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Error trinity partition #23

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rafaeltiveron opened this issue Mar 27, 2019 · 3 comments
Closed

Error trinity partition #23

rafaeltiveron opened this issue Mar 27, 2019 · 3 comments

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@rafaeltiveron
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rafaeltiveron commented Mar 27, 2019 •
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I've been encountering this error below:

succeeded(2217)   2.81867% completed.    
succeeded(2218)   2.81995% completed.    
succeeded(2219)   2.82122% completed.    

Error encountered::  <!----
CMD: /home/rafael/programas/ORP/software/anaconda/install/envs/orp_v2/opt/trinity-2.8.4/util/support_scripts/salmon_runner.pl /home/rafael/.../assemblies/Rmontenegrensis.trinity/read_partitions/Fb_0/CBin_616/c61724.trinity.reads.fa.out/Trinity.tmp.fasta /home/rafael/.../assemblies/Rmontenegrensis.trinity/read_partitions/Fb_0/CBin_616/c61724.trinity.reads.fa.out/single.fa 2>tmp.27300.1553597564.stderr

Errmsg:
CMD: salmon --no-version-check index -t /home/rafael/.../assemblies/Rmontenegrensis.trinity/read_partitions/Fb_0/CBin_616/c61724.trinity.reads.fa.out/Trinity.tmp.fasta -i /home/rafael/.../assemblies/Rmontenegrensis.trinity/read_partitions/Fb_0/CBin_616/c61724.trinity.reads.fa.out/Trinity.tmp.fasta.salmon.idx --type quasi -k 25 -p 1
index ["/home/rafael/.../assemblies/Rmontenegrensis.trinity/read_partitions/Fb_0/CBin_616/c61724.trinity.reads.fa.out/Trinity.tmp.fasta.salmon.idx"] did not previously exist  . . . creating it
[2019-03-26 07:52:44.707] [jLog] [info] building index
[2019-03-26 07:52:44.707] [jointLog] [info] [Step 1 of 4] : counting k-mers
Elapsed time: 0.000644187s

[2019-03-26 07:52:44.708] [jointLog] [info] Replaced 0 non-ATCG nucleotides
[2019-03-26 07:52:44.708] [jointLog] [info] Clipped poly-A tails from 0 transcripts
[2019-03-26 07:52:44.708] [jointLog] [info] Building rank-select dictionary and saving to disk
[2019-03-26 07:52:44.708] [jointLog] [info] done
Elapsed time: 1.0819e-05s
[2019-03-26 07:52:44.708] [jointLog] [info] Writing sequence data to file . . . 
[2019-03-26 07:52:44.708] [jointLog] [info] done
Elapsed time: 1.3754e-05s
[2019-03-26 07:52:44.708] [jointLog] [info] Building 32-bit suffix array (length of generalized text is 443)
[2019-03-26 07:52:44.708] [jointLog] [info] Building suffix array . . . 
success
saving to disk . . . done
Elapsed time: 1.823e-05s
done
Elapsed time: 0.000446444s


processed 0 positions[2019-03-26 07:52:44.709] [jointLog] [info] khash had 393 keys
[2019-03-26 07:52:44.709] [jointLog] [info] saving hash to disk . . . 
[2019-03-26 07:52:44.709] [jointLog] [info] done
Elapsed time: 6.3439e-05s
[2019-03-26 07:52:44.709] [jLog] [info] done building index
CMD: salmon --no-version-check quant -i /home/rafael/.../assemblies/Rmontenegrensis.trinity/read_partitions/Fb_0/CBin_616/c61724.trinity.reads.fa.out/Trinity.tmp.fasta.salmon.idx -l U -r /home/rafael/.../assemblies/Rmontenegrensis.trinity/read_partitions/Fb_0/CBin_616/c61724.trinity.reads.fa.out/single.fa -o salmon_outdir -p 1 --minAssignedFrags 1 
### salmon (mapping-based) v0.12.0
### [ program ] => salmon 
### [ command ] => quant 
### [ index ] => { /home/rafael/.../assemblies/Rmontenegrensis.trinity/read_partitions/Fb_0/CBin_616/c61724.trinity.reads.fa.out/Trinity.tmp.fasta.salmon.idx }
### [ libType ] => { U }
### [ unmatedReads ] => { /home/rafael/.../assemblies/Rmontenegrensis.trinity/read_partitions/Fb_0/CBin_616/c61724.trinity.reads.fa.out/single.fa }
### [ output ] => { salmon_outdir }
### [ threads ] => { 1 }
### [ minAssignedFrags ] => { 1 }
Logs will be written to salmon_outdir/logs
[2019-03-26 07:52:44.734] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2019-03-26 07:52:44.734] [jointLog] [warning] 

NOTE: It appears you are running salmon without the `--validateMappings` option.
Mapping validation can generally improve both the sensitivity and specificity of mapping,
with only a moderate increase in use of computational resources. 
Unless there is a specific reason to do this (e.g. testing on clean simulated data),
`--validateMappings` is generally recommended.

[2019-03-26 07:52:44.734] [jointLog] [info] parsing read library format
[2019-03-26 07:52:44.734] [jointLog] [info] There is 1 library.
[2019-03-26 07:52:44.771] [jointLog] [info] Loading Quasi index
[2019-03-26 07:52:44.771] [jointLog] [info] Loading 32-bit quasi index
[2019-03-26 07:52:44.771] [jointLog] [info] done
[2019-03-26 07:52:44.771] [jointLog] [info] Index contained 2 targets
[2019-03-26 07:52:44.771] [stderrLog] [info] Loading Suffix Array 
[2019-03-26 07:52:44.771] [stderrLog] [info] Loading Transcript Info 
[2019-03-26 07:52:44.771] [stderrLog] [info] Loading Rank-Select Bit Array
[2019-03-26 07:52:44.771] [stderrLog] [info] There were 2 set bits in the bit array
[2019-03-26 07:52:44.771] [stderrLog] [info] Computing transcript lengths
[2019-03-26 07:52:44.771] [stderrLog] [info] Waiting to finish loading hash
[2019-03-26 07:52:44.771] [stderrLog] [info] Done loading index




Error, cmd:
salmon --no-version-check quant -i /home/rafael/.../assemblies/Rmontenegrensis.trinity/read_partitions/Fb_0/CBin_616/c61724.trinity.reads.fa.out/Trinity.tmp.fasta.salmon.idx -l U -r /home/rafael/.../assemblies/Rmontenegrensis.trinity/read_partitions/Fb_0/CBin_616/c61724.trinity.reads.fa.out/single.fa -o salmon_outdir -p 1 --minAssignedFrags 1 
 died with ret (256) at /home/rafael/programas/ORP/software/anaconda/install/envs/orp_v2/opt/trinity-2.8.4/util/support_scripts/../../PerlLib/Process_cmd.pm line 19.
	Process_cmd::process_cmd("salmon --no-version-check quant -i /home/rafael/..."...) called at /home/rafael/programas/ORP/software/anaconda/install/envs/orp_v2/opt/trinity-2.8.4/util/support_scripts/salmon_runner.pl line 26

--->

-salmon error reported: Error, cmd: /home/rafael/programas/ORP/software/anaconda/install/envs/orp_v2/opt/trinity-2.8.4/util/support_scripts/salmon_runner.pl /home/rafael/.../assemblies/Rmontenegrensis.trinity/read_partitions/Fb_0/CBin_616/c61724.trinity.reads.fa.out/Trinity.tmp.fasta /home/rafael/.../assemblies/Rmontenegrensis.trinity/read_partitions/Fb_0/CBin_616/c61724.trinity.reads.fa.out/single.fa 2>tmp.27300.1553597564.stderr died with ret 256  at /home/rafael/programas/ORP/software/anaconda/install/envs/orp_v2/opt/trinity-2.8.4/PerlLib/Pipeliner.pm line 186.
	Pipeliner::run(Pipeliner=HASH(0x564e71a255d8)) called at /home/rafael/programas/ORP/software/anaconda/install/envs/orp_v2/opt/trinity-2.8.4/util/support_scripts/../../Trinity line 1778
	eval {...} called at /home/rafael/programas/ORP/software/anaconda/install/envs/orp_v2/opt/trinity-2.8.4/util/support_scripts/../../Trinity line 1777
	main::run_Trinity() called at /home/rafael/programas/ORP/software/anaconda/install/envs/orp_v2/opt/trinity-2.8.4/util/support_scripts/../../Trinity line 1345
	eval {...} called at /home/rafael/programas/ORP/software/anaconda/install/envs/orp_v2/opt/trinity-2.8.4/util/support_scripts/../../Trinity line 1344
WARNING - salmon failure mode not recognized by Trinity:
Error, cmd: /home/rafael/programas/ORP/software/anaconda/install/envs/orp_v2/opt/trinity-2.8.4/util/support_scripts/salmon_runner.pl /home/rafael/.../assemblies/Rmontenegrensis.trinity/read_partitions/Fb_0/CBin_616/c61724.trinity.reads.fa.out/Trinity.tmp.fasta /home/rafael/.../assemblies/Rmontenegrensis.trinity/read_partitions/Fb_0/CBin_616/c61724.trinity.reads.fa.out/single.fa 2>tmp.27300.1553597564.stderr died with ret 256  at /home/rafael/programas/ORP/software/anaconda/install/envs/orp_v2/opt/trinity-2.8.4/PerlLib/Pipeliner.pm line 186.
	Pipeliner::run(Pipeliner=HASH(0x564e71a255d8)) called at /home/rafael/programas/ORP/software/anaconda/install/envs/orp_v2/opt/trinity-2.8.4/util/support_scripts/../../Trinity line 1778
	eval {...} called at /home/rafael/programas/ORP/software/anaconda/install/envs/orp_v2/opt/trinity-2.8.4/util/support_scripts/../../Trinity line 1777
	main::run_Trinity() called at /home/rafael/programas/ORP/software/anaconda/install/envs/orp_v2/opt/trinity-2.8.4/util/support_scripts/../../Trinity line 1345
	eval {...} called at /home/rafael/programas/ORP/software/anaconda/install/envs/orp_v2/opt/trinity-2.8.4/util/support_scripts/../../Trinity line 1344

 - retaining Trinity transcripts provided as input to salmon, w/o filtering (pre-salmon mode).

succeeded(2220)   2.82249% completed.    
succeeded(2221)   2.82376% completed.    
succeeded(2222)   2.82503% completed.

This error repeats with more following "succeeded" steps. Why Trinity is not partitioning correctly? Paired-ends are 8gb of data, too many reads, compacted in .gz file. Is this a problem?
@macmanes
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Hmm, this is a Trinity problem, so it might be best posted over there. In reading some of those messages, it looks like some of the issue might be related to version incompatabilities. What versions of Salmon and Trinity are you using?

@rafaeltiveron
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Versions:
Oyster River Protocol 2.1.0, with:

  • Trinity 2.8.4
  • Salmon 0.12.0

@rafaeltiveron
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I've fixed. I was running two fastq files that are not paired-end to each other. So, no mapping conditions were found, like not closing gaps. With the correct files, everything was gone ok. Sorry for this inconvenience.

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@macmanes @rafaeltiveron