Problem with a Trinity run

[Baradwaj]

Hi Brian,

Trinity run stopped with an error during Jellyfish step.

The relavent log section is as below.

I searched for the "DD63XKN1:378:C5NFFACXX:1:1104:7590:8635/2" stat in the "right.fa.K25.stats.sort" file which is indeed missing the fields. How can I move forward?

Please help!

-------------------------------------------
----------- Jellyfish  --------------------
-- (building a k-mer catalog from reads) --
-------------------------------------------

CMD: jellyfish count -t 6 -m 25 -s 100000000  --canonical  both.fa
CMD finished (3449 seconds)
CMD: jellyfish histo -t 6 -o jellyfish.K25.min2.kmers.fa.histo mer_counts.jf
CMD finished (37 seconds)
CMD: jellyfish dump -L 2 mer_counts.jf > jellyfish.K25.min2.kmers.fa
CMD finished (140 seconds)
CMD: touch jellyfish.K25.min2.kmers.fa.success
CMD finished (0 seconds)
-generating stats files
CMD: /usr/local/bin/util/..//Inchworm/bin/fastaToKmerCoverageStats --reads left.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25  --num_threads 3  --DS  > left.fa.K25.stats
CMD: /usr/local/bin/util/..//Inchworm/bin/fastaToKmerCoverageStats --reads right.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25  --num_threads 3  --DS  > right.fa.K25.stats
-reading Kmer occurrences...
-reading Kmer occurrences...

 done parsing 438614125 Kmers, 438614125 added, taking 459 seconds.

 done parsing 438614125 Kmers, 438614125 added, taking 460 seconds.
STATS_GENERATION_TIME: 8196 seconds.
CMD finished (8745 seconds)
STATS_GENERATION_TIME: 8657 seconds.
CMD finished (9198 seconds)
CMD: touch left.fa.K25.stats.ok
CMD finished (0 seconds)
CMD: touch right.fa.K25.stats.ok
CMD finished (0 seconds)
-sorting each stats file by read name.
CMD: head -n1 left.fa.K25.stats > left.fa.K25.stats.sort && tail -n +2 left.fa.K25.stats | /usr/bin/sort --parallel=6 -k1,1 -T . -S 27G >> left.fa.K25.stats.sort
CMD: head -n1 right.fa.K25.stats > right.fa.K25.stats.sort && tail -n +2 right.fa.K25.stats | /usr/bin/sort --parallel=6 -k1,1 -T . -S 27G >> right.fa.K25.stats.sort
CMD finished (1357 seconds)
CMD finished (2962 seconds)
CMD: touch left.fa.K25.stats.sort.ok
CMD finished (0 seconds)
CMD: touch right.fa.K25.stats.sort.ok
CMD finished (0 seconds)
-defining normalized reads
CMD: /usr/local/bin/util/..//util/support_scripts//nbkc_merge_left_right_stats.pl --left left.fa.K25.stats.sort --right right.fa.K25.stats.sort --sorted > pairs.K25.stats
-opening left.fa.K25.stats.sort
-opening right.fa.K25.stats.sort
-done opening files.
Error, line: [DD63XKN1:378:C5NFFACXX:1:1104:7590:8635/2 15514
] $VAR1 = [
          'DD63XKN1:378:C5NFFACXX:1:1104:7590:8635/2',
          '15514'
        ];
 is lacking 5 fields: $VAR1 = [
          'acc',
          'median_cov',
          'mean_cov',
          'stdev',
          'tid'
        ];
 at /usr/local/bin/util/support_scripts/../../PerlLib/DelimParser.pm line 162, <$right_fh> line 3863767.
DelimParser::Reader::get_row(DelimParser::Reader=HASH(0x5f5c7ed73150)) called at /usr/local/bin/util/..//util/support_scripts//nbkc_merge_left_right_stats.pl line 146
Error, cmd: /usr/local/bin/util/..//util/support_scripts//nbkc_merge_left_right_stats.pl --left left.fa.K25.stats.sort --right right.fa.K25.stats.sort --sorted > pairs.K25.stats died with ret 6400 at /usr/local/bin/util/insilico_read_normalization.pl line 807.
Error, cmd: /usr/local/bin/util/insilico_read_normalization.pl --seqType fq --JM 55G  --max_cov 200 --min_cov 1 --CPU 6 --output /media/baradwaj/Research/Sandlewood/Trinity_Runs/insilico_read_normalization --max_CV 10000  --left SRR2541771_1.fastq.PwU.qtrim.fq,SRR2541774_1.fastq.PwU.qtrim.fq,SRR2541775_1.fastq.PwU.qtrim.fq,SRR2541780_1.fastq.PwU.qtrim.fq,SRR2541781_1.fastq.PwU.qtrim.fq,SRR2541808_1.fastq.PwU.qtrim.fq,SRR2541809_1.fastq.PwU.qtrim.fq,SRR2541772_1.fastq.PwU.qtrim.fq,SRR2541776_1.fastq.PwU.qtrim.fq,SRR2541777_1.fastq.PwU.qtrim.fq,SRR2541792_1.fastq.PwU.qtrim.fq,SRR2541798_1.fastq.PwU.qtrim.fq,SRR2541810_1.fastq.PwU.qtrim.fq,SRR2541811_1.fastq.PwU.qtrim.fq,SRR2541773_1.fastq.PwU.qtrim.fq,SRR2541778_1.fastq.PwU.qtrim.fq,SRR2541779_1.fastq.PwU.qtrim.fq,SRR2541801_1.fastq.PwU.qtrim.fq,SRR2541805_1.fastq.PwU.qtrim.fq,SRR2541812_1.fastq.PwU.qtrim.fq,SRR2541813_1.fastq.PwU.qtrim.fq --right SRR2541771_2.fastq.PwU.qtrim.fq,SRR2541774_2.fastq.PwU.qtrim.fq,SRR2541775_2.fastq.PwU.qtrim.fq,SRR2541780_2.fastq.PwU.qtrim.fq,SRR2541781_2.fastq.PwU.qtrim.fq,SRR2541808_2.fastq.PwU.qtrim.fq,SRR2541809_2.fastq.PwU.qtrim.fq,SRR2541772_2.fastq.PwU.qtrim.fq,SRR2541776_2.fastq.PwU.qtrim.fq,SRR2541777_2.fastq.PwU.qtrim.fq,SRR2541792_2.fastq.PwU.qtrim.fq,SRR2541798_2.fastq.PwU.qtrim.fq,SRR2541810_2.fastq.PwU.qtrim.fq,SRR2541811_2.fastq.PwU.qtrim.fq,SRR2541773_2.fastq.PwU.qtrim.fq,SRR2541778_2.fastq.PwU.qtrim.fq,SRR2541779_2.fastq.PwU.qtrim.fq,SRR2541801_2.fastq.PwU.qtrim.fq,SRR2541805_2.fastq.PwU.qtrim.fq,SRR2541812_2.fastq.PwU.qtrim.fq,SRR2541813_2.fastq.PwU.qtrim.fq --pairs_together  --PARALLEL_STATS   died with ret 512 at /usr/local/bin/Trinity line 2919.
main::process_cmd("/usr/local/bin/util/insilico_read_normalization.pl --seqType "...) called at /usr/local/bin/Trinity line 3472
main::normalize("/media/baradwaj/Research/Sandlewood/Trinity_Runs/insilico_rea"..., 200, ARRAY(0x5ce4a24f0840), ARRAY(0x5ce4a24f0870)) called at /usr/local/bin/Trinity line 3412
main::run_normalization(200, ARRAY(0x5ce4a24f0840), ARRAY(0x5ce4a24f0870)) called at /usr/local/bin/Trinity line 1450

--------------------------------------------------------------------------------------------

With best regards,

Baradwaj

    

    

[Brian Haas]

Hi,

It looks like something got corrupted there.

You might try removing the directory that has the pairs.K25.stats file in it, and then rerunning Trinity with the '--no_parallel_norm_stats'  parameter.   It should pick up around where it left off and use less resources and less chance of something getting corrupted along the way.

--

--
Brian J. Haas
The Broad Institute
http://broadinstitute.org/~bhaas

 

[Baradwaj]

Hello Brian,

It worked :)

With best regards 

Baradwaj 

[Brian Haas]

Excellent!  Always great to hear!