Ask away!
I have tried to run epi2me for differential gene expression (the normal commands from epi2me) but I keep getting the errors pasted below. I was wondering if this is something I can fix or if I need to contact IT?
Doing reference based transcript analysis
executor > local (5)
[4f/ba4c4e] checkBamHeaders (1) | 0 of 1
[- ] fastcat -
[53/4d7ca9] pip…:preprocess_ref_annotation | 0 of 1
[- ] pip…ctFastqIngressResultsInDir -
[da/d02661] pipeline:getVersions | 1 of 1, failed: 1 ✘
[76/8c1c4d] pipeline:getParams | 1 of 1, failed: 1 ✘
[- ] pipeline:preprocess_reads -
[e6/106f3f] pip…ne:build_minimap_index (1) | 1 of 1, failed: 1 ✘
[- ] pip…ference_assembly:map_reads -
[- ] pipeline:split_bam -
[- ] pipeline:assemble_transcripts -
[- ] pipeline:merge_gff_bundles -
[- ] pipeline:run_gffcompare -
[- ] pipeline:get_transcriptome -
[- ] pipeline:makeReport -
[- ] publish_results -
Doing reference based transcript analysis
ERROR ~ Error executing process > 'pipeline:preprocess_ref_annotation'
Caused by:
Process pipeline:preprocess_ref_annotation terminated with an error exit status (127)
Command executed:
sed -i -e 's/transcript_id "";//g' gencode.v22.annotation.chr20.gtf
mv gencode.v22.annotation.chr20.gtf "amended.gencode.v22.annotation.chr20.gtf"
Command exit status:
127
Command output:
(empty)
Command error:
.command.run: line 296: docker: command not found
Work dir:
/mnt/scratch/users/prc547/work/53/4d7ca981c27f9c927d3ebf36edcc54
Container:
ontresearch/wf-transcriptomes:shaaaf20a5a0e76f9e18bad21af639a6b69e4a31a2f
Tip: view the complete command output by changing to the process work dir and entering the command cat .command.out
-- Check '.nextflow.log' file for details
WARN: Killing running tasks (1)
Ask away!
I have tried to run epi2me for differential gene expression (the normal commands from epi2me) but I keep getting the errors pasted below. I was wondering if this is something I can fix or if I need to contact IT?
Doing reference based transcript analysis
executor > local (5)
[4f/ba4c4e] checkBamHeaders (1) | 0 of 1
[- ] fastcat -
[53/4d7ca9] pip…:preprocess_ref_annotation | 0 of 1
[- ] pip…ctFastqIngressResultsInDir -
[da/d02661] pipeline:getVersions | 1 of 1, failed: 1 ✘
[76/8c1c4d] pipeline:getParams | 1 of 1, failed: 1 ✘
[- ] pipeline:preprocess_reads -
[e6/106f3f] pip…ne:build_minimap_index (1) | 1 of 1, failed: 1 ✘
[- ] pip…ference_assembly:map_reads -
[- ] pipeline:split_bam -
[- ] pipeline:assemble_transcripts -
[- ] pipeline:merge_gff_bundles -
[- ] pipeline:run_gffcompare -
[- ] pipeline:get_transcriptome -
[- ] pipeline:makeReport -
[- ] publish_results -
Doing reference based transcript analysis
ERROR ~ Error executing process > 'pipeline:preprocess_ref_annotation'
Caused by:
Process
pipeline:preprocess_ref_annotationterminated with an error exit status (127)Command executed:
sed -i -e 's/transcript_id "";//g' gencode.v22.annotation.chr20.gtf
mv gencode.v22.annotation.chr20.gtf "amended.gencode.v22.annotation.chr20.gtf"
Command exit status:
127
Command output:
(empty)
Command error:
.command.run: line 296: docker: command not found
Work dir:
/mnt/scratch/users/prc547/work/53/4d7ca981c27f9c927d3ebf36edcc54
Container:
ontresearch/wf-transcriptomes:shaaaf20a5a0e76f9e18bad21af639a6b69e4a31a2f
Tip: view the complete command output by changing to the process work dir and entering the command
cat .command.out-- Check '.nextflow.log' file for details
WARN: Killing running tasks (1)