guigolab / ipsa-nf Goto Github PK

@emi80, currently only .fa files are recognized. However many users may use .fasta extension for their genome files. It would be useful to add .fasta to the default extensions for the genome reference.

I'm not sure if this is an issue with ipsa-nf or nextflow in general, so please redirect me if there's a better place to get help...

I have been trying to run this pipeline on google cloud and it keeps failing with a 412 "Precondition Failed" error, which is thrown after the first successful completion of an sjcount process. See the attached log file, line 785.
nextflow.log It seems there is some issue copying the .ssc and .ssj from the work directory to the A01 folder in the results directory. The pipeline runs fine for me on the included test dataset, so if there's any issue you know that may be causing this problem, I would be very appreciative!

Thanks for your help!

Hi dear,

my working directory where I run IPSA pipeline is located directly on my home directory.
While trying to run the IPSA pipeline I got the following error:
command run : ./nextflow run guigolab/ipsa-nf

Success : false
workDir : /home/jelhasnaoui/IPSA/work
exit status : 127
Error report: Error executing process > 'aggregateSSJ (E14_rep2.A02.ssj)'
Caused by:
Process aggregateSSJ (E14_rep2.A02.ssj) terminated with an error exit status (127)
Command executed:
aggregate.awk -v degree=1 -v readLength= -v margin=5 -v prefix= -v logfile=E14_rep2.A02.ssj.log E14_rep2.A01.ssj.tsv > E14_rep2.A02.ssj.tsv
Command exit status:
127
Command output:
(empty)
Command error:
.command.sh: line 2: aggregate.awk: command not found
Work dir:
/home/jelhasnaoui/IPSA/work/93/81fb6b38edf80890ad1b622455d148
Tip: view the complete command output by changing to the process work dir and entering the command cat .command.out
WARN: Killing pending tasks (7)
Error executing process > 'aggregateSSJ (E14_rep2.A02.ssj)'
Caused by:
Process aggregateSSJ (E14_rep2.A02.ssj) terminated with an error exit status (127)
Command executed:
aggregate.awk -v degree=1 -v readLength= -v margin=5 -v prefix= -v logfile=E14_rep2.A02.ssj.log E14_rep2.A01.ssj.tsv > E14_rep2.A02.ssj.tsv
Command exit status:
127
Command output:
(empty)
Command error:
.command.sh: line 2: aggregate.awk: command not found
Work dir:
/home/jelhasnaoui/IPSA/work/93/81fb6b38edf80890ad1b622455d148
Tip: view the complete command output by changing to the process work dir and entering the command cat .command.out

The error says that the aggregate.awk command is not found, like if the program is not able to recognize it.

Could you please help me to fix this issue?
Thank you in advance!

Best regards,
Jamal.

In the pipeline results section there is no mention of the merged output, i.e. all.A.psi.tsv, all.A.cosi.tsv, etc.

Also it would be nice if there is a small description of how the pipeline work. Maybe you can just add a link to this pdf from ipsa-full. It helped me understand a bit better the output of the pipeline.

Dear,

Thank you for sharing and making publicly available the great tool IPSA.

While running the test pipeline with the following command:
./nextflow run guigolab/ipsa-nf

I got the following error:
exit status : 2
Error report: Error executing process > 'annotate (E14_rep1.A03.ssj)'

Caused by:
Process annotate (E14_rep1.A03.ssj) terminated with an error exit status (2)

Command executed:

annotate.pl -annot annotation.gfx -dbx genome.dbx -idx genome.idx -deltaSS 10 -in E14_rep1.A02.ssj.tsv > E14_rep1.A03.ssj.tsv

Command exit status:
2

Command output:
(empty)

Command error:
Can't locate Perl/utils.pm in @inc (you may need to install the Perl::utils module) (@inc contains: /home/jelhasnaoui/.nextflow/assets/guigolab/ipsa-nf /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.20.2 /usr/local/share/perl/5.20.2 /usr/lib/x86_64-linux-gnu/perl5/5.20 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.20 /usr/share/perl/5.20 /usr/local/lib/site_perl .) at /home/jelhasnaoui/.nextflow/assets/guigolab/ipsa-nf/bin/annotate.pl line 2.
BEGIN failed--compilation aborted at /home/jelhasnaoui/.nextflow/assets/guigolab/ipsa-nf/bin/annotate.pl line 2.

Work dir:
/vol3/Reference/OriginalData/DeBortoli/03_2016_RNASeq_Noncoding/pipelines/IPSA/work/98/a1b7a3951b7f892b36677c61b4337b

Tip: when you have fixed the problem you can continue the execution appending to the nextflow command line the option -resume
WARN: Killing pending tasks (3)
ERROR ~ Error executing process > 'annotate (E14_rep1.A03.ssj)'

Caused by:
Process annotate (E14_rep1.A03.ssj) terminated with an error exit status (2)

Command executed:

annotate.pl -annot annotation.gfx -dbx genome.dbx -idx genome.idx -deltaSS 10 -in E14_rep1.A02.ssj.tsv > E14_rep1.A03.ssj.tsv

Command exit status:
2

Command output:
(empty)

Command error:
Can't locate Perl/utils.pm in @inc (you may need to install the Perl::utils module) (@inc contains: /home/jelhasnaoui/.nextflow/assets/guigolab/ipsa-nf /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.20.2 /usr/local/share/perl/5.20.2 /usr/lib/x86_64-linux-gnu/perl5/5.20 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.20 /usr/share/perl/5.20 /usr/local/lib/site_perl .) at /home/jelhasnaoui/.nextflow/assets/guigolab/ipsa-nf/bin/annotate.pl line 2.
BEGIN failed--compilation aborted at /home/jelhasnaoui/.nextflow/assets/guigolab/ipsa-nf/bin/annotate.pl line 2.

Work dir:
/vol3/Reference/OriginalData/DeBortoli/03_2016_RNASeq_Noncoding/pipelines/IPSA/work/98/a1b7a3951b7f892b36677c61b4337b

Tip: when you have fixed the problem you can continue the execution appending to the nextflow command line the option -resume

-- Check '.nextflow.log' file for details

I checked the location of the utils.pm file and it's located at :
/home/jelhasnaoui/.nextflow/assets/guigolab/ipsa-nf/Perl/utils.pm

I think that the problem is related to the location of the utils.pm file at the annotate process step. Could you please help me to fix this bug?
Thank you so much in advance!
Best regards,
Jamal.