Heading ##Hello everybody!! I ran the following command
(base) [ntilikj@login1 clean_data]$ #!/bin/bash
(base) [ntilikj@login1 clean_data]$ #SBATCH -p short #nombre cola
(base) [ntilikj@login1 clean_data]$ #SBATCH -J AssemblyTrinityCUATRO #nombre trabajo
(base) [ntilikj@login1 clean_data]$ #SBATCH -t 0-02:00:00 # Duración (D-HH:MM:SS)
(base) [ntilikj@login1 clean_data]$ #SBATCH -N 1 # Numero de nodes
(base) [ntilikj@login1 clean_data]$ #SBATCH -n 25 # Numero de cores (CPUs)
(base) [ntilikj@login1 clean_data]$ #SBATCH --mem 60G #Bloque memoria para tdos los nodos
(base) [ntilikj@login1 clean_data]$ #SBATCH -o trinity.%j.out #Nombre de archivo de salida
(base) [ntilikj@login1 clean_data]$ #SBATCH -e trinity.%j.err # Nombre archivo de errores
(base) [ntilikj@login1 clean_data]$ #SBATCH --mail-type=END, FAIL # Notificacion mail interno cuando el trabajo termina o falla
(base) [ntilikj@login1 clean_data]$ Trinity --normalize_reads --seqType fq --max_memory 50G --left DD1_1.clean.fq.gz --right DD1_2.clean.fq.gz --output trinity_asemb_DD1 --CPU 22 --full_cleanup
and I'm getting this error
Error, cmd: jellyfish count -t 22 -m 25 -s 6339913254 --canonical both.fa died with ret 9 at /mnt/lustre/home/ntilikj/miniconda3/opt/trinity-2.1.1/util/insilico_read_normalization.pl line 733. Error, cmd: /mnt/lustre/home/ntilikj/miniconda3/opt/trinity-2.1.1/util/insilico_read_normalization.pl --seqType fq --JM 50G --max_cov 50 --CPU 22 --output /mnt/lustre/home/ntilikj/D1_D2_LP/clean_data/trinity_asemb_DD1/insilico_read_normalization --left /mnt/lustre/home/ntilikj/D1_D2_LP/clean_data/DD1_1.clean.fq.gz --right /mnt/lustre/home/ntilikj/D1_D2_LP/clean_data/DD1_2.clean.fq.gz --pairs_together --PARALLEL_STATS died with ret 512 at /home/ntilikj/miniconda3/bin/Trinity line 2183.
As suggested from other issues I tried to do it step by step
perl /mnt/lustre/home/ntilikj/miniconda3/bin/insilico_read_normalization.pl --seqType fq --JM 100G --max_cov 50 --CPU 8 --output normalization_DD1a --left DD1_1.clean.fq.gz --right DD1_2.clean.fq.gz
However I stumbeled on the same error Error, cmd: jellyfish count -t 8 -m 25 -s 1738162579 --canonical both.fa died with ret 9 at /mnt/lustre/home/ntilikj/miniconda3/bin/insilico_read_normalization.pl line 733.
I'm fairly new to RNAseq analysis so any help/advice or additional tutorial would be helpful
