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error sampling paired fastq #27

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afmcc opened this issue Nov 1, 2018 · 0 comments
Open

error sampling paired fastq #27

afmcc opened this issue Nov 1, 2018 · 0 comments

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@afmcc
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afmcc commented Nov 1, 2018

iramohio-01$ tardis --hpctype local -s .5 cat _condition_paired_fastq_input_test_R1.fastq.gz > R1_sample.fastq ; _condition_paired_fastq_inple.fastq
reading config from /etc/tardis/tardis.toml
tool args = ['cat', '_condition_paired_fastq_input_test_R1.fastq.gz', '>', 'R1_sample.fastq', ';', '_condition_paired_fastq_input_test_R2.fast
tardis.py : logging this session to /bifo/active/gseq_processing/bin/resequencing_prism/test/tardis_UcZQHv
Traceback (most recent call last):
File "/stash/miniconda3/envs/universal2/bin/tardis", line 11, in
sys.exit(tardis_main())
File "/stash/miniconda3/envs/universal2/lib/python2.7/site-packages/tardis/run.py", line 244, in tardis_main
(exit_code, factory) = run(command_args, options, checkCommandIsValid = False)
File "/stash/miniconda3/envs/universal2/lib/python2.7/site-packages/tardis/run.py", line 65, in run
for conditionedInputs in conditionedInputGenerators:
File "/stash/miniconda3/envs/universal2/lib/python2.7/site-packages/tardis/conditioner/text.py", line 726, in _slow_get_conditioned_filename
sampleBool = tutils.getSampleBool(samplerate) # 1 or 0 (always 1 if not sampling)
File "/stash/miniconda3/envs/universal2/lib/python2.7/site-packages/tardis/tutils/tutils.py", line 42, in getSampleBool
uniform = random.random()
NameError: global name 'random' is not defined

Also a different error in dev

iramohio-01$ \vi test1.sh
iramohio-01$ ./test1.sh
reading config from /etc/tardis/tardis.toml
reading config from tardis.toml
tool args = ['cat', 'condition_paired_fastq_input/dataset/bioinformatics_dev/active/tardis/tardis/test/R1.fastq', '>', 'R1_sample.fastq', ';', 'cat', 'condition_paired_fastq_input/dataset/bioinformatics_dev/active/tardis/tardis/test/R2.fastq', '>', 'R2_sample.fastq', ';']
tardis.py : logging this session to /bifo/active/bioinformatics_dev/tardis/tardis/test/tardis_MvO6Sy
Traceback (most recent call last):
File "/stash/miniconda3/envs/universal2/bin/tardis", line 11, in
sys.exit(tardis_main())
File "/dataset/bioinformatics_dev/active/tardis/tardis/tardis/run.py", line 244, in tardis_main
(exit_code, factory) = run(command_args, options, checkCommandIsValid = False)
File "/dataset/bioinformatics_dev/active/tardis/tardis/tardis/run.py", line 65, in run
for conditionedInputs in conditionedInputGenerators:
File "/dataset/bioinformatics_dev/active/tardis/tardis/tardis/conditioner/text.py", line 796, in _slow_get_conditioned_filenames
if not pairBond(record1 , record2):
File "/dataset/bioinformatics_dev/active/tardis/tardis/tardis/conditioner/fastq.py", line 26, in
pairBond = lambda cls,x,y: fastqPairedNamesEqual(x.name, y.name) # x, y is a biopython seqrecord object
NameError: global name 'fastqPairedNamesEqual' is not defined

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