Error normalization process Trinity

Question

[weimabri]

Hello I hope everyone is well. I have a question with this error in the normalization of the data.

I use this command

./Trinity --seqType fq --left /home/danielurrea/Escritorio/Paula_Manuela/SRR7942798_1.fastq --right /home/danielurrea/Escritorio/Paula_Manuela/SRR7942798_2.fastq --CPU 6 --max_memory 8G

The error thi's here.

Error, no reads made it to the normalization process...   at /home/danielurrea/Programas/trinityrnaseq-v2.13.2/util/..//util/support_scripts//nbkc_normalize.pl line 119.
Error, cmd: /home/danielurrea/Programas/trinityrnaseq-v2.13.2/util/..//util/support_scripts//nbkc_normalize.pl --stats_file pairs.K25.stats --max_cov 200  --min_cov 1 --max_CV 10000 > pairs.K25.stats.C200.maxCV10000.accs died with ret 65280 at /home/danielurrea/Programas/trinityrnaseq-v2.13.2/util/insilico_read_normalization.pl line 795.
Error, cmd: /home/danielurrea/Programas/trinityrnaseq-v2.13.2/util/insilico_read_normalization.pl --seqType fq --JM 8G  --max_cov 200 --min_cov 1 --CPU 6 --output /home/danielurrea/Programas/trinityrnaseq-v2.13.2/trinity_out_dir/insilico_read_normalization --max_CV 10000  --left /home/danielurrea/Escritorio/Paula_Manuela/SRR7942798_1.fastq --right /home/danielurrea/Escritorio/Paula_Manuela/SRR7942798_2.fastq --pairs_together  --PARALLEL_STATS   died with ret 512 at ./Trinity line 2863.
    main::process_cmd("/home/danielurrea/Programas/trinityrnaseq-v2.13.2/util/insili"...) called at ./Trinity line 3416
    main::normalize("/home/danielurrea/Programas/trinityrnaseq-v2.13.2/trinity_out"..., 200, ARRAY(0x55c0c6cd7f00), ARRAY(0x55c0c6ff5118)) called at ./Trinity line 3356
    main::run_normalization(200, ARRAY(0x55c0c6cd7f00), ARRAY(0x55c0c6ff5118)) called at ./Trinity line 1394

Thanks for the help

[GenoMax]

--max_memory 8G

With Trinity you need 1GB of RAM per million reads. So keep that mind.

[weimabri]

my pc have 16 Ram, i use the --max_memory 16G, and the problem continues.

Error, no reads made it to the normalization process...   at /home/danielurrea/Programas/trinityrnaseq-v2.13.2/util/..//util/support_scripts//nbkc_normalize.pl line 119.
Error, cmd: /home/danielurrea/Programas/trinityrnaseq-v2.13.2/util/..//util/support_scripts//nbkc_normalize.pl --stats_file pairs.K25.stats --max_cov 200  --min_cov 1 --max_CV 10000 > pairs.K25.stats.C200.maxCV10000.accs died with ret 65280 at /home/danielurrea/Programas/trinityrnaseq-v2.13.2/util/insilico_read_normalization.pl line 795.
Error, cmd: /home/danielurrea/Programas/trinityrnaseq-v2.13.2/util/insilico_read_normalization.pl --seqType fq --JM 16G  --max_cov 200 --min_cov 1 --CPU 6 --output /home/danielurrea/Programas/trinityrnaseq-v2.13.2/trinity_out_dir/insilico_read_normalization --max_CV 10000  --left /home/danielurrea/Escritorio/Paula_Manuela/SRR7942798_1.fastq --right /home/danielurrea/Escritorio/Paula_Manuela/SRR7942798_2.fastq --pairs_together  --PARALLEL_STATS   died with ret 512 at ./Trinity line 2863.
    main::process_cmd("/home/danielurrea/Programas/trinityrnaseq-v2.13.2/util/insili"...) called at ./Trinity line 3416
    main::normalize("/home/danielurrea/Programas/trinityrnaseq-v2.13.2/trinity_out"..., 200, ARRAY(0x557bb5db0220), ARRAY(0x557bb6157e18)) called at ./Trinity line 3356
    main::run_normalization(200, ARRAY(0x557bb5db0220), ARRAY(0x557bb6157e18)) called at ./Trinity line 1394

The read are DEV2, they are relatively small.