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atulkakrana / PHASIS

Suite for phased clusters discovery, comparison, annotation and to identify miRNA triggers - uses MapReduce model [In review]
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Stuck at Clusters have been scored #15

Open mictadlo opened 5 years ago

mictadlo commented 5 years ago

Hi, It appears that PHASIS get stuck at the second round of clusters have been scored

#### Fn: phaser #############################
sRNA library located - Running phasing analysis
SRR1555764.fix.fastp.fas
** Problem with Phasing script - Return code not 0
Thu Aug 29 07:57:10 2019: Clusters have been scored...
# reads processed: 2971890
# reads with at least one reported alignment: 1335851 (44.95%)
# reads that failed to align: 1136504 (38.24%)
# reads with alignments suppressed due to -m: 499535 (16.81%)
Reported 3187434 alignments
# reads processed: 4152909
# reads with at least one reported alignment: 1743245 (41.98%)
# reads that failed to align: 1791404 (43.14%)
# reads with alignments suppressed due to -m: 618260 (14.89%)
Reported 4013018 alignments
Thu Aug 29 07:57:26 2019: aligning is done
Thu Aug 29 07:57:39 2019: finished the loading of sRNA alignment data.
Thu Aug 29 07:57:41 2019: finished the sorting of presplitted sRNA clusters data
Thu Aug 29 07:57:41 2019: total 2599 presplitted sRNA clusters
# reads processed: 7739944
# reads with at least one reported alignment: 5575799 (72.04%)
# reads that failed to align: 1174960 (15.18%)
# reads with alignments suppressed due to -m: 989185 (12.78%)
Reported 10475353 alignments
Thu Aug 29 07:57:30 2019: aligning is done
Thu Aug 29 07:57:43 2019: finished the loading of sRNA alignment data.
Thu Aug 29 07:57:44 2019: finished the sorting of presplitted sRNA clusters data
Thu Aug 29 07:57:45 2019: total 2796 presplitted sRNA clusters
Thu Aug 29 07:58:07 2019: Clusters have been scored...
Thu Aug 29 07:57:43 2019: aligning is done
Thu Aug 29 07:58:09 2019: finished the loading of sRNA alignment data.
Thu Aug 29 07:58:14 2019: finished the sorting of presplitted sRNA clusters data
Thu Aug 29 07:58:17 2019: total 41726 presplitted sRNA clusters
Thu Aug 29 07:58:17 2019: Clusters have been scored...
Thu Aug 29 08:02:16 2019: Clusters have been scored...
=>> PBS: job killed: walltime 154899 exceeded limit 154800

What did I miss?

Thank you in advance,

Michal

atulkakrana commented 5 years ago

Could you please paste content of your settings file?

Atul

mictadlo commented 5 years ago 
@runType                = G
@reference              = /scratch/NbV1ChF.fasta
@userLibs               = SRR1555764.fix.fastp.fasta,SRR1555765.fix.fastp.fasta,SRR6074038.fastp.fasta,SRR6074039.fastp.fasta,SRR935013.fastp.fasta,SRR947064.fastp.fasta

@libFormat              = F                                     
@phase          = 21

<<< Optional Settings, leave empty to make index on fly and reuse, value in text>>>
@index          = /scratch/NbV1ChF_index/NbV1ChF 

<<< Advanced Settings, value in text>>>
@minDepth               = 3
@clustBuffer    = 300
@mismat         = 3