Error in step1

[baravalle]

Hi, I'm trying step 1: bash HashCounting.sh 6 33 22

but I get some problems with the parallel call. The option --no-notice doesn't seem to be available in my version - so I have removed it.

This is what I get, with bash -x (the CreateHash code seems to be working, so I have commented the lines after the first execution):

bash -x HashCounting.sh 6 33 22 \+ '[' 3 -ne 3 ']' \+ numThreads=6 \+ kmerLen=33 \+ export hashSize=22 \+ hashSize=22 \+ mkdir Logs mkdir: cannot create directoryLogs': File exists ++ grep '^-' ++ wc -l ++ ls -l original_reads/SRR492065.10kReads.plusSpike.fastq original_reads/SRR492066.10kReads.plusSpike.fastq original_reads/SRR492182.10kReads.plusSpike.fastq original_reads/SRR492183.10kReads.plusSpike.fastq original_reads/SRR492184.10kReads.plusSpike.fastq originalreads/SRR492185.10kReads.plusSpike.fastq original reads/SRR492186.10kReads.plusSpike.fastq original_reads/SRR492187.10kReads.plusSpike.fastq original_reads/SRR492188.10kReads.plusSpike.fastq original_reads/SRR 492189.10kReads.plusSpike.fastq original_reads/SRR492190.10kReads.plusSpike.fastq original_reads/SRR492191.10kReads.plusSpike.fastq original_reads/SRR492192.10 kReads.plusSpike.fastq original_reads/SRR492193.10kReads.plusSpike.fastq original_reads/SRR492194.10kReads.plusSpike.fastq original_reads/SRR492195.10kReads.pl usSpike.fastq original_reads/SRR492196.10kReads.plusSpike.fastq original_reads/SRR492197.10kReads.plusSpike.fastq

• numInputFiles=18 ++ seq 1 18
• parallel -j 6 --halt-on-error 2 'echo $(date) hashing reads in file {}; \ python LSA/hash_fastq_reads.py -r {} -i original_reads/ -o hashed_reads/ >> Logs/HashReads.log 2>&1' ::: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 parallel: Warning: YOU ARE USING --tollef. IF THINGS ARE ACTING WEIRD USE --gnu. parallel: Warning: --tollef is obsolete and will be retired 20140222. parallel: Warning: See: http://lists.gnu.org/archive/html/parallel/2013-02/msg00018.html Thu Feb 4 23:55:26 GMT 2016 hashing reads in file {} /bin/bash: :::: command not found /bin/bash: 1: command not found /bin/bash: 2: command not found parallel: This job failed: /bin/bash -c ::: /bin/bash: 3: command not found
• '[' 127 -ne 0 ']'
• echo 'printing end of last log file...' printing end of last log file...
• tail Logs/HashReads.log /bin/bash: 4: command not found fr = int(arg) - 1 ValueError: invalid literal for int() with base 10: '{}' Traceback (most recent call last): File "LSA/hash_fastq_reads.py", line 54, in fr = int(arg) - 1 ValueError: invalid literal for int() with base 10: '{}' Traceback (most recent call last): File "LSA/hash_fastq_reads.py", line 54, in fr = int(arg) - 1 ValueError: invalid literal for int() with base 10: '{}'
• exit 1`

Any ideas of what this could be?

  Andres

[baravalle]

Hi all, the problem was in the library versions - with more up to date libraries I managed to go through the test data.

 Andres