1411)
	at uk.ac.babraham.FastQC.Report.HTMLReportArchive.base64ForIcon(HTMLReportArchive.java:383)
	at uk.ac.babraham.FastQC.Report.HTMLReportArchive.startDocument(HTMLReportArchive.java:351)
	at uk.ac.babraham.FastQC.Report.HTMLReportArchive.<init>(HTMLReportArchive.java:84)
	at uk.ac.babraham.FastQC.Analysis.OfflineRunner.analysisComplete(OfflineRunner.java:189)
	at uk.ac.babraham.FastQC.Analysis.AnalysisRunner.run(AnalysisRunner.java:123)
	at java.base/java.lang.Thread.run(Thread.java:833)
Caused by: java.nio.file.FileSystemException: /tmp/imageio1683603687249839151.tmp: No space left on device
	at java.base/sun.nio.fs.UnixException.translateToIOException(UnixException.java:100)
	at java.base/sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:106)
	at java.base/sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:111)
	at java.base/sun.nio.fs.UnixFileSystemProvider.newByteChannel(UnixFileSystemProvider.java:218)
	at java.base/java.nio.file.Files.newByteChannel(Files.java:380)
	at java.base/java.nio.file.Files.createFile(Files.java:658)
	at java.base/java.nio.file.TempFileHelper.create(TempFileHelper.java:136)
	at java.base/java.nio.file.TempFileHelper.createTempFile(TempFileHelper.java:159)
	at java.base/java.nio.file.Files.createTempFile(Files.java:923)
	at java.desktop/javax.imageio.stream.FileCacheImageInputStream.<init>(FileCacheImageInputStream.java:102)
	at java.desktop/com.sun.imageio.spi.InputStreamImageInputStreamSpi.createInputStreamInstance(InputStreamImageInputStreamSpi.java:69)
	at java.desktop/javax.imageio.ImageIO.createImageInputStream(ImageIO.java:359)
	... 7 more
javax.imageio.IIOException: Can't create cache file!
	at java.desktop/javax.imageio.ImageIO.createImageInputStream(ImageIO.java:363)
	at java.desktop/javax.imageio.ImageIO.read(ImageIO.java:1411)
	at uk.ac.babraham.FastQC.Report.HTMLReportArchive.base64ForIcon(HTMLReportArchive.java:383)
	at uk.ac.babraham.FastQC.Report.HTMLReportArchive.startDocument(HTMLReportArchive.java:351)
	at uk.ac.babraham.FastQC.Report.HTMLReportArchive.<init>(HTMLReportArchive.java:84)
	at uk.ac.babraham.FastQC.Analysis.OfflineRunner.analysisComplete(OfflineRunner.java:189)
	at uk.ac.babraham.FastQC.Analysis.AnalysisRunner.run(AnalysisRunner.java:123)
	at java.base/java.lang.Thread.run(Thread.java:833)
Caused by: java.nio.file.FileSystemException: /tmp/imageio718524993707708350.tmp: No space left on device
	at java.base/sun.nio.fs.UnixException.translateToIOException(UnixException.java:100)
	at java.base/sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:106)
	at java.base/sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:111)
	at java.base/sun.nio.fs.UnixFileSystemProvider.newByteChannel(UnixFileSystemProvider.java:218)
	at java.base/java.nio.file.Files.newByteChannel(Files.java:380)
	at java.base/java.nio.file.Files.createFile(Files.java:658)
	at java.base/java.nio.file.TempFileHelper.create(TempFileHelper.java:136)
	at java.base/java.nio.file.TempFileHelper.createTempFile(TempFileHelper.java:159)
	at java.base/java.nio.file.Files.createTempFile(Files.java:923)
	at java.desktop/javax.imageio.stream.FileCacheImageInputStream.<init>(FileCacheImageInputStream.java:102)
	at java.desktop/com.sun.imageio.spi.InputStreamImageInputStreamSpi.createInputStreamInstance(InputStreamImageInputStreamSpi.java:69)
	at java.desktop/javax.imageio.ImageIO.createImageInputStream(ImageIO.java:359)
	... 7 more
javax.imageio.IIOException: Can't create cache file!
	at java.desktop/javax.imageio.ImageIO.createImageInputStream(ImageIO.java:363)
	at java.desktop/javax.imageio.ImageIO.read(ImageIO.java:1411)
	at uk.ac.babraham.FastQC.Report.HTMLReportArchive.base64ForIcon(HTMLReportArchive.java:383)
	at uk.ac.babraham.FastQC.Report.HTMLReportArchive.startDocument(HTMLReportArchive.java:351)
	at uk.ac.babraham.FastQC.Report.HTMLReportArchive.<init>(HTMLReportArchive.java:84)
	at uk.ac.babraham.FastQC.Analysis.OfflineRunner.analysisComplete(OfflineRunner.java:189)
	at uk.ac.babraham.FastQC.Analysis.AnalysisRunner.run(AnalysisRunner.java:123)
	at java.base/java.lang.Thread.run(Thread.java:833)
Caused by: java.nio.file.FileSystemException: /tmp/imageio2538243578795743500.tmp: No space left on device
	at java.base/sun.nio.fs.UnixException.translateToIOException(UnixException.java:100)
	at java.base/sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:106)
	at java.base/sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:111)
	at java.base/sun.nio.fs.UnixFileSystemProvider.newByteChannel(UnixFileSystemProvider.java:218)
	at java.base/java.nio.file.Files.newByteChannel(Files.java:380)
	at java.base/java.nio.file.Files.createFile(Files.java:658)
	at java.base/java.nio.file.TempFileHelper.create(TempFileHelper.java:136)
	at java.base/java.nio.file.TempFileHelper.createTempFile(TempFileHelper.java:159)
	at java.base/java.nio.file.Files.createTempFile(Files.java:923)
	at java.desktop/javax.imageio.stream.FileCacheImageInputStream.<init>(FileCacheImageInputStream.java:102)
	at java.desktop/com.sun.imageio.spi.InputStreamImageInputStreamSpi.createInputStreamInstance(InputStreamImageInputStreamSpi.java:69)
	at java.desktop/javax.imageio.ImageIO.createImageInputStream(ImageIO.java:359)
	... 7 more
javax.imageio.IIOException: Can't create cache file!
	at java.desktop/javax.imageio.ImageIO.createImageInputStream(ImageIO.java:363)
	at java.desktop/javax.imageio.ImageIO.read(ImageIO.java:1411)
	at uk.ac.babraham.FastQC.Report.HTMLReportArchive.base64ForIcon(HTMLReportArchive.java:383)
	at uk.ac.babraham.FastQC.Report.HTMLReportArchive.startDocument(HTMLReportArchive.java:351)
	at uk.ac.babraham.FastQC.Report.HTMLReportArchive.<init>(HTMLReportArchive.java:84)
	at uk.ac.babraham.FastQC.Analysis.OfflineRunner.analysisComplete(OfflineRunner.java:189)
	at uk.ac.babraham.FastQC.Analysis.AnalysisRunner.run(AnalysisRunner.java:123)
	at java.base/java.lang.Thread.run(Thread.java:833)
Caused by: java.nio.file.FileSystemException: /tmp/imageio2822899787946026586.tmp: No space left on device
	at java.base/sun.nio.fs.UnixException.translateToIOException(UnixException.java:100)
	at java.base/sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:106)
	at java.base/sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:111)
	at java.base/sun.nio.fs.UnixFileSystemProvider.newByteChannel(UnixFileSystemProvider.java:218)
	at java.base/java.nio.file.Files.newByteChannel(Files.java:380)
	at java.base/java.nio.file.Files.createFile(Files.java:658)
	at java.base/java.nio.file.TempFileHelper.create(TempFileHelper.java:136)
	at java.base/java.nio.file.TempFileHelper.createTempFile(TempFileHelper.java:159)
	at java.base/java.nio.file.Files.createTempFile(Files.java:923)
	at java.desktop/javax.imageio.stream.FileCacheImageInputStream.<init>(FileCacheImageInputStream.java:102)
	at java.desktop/com.sun.imageio.spi.InputStreamImageInputStreamSpi.createInputStreamInstance(InputStreamImageInputStreamSpi.java:69)
	at java.desktop/javax.imageio.ImageIO.createImageInputStream(ImageIO.java:359)
	... 7 more
javax.imageio.IIOException: Can't create cache file!
	at java.desktop/javax.imageio.ImageIO.createImageInputStream(ImageIO.java:363)
	at java.desktop/javax.imageio.ImageIO.read(ImageIO.java:1411)
	at uk.ac.babraham.FastQC.Report.HTMLReportArchive.base64ForIcon(HTMLReportArchive.java:383)
	at uk.ac.babraham.FastQC.Report.HTMLReportArchive.startDocument(HTMLReportArchive.java:351)
	at uk.ac.babraham.FastQC.Report.HTMLReportArchive.<init>(HTMLReportArchive.java:84)
	at uk.ac.babraham.FastQC.Analysis.OfflineRunner.analysisComplete(OfflineRunner.java:189)
	at uk.ac.babraham.FastQC.Analysis.AnalysisRunner.run(AnalysisRunner.java:123)
	at java.base/java.lang.Thread.run(Thread.java:833)
Caused by: java.nio.file.FileSystemException: /tmp/imageio7678752523632863695.tmp: No space left on device
	at java.base/sun.nio.fs.UnixException.translateToIOException(UnixException.java:100)
	at java.base/sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:106)
	at java.base/sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:111)
	at java.base/sun.nio.fs.UnixFileSystemProvider.newByteChannel(UnixFileSystemProvider.java:218)
	at java.base/java.nio.file.Files.newByteChannel(Files.java:380)
	at java.base/java.nio.file.Files.createFile(Files.java:658)
	at java.base/java.nio.file.TempFileHelper.create(TempFileHelper.java:136)
	at java.base/java.nio.file.TempFileHelper.createTempFile(TempFileHelper.java:159)
	at java.base/java.nio.file.Files.createTempFile(Files.java:923)
	at java.desktop/javax.imageio.stream.FileCacheImageInputStream.<init>(FileCacheImageInputStream.java:102)
	at java.desktop/com.sun.imageio.spi.InputStreamImageInputStreamSpi.createInputStreamInstance(InputStreamImageInputStreamSpi.java:69)
	at java.desktop/javax.imageio.ImageIO.createImageInputStream(ImageIO.java:359)
	... 7 more
javax.imageio.IIOException: Can't create cache file!
	at java.desktop/javax.imageio.ImageIO.createImageInputStream(ImageIO.java:363)
	at java.desktop/javax.imageio.ImageIO.read(ImageIO.java:1411)
	at uk.ac.babraham.FastQC.Report.HTMLReportArchive.base64ForIcon(HTMLReportArchive.java:383)
	at uk.ac.babraham.FastQC.Report.HTMLReportArchive.startDocument(HTMLReportArchive.java:351)
	at uk.ac.babraham.FastQC.Report.HTMLReportArchive.<init>(HTMLReportArchive.java:84)
	at uk.ac.babraham.FastQC.Analysis.OfflineRunner.analysisComplete(OfflineRunner.java:189)
	at uk.ac.babraham.FastQC.Analysis.AnalysisRunner.run(AnalysisRunner.java:123)
	at java.base/java.lang.Thread.run(Thread.java:833)
Caused by: java.nio.file.FileSystemException: /tmp/imageio10275866623082248172.tmp: No space left on device
	at java.base/sun.nio.fs.UnixException.translateToIOException(UnixException.java:100)
	at java.base/sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:106)
	at java.base/sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:111)
	at java.base/sun.nio.fs.UnixFileSystemProvider.newByteChannel(UnixFileSystemProvider.java:218)
	at java.base/java.nio.file.Files.newByteChannel(Files.java:380)
	at java.base/java.nio.file.Files.createFile(Files.java:658)
	at java.base/java.nio.file.TempFileHelper.create(TempFileHelper.java:136)
	at java.base/java.nio.file.TempFileHelper.createTempFile(TempFileHelper.java:159)
	at java.base/java.nio.file.Files.createTempFile(Files.java:923)
	at java.desktop/javax.imageio.stream.FileCacheImageInputStream.<init>(FileCacheImageInputStream.java:102)
	at java.desktop/com.sun.imageio.spi.InputStreamImageInputStreamSpi.createInputStreamInstance(InputStreamImageInputStreamSpi.java:69)
	at java.desktop/javax.imageio.ImageIO.createImageInputStream(ImageIO.java:359)
	... 7 more
javax.imageio.IIOException: Can't create cache file!
	at java.desktop/javax.imageio.ImageIO.createImageInputStream(ImageIO.java:363)
	at java.desktop/javax.imageio.ImageIO.read(ImageIO.java:1411)
	at uk.ac.babraham.FastQC.Report.HTMLReportArchive.base64ForIcon(HTMLReportArchive.java:383)
	at uk.ac.babraham.FastQC.Report.HTMLReportArchive.startDocument(HTMLReportArchive.java:351)
	at uk.ac.babraham.FastQC.Report.HTMLReportArchive.<init>(HTMLReportArchive.java:84)
	at uk.ac.babraham.FastQC.Analysis.OfflineRunner.analysisComplete(OfflineRunner.java:189)
	at uk.ac.babraham.FastQC.Analysis.AnalysisRunner.run(AnalysisRunner.java:123)
	at java.base/java.lang.Thread.run(Thread.java:833)
Caused by: java.nio.file.FileSystemException: /tmp/imageio10099959907746237469.tmp: No space left on device
	at java.base/sun.nio.fs.UnixException.translateToIOException(UnixException.java:100)
	at java.base/sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:106)
	at java.base/sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:111)
	at java.base/sun.nio.fs.UnixFileSystemProvider.newByteChannel(UnixFileSystemProvider.java:218)
	at java.base/java.nio.file.Files.newByteChannel(Files.java:380)
	at java.base/java.nio.file.Files.createFile(Files.java:658)
	at java.base/java.nio.file.TempFileHelper.create(TempFileHelper.java:136)
	at java.base/java.nio.file.TempFileHelper.createTempFile(TempFileHelper.java:159)
	at java.base/java.nio.file.Files.createTempFile(Files.java:923)
	at java.desktop/javax.imageio.stream.FileCacheImageInputStream.<init>(FileCacheImageInputStream.java:102)
	at java.desktop/com.sun.imageio.spi.InputStreamImageInputStreamSpi.createInputStreamInstance(InputStreamImageInputStreamSpi.java:69)
	at java.desktop/javax.imageio.ImageIO.createImageInputStream(ImageIO.java:359)
	... 7 more
javax.imageio.IIOException: Can't create cache file!
	at java.desktop/javax.imageio.ImageIO.createImageInputStream(ImageIO.java:363)
	at java.desktop/javax.imageio.ImageIO.read(ImageIO.java:1411)
	at uk.ac.babraham.FastQC.Report.HTMLReportArchive.base64ForIcon(HTMLReportArchive.java:383)
	at uk.ac.babraham.FastQC.Report.HTMLReportArchive.startDocument(HTMLReportArchive.java:346)
	at uk.ac.babraham.FastQC.Report.HTMLReportArchive.<init>(HTMLReportArchive.java:84)
	at uk.ac.babraham.FastQC.Analysis.OfflineRunner.analysisComplete(OfflineRunner.java:189)
	at uk.ac.babraham.FastQC.Analysis.AnalysisRunner.run(AnalysisRunner.java:123)
	at java.base/java.lang.Thread.run(Thread.java:833)
Caused by: java.nio.file.FileSystemException: /tmp/imageio8904933919996448080.tmp: No space left on device
	at java.base/sun.nio.fs.UnixException.translateToIOException(UnixException.java:100)
	at java.base/sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:106)
	at java.base/sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:111)
	at java.base/sun.nio.fs.UnixFileSystemProvider.newByteChannel(UnixFileSystemProvider.java:218)
	at java.base/java.nio.file.Files.newByteChannel(Files.java:380)
	at java.base/java.nio.file.Files.createFile(Files.java:658)
	at java.base/java.nio.file.TempFileHelper.create(TempFileHelper.java:136)
	at java.base/java.nio.file.TempFileHelper.createTempFile(TempFileHelper.java:159)
	at java.base/java.nio.file.Files.createTempFile(Files.java:923)
	at java.desktop/javax.imageio.stream.FileCacheImageInputStream.<init>(FileCacheImageInputStream.java:102)
	at java.desktop/com.sun.imageio.spi.InputStreamImageInputStreamSpi.createInputStreamInstance(InputStreamImageInputStreamSpi.java:69)
	at java.desktop/javax.imageio.ImageIO.createImageInputStream(ImageIO.java:359)
	... 7 more
javax.imageio.IIOException: Can't create cache file!
	at java.desktop/javax.imageio.ImageIO.createImageInputStream(ImageIO.java:363)
	at java.desktop/javax.imageio.ImageIO.read(ImageIO.java:1411)
	at uk.ac.babraham.FastQC.Report.HTMLReportArchive.base64ForIcon(HTMLReportArchive.java:383)
	at uk.ac.babraham.FastQC.Report.HTMLReportArchive.startDocument(HTMLReportArchive.java:351)
	at uk.ac.babraham.FastQC.Report.HTMLReportArchive.<init>(HTMLReportArchive.java:84)
	at uk.ac.babraham.FastQC.Analysis.OfflineRunner.analysisComplete(OfflineRunner.java:189)
	at uk.ac.babraham.FastQC.Analysis.AnalysisRunner.run(AnalysisRunner.java:123)
	at java.base/java.lang.Thread.run(Thread.java:833)
Caused by: java.nio.file.FileSystemException: /tmp/imageio1836383862602129082.tmp: No space left on device
	at java.base/sun.nio.fs.UnixException.translateToIOException(UnixException.java:100)
	at java.base/sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:106)
	at java.base/sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:111)
	at java.base/sun.nio.fs.UnixFileSystemProvider.newByteChannel(UnixFileSystemProvider.java:218)
	at java.base/java.nio.file.Files.newByteChannel(Files.java:380)
	at java.base/java.nio.file.Files.createFile(Files.java:658)
	at java.base/java.nio.file.TempFileHelper.create(TempFileHelper.java:136)
	at java.base/java.nio.file.TempFileHelper.createTempFile(TempFileHelper.java:159)
	at java.base/java.nio.file.Files.createTempFile(Files.java:923)
	at java.desktop/javax.imageio.stream.FileCacheImageInputStream.<init>(FileCacheImageInputStream.java:102)
	at java.desktop/com.sun.imageio.spi.InputStreamImageInputStreamSpi.createInputStreamInstance(InputStreamImageInputStreamSpi.java:69)
	at java.desktop/javax.imageio.ImageIO.createImageInputStream(ImageIO.java:359)
	... 7 more
javax.imageio.IIOException: Can't create cache file!
	at java.desktop/javax.imageio.ImageIO.createImageInputStream(ImageIO.java:363)
	at java.desktop/javax.imageio.ImageIO.read(ImageIO.java:1411)
	at uk.ac.babraham.FastQC.Report.HTMLReportArchive.base64ForIcon(HTMLReportArchive.java:383)
	at uk.ac.babraham.FastQC.Report.HTMLReportArchive.startDocument(HTMLReportArchive.java:351)
	at uk.ac.babraham.FastQC.Report.HTMLReportArchive.<init>(HTMLReportArchive.java:84)
	at uk.ac.babraham.FastQC.Analysis.OfflineRunner.analysisComplete(OfflineRunner.java:189)
	at uk.ac.babraham.FastQC.Analysis.AnalysisRunner.run(AnalysisRunner.java:123)
	at java.base/java.lang.Thread.run(Thread.java:833)
Caused by: java.nio.file.FileSystemException: /tmp/imageio12060475804005699787.tmp: No space left on device
	at java.base/sun.nio.fs.UnixException.translateToIOException(UnixException.java:100)
	at java.base/sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:106)
	at java.base/sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:111)
	at java.base/sun.nio.fs.UnixFileSystemProvider.newByteChannel(UnixFileSystemProvider.java:218)
	at java.base/java.nio.file.Files.newByteChannel(Files.java:380)
	at java.base/java.nio.file.Files.createFile(Files.java:658)
	at java.base/java.nio.file.TempFileHelper.create(TempFileHelper.java:136)
	at java.base/java.nio.file.TempFileHelper.createTempFile(TempFileHelper.java:159)
	at java.base/java.nio.file.Files.createTempFile(Files.java:923)
	at java.desktop/javax.imageio.stream.FileCacheImageInputStream.<init>(FileCacheImageInputStream.java:102)
	at java.desktop/com.sun.imageio.spi.InputStreamImageInputStreamSpi.createInputStreamInstance(InputStreamImageInputStreamSpi.java:69)
	at java.desktop/javax.imageio.ImageIO.createImageInputStream(ImageIO.java:359)
	... 7 more
javax.imageio.IIOException: Can't create cache file!
	at java.desktop/javax.imageio.ImageIO.createImageInputStream(ImageIO.java:363)
	at java.desktop/javax.imageio.ImageIO.read(ImageIO.java:1411)
	at uk.ac.babraham.FastQC.Report.HTMLReportArchive.base64ForIcon(HTMLReportArchive.java:383)
	at uk.ac.babraham.FastQC.Report.HTMLReportArchive.startDocument(HTMLReportArchive.java:341)
	at uk.ac.babraham.FastQC.Report.HTMLReportArchive.<init>(HTMLReportArchive.java:84)
	at uk.ac.babraham.FastQC.Analysis.OfflineRunner.analysisComplete(OfflineRunner.java:189)
	at uk.ac.babraham.FastQC.Analysis.AnalysisRunner.run(AnalysisRunner.java:123)
	at java.base/java.lang.Thread.run(Thread.java:833)
Caused by: java.nio.file.FileSystemException: /tmp/imageio10916884665183464442.tmp: No space left on device
	at java.base/sun.nio.fs.UnixException.translateToIOException(UnixException.java:100)
	at java.base/sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:106)
	at java.base/sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:111)
	at java.base/sun.nio.fs.UnixFileSystemProvider.newByteChannel(UnixFileSystemProvider.java:218)
	at java.base/java.nio.file.Files.newByteChannel(Files.java:380)
	at java.base/java.nio.file.Files.createFile(Files.java:658)
	at java.base/java.nio.file.TempFileHelper.create(TempFileHelper.java:136)
	at java.base/java.nio.file.TempFileHelper.createTempFile(TempFileHelper.java:159)
	at java.base/java.nio.file.Files.createTempFile(Files.java:923)
	at java.desktop/javax.imageio.stream.FileCacheImageInputStream.<init>(FileCacheImageInputStream.java:102)
	at java.desktop/com.sun.imageio.spi.InputStreamImageInputStreamSpi.createInputStreamInstance(InputStreamImageInputStreamSpi.java:69)
	at java.desktop/javax.imageio.ImageIO.createImageInputStream(ImageIO.java:359)
	... 7 more
javax.imageio.IIOException: Can't create cache file!
	at java.desktop/javax.imageio.ImageIO.createImageInputStream(ImageIO.java:363)
	at java.desktop/javax.imageio.ImageIO.read(ImageIO.java:1411)
	at uk.ac.babraham.FastQC.Report.HTMLReportArchive.base64ForIcon(HTMLReportArchive.java:383)
	at uk.ac.babraham.FastQC.Report.HTMLReportArchive.<init>(HTMLReportArchive.java:111)
	at uk.ac.babraham.FastQC.Analysis.OfflineRunner.analysisComplete(OfflineRunner.java:189)
	at uk.ac.babraham.FastQC.Analysis.AnalysisRunner.run(AnalysisRunner.java:123)
	at java.base/java.lang.Thread.run(Thread.java:833)
Caused by: java.nio.file.FileSystemException: /tmp/imageio1315059535426717720.tmp: No space left on device
	at java.base/sun.nio.fs.UnixException.translateToIOException(UnixException.java:100)
	at java.base/sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:106)
	at java.base/sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:111)
	at java.base/sun.nio.fs.UnixFileSystemProvider.newByteChannel(UnixFileSystemProvider.java:218)
	at java.base/java.nio.file.Files.newByteChannel(Files.java:380)
	at java.base/java.nio.file.Files.createFile(Files.java:658)
	at java.base/java.nio.file.TempFileHelper.create(TempFileHelper.java:136)
	at java.base/java.nio.file.TempFileHelper.createTempFile(TempFileHelper.java:159)
	at java.base/java.nio.file.Files.createTempFile(Files.java:923)
	at java.desktop/javax.imageio.stream.FileCacheImageInputStream.<init>(FileCacheImageInputStream.java:102)
	at java.desktop/com.sun.imageio.spi.InputStreamImageInputStreamSpi.createInputStreamInstance(InputStreamImageInputStreamSpi.java:69)
	at java.desktop/javax.imageio.ImageIO.createImageInputStream(ImageIO.java:359)
	... 6 more
javax.imageio.IIOException: Can't create cache file!
	at java.desktop/javax.imageio.ImageIO.createImageInputStream(ImageIO.java:363)
	at java.desktop/javax.imageio.ImageIO.read(ImageIO.java:1411)
	at uk.ac.babraham.FastQC.Report.HTMLReportArchive.base64ForIcon(HTMLReportArchive.java:383)
	at uk.ac.babraham.FastQC.Report.HTMLReportArchive.<init>(HTMLReportArchive.java:111)
	at uk.ac.babraham.FastQC.Analysis.OfflineRunner.analysisComplete(OfflineRunner.java:189)
	at uk.ac.babraham.FastQC.Analysis.AnalysisRunner.run(AnalysisRunner.java:123)
	at java.base/java.lang.Thread.run(Thread.java:833)
Caused by: java.nio.file.FileSystemException: /tmp/imageio7856324536660743783.tmp: No space left on device
	at java.base/sun.nio.fs.UnixException.translateToIOException(UnixException.java:100)
	at java.base/sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:106)
	at java.base/sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:111)
	at java.base/sun.nio.fs.UnixFileSystemProvider.newByteChannel(UnixFileSystemProvider.java:218)
	at java.base/java.nio.file.Files.newByteChannel(Files.java:380)
	at java.base/java.nio.file.Files.createFile(Files.java:658)
	at java.base/java.nio.file.TempFileHelper.create(TempFileHelper.java:136)
	at java.base/java.nio.file.TempFileHelper.createTempFile(TempFileHelper.java:159)
	at java.base/java.nio.file.Files.createTempFile(Files.java:923)
	at java.desktop/javax.imageio.stream.FileCacheImageInputStream.<init>(FileCacheImageInputStream.java:102)
	at java.desktop/com.sun.imageio.spi.InputStreamImageInputStreamSpi.createInputStreamInstance(InputStreamImageInputStreamSpi.java:69)
	at java.desktop/javax.imageio.ImageIO.createImageInputStream(ImageIO.java:359)
	... 6 more
Failed to process file P25_1.fastq.gz
javax.imageio.IIOException: Can't create cache file!
	at java.desktop/javax.imageio.ImageIO.createImageOutputStream(ImageIO.java:425)
	at java.desktop/javax.imageio.ImageIO.write(ImageIO.java:1591)
	at uk.ac.babraham.FastQC.Modules.AbstractQCModule.writeDefaultImage(AbstractQCModule.java:91)
	at uk.ac.babraham.FastQC.Modules.PerBaseQualityScores.makeReport(PerBaseQualityScores.java:199)
	at uk.ac.babraham.FastQC.Report.HTMLReportArchive.<init>(HTMLReportArchive.java:131)
	at uk.ac.babraham.FastQC.Analysis.OfflineRunner.analysisComplete(OfflineRunner.java:189)
	at uk.ac.babraham.FastQC.Analysis.AnalysisRunner.run(AnalysisRunner.java:123)
	at java.base/java.lang.Thread.run(Thread.java:833)
Caused by: java.nio.file.FileSystemException: /tmp/imageio11143121003080160356.tmp: No space left on device
	at java.base/sun.nio.fs.UnixException.translateToIOException(UnixException.java:100)
	at java.base/sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:106)
	at java.base/sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:111)
	at java.base/sun.nio.fs.UnixFileSystemProvider.newByteChannel(UnixFileSystemProvider.java:218)
	at java.base/java.nio.file.Files.newByteChannel(Files.java:380)
	at java.base/java.nio.file.Files.createFile(Files.java:658)
	at java.base/java.nio.file.TempFileHelper.create(TempFileHelper.java:136)
	at java.base/java.nio.file.TempFileHelper.createTempFile(TempFileHelper.java:159)
	at java.base/java.nio.file.Files.createTempFile(Files.java:923)
	at java.desktop/javax.imageio.stream.FileCacheImageOutputStream.<init>(FileCacheImageOutputStream.java:88)
	at java.desktop/com.sun.imageio.spi.OutputStreamImageOutputStreamSpi.createOutputStreamInstance(OutputStreamImageOutputStreamSpi.java:68)
	at java.desktop/javax.imageio.ImageIO.createImageOutputStream(ImageIO.java:421)
	... 7 more
Started analysis of P25_2.fastq.gz
Approx 5% complete for P25_2.fastq.gz
Approx 10% complete for P25_2.fastq.gz
Approx 15% complete for P25_2.fastq.gz
Approx 20% complete for P25_2.fastq.gz
Approx 25% complete for P25_2.fastq.gz
Approx 30% complete for P25_2.fastq.gz
Approx 35% complete for P25_2.fastq.gz
Approx 40% complete for P25_2.fastq.gz
Approx 45% complete for P25_2.fastq.gz
Approx 50% complete for P25_2.fastq.gz
Approx 55% complete for P25_2.fastq.gz
Approx 60% complete for P25_2.fastq.gz
Approx 65% complete for P25_2.fastq.gz
Approx 70% complete for P25_2.fastq.gz
Approx 75% complete for P25_2.fastq.gz
Approx 80% complete for P25_2.fastq.gz
Approx 85% complete for P25_2.fastq.gz
Approx 90% complete for P25_2.fastq.gz
Approx 95% complete for P25_2.fastq.gz
Analysis complete for P25_2.fastq.gz
javax.imageio.IIOException: Can't create cache file!
	at java.desktop/javax.imageio.ImageIO.createImageInputStream(ImageIO.java:363)
	at java.desktop/javax.imageio.ImageIO.read(ImageIO.java:1411)
	at uk.ac.babraham.FastQC.Report.HTMLReportArchive.base64ForIcon(HTMLReportArchive.java:383)
	at uk.ac.babraham.FastQC.Report.HTMLReportArchive.startDocument(HTMLReportArchive.java:307)
	at uk.ac.babraham.FastQC.Report.HTMLReportArchive.<init>(HTMLReportArchive.java:84)
	at uk.ac.babraham.FastQC.Analysis.OfflineRunner.analysisComplete(OfflineRunner.java:189)
	at uk.ac.babraham.FastQC.Analysis.AnalysisRunner.run(AnalysisRunner.java:123)
	at java.base/java.lang.Thread.run(Thread.java:833)
Caused by: java.nio.file.FileSystemException: /tmp/imageio1994634053410900560.tmp: No space left on device
	at java.base/sun.nio.fs.UnixException.translateToIOException(UnixException.java:100)
	at java.base/sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:106)
	at java.base/sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:111)
	at java.base/sun.nio.fs.UnixFileSystemProvider.newByteChannel(UnixFileSystemProvider.java:218)
	at java.base/java.nio.file.Files.newByteChannel(Files.java:380)
	at java.base/java.nio.file.Files.createFile(Files.java:658)
	at java.base/java.nio.file.TempFileHelper.create(TempFileHelper.java:136)
	at java.base/java.nio.file.TempFileHelper.createTempFile(TempFileHelper.java:159)
	at java.base/java.nio.file.Files.createTempFile(Files.java:923)
	at java.desktop/javax.imageio.stream.FileCacheImageInputStream.<init>(FileCacheImageInputStream.java:102)
	at java.desktop/com.sun.imageio.spi.InputStreamImageInputStreamSpi.createInputStreamInstance(InputStreamImageInputStreamSpi.java:69)
	at java.desktop/javax.imageio.ImageIO.createImageInputStream(ImageIO.java:359)
	... 7 more
javax.imageio.IIOException: Can't create cache file!
	at java.desktop/javax.imageio.ImageIO.createImageInputStream(ImageIO.java:363)
	at java.desktop/javax.imageio.ImageIO.read(ImageIO.java:1411)
	at uk.ac.babraham.FastQC.Report.HTMLReportArchive.base64ForIcon(HTMLReportArchive.java:383)
	at uk.ac.babraham.FastQC.Report.HTMLReportArchive.startDocument(HTMLReportArchive.java:351)
	at uk.ac.babraham.FastQC.Report.HTMLReportArchive.<init>(HTMLReportArchive.java:84)
	at uk.ac.babraham.FastQC.Analysis.OfflineRunner.analysisComplete(OfflineRunner.java:189)
	at uk.ac.babraham.FastQC.Analysis.AnalysisRunner.run(AnalysisRunner.java:123)
	at java.base/java.lang.Thread.run(Thread.java:833)
Caused by: java.nio.file.FileSystemException: /tmp/imageio12292755026493933526.tmp: No space left on device
	at java.base/sun.nio.fs.UnixException.translateToIOException(UnixException.java:100)
	at java.base/sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:106)
	at java.base/sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:111)
	at java.base/sun.nio.fs.UnixFileSystemProvider.newByteChannel(UnixFileSystemProvider.java:218)
	at java.base/java.nio.file.Files.newByteChannel(Files.java:380)
	at java.base/java.nio.file.Files.createFile(Files.java:658)
	at java.base/java.nio.file.TempFileHelper.create(TempFileHelper.java:136)
	at java.base/java.nio.file.TempFileHelper.createTempFile(TempFileHelper.java:159)
	at java.base/java.nio.file.Files.createTempFile(Files.java:923)
	at java.desktop/javax.imageio.stream.FileCacheImageInputStream.<init>(FileCacheImageInputStream.java:102)
	at java.desktop/com.sun.imageio.spi.InputStreamImageInputStreamSpi.createInputStreamInstance(InputStreamImageInputStreamSpi.java:69)
	at java.desktop/javax.imageio.ImageIO.createImageInputStream(ImageIO.java:359)
	... 7 more
javax.imageio.IIOException: Can't create cache file!
	at java.desktop/javax.imageio.ImageIO.createImageInputStream(ImageIO.java:363)
	at java.desktop/javax.imageio.ImageIO.read(ImageIO.java:1411)
	at uk.ac.babraham.FastQC.Report.HTMLReportArchive.base64ForIcon(HTMLReportArchive.java:383)
	at uk.ac.babraham.FastQC.Report.HTMLReportArchive.startDocument(HTMLReportArchive.java:351)
	at uk.ac.babraham.FastQC.Report.HTMLReportArchive.<init>(HTMLReportArchive.java:84)
	at uk.ac.babraham.FastQC.Analysis.OfflineRunner.analysisComplete(OfflineRunner.java:189)
	at uk.ac.babraham.FastQC.Analysis.AnalysisRunner.run(AnalysisRunner.java:123)
	at java.base/java.lang.Thread.run(Thread.java:833)
Caused by: java.nio.file.FileSystemException: /tmp/imageio14752638154297097020.tmp: No space left on device
	at java.base/sun.nio.fs.UnixException.translateToIOException(UnixException.java:100)
	at java.base/sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:106)
	at java.base/sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:111)
	at java.base/sun.nio.fs.UnixFileSystemProvider.newByteChannel(UnixFileSystemProvider.java:218)
	at java.base/java.nio.file.Files.newByteChannel(Files.java:380)
	at java.base/java.nio.file.Files.createFile(Files.java:658)
	at java.base/java.nio.file.TempFileHelper.create(TempFileHelper.java:136)
	at java.base/java.nio.file.TempFileHelper.createTempFile(TempFileHelper.java:159)
	at java.base/java.nio.file.Files.createTempFile(Files.java:923)
	at java.desktop/javax.imageio.stream.FileCacheImageInputStream.<init>(FileCacheImageInputStream.java:102)
	at java.desktop/com.sun.imageio.spi.InputStreamImageInputStreamSpi.createInputStreamInstance(InputStreamImageInputStreamSpi.java:69)
	at java.desktop/javax.imageio.ImageIO.createImageInputStream(ImageIO.java:359)
	... 7 more
javax.imageio.IIOException: Can't create cache file!
	at java.desktop/javax.imageio.ImageIO.createImageInputStream(ImageIO.java:363)
	at java.desktop/javax.imageio.ImageIO.read(ImageIO.java:1411)
	at uk.ac.babraham.FastQC.Report.HTMLReportArchive.base64ForIcon(HTMLReportArchive.java:383)
	at uk.ac.babraham.FastQC.Report.HTMLReportArchive.startDocument(HTMLReportArchive.java:351)
	at uk.ac.babraham.FastQC.Report.HTMLReportArchive.<init>(HTMLReportArchive.java:84)
	at uk.ac.babraham.FastQC.Analysis.OfflineRunner.analysisComplete(OfflineRunner.java:189)
	at uk.ac.babraham.FastQC.Analysis.AnalysisRunner.run(AnalysisRunner.java:123)
	at java.base/java.lang.Thread.run(Thread.java:833)
Caused by: java.nio.file.FileSystemException: /tmp/imageio13669323324678669618.tmp: No space left on device
	at java.base/sun.nio.fs.UnixException.translateToIOException(UnixException.java:100)
	at java.base/sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:106)
	at java.base/sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:111)
	at java.base/sun.nio.fs.UnixFileSystemProvider.newByteChannel(UnixFileSystemProvider.java:218)
	at java.base/java.nio.file.Files.newByteChannel(Files.java:380)
	at java.base/java.nio.file.Files.createFile(Files.java:658)
	at java.base/java.nio.file.TempFileHelper.create(TempFileHelper.java:136)
	at java.base/java.nio.file.TempFileHelper.createTempFile(TempFileHelper.java:159)
	at java.base/java.nio.file.Files.createTempFile(Files.java:923)
	at java.desktop/javax.imageio.stream.FileCacheImageInputStream.<init>(FileCacheImageInputStream.java:102)
	at java.desktop/com.sun.imageio.spi.InputStreamImageInputStreamSpi.createInputStreamInstance(InputStreamImageInputStreamSpi.java:69)
	at java.desktop/javax.imageio.ImageIO.createImageInputStream(ImageIO.java:359)
	... 7 more
javax.imageio.IIOException: Can't create cache file!
	at java.desktop/javax.imageio.ImageIO.createImageInputStream(ImageIO.java:363)
	at java.desktop/javax.imageio.ImageIO.read(ImageIO.java:1411)
	at uk.ac.babraham.FastQC.Report.HTMLReportArchive.base64ForIcon(HTMLReportArchive.java:383)
	at uk.ac.babraham.FastQC.Report.HTMLReportArchive.startDocument(HTMLReportArchive.java:351)
	at uk.ac.babraham.FastQC.Report.HTMLReportArchive.<init>(HTMLReportArchive.java:84)
	at uk.ac.babraham.FastQC.Analysis.OfflineRunner.analysisComplete(OfflineRunner.java:189)
	at uk.ac.babraham.FastQC.Analysis.AnalysisRunner.run(AnalysisRunner.java:123)
	at java.base/java.lang.Thread.run(Thread.java:833)
Caused by: java.nio.file.FileSystemException: /tmp/imageio1932005552871342498.tmp: No space left on device
	at java.base/sun.nio.fs.UnixException.translateToIOException(UnixException.java:100)
	at java.base/sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:106)
	at java.base/sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:111)
	at java.base/sun.nio.fs.UnixFileSystemProvider.newByteChannel(UnixFileSystemProvider.java:218)
	at java.base/java.nio.file.Files.newByteChannel(Files.java:380)
	at java.base/java.nio.file.Files.createFile(Files.java:658)
	at java.base/java.nio.file.TempFileHelper.create(TempFileHelper.java:136)
	at java.base/java.nio.file.TempFileHelper.createTempFile(TempFileHelper.java:159)
	at java.base/java.nio.file.Files.createTempFile(Files.java:923)
	at java.desktop/javax.imageio.stream.FileCacheImageInputStream.<init>(FileCacheImageInputStream.java:102)
	at java.desktop/com.sun.imageio.spi.InputStreamImageInputStreamSpi.createInputStreamInstance(InputStreamImageInputStreamSpi.java:69)
	at java.desktop/javax.imageio.ImageIO.createImageInputStream(ImageIO.java:359)
	... 7 more
javax.imageio.IIOException: Can't create cache file!
	at java.desktop/javax.imageio.ImageIO.createImageInputStream(ImageIO.java:363)
	at java.desktop/javax.imageio.ImageIO.read(ImageIO.java:1411)
	at uk.ac.babraham.FastQC.Report.HTMLReportArchive.base64ForIcon(HTMLReportArchive.java:383)
	at uk.ac.babraham.FastQC.Report.HTMLReportArchive.startDocument(HTMLReportArchive.java:351)
	at uk.ac.babraham.FastQC.Report.HTMLReportArchive.<init>(HTMLReportArchive.java:84)
	at uk.ac.babraham.FastQC.Analysis.OfflineRunner.analysisComplete(OfflineRunner.java:189)
	at uk.ac.babraham.FastQC.Analysis.AnalysisRunner.run(AnalysisRunner.java:123)
	at java.base/java.lang.Thread.run(Thread.java:833)
Caused by: java.nio.file.FileSystemException: /tmp/imageio8348799664233890142.tmp: No space left on device
	at java.base/sun.nio.fs.UnixException.translateToIOException(UnixException.java:100)
	at java.base/sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:106)
	at java.base/sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:111)
	at java.base/sun.nio.fs.UnixFileSystemProvider.newByteChannel(UnixFileSystemProvider.java:218)
	at java.base/java.nio.file.Files.newByteChannel(Files.java:380)
	at java.base/java.nio.file.Files.createFile(Files.java:658)
	at java.base/java.nio.file.TempFileHelper.create(TempFileHelper.java:136)
	at java.base/java.nio.file.TempFileHelper.createTempFile(TempFileHelper.java:159)
	at java.base/java.nio.file.Files.createTempFile(Files.java:923)
	at java.desktop/javax.imageio.stream.FileCacheImageInputStream.<init>(FileCacheImageInputStream.java:102)
	at java.desktop/com.sun.imageio.spi.InputStreamImageInputStreamSpi.createInputStreamInstance(InputStreamImageInputStreamSpi.java:69)
	at java.desktop/javax.imageio.ImageIO.createImageInputStream(ImageIO.java:359)
	... 7 more
javax.imageio.IIOException: Can't create cache file!
	at java.desktop/javax.imageio.ImageIO.createImageInputStream(ImageIO.java:363)
	at java.desktop/javax.imageio.ImageIO.read(ImageIO.java:1411)
	at uk.ac.babraham.FastQC.Report.HTMLReportArchive.base64ForIcon(HTMLReportArchive.java:383)
	at uk.ac.babraham.FastQC.Report.HTMLReportArchive.startDocument(HTMLReportArchive.java:351)
	at uk.ac.babraham.FastQC.Report.HTMLReportArchive.<init>(HTMLReportArchive.java:84)
	at uk.ac.babraham.FastQC.Analysis.OfflineRunner.analysisComplete(OfflineRunner.java:189)
	at uk.ac.babraham.FastQC.Analysis.AnalysisRunner.run(AnalysisRunner.java:123)
	at java.base/java.lang.Thread.run(Thread.java:833)
Caused by: java.nio.file.FileSystemException: /tmp/imageio5551075560791837984.tmp: No space left on device
	at java.base/sun.nio.fs.UnixException.translateToIOException(UnixException.java:100)
	at java.base/sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:106)
	at java.base/sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:111)
	at java.base/sun.nio.fs.UnixFileSystemProvider.newByteChannel(UnixFileSystemProvider.java:218)
	at java.base/java.nio.file.Files.newByteChannel(Files.java:380)
	at java.base/java.nio.file.Files.createFile(Files.java:658)
	at java.base/java.nio.file.TempFileHelper.create(TempFileHelper.java:136)
	at java.base/java.nio.file.TempFileHelper.createTempFile(TempFileHelper.java:159)
	at java.base/java.nio.file.Files.createTempFile(Files.java:923)
	at java.desktop/javax.imageio.stream.FileCacheImageInputStream.<init>(FileCacheImageInputStream.java:102)
	at java.desktop/com.sun.imageio.spi.InputStreamImageInputStreamSpi.createInputStreamInstance(InputStreamImageInputStreamSpi.java:69)
	at java.desktop/javax.imageio.ImageIO.createImageInputStream(ImageIO.java:359)
	... 7 more
javax.imageio.IIOException: Can't create cache file!
	at java.desktop/javax.imageio.ImageIO.createImageInputStream(ImageIO.java:363)
	at java.desktop/javax.imageio.ImageIO.read(ImageIO.java:1411)
	at uk.ac.babraham.FastQC.Report.HTMLReportArchive.base64ForIcon(HTMLReportArchive.java:383)
	at uk.ac.babraham.FastQC.Report.HTMLReportArchive.startDocument(HTMLReportArchive.java:351)
	at uk.ac.babraham.FastQC.Report.HTMLReportArchive.<init>(HTMLReportArchive.java:84)
	at uk.ac.babraham.FastQC.Analysis.OfflineRunner.analysisComplete(OfflineRunner.java:189)
	at uk.ac.babraham.FastQC.Analysis.AnalysisRunner.run(AnalysisRunner.java:123)
	at java.base/java.lang.Thread.run(Thread.java:833)
Caused by: java.nio.file.FileSystemException: /tmp/imageio9688800796617086534.tmp: No space left on device
	at java.base/sun.nio.fs.UnixException.translateToIOException(UnixException.java:100)
	at java.base/sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:106)
	at java.base/sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:111)
	at java.base/sun.nio.fs.UnixFileSystemProvider.newByteChannel(UnixFileSystemProvider.java:218)
	at java.base/java.nio.file.Files.newByteChannel(Files.java:380)
	at java.base/java.nio.file.Files.createFile(Files.java:658)
	at java.base/java.nio.file.TempFileHelper.create(TempFileHelper.java:136)
	at java.base/java.nio.file.TempFileHelper.createTempFile(TempFileHelper.java:159)
	at java.base/java.nio.file.Files.createTempFile(Files.java:923)
	at java.desktop/javax.imageio.stream.FileCacheImageInputStream.<init>(FileCacheImageInputStream.java:102)
	at java.desktop/com.sun.imageio.spi.InputStreamImageInputStreamSpi.createInputStreamInstance(InputStreamImageInputStreamSpi.java:69)
	at java.desktop/javax.imageio.ImageIO.createImageInputStream(ImageIO.java:359)
	... 7 more
javax.imageio.IIOException: Can't create cache file!
	at java.desktop/javax.imageio.ImageIO.createImageInputStream(ImageIO.java:363)
	at java.desktop/javax.imageio.ImageIO.read(ImageIO.java:1411)
	at uk.ac.babraham.FastQC.Report.HTMLReportArchive.base64ForIcon(HTMLReportArchive.java:383)
	at uk.ac.babraham.FastQC.Report.HTMLReportArchive.startDocument(HTMLReportArchive.java:346)
	at uk.ac.babraham.FastQC.Report.HTMLReportArchive.<init>(HTMLReportArchive.java:84)
	at uk.ac.babraham.FastQC.Analysis.OfflineRunner.analysisComplete(OfflineRunner.java:189)
	at uk.ac.babraham.FastQC.Analysis.AnalysisRunner.run(AnalysisRunner.java:123)
	at java.base/java.lang.Thread.run(Thread.java:833)
Caused by: java.nio.file.FileSystemException: /tmp/imageio7304443227837905039.tmp: No space left on device
	at java.base/sun.nio.fs.UnixException.translateToIOException(UnixException.java:100)
	at java.base/sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:106)
	at java.base/sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:111)
	at java.base/sun.nio.fs.UnixFileSystemProvider.newByteChannel(UnixFileSystemProvider.java:218)
	at java.base/java.nio.file.Files.newByteChannel(Files.java:380)
	at java.base/java.nio.file.Files.createFile(Files.java:658)
	at java.base/java.nio.file.TempFileHelper.create(TempFileHelper.java:136)
	at java.base/java.nio.file.TempFileHelper.createTempFile(TempFileHelper.java:159)
	at java.base/java.nio.file.Files.createTempFile(Files.java:923)
	at java.desktop/javax.imageio.stream.FileCacheImageInputStream.<init>(FileCacheImageInputStream.java:102)
	at java.desktop/com.sun.imageio.spi.InputStreamImageInputStreamSpi.createInputStreamInstance(InputStreamImageInputStreamSpi.java:69)
	at java.desktop/javax.imageio.ImageIO.createImageInputStream(ImageIO.java:359)
	... 7 more
javax.imageio.IIOException: Can't create cache file!
	at java.desktop/javax.imageio.ImageIO.createImageInputStream(ImageIO.java:363)
	at java.desktop/javax.imageio.ImageIO.read(ImageIO.java:1411)
	at uk.ac.babraham.FastQC.Report.HTMLReportArchive.base64ForIcon(HTMLReportArchive.java:383)
	at uk.ac.babraham.FastQC.Report.HTMLReportArchive.startDocument(HTMLReportArchive.java:351)
	at uk.ac.babraham.FastQC.Report.HTMLReportArchive.<init>(HTMLReportArchive.java:84)
	at uk.ac.babraham.FastQC.Analysis.OfflineRunner.analysisComplete(OfflineRunner.java:189)
	at uk.ac.babraham.FastQC.Analysis.AnalysisRunner.run(AnalysisRunner.java:123)
	at java.base/java.lang.Thread.run(Thread.java:833)
Caused by: java.nio.file.FileSystemException: /tmp/imageio14220729957678428228.tmp: No space left on device
	at java.base/sun.nio.fs.UnixException.translateToIOException(UnixException.java:100)
	at java.base/sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:106)
	at java.base/sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:111)
	at java.base/sun.nio.fs.UnixFileSystemProvider.newByteChannel(UnixFileSystemProvider.java:218)
	at java.base/java.nio.file.Files.newByteChannel(Files.java:380)
	at java.base/java.nio.file.Files.createFile(Files.java:658)
	at java.base/java.nio.file.TempFileHelper.create(TempFileHelper.java:136)
	at java.base/java.nio.file.TempFileHelper.createTempFile(TempFileHelper.java:159)
	at java.base/java.nio.file.Files.createTempFile(Files.java:923)
	at java.desktop/javax.imageio.stream.FileCacheImageInputStream.<init>(FileCacheImageInputStream.java:102)
	at java.desktop/com.sun.imageio.spi.InputStreamImageInputStreamSpi.createInputStreamInstance(InputStreamImageInputStreamSpi.java:69)
	at java.desktop/javax.imageio.ImageIO.createImageInputStream(ImageIO.java:359)
	... 7 more
javax.imageio.IIOException: Can't create cache file!
	at java.desktop/javax.imageio.ImageIO.createImageInputStream(ImageIO.java:363)
	at java.desktop/javax.imageio.ImageIO.read(ImageIO.java:1411)
	at uk.ac.babraham.FastQC.Report.HTMLReportArchive.base64ForIcon(HTMLReportArchive.java:383)
	at uk.ac.babraham.FastQC.Report.HTMLReportArchive.startDocument(HTMLReportArchive.java:351)
	at uk.ac.babraham.FastQC.Report.HTMLReportArchive.<init>(HTMLReportArchive.java:84)
	at uk.ac.babraham.FastQC.Analysis.OfflineRunner.analysisComplete(OfflineRunner.java:189)
	at uk.ac.babraham.FastQC.Analysis.AnalysisRunner.run(AnalysisRunner.java:123)
	at java.base/java.lang.Thread.run(Thread.java:833)
Caused by: java.nio.file.FileSystemException: /tmp/imageio8781950222711960529.tmp: No space left on device
	at java.base/sun.nio.fs.UnixException.translateToIOException(UnixException.java:100)
	at java.base/sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:106)
	at java.base/sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:111)
	at java.base/sun.nio.fs.UnixFileSystemProvider.newByteChannel(UnixFileSystemProvider.java:218)
	at java.base/java.nio.file.Files.newByteChannel(Files.java:380)
	at java.base/java.nio.file.Files.createFile(Files.java:658)
	at java.base/java.nio.file.TempFileHelper.create(TempFileHelper.java:136)
	at java.base/java.nio.file.TempFileHelper.createTempFile(TempFileHelper.java:159)
	at java.base/java.nio.file.Files.createTempFile(Files.java:923)
	at java.desktop/javax.imageio.stream.FileCacheImageInputStream.<init>(FileCacheImageInputStream.java:102)
	at java.desktop/com.sun.imageio.spi.InputStreamImageInputStreamSpi.createInputStreamInstance(InputStreamImageInputStreamSpi.java:69)
	at java.desktop/javax.imageio.ImageIO.createImageInputStream(ImageIO.java:359)
	... 7 more
javax.imageio.IIOException: Can't create cache file!
	at java.desktop/javax.imageio.ImageIO.createImageInputStream(ImageIO.java:363)
	at java.desktop/javax.imageio.ImageIO.read(ImageIO.java:1411)
	at uk.ac.babraham.FastQC.Report.HTMLReportArchive.base64ForIcon(HTMLReportArchive.java:383)
	at uk.ac.babraham.FastQC.Report.HTMLReportArchive.startDocument(HTMLReportArchive.java:341)
	at uk.ac.babraham.FastQC.Report.HTMLReportArchive.<init>(HTMLReportArchive.java:84)
	at uk.ac.babraham.FastQC.Analysis.OfflineRunner.analysisComplete(OfflineRunner.java:189)
	at uk.ac.babraham.FastQC.Analysis.AnalysisRunner.run(AnalysisRunner.java:123)
	at java.base/java.lang.Thread.run(Thread.java:833)
Caused by: java.nio.file.FileSystemException: /tmp/imageio8460229244872507121.tmp: No space left on device
	at java.base/sun.nio.fs.UnixException.translateToIOException(UnixException.java:100)
	at java.base/sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:106)
	at java.base/sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:111)
	at java.base/sun.nio.fs.UnixFileSystemProvider.newByteChannel(UnixFileSystemProvider.java:218)
	at java.base/java.nio.file.Files.newByteChannel(Files.java:380)
	at java.base/java.nio.file.Files.createFile(Files.java:658)
	at java.base/java.nio.file.TempFileHelper.create(TempFileHelper.java:136)
	at java.base/java.nio.file.TempFileHelper.createTempFile(TempFileHelper.java:159)
	at java.base/java.nio.file.Files.createTempFile(Files.java:923)
	at java.desktop/javax.imageio.stream.FileCacheImageInputStream.<init>(FileCacheImageInputStream.java:102)
	at java.desktop/com.sun.imageio.spi.InputStreamImageInputStreamSpi.createInputStreamInstance(InputStreamImageInputStreamSpi.java:69)
	at java.desktop/javax.imageio.ImageIO.createImageInputStream(ImageIO.java:359)
	... 7 more
javax.imageio.IIOException: Can't create cache file!
	at java.desktop/javax.imageio.ImageIO.createImageInputStream(ImageIO.java:363)
	at java.desktop/javax.imageio.ImageIO.read(ImageIO.java:1411)
	at uk.ac.babraham.FastQC.Report.HTMLReportArchive.base64ForIcon(HTMLReportArchive.java:383)
	at uk.ac.babraham.FastQC.Report.HTMLReportArchive.<init>(HTMLReportArchive.java:111)
	at uk.ac.babraham.FastQC.Analysis.OfflineRunner.analysisComplete(OfflineRunner.java:189)
	at uk.ac.babraham.FastQC.Analysis.AnalysisRunner.run(AnalysisRunner.java:123)
	at java.base/java.lang.Thread.run(Thread.java:833)
Caused by: java.nio.file.FileSystemException: /tmp/imageio2999279431954900278.tmp: No space left on device
	at java.base/sun.nio.fs.UnixException.translateToIOException(UnixException.java:100)
	at java.base/sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:106)
	at java.base/sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:111)
	at java.base/sun.nio.fs.UnixFileSystemProvider.newByteChannel(UnixFileSystemProvider.java:218)
	at java.base/java.nio.file.Files.newByteChannel(Files.java:380)
	at java.base/java.nio.file.Files.createFile(Files.java:658)
	at java.base/java.nio.file.TempFileHelper.create(TempFileHelper.java:136)
	at java.base/java.nio.file.TempFileHelper.createTempFile(TempFileHelper.java:159)
	at java.base/java.nio.file.Files.createTempFile(Files.java:923)
	at java.desktop/javax.imageio.stream.FileCacheImageInputStream.<init>(FileCacheImageInputStream.java:102)
	at java.desktop/com.sun.imageio.spi.InputStreamImageInputStreamSpi.createInputStreamInstance(InputStreamImageInputStreamSpi.java:69)
	at java.desktop/javax.imageio.ImageIO.createImageInputStream(ImageIO.java:359)
	... 6 more
javax.imageio.IIOException: Can't create cache file!
	at java.desktop/javax.imageio.ImageIO.createImageInputStream(ImageIO.java:363)
	at java.desktop/javax.imageio.ImageIO.read(ImageIO.java:1411)
	at uk.ac.babraham.FastQC.Report.HTMLReportArchive.base64ForIcon(HTMLReportArchive.java:383)
	at uk.ac.babraham.FastQC.Report.HTMLReportArchive.<init>(HTMLReportArchive.java:111)
	at uk.ac.babraham.FastQC.Analysis.OfflineRunner.analysisComplete(OfflineRunner.java:189)
	at uk.ac.babraham.FastQC.Analysis.AnalysisRunner.run(AnalysisRunner.java:123)
	at java.base/java.lang.Thread.run(Thread.java:833)
Caused by: java.nio.file.FileSystemException: /tmp/imageio7584080601426569510.tmp: No space left on device
	at java.base/sun.nio.fs.UnixException.translateToIOException(UnixException.java:100)
	at java.base/sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:106)
	at java.base/sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:111)
	at java.base/sun.nio.fs.UnixFileSystemProvider.newByteChannel(UnixFileSystemProvider.java:218)
	at java.base/java.nio.file.Files.newByteChannel(Files.java:380)
	at java.base/java.nio.file.Files.createFile(Files.java:658)
	at java.base/java.nio.file.TempFileHelper.create(TempFileHelper.java:136)
	at java.base/java.nio.file.TempFileHelper.createTempFile(TempFileHelper.java:159)
	at java.base/java.nio.file.Files.createTempFile(Files.java:923)
	at java.desktop/javax.imageio.stream.FileCacheImageInputStream.<init>(FileCacheImageInputStream.java:102)
	at java.desktop/com.sun.imageio.spi.InputStreamImageInputStreamSpi.createInputStreamInstance(InputStreamImageInputStreamSpi.java:69)
	at java.desktop/javax.imageio.ImageIO.createImageInputStream(ImageIO.java:359)
	... 6 more
Failed to process file P25_2.fastq.gz
javax.imageio.IIOException: Can't create cache file!
	at java.desktop/javax.imageio.ImageIO.createImageOutputStream(ImageIO.java:425)
	at java.desktop/javax.imageio.ImageIO.write(ImageIO.java:1591)
	at uk.ac.babraham.FastQC.Modules.AbstractQCModule.writeDefaultImage(AbstractQCModule.java:91)
	at uk.ac.babraham.FastQC.Modules.PerBaseQualityScores.makeReport(PerBaseQualityScores.java:199)
	at uk.ac.babraham.FastQC.Report.HTMLReportArchive.<init>(HTMLReportArchive.java:131)
	at uk.ac.babraham.FastQC.Analysis.OfflineRunner.analysisComplete(OfflineRunner.java:189)
	at uk.ac.babraham.FastQC.Analysis.AnalysisRunner.run(AnalysisRunner.java:123)
	at java.base/java.lang.Thread.run(Thread.java:833)
Caused by: java.nio.file.FileSystemException: /tmp/imageio13960045539872474523.tmp: No space left on device
	at java.base/sun.nio.fs.UnixException.translateToIOException(UnixException.java:100)
	at java.base/sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:106)
	at java.base/sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:111)
	at java.base/sun.nio.fs.UnixFileSystemProvider.newByteChannel(UnixFileSystemProvider.java:218)
	at java.base/java.nio.file.Files.newByteChannel(Files.java:380)
	at java.base/java.nio.file.Files.createFile(Files.java:658)
	at java.base/java.nio.file.TempFileHelper.create(TempFileHelper.java:136)
	at java.base/java.nio.file.TempFileHelper.createTempFile(TempFileHelper.java:159)
	at java.base/java.nio.file.Files.createTempFile(Files.java:923)
	at java.desktop/javax.imageio.stream.FileCacheImageOutputStream.<init>(FileCacheImageOutputStream.java:88)
	at java.desktop/com.sun.imageio.spi.OutputStreamImageOutputStreamSpi.createOutputStreamInstance(OutputStreamImageOutputStreamSpi.java:68)
	at java.desktop/javax.imageio.ImageIO.createImageOutputStream(ImageIO.java:421)
	... 7 more
[Wed Nov  8 08:05:

Sunbeam version
sunbeam v4.1.0

Additional context
@benyoung93 benyoung93 added the bug label Nov 8, 2023
@benyoung93
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Just to add some additional information, I went into the fastqc env (/projects/beyo2625/programs/sunbeam4.0.0/.snakemake/e972c15c96b9e03c5f212c45f1887dc5_/bin) and inspected the FastQC executable.

This showed

and this if ($temp_directory) {
        unless (-e $temp_directory and -d $temp_directory and -w $temp_directory) {
                die "Temp directory '$temp_directory' doesn't exist, or can't be written to\n";
        }
        push @java_args, "-Djava.io.tmpdir=$temp_directory";

As such I have added expoert temp_directory=path/to/scratch to my script file to see if this will fix the error. I can relay if this did it otherwise any additional fixes/aid would still be needed :).

Ben

@Ulthran
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Ulthran commented Nov 8, 2023

Hi @benyoung93 thanks for using sunbeam! It looks like maybe fastqc provides an option for rerouting tmp files with -d/--dir (bottom of this page). Could you try modifying the fastqc rule directly in your sunbeam/workflow/rules/qc.smk file to see if that works?

Charlie

@benyoung93
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benyoung93 commented Nov 8, 2023 •
edited
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HI @Ulthran :)

thanks for the reply yes I can try that, so far it has not crashed yet with the temp_directory addition but I will test the rule edit this week.

Just to double check, ive put the editied command below just want to make sure it is in the correct place :).

rule fastqc:
    input:
        reads=expand(QC_FP / "02_trimmomatic" / "{{sample}}_{rp}.fastq.gz", rp=Pairs),
    output:
        expand(QC_FP / "reports" / "{{sample}}_{rp}_fastqc/fastqc_data.txt", rp=Pairs),
    log:
        LOG_FP / "fastqc_{sample}.log",
    benchmark:
        BENCHMARK_FP / "fastqc_{sample}.tsv"
    params:
        outdir=QC_FP / "reports",
    conda:
        "../envs/qc.yml"
    shell:
        "fastqc -o {params.outdir} -d /rc_scratch/beyo2625/temp_space {input.reads} -extract 2>&1 | tee {log}"

@Ulthran
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Ulthran commented Nov 8, 2023

Looks right to me!

@benyoung93
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quick update, my temp_directory failed miserably lol, so now I am trying the fix suggested by @Ulthran.

throwing the -d flag however gives the following error

Option d is ambiguous (delete, dir, dup_length)

So I am now retrying it with --dir instead. This has not thrown the error when running the command within the rule_fastqc (copied below) and it seems to work well. Please note that my login nodes have 8Gb of /tmp, while compute nodes have /tmp of 2Gb, so while this test seems to of worked I will update if the actual snakemake execution also works.

(/projects/beyo2625/programs/sunbeam4.0.0/.snakemake/e972c15c96b9e03c5f212c45f1887dc5_) [beyo2625@login10 sunbeam]$ fastqc -o /rc_scratch/beyo2625/sunbeam/sunbeam_output/qc/reports --dir /rc_scratch/beyo2625/temp_space /rc_scratch/beyo2625/sunbeam/sunbeam_output/qc/02_trimmomatic/P20_1.fastq.gz /rc_scratch/beyo2625/sunbeam/sunbeam_output/qc/02_trimmomatic/P20_2.fastq.gz -extract 2>&1 | tee /rc_scratch/beyo2625/sunbeam/sunbeam_output/logs/fastqc_P20.log

Ben

@benyoung93
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benyoung93 commented Nov 8, 2023 •
edited
Loading

Adding in the --dir to the fastqc command in the qc.smk has successfully solved the problem woooooooooooooooooooooooooo. Thank you so much for the help I really appreciate it !

FIngers crossed the rest of the pipeline now completes :).

Ben

@Ulthran
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Ulthran commented Nov 9, 2023

Glad that's working for you!

Part of me wants to include config options for every rule's CLI to easily add in options like this. But then the other part of me doesn't want to add a hundred new config options and muck up the config file... I'll keep thinking on this one.

@benyoung93
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Personally, I think it would be alot of work and, as you said, potentially mess up config files thus creating more effort than it is worth.

A potential middle ground could be to incorporate a small section in the manual about adding in additional CLI options for the tools. For example pointing to the workflow directory and relevant .smk files (which I know is alreadty mentioned in the software structure section of the docs), and then a potential list of the tools used and links to the flags for each software.

Just an idea which is again a wee but of work but could be a nice middle ground :).

Ben

@rzelle-lallemand rzelle-lallemand mentioned this issue Oct 17, 2024
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