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Oshlack / JAFFA

JAFFA is a multi-step pipeline that takes either raw RNA-Seq reads, or pre-assembled transcripts, then searches for gene fusions
https://github.com/Oshlack/JAFFA/wiki
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jaffal error #61

Closed readmanchiu closed 3 years ago

readmanchiu commented 3 years ago

Hi,

I was trying to do run jaffal and stopped by the following error:

cat SRR12010483.sra.fastq/SRR12010483.sra.fastq.txt | awk '{print $1}' > SRR12010483.sra.fastq/SRR12010483.sra.fastq.fusions.fa.temp ;                 /projects/xxx/yyy/jaffa/JAFFA-version-2.1/tools/bin/reformat in=SRR12010483.sra.fastq/SRR12010483.sra.fastq.fasta out=stdout.fasta fastawrap=0 |  SRR12010483.sra.fastq/SRR12010483.sra.fastq.fusions.fa.temp > SRR12010483.sra.fastq/SRR12010483.sra.fastq.fusions.fa ;                 rm SRR12010483.sra.fastq/SRR12010483.sra.fastq.fusions.fa.temp ;

should there be some executable after the pipe in the command???

|  SRR12010483.sra.fastq/SRR12010483.sra.fastq.fusions.fa.temp > SRR12010483.sra.fastq/SRR12010483.sra.fastq.fusions.fa

Output after running bpipe errors:

============================= Found 1 failed commands from run 159543 ==============================

============================================ Command 9 =============================================

Command    : cat SRR12010483.sra.fastq/SRR12010483.sra.fastq.txt | awk '{print $1}' > SRR12010483.sra.fastq/SRR12010483.sra.fastq.fusions.fa.temp ;                 /projects/xxx/yyy/jaffa/JAFFA-version-2.1/tools/bin/reformat in=SRR12010483.sra.fastq/SRR12010483.sra.fastq.fasta out=stdout.fasta fastawrap=0 |  SRR12010483.sra.fastq/SRR12010483.sra.fastq.fusions.fa.temp > SRR12010483.sra.fastq/SRR12010483.sra.fastq.fusions.fa ;                 rm SRR12010483.sra.fastq/SRR12010483.sra.fastq.fusions.fa.temp ;
Exit Code  : 1
Output     : 

No command output found in most recent log file
nadiadavidson commented 3 years ago

Yes, you are right, there should be a "extract_seq_from_fasta" after the pipe. This likely means that it was not installed. You can check in tools.groovy in the directory where you installed JAFFA and it's likely the path to this program will be empty. When you ran ./install_linux64.sh, if should have compiled it or thrown an error. You can try rerunning this script and send me the output to see what's gone wrong. Otherwise you can compile/install manually: from the directory when you ran install_linux64.sh, "cd tools" then "g++ -O3 -o bin/extract_seq_from_fasta ../src/extract_seq_from_fasta.c++", and let me know what it does.

Cheers, Nadia.

nadiadavidson commented 3 years ago

This flag has now been added to the master code branch.