Trinity Error

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Banisha Phukela

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Feb 15, 2024, 1:44:14 PMFeb 15
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Dear Trinity users,

I have tried to run trinity file for de novo seq assembly. I got an error which i really don't understand. Could you please help?

I am attaching the error file that shows:

-file doesn't yet exist: /splice-jbod/vanessaroy/projects/trinity_banisha/trinity/banisha_output_trinity/insilico_read_normalization/left.norm.fq

Thursday, February 15, 2024: 18:51:31   CMD: /storage/apps/mamba/envs/trinity-2.15/opt/trinity-2.15.1/util/insilico_read_normalization.pl --seqType fq --JM 200G  --max_cov 200 --min_cov 1 --CPU 24 --output /splice-jbod/vanessaroy/projects/trinity_banisha/trinity/banisha_output_trinity/insilico_read_normalization --max_CV 10000  --SS_lib_type RF  --left /splice-jbod/vanessaroy/projects/trinity_banisha/trinity/257_R1_trimmed.fastq.gz,/splice-jbod/vanessaroy/projects/trinity_banisha/trinity/264_R1_trimmed.fastq.gz,/splice-jbod/vanessaroy/projects/trinity_banisha/trinity/315_R1_trimmed.fastq.gz,/splice-jbod/vanessaroy/projects/trinity_banisha/trinity/316_R1_trimmed.fastq.gz,/splice-jbod/vanessaroy/projects/trinity_banisha/trinity/ACP1_R1_trimmed.fastq.gz,/splice-jbod/vanessaroy/projects/trinity_banisha/trinity/ACP3_R1_trimmed.fastq.gz,/splice-jbod/vanessaroy/projects/trinity_banisha/trinity/ACR2_2_R1_trimmed.fastq.gz,/splice-jbod/vanessaroy/projects/trinity_banisha/trinity/ACR3_3_R1_trimmed.fastq.gz,/splice-jbod/vanessaroy/projects/trinity_banisha/trinity/ACW11_2_R1_trimmed.fastq.gz,/splice-jbod/vanessaroy/projects/trinity_banisha/trinity/ACW11_3_R1_trimmed.fastq.gz,/splice-jbod/vanessaroy/projects/trinity_banisha/trinity/ACW2_R1_trimmed.fastq.gz,/splice-jbod/vanessaroy/projects/trinity_banisha/trinity/APC2_R1_trimmed.fastq.gz,/splice-jbod/vanessaroy/projects/trinity_banisha/trinity/R21_R1_trimmed.fastq.gz --right /splice-jbod/vanessaroy/projects/trinity_banisha/trinity/257_R2_trimmed.fastq.gz,/splice-jbod/vanessaroy/projects/trinity_banisha/trinity/264_R2_trimmed.fastq.gz,/splice-jbod/vanessaroy/projects/trinity_banisha/trinity/315_R2_trimmed.fastq.gz,/splice-jbod/vanessaroy/projects/trinity_banisha/trinity/316_R2_trimmed.fastq.gz,/splice-jbod/vanessaroy/projects/trinity_banisha/trinity/ACP1_R2_trimmed.fastq.gz,/splice-jbod/vanessaroy/projects/trinity_banisha/trinity/ACP3_R2_trimmed.fastq.gz,/splice-jbod/vanessaroy/projects/trinity_banisha/trinity/ACR2_2_R2_trimmed.fastq.gz,/splice-jbod/vanessaroy/projects/trinity_banisha/trinity/ACR3_3_R2_trimmed.fastq.gz,/splice-jbod/vanessaroy/projects/trinity_banisha/trinity/ACW11_2_R2_trimmed.fastq.gz,/splice-jbod/vanessaroy/projects/trinity_banisha/trinity/ACW11_3_R2_trimmed.fastq.gz,/splice-jbod/vanessaroy/projects/trinity_banisha/trinity/ACW2_R2_trimmed.fastq.gz,/splice-jbod/vanessaroy/projects/trinity_banisha/trinity/APC2_R2_trimmed.fastq.gz,/splice-jbod/vanessaroy/projects/trinity_banisha/trinity/R21_R2_trimmed.fastq.gz --pairs_together  --PARALLEL_STATS

Can't locate DB_File.pm in @INC (you may need to install the DB_File module) (@INC contains: /storage/apps/mamba/envs/trinity-2.15/opt/trinity-2.15.1/util/../PerlLib /storage/apps/python-anaconda3-5.3.1/envs/bowtie2/lib/site_perl/5.26.2/x86_64-linux-thread-multi /storage/apps/python-anaconda3-5.3.1/envs/bowtie2/lib/site_perl/5.26.2 /storage/apps/python-anaconda3-5.3.1/envs/bowtie2/lib/5.26.2/x86_64-linux-thread-multi /storage/apps/python-anaconda3-5.3.1/envs/bowtie2/lib/5.26.2 .) at /storage/apps/mamba/envs/trinity-2.15/opt/trinity-2.15.1/util/insilico_read_normalization.pl line 19.

BEGIN failed--compilation aborted at /storage/apps/mamba/envs/trinity-2.15/opt/trinity-2.15.1/util/insilico_read_normalization.pl line 19.

Error, cmd: /storage/apps/mamba/envs/trinity-2.15/opt/trinity-2.15.1/util/insilico_read_normalization.pl --seqType fq --JM 200G  --max_cov 200 --min_cov 1 --CPU 24 --output /splice-jbod/vanessaroy/projects/trinity_banisha/trinity/banisha_output_trinity/insilico_read_normalization --max_CV 10000  --SS_lib_type RF  --left /splice-jbod/vanessaroy/projects/trinity_banisha/trinity/257_R1_trimmed.fastq.gz,/splice-jbod/vanessaroy/projects/trinity_banisha/trinity/264_R1_trimmed.fastq.gz,/splice-jbod/vanessaroy/projects/trinity_banisha/trinity/315_R1_trimmed.fastq.gz,/splice-jbod/vanessaroy/projects/trinity_banisha/trinity/316_R1_trimmed.fastq.gz,/splice-jbod/vanessaroy/projects/trinity_banisha/trinity/ACP1_R1_trimmed.fastq.gz,/splice-jbod/vanessaroy/projects/trinity_banisha/trinity/ACP3_R1_trimmed.fastq.gz,/splice-jbod/vanessaroy/projects/trinity_banisha/trinity/ACR2_2_R1_trimmed.fastq.gz,/splice-jbod/vanessaroy/projects/trinity_banisha/trinity/ACR3_3_R1_trimmed.fastq.gz,/splice-jbod/vanessaroy/projects/trinity_banisha/trinity/ACW11_2_R1_trimmed.fastq.gz,/splice-jbod/vanessaroy/projects/trinity_banisha/trinity/ACW11_3_R1_trimmed.fastq.gz,/splice-jbod/vanessaroy/projects/trinity_banisha/trinity/ACW2_R1_trimmed.fastq.gz,/splice-jbod/vanessaroy/projects/trinity_banisha/trinity/APC2_R1_trimmed.fastq.gz,/splice-jbod/vanessaroy/projects/trinity_banisha/trinity/R21_R1_trimmed.fastq.gz --right /splice-jbod/vanessaroy/projects/trinity_banisha/trinity/257_R2_trimmed.fastq.gz,/splice-jbod/vanessaroy/projects/trinity_banisha/trinity/264_R2_trimmed.fastq.gz,/splice-jbod/vanessaroy/projects/trinity_banisha/trinity/315_R2_trimmed.fastq.gz,/splice-jbod/vanessaroy/projects/trinity_banisha/trinity/316_R2_trimmed.fastq.gz,/splice-jbod/vanessaroy/projects/trinity_banisha/trinity/ACP1_R2_trimmed.fastq.gz,/splice-jbod/vanessaroy/projects/trinity_banisha/trinity/ACP3_R2_trimmed.fastq.gz,/splice-jbod/vanessaroy/projects/trinity_banisha/trinity/ACR2_2_R2_trimmed.fastq.gz,/splice-jbod/vanessaroy/projects/trinity_banisha/trinity/ACR3_3_R2_trimmed.fastq.gz,/splice-jbod/vanessaroy/projects/trinity_banisha/trinity/ACW11_2_R2_trimmed.fastq.gz,/splice-jbod/vanessaroy/projects/trinity_banisha/trinity/ACW11_3_R2_trimmed.fastq.gz,/splice-jbod/vanessaroy/projects/trinity_banisha/trinity/ACW2_R2_trimmed.fastq.gz,/splice-jbod/vanessaroy/projects/trinity_banisha/trinity/APC2_R2_trimmed.fastq.gz,/splice-jbod/vanessaroy/projects/trinity_banisha/trinity/R21_R2_trimmed.fastq.gz --pairs_together  --PARALLEL_STATS   died with ret 512 at /home/apps/mamba/envs/trinity-2.15/bin/Trinity line 2919.

        main::process_cmd("/storage/apps/mamba/envs/trinity-2.15/opt/trinity-2.15.1/util"...) called at /home/apps/mamba/envs/trinity-2.15/bin/Trinity line 3472

        main::normalize("/splice-jbod/vanessaroy/projects/trinity_banisha/trinity/bani"..., 200, ARRAY(0x56342ff58f68), ARRAY(0x56342ff58f98)) called at /home/apps/mamba/envs/trinity-2.15/bin/Trinity line 3412

        main::run_normalization(200, ARRAY(0x56342ff58f68), ARRAY(0x56342ff58f98)) called at /home/apps/mamba/envs/trinity-2.15/bin/Trinity line 1450


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