error when processing own data

[markziemann]

ran the following command:

$ docker run -v $(pwd):/mnt -it mziemann/tallyup /root/code/volunteer_pipeline.sh ecoli -f e-BC24_CB2EYANXX_ATTCCT_L001_R1.fastq.gz e-BC24_CB2EYANXX_ATTCCT_L002_R1.fastq.gz

and got the following error:

+ echo Processing fastq files /mnt/e-BC24_CB2EYANXX_ATTCCT_L001_R1.fastq.gz and /mnt/e-BC24_CB2EYANXX_ATTCCT_L002_R1.fastq.gz in paired end mode
Processing fastq files /mnt/e-BC24_CB2EYANXX_ATTCCT_L001_R1.fastq.gz and /mnt/e-BC24_CB2EYANXX_ATTCCT_L002_R1.fastq.gz in paired end mode
+ FQ1=/mnt/e-BC24_CB2EYANXX_ATTCCT_L001_R1.fastq.gz
+ FQ2=/mnt/e-BC24_CB2EYANXX_ATTCCT_L002_R1.fastq.gz
++ basename /mnt/e-BC24_CB2EYANXX_ATTCCT_L001_R1.fastq.gz
++ cut -d . -f1
+ SRR=e-BC24_CB2EYANXX_ATTCCT_L001_R1
+ RDS=PE
+ '[' '!' -r /mnt/e-BC24_CB2EYANXX_ATTCCT_L001_R1.fastq.gz ']'
+ '[' '!' -r /mnt/e-BC24_CB2EYANXX_ATTCCT_L002_R1.fastq.gz ']'
+ mkdir e-BC24_CB2EYANXX_ATTCCT_L001_R1
+ cp /root/code/volunteer_pipeline.sh e-BC24_CB2EYANXX_ATTCCT_L001_R1
+ cd e-BC24_CB2EYANXX_ATTCCT_L001_R1
+ cp /mnt/e-BC24_CB2EYANXX_ATTCCT_L001_R1.fastq.gz /mnt/e-BC24_CB2EYANXX_ATTCCT_L002_R1.fastq.gz .
++ basename /mnt/e-BC24_CB2EYANXX_ATTCCT_L001_R1.fastq.gz
+ FQ1=e-BC24_CB2EYANXX_ATTCCT_L001_R1.fastq.gz
++ basename /mnt/e-BC24_CB2EYANXX_ATTCCT_L002_R1.fastq.gz
+ FQ2=e-BC24_CB2EYANXX_ATTCCT_L002_R1.fastq.gz
+ echo 'Starting /root/code/volunteer_pipeline.sh e-BC24_CB2EYANXX_ATTCCT_L001_R1
      current disk space = 842849864
      free memory = 131294344 '
+ tee -a e-BC24_CB2EYANXX_ATTCCT_L001_R1.log
Starting /root/code/volunteer_pipeline.sh e-BC24_CB2EYANXX_ATTCCT_L001_R1
      current disk space = 842849864
      free memory = 131294344 
++ echo e-BC24_CB2EYANXX_ATTCCT_L001_R1.fastq.gz e-BC24_CB2EYANXX_ATTCCT_L002_R1.fastq.gz
++ tr ' ' '\n'
++ grep -c '.gz$'
+ ISGZ=2
+ '[' 2 -eq 2 ']'
+ pigz -t e-BC24_CB2EYANXX_ATTCCT_L001_R1.fastq.gz
+ pigz -t e-BC24_CB2EYANXX_ATTCCT_L002_R1.fastq.gz
+ GZTEST=OK
+ '[' OK == OK ']'
+ pigz -d e-BC24_CB2EYANXX_ATTCCT_L001_R1.fastq.gz e-BC24_CB2EYANXX_ATTCCT_L002_R1.fastq.gz
++ basename e-BC24_CB2EYANXX_ATTCCT_L001_R1.fastq.gz .gz
+ FQ1=e-BC24_CB2EYANXX_ATTCCT_L001_R1.fastq
++ basename e-BC24_CB2EYANXX_ATTCCT_L002_R1.fastq.gz .gz
+ FQ2=e-BC24_CB2EYANXX_ATTCCT_L002_R1.fastq
++ echo e-BC24_CB2EYANXX_ATTCCT_L001_R1.fastq e-BC24_CB2EYANXX_ATTCCT_L002_R1.fastq
++ tr ' ' '\n'
++ grep -c '.bz2$'
+ ISBZ=0
+ '[' 0 -eq 2 ']'
++ echo e-BC24_CB2EYANXX_ATTCCT_L001_R1.fastq
++ egrep -c '(.fq$|.fastq$)'
+ ISFQ=1
+ '[' 1 -ne 2 ']'
+ echo Error. Unknown input file format. Input file extension should match .fastq or '.fq$'
Error. Unknown input file format. Input file extension should match .fastq or .fq$
+ exit1
+ rm e-BC24_CB2EYANXX_ATTCCT_L001_R1.fastq e-BC24_CB2EYANXX_ATTCCT_L002_R1.fastq '*.sra' '*tsv'
rm: cannot remove '*.sra': No such file or directory
rm: cannot remove '*tsv': No such file or directory
+ return 1
+ '[' 2 -eq 1 ']'
+ '[' -z PE ']'
+ exit

[markziemann]

multiple problems with this chunk of code

    ISFQ=$(echo $FQ1 | egrep -c '(.fq$|.fastq$)' )
    if [ $ISFQ -ne "2" ] ; then
      echo Error. Unknown input file format. Input file extension should match ".fastq" or ".fq"$
      exit1 ; return 1
    fi

[markziemann]

Looks to be fixed in the latest commit