gmap error after about 24 hours of running OK #88
Comments
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Hi,
I've had trouble with different versions of gmap. The one that's worked
well for me is:
http://research-pub.gene.com/gmap/src/gmap-gsnap-2017-11-15.tar.gz
The 'no paths found' is just reported when the transcript isn't found to
align to the target genome. It did seem to crash, though, at some point.
~b
…On Wed, Sep 26, 2018 at 10:34 AM jamlover ***@***.***> wrote:
Hi. I started a run yesterday morning with Trinity assembled reads (denovo
and genome guided) as inputs and things seemed to be going fine, but when I
looked this morming I found a gmap error in the output stream -
....No paths found for TRINITY_GG_125659_c0_g2_i2
No paths found for TRINITY_GG_125665_c0_g1_i1
No paths found for TRINITY_GG_125667_c0_g1_i1
....No paths found for TRINITY_GG_125743_c5_g4_i1
..No paths found for TRINITY_GG_125767_c12_g1_i18
............Error, cmd: gmap -D . -d fish_29Aug2018_8Ahzp.fasta.gmap
Trinity.all.fasta -f 3 -n 0 -x 50 -t 24 -B 5
--max-intronlength-middle=500000 --max-intronlength-ends=500000 died with
ret (9) at
/data/progs/PASA/scripts/process_GMAP_alignments_gff3_chimeras_ok.pl line
115.
Thread 1 terminated abnormally: Error, cmd:
/data/progs/PASA/scripts/process_GMAP_alignments_gff3_chimeras_ok.pl
--genome fish_29Aug2018_8Ahzp.fasta --transcripts Trinity.all.fasta --CPU
24 -N 1 -I 500000 > gmap.spliced_alignments.gff3
died with ret (65280) at
/data/progs/PASA/scripts/../PerlLib/Process_cmd.pm line 18 thread 1.
Process_cmd::process_cmd("/data/progs/PASA/scripts/process_GMAP_alignments_gff3_chimera"...)
called at /data/progs/PASA/scripts/run_spliced_aligners.pl line 109
thread 1
main::run_gmap() called at /data/progs/PASA/scripts/
run_spliced_aligners.pl line 70 thread 1
eval {...} called at /data/progs/PASA/scripts/run_spliced_aligners.pl
line 70 thread 1
ERROR, thread 1 exited with error Error, cmd:
/data/progs/PASA/scripts/process_GMAP_alignments_gff3_chimeras_ok.pl
--genome fish_29Aug2018_8Ahzp.fasta --transcripts Trinity.all.fasta --CPU
24 -N 1 -I 500000 > gmap.spliced_alignments.gff3
died with ret (65280) at
/data/progs/PASA/scripts/../PerlLib/Process_cmd.pm line 18 thread 1.
Process_cmd::process_cmd("/data/progs/PASA/scripts/process_GMAP_alignments_gff3_chimera"...)
called at /data/progs/PASA/scripts/run_spliced_aligners.pl line 109
thread 1
main::run_gmap() called at /data/progs/PASA/scripts/
run_spliced_aligners.pl line 70 thread 1
eval {...} called at /data/progs/PASA/scripts/run_spliced_aligners.pl
line 70 thread 1
.............................................................................................Searched
86718589 bases in 130840 sequences
.......................................................................................................................................................................................................................
The blat alignments are still churning away happily at this point. The
file gmap.spliced_alignments.gff3 is definitely truncated, but has 885072
lines of with alignments of reads to 5894 of my 6043 total scaffolds.
Any idea on what the problem might be and/or what I should do next? I've
attached the whol output stream file for reference. The error message above
was copied from the bottom of it.
Thanks,
John Martinson
output.log
<//www.greatytc.com/PASApipeline/PASApipeline/files/2420187/output.log>
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So, a few things.
Thanks again, John |
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Hi John,
responses below:
On Wed, Sep 26, 2018 at 1:52 PM jamlover ***@***.***> wrote:
So, a few things.
1. Should I just let the run continue for now or do you think I should
stop it? Could I possibly try running gmap outside the pipeline (see 2
below) and see if I can generate the "missing" results and resume the
pipeline somehow after doing that without having to redo everything?
Install the version of gmap you use and try the whole thing (or somehow
resume) again? What do you think?
I'd kill it. Since the gmap step crashed, it's going to fully crash once
the blat step finishes.
1. I did use this version of gmap successfully (I believe) on an
earlier run (there was an empty "gmap.spliced_alignments.gff3.completed"
file generated which I assume means it completed successfully). Assuming
I'm correct that it finished successfully, I wonder what was different this
time? I did have new Trinity assembled reads and a revised genome, but that
seems like it would be relatively trivial. I wonder if I just hit a memory
spike or something like that. Maybe I should try again and back down the
-CPUs a little. Just thinking aloud here I guess.
Not sure... gmap is great software, but I've had different versions crash
for a variety of different reasons. If you're using the latest version,
you can send the example sequence and target to the gmap author and he'll
be able to look into the reason for the crash. If you're not using the
version of gmap I suggested, then I'd suggest giving it a whirl. It's been
fairly stable wrt PASA, or you could try going with BLAT alone for now.
1. As far as the "No paths found" messages, it appears that about
2.5-3% of all input reads didn't or weren't going to map to the genome. I
assume that's probably not that unusual but was wondering if you had any
comment. The genome is about 1.4 Gb and there about 3.1 million Trinity
assembled reads (combined genome-guided and denovo) being aligned.
The percentage varies from sample to sample. If you have some low level
contamination, those transcripts won't map. Others could be de novo
assembly artifacts. Other cases are those where the reference is incomplete
(lots of gaps), or the sample isn't a perfect match to the reference genome
('novel' genes). Doing blast searches on the transcripts that don't match
should give some insights here.
hope this helps,
~b
…
Thanks again,
John
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Ok, I will assume there's not really an easy way to resume a partially completed run unless I hear something more from you. Thanks again for the guidance and thoughts. John |
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I don't think there's an easy way to resume a partially failed run. If it
crashes in this step, I think it'll warn you about it first deleting all
the results and then starting over.
…On Wed, Sep 26, 2018 at 2:47 PM jamlover ***@***.***> wrote:
Ok, I will assume there's not really an easy way to resume a partially
completed run unless I hear something more from you. Thanks again for the
guidance and thoughts.
John
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Brian, I upgraded to your suggested version of gmap and it worked. Thanks! John |
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great to hear!!
…On Fri, Sep 28, 2018 at 9:03 AM jamlover ***@***.***> wrote:
Closed #88 <#88>.
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Hi Brian, No paths found for TRINITY_DN59176_c0_g1_i1 How to know if the above log is created when the particular transcript isn't found or if there is an error in PASA? I have a long list of such occurrences but my PASA run is always "complete" , reached the end and creates a valid and failed for both gmap and blat with the main PASA gff3. I am using the above suggested version of gmap(gmap-gsnap-2017-11-15.tar.gz). Thanks! |
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The 'no paths found' is reported by gmap in those cases where it couldn't
find an alignment for the transcript.
In the case of the 'comprehensive transcript database':
//www.greatytc.com/PASApipeline/PASApipeline/wiki/PASA_comprehensive_db
those unaligned transcripts continue to be output as part of the final
'comprehensive' database.
Reasons for not aligning:
- novel transcript not represented by the genome (draft genome or sample
gene content difference with respect to reference)
- contaminant transcript in the sample sequenced/assembled
- some unusual assembly artifact
…On Mon, Oct 11, 2021 at 9:27 AM bioinfouser123 ***@***.***> wrote:
Hi Brian,
No paths found for TRINITY_DN59176_c0_g1_i1
How to know if the above log is created when the particular transcript
isn't found or if there is an error in PASA? I have a long list of such
occurrences but my PASA run is always "complete" , reached the end and
creates a valid and failed for both gmap and blat with the main PASA gff3.
I am using the above suggested version of
gmap(gmap-gsnap-2017-11-15.tar.gz).
Thanks!
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Hi. I started a run yesterday morning with Trinity assembled reads (denovo and genome guided) as inputs and things seemed to be going fine, but when I looked this morming I found a gmap error in the output stream -
....No paths found for TRINITY_GG_125659_c0_g2_i2
No paths found for TRINITY_GG_125665_c0_g1_i1
No paths found for TRINITY_GG_125667_c0_g1_i1
....No paths found for TRINITY_GG_125743_c5_g4_i1
..No paths found for TRINITY_GG_125767_c12_g1_i18
............Error, cmd: gmap -D . -d fish_29Aug2018_8Ahzp.fasta.gmap Trinity.all.fasta -f 3 -n 0 -x 50 -t 24 -B 5 --max-intronlength-middle=500000 --max-intronlength-ends=500000 died with ret (9) at /data/progs/PASA/scripts/process_GMAP_alignments_gff3_chimeras_ok.pl line 115.
Thread 1 terminated abnormally: Error, cmd:
/data/progs/PASA/scripts/process_GMAP_alignments_gff3_chimeras_ok.pl --genome fish_29Aug2018_8Ahzp.fasta --transcripts Trinity.all.fasta --CPU 24 -N 1 -I 500000 > gmap.spliced_alignments.gff3
died with ret (65280) at /data/progs/PASA/scripts/../PerlLib/Process_cmd.pm line 18 thread 1.
Process_cmd::process_cmd("/data/progs/PASA/scripts/process_GMAP_alignments_gff3_chimera"...) called at /data/progs/PASA/scripts/run_spliced_aligners.pl line 109 thread 1
main::run_gmap() called at /data/progs/PASA/scripts/run_spliced_aligners.pl line 70 thread 1
eval {...} called at /data/progs/PASA/scripts/run_spliced_aligners.pl line 70 thread 1
ERROR, thread 1 exited with error Error, cmd:
/data/progs/PASA/scripts/process_GMAP_alignments_gff3_chimeras_ok.pl --genome fish_29Aug2018_8Ahzp.fasta --transcripts Trinity.all.fasta --CPU 24 -N 1 -I 500000 > gmap.spliced_alignments.gff3
died with ret (65280) at /data/progs/PASA/scripts/../PerlLib/Process_cmd.pm line 18 thread 1.
Process_cmd::process_cmd("/data/progs/PASA/scripts/process_GMAP_alignments_gff3_chimera"...) called at /data/progs/PASA/scripts/run_spliced_aligners.pl line 109 thread 1
main::run_gmap() called at /data/progs/PASA/scripts/run_spliced_aligners.pl line 70 thread 1
eval {...} called at /data/progs/PASA/scripts/run_spliced_aligners.pl line 70 thread 1
.............................................................................................Searched 86718589 bases in 130840 sequences
.......................................................................................................................................................................................................................
The blat alignments are still churning away happily at this point. The file gmap.spliced_alignments.gff3 is definitely truncated, but has 885072 lines of with alignments of reads to 5894 of my 6043 total scaffolds.
Any idea on what the problem might be and/or what I should do next? I've attached the whol output stream file for reference. The error message above was copied from the bottom of it.
Thanks,
John Martinson
output.log
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