Jellyfish errors

[Robert García Mendoza]

Hi, I got these errors. The first one is when I set Trinity without "--normalize_by_read_set"; the second is when I set it with "--normalize_by_read_set". Although when I ran a test with short datasets (50 million reads per dataset), Trinity worked well without any errors. But when I ran it with my datasets (100 million reads per dataset), I got these errors.

First errors

CMD: jellyfish count -t 6 -m 25 -s 50000000  --canonical  both.fa
Error, cmd: jellyfish count -t 6 -m 25 -s 50000000  --canonical  both.fa died with ret 9 at /home/dna/anaconda3/envs/trinity/opt/trinity-2.15.2/util/insilico_read_normalization.pl line 807.
Error, cmd: /home/dna/anaconda3/envs/trinity/opt/trinity-2.15.2/util/insilico_read_normalization.pl --seqType fq --JM 100G  --max_cov 50 --min_cov 1 --CPU 6 --output /mnt/d/trinity/trinity_out/insilico_read_normalization --max_CV 10000  --left /mnt/d/trinity/MCF_7_ctrl_1_R1.fq.gz,/mnt/d/trinity/MCF_7_ctrl_2_R1.fq.gz,/mnt/d/trinity/MCF_7_ctrl_3_R1.fq.gz,/mnt/d/trinity/MCF_7_fascinato_1_R1.fq.gz,/mnt/d/trinity/MCF_7_fascinato_2_R1.fq.gz,/mnt/d/trinity/MCF_7_fascinato_3_R1.fq.gz --right /mnt/d/trinity/MCF_7_ctrl_1_R2.fq.gz,/mnt/d/trinity/MCF_7_ctrl_2_R2.fq.gz,/mnt/d/trinity/MCF_7_ctrl_3_R2.fq.gz,/mnt/d/trinity/MCF_7_fascinato_1_R2.fq.gz,/mnt/d/trinity/MCF_7_fascinato_2_R2.fq.gz,/mnt/d/trinity/MCF_7_fascinato_3_R2.fq.gz --pairs_together  --PARALLEL_STATS   died with ret 512 at /home/dna/anaconda3/envs/trinity/bin/Trinity line 2919.
main::process_cmd("/home/dna/anaconda3/envs/trinity/opt/trinity-2.15.2/util/insi"...) called at /home/dna/anaconda3/envs/trinity/bin/Trinity line 3472
main::normalize("/mnt/d/trinity/trinity_out/insilico_read_normalization", 50, ARRAY(0x563ad2011548), ARRAY(0x563ad2011578)) called at /home/dna/anaconda3/envs/trinity/bin/Trinity line 3412

main::run_normalization(50, ARRAY(0x563ad2011548), ARRAY(0x563ad2011578)) called at /home/dna/anaconda3/envs/trinity/bin/Trinity line 1450

Second errors

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

CMD: jellyfish count -t 4 -m 25 -s 1095434790  --canonical  both.fa
CMD finished (700 seconds)
CMD: jellyfish histo -t 4 -o jellyfish.K25.min2.kmers.fa.histo mer_counts.jf
CMD finished (225 seconds)
CMD: jellyfish dump -L 2 mer_counts.jf > jellyfish.K25.min2.kmers.fa
CMD finished (674 seconds)
CMD: touch jellyfish.K25.min2.kmers.fa.success
CMD finished (0 seconds)
-generating stats files
CMD: /home/dna/anaconda3/envs/trinity/opt/trinity-2.15.2/util/..//Inchworm/bin/fastaToKmerCoverageStats --reads left.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25  --num_threads 2  --DS  > left.fa.K25.stats
CMD: /home/dna/anaconda3/envs/trinity/opt/trinity-2.15.2/util/..//Inchworm/bin/fastaToKmerCoverageStats --reads right.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25  --num_threads 2  --DS  > right.fa.K25.stats
-reading Kmer occurrences...
-reading Kmer occurrences...
bash: line 1: 35681 Killed                  /home/dna/anaconda3/envs/trinity/opt/trinity-2.15.2/util/..//Inchworm/bin/fastaToKmerCoverageStats --reads right.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25 --num_threads 2 --DS > right.fa.K25.stats
Thread 4 terminated abnormally: Error, cmd: /home/dna/anaconda3/envs/trinity/opt/trinity-2.15.2/util/..//Inchworm/bin/fastaToKmerCoverageStats --reads right.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25  --num_threads 2  --DS  > right.fa.K25.stats died with ret 35072 at /home/dna/anaconda3/envs/trinity/opt/trinity-2.15.2/util/insilico_read_normalization.pl line 807.
bash: line 1: 35680 Killed                  /home/dna/anaconda3/envs/trinity/opt/trinity-2.15.2/util/..//Inchworm/bin/fastaToKmerCoverageStats --reads left.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25 --num_threads 2 --DS > left.fa.K25.stats
Thread 3 terminated abnormally: Error, cmd: /home/dna/anaconda3/envs/trinity/opt/trinity-2.15.2/util/..//Inchworm/bin/fastaToKmerCoverageStats --reads left.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25  --num_threads 2  --DS  > left.fa.K25.stats died with ret 35072 at /home/dna/anaconda3/envs/trinity/opt/trinity-2.15.2/util/insilico_read_normalization.pl line 807.
Error, thread exited with error Error, cmd: /home/dna/anaconda3/envs/trinity/opt/trinity-2.15.2/util/..//Inchworm/bin/fastaToKmerCoverageStats --reads left.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25  --num_threads 2  --DS  > left.fa.K25.stats died with ret 35072 at /home/dna/anaconda3/envs/trinity/opt/trinity-2.15.2/util/insilico_read_normalization.pl line 807.

Error, thread exited with error Error, cmd: /home/dna/anaconda3/envs/trinity/opt/trinity-2.15.2/util/..//Inchworm/bin/fastaToKmerCoverageStats --reads right.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25  --num_threads 2  --DS  > right.fa.K25.stats died with ret 35072 at /home/dna/anaconda3/envs/trinity/opt/trinity-2.15.2/util/insilico_read_normalization.pl line 807.

Error, 2 threads errored out at /home/dna/anaconda3/envs/trinity/opt/trinity-2.15.2/util/insilico_read_normalization.pl line 1011.
Error, cmd: /home/dna/anaconda3/envs/trinity/opt/trinity-2.15.2/util/insilico_read_normalization.pl --seqType fq --JM 100G  --max_cov 200 --min_cov 1 --CPU 4 --output /mnt/z/RNAseqMCF7/MCF_7/trinity/trinity_out/norm_for_read_set_1 --max_CV 10000  --left /mnt/z/RNAseqMCF7/MCF_7/trinity/MCF_7_ctrl_1_R1.fq.gz --right /mnt/z/RNAseqMCF7/MCF_7/trinity/MCF_7_ctrl_1_R2.fq.gz --pairs_together  --PARALLEL_STATS   died with ret 7424 at /home/dna/anaconda3/envs/trinity/bin/Trinity line 2919.
main::process_cmd("/home/dna/anaconda3/envs/trinity/opt/trinity-2.15.2/util/insi"...) called at /home/dna/anaconda3/envs/trinity/bin/Trinity line 3472
main::normalize("/mnt/z/RNAseqMCF7/MCF_7/trinity/trinity_out/norm_for_read_set_1", 200, ARRAY(0x5613ce8ee138), ARRAY(0x5613ce8f1a08)) called at /home/dna/anaconda3/envs/trinity/bin/Trinity line 3389
main::run_normalization(200, ARRAY(0x5613ce6bbf10), ARRAY(0x5613ce6bbf28)) called at /home/dna/anaconda3/envs/trinity/bin/Trinity line 1450