lukasv@gnkm:~/projects/sekoskaita/mokymai/nanopore/denbi$ porechop -i ./data_arctic/barcode_tiny/basecall_tiny.fastq.gz -o data_artic/basecall_tiny_porechopped.fastq.gz -t 10 Loading reads ./data_arctic/barcode_tiny/basecall_tiny.fastq.gz 3,920 reads loaded Looking for known adapter sets 3,920 / 3,920 (100.0%) Best read Best start read end Set %ID %ID SQK-NSK007 100.0 77.3 Rapid 63.6 0.0 RBK004_upstream 82.1 0.0 SQK-MAP006 74.2 78.3 SQK-MAP006 short 73.1 75.0 PCR adapters 1 75.0 75.0 PCR adapters 2 81.8 78.3 PCR adapters 3 72.0 75.0 1D^2 part 1 74.1 72.4 1D^2 part 2 88.6 73.3 cDNA SSP 66.7 67.4 Barcode 1 (reverse) 100.0 100.0 Barcode 2 (reverse) 100.0 100.0 Barcode 3 (reverse) 100.0 77.8 Barcode 4 (reverse) 100.0 100.0 Barcode 5 (reverse) 100.0 100.0 Barcode 6 (reverse) 80.0 76.9 Barcode 7 (reverse) 75.0 76.0 Barcode 8 (reverse) 73.1 75.0 Barcode 9 (reverse) 75.0 75.0 Barcode 10 (reverse) 73.1 74.1 Barcode 11 (reverse) 75.0 73.1 Barcode 12 (reverse) 80.8 79.2 Barcode 1 (forward) 73.1 100.0 Barcode 2 (forward) 75.0 83.3 Barcode 3 (forward) 75.0 75.0 Barcode 4 (forward) 75.0 72.4 Barcode 5 (forward) 72.4 75.0 Barcode 6 (forward) 80.0 79.2 Barcode 7 (forward) 73.1 75.0 Barcode 8 (forward) 73.1 76.9 Barcode 9 (forward) 75.0 76.0 Barcode 10 (forward) 73.1 73.1 Barcode 11 (forward) 72.0 72.0 Barcode 12 (forward) 77.8 77.8 Barcode 13 (forward) 76.9 76.0 Barcode 14 (forward) 73.1 74.1 Barcode 15 (forward) 76.0 75.0 Barcode 16 (forward) 72.0 74.1 Barcode 17 (forward) 80.0 73.1 Barcode 18 (forward) 71.4 74.1 Barcode 19 (forward) 74.1 76.0 Barcode 20 (forward) 73.1 76.0 Barcode 21 (forward) 76.0 75.0 Barcode 22 (forward) 75.0 75.0 Barcode 23 (forward) 73.1 76.0 Barcode 24 (forward) 77.8 77.8 Barcode 25 (forward) 76.9 76.0 Barcode 26 (forward) 75.0 75.0 Barcode 27 (forward) 71.4 76.0 Barcode 28 (forward) 72.0 74.1 Barcode 29 (forward) 77.8 77.8 Barcode 30 (forward) 72.0 75.0 Barcode 31 (forward) 76.0 77.8 Barcode 32 (forward) 75.0 76.0 Barcode 33 (forward) 72.4 75.0 Barcode 34 (forward) 75.0 75.0 Barcode 35 (forward) 74.1 72.0 Barcode 36 (forward) 70.8 72.0 Barcode 37 (forward) 75.0 75.0 Barcode 38 (forward) 74.1 76.0 Barcode 39 (forward) 72.0 75.0 Barcode 40 (forward) 73.1 75.0 Barcode 41 (forward) 75.0 75.0 Barcode 42 (forward) 74.1 76.9 Barcode 43 (forward) 73.1 75.0 Barcode 44 (forward) 71.4 75.0 Barcode 45 (forward) 72.0 75.0 Barcode 46 (forward) 73.1 73.1 Barcode 47 (forward) 76.0 72.0 Barcode 48 (forward) 72.0 73.1 Barcode 49 (forward) 73.3 76.9 Barcode 50 (forward) 75.0 79.2 Barcode 51 (forward) 70.8 79.2 Barcode 52 (forward) 75.0 75.0 Barcode 53 (forward) 75.0 73.1 Barcode 54 (forward) 76.9 76.9 Barcode 55 (forward) 72.0 73.1 Barcode 56 (forward) 76.0 76.0 Barcode 57 (forward) 75.0 74.1 Barcode 58 (forward) 71.4 73.1 Barcode 59 (forward) 73.1 75.0 Barcode 60 (forward) 73.1 76.9 Barcode 61 (forward) 73.1 73.1 Barcode 62 (forward) 83.3 83.3 Barcode 63 (forward) 72.0 72.0 Barcode 64 (forward) 76.9 75.0 Barcode 65 (forward) 76.0 77.8 Barcode 66 (forward) 73.1 74.1 Barcode 67 (forward) 76.0 76.0 Barcode 68 (forward) 75.0 76.0 Barcode 69 (forward) 79.2 75.0 Barcode 70 (forward) 72.4 72.4 Barcode 71 (forward) 73.1 73.1 Barcode 72 (forward) 76.0 79.2 Barcode 73 (forward) 74.1 76.0 Barcode 74 (forward) 73.1 74.1 Barcode 75 (forward) 75.0 75.0 Barcode 76 (forward) 76.9 76.9 Barcode 77 (forward) 75.0 74.1 Barcode 78 (forward) 76.9 76.0 Barcode 79 (forward) 73.1 73.1 Barcode 80 (forward) 70.8 74.1 Barcode 81 (forward) 79.2 76.0 Barcode 82 (forward) 76.9 76.0 Barcode 83 (forward) 72.0 73.1 Barcode 84 (forward) 74.1 73.1 Barcode 85 (forward) 75.0 79.2 Barcode 86 (forward) 70.8 74.1 Barcode 87 (forward) 72.0 73.1 Barcode 88 (forward) 75.9 75.0 Barcode 89 (forward) 75.0 76.0 Barcode 90 (forward) 72.0 72.0 Barcode 91 (forward) 74.1 76.0 Barcode 92 (forward) 75.0 72.0 Barcode 93 (forward) 74.1 77.8 Barcode 94 (forward) 80.0 76.0 Barcode 95 (forward) 72.0 75.0 Barcode 96 (forward) 75.0 73.1 Trimming adapters from read ends SQK-NSK007_Y_Top: AATGTACTTCGTTCAGTTACGTATTGCT SQK-NSK007_Y_Bottom: GCAATACGTAACTGAACGAAGT BC01_rev: CACAAAGACACCGACAACTTTCTT BC01: AAGAAAGTTGTCGGTGTCTTTGTG BC02_rev: ACAGACGACTACAAACGGAATCGA BC02: TCGATTCCGTTTGTAGTCGTCTGT BC03_rev: CCTGGTAACTGGGACACAAGACTC BC03: GAGTCTTGTGTCCCAGTTACCAGG BC04_rev: TAGGGAAACACGATAGAATCCGAA BC04: TTCGGATTCTATCGTGTTTCCCTA BC05_rev: AAGGTTACACAAACCCTGGACAAG BC05: CTTGTCCAGGGTTTGTGTAACCTT BC01: AAGAAAGTTGTCGGTGTCTTTGTG BC01_rev: CACAAAGACACCGACAACTTTCTT NB01_start: AATGTACTTCGTTCAGTTACGTATTGCTAAGGTTAACACAAAGACACCGACAACTTTCTTCAGCACCT NB01_end: AGGTGCTGAAGAAAGTTGTCGGTGTCTTTGTGTTAACCTTAGCAATACGTAACTGAACGAAGT NB02_start: AATGTACTTCGTTCAGTTACGTATTGCTAAGGTTAAACAGACGACTACAAACGGAATCGACAGCACCT NB02_end: AGGTGCTGTCGATTCCGTTTGTAGTCGTCTGTTTAACCTTAGCAATACGTAACTGAACGAAGT NB03_start: AATGTACTTCGTTCAGTTACGTATTGCTAAGGTTAACCTGGTAACTGGGACACAAGACTCCAGCACCT NB03_end: AGGTGCTGGAGTCTTGTGTCCCAGTTACCAGGTTAACCTTAGCAATACGTAACTGAACGAAGT NB04_start: AATGTACTTCGTTCAGTTACGTATTGCTAAGGTTAATAGGGAAACACGATAGAATCCGAACAGCACCT NB04_end: AGGTGCTGTTCGGATTCTATCGTGTTTCCCTATTAACCTTAGCAATACGTAACTGAACGAAGT NB05_start: AATGTACTTCGTTCAGTTACGTATTGCTAAGGTTAAAAGGTTACACAAACCCTGGACAAGCAGCACCT NB05_end: AGGTGCTGCTTGTCCAGGGTTTGTGTAACCTTTTAACCTTAGCAATACGTAACTGAACGAAGT 3,920 / 3,920 (100.0%) 3,915 / 3,920 reads had adapters trimmed from their start (275,440 bp removed) 2,018 / 3,920 reads had adapters trimmed from their end (74,241 bp removed) Splitting reads containing middle adapters 3,920 / 3,920 (100.0%) 31 / 3,920 reads were split based on middle adapters Saving trimmed reads to file pigz found - using it to compress instead of gzip Traceback (most recent call last): File "/usr/local/bin/porechop", line 33, in sys.exit(load_entry_point('porechop==0.2.4', 'console_scripts', 'porechop')()) File "/usr/local/lib/python3.10/dist-packages/porechop/porechop.py", line 76, in main output_reads(reads, args.format, args.output, read_type, args.verbosity, File "/usr/local/lib/python3.10/dist-packages/porechop/porechop.py", line 727, in output_reads subprocess.check_output(gzip_command + ' -c ' + out_filename + ' > ' + output, File "/usr/lib/python3.10/subprocess.py", line 421, in check_output return run(*popenargs, stdout=PIPE, timeout=timeout, check=True, File "/usr/lib/python3.10/subprocess.py", line 526, in run raise CalledProcessError(retcode, process.args, subprocess.CalledProcessError: Command 'pigz -p 10 -c TEMP_60624.fastq > data_artic/basecall_tiny_porechopped.fastq.gz' returned non-zero exit status 2.