Open hcph opened 2 years ago
Hi, I am so sad that my alignment job was disturbed when already have run for half a month. Could you please tell me whether there is any way to continue running this job or not? Thank you very much!
My job is like that: bsub -J ${index} -n 4 -o %J.${index}.out -e %J.${index}.err -q smp -R "rusage[mem=80GB]" "python /public/home/chaohe/BSseeker2-2.1.1/bs_seeker2-align.py -1 ${prefix}/${index}_R1_001_val_1.fq.gz -2 ${prefix}/${index}_R2_001_val_2.fq.gz -g IWGSC_v1.fasta --aligner=bowtie2 -o ${index}.bam -f bam --bt-p 8"
And the error output is : (ERR): bowtie2-align died with signal 6 (ABRT) (core dumped) ERROR: ('/public/home/chaohe/miniconda3/envs/py2/bin/bowtie2 --local --quiet -D 50 --no-mixed --norc --sam-nohead --no-discordant -k 2 -p 8 -X 500 --fr -x /public/home/chaohe/BSseeker2-2.1.1/bs_utils/reference_genomes/IWGSC_v1.fasta_bowtie2/W_C2T -f -1 /tmp/bs_seeker2_BS-7-1_S1L003.bam-bowtie2-local-TMP-fMDSV0/Trimed_FCT_1.fa.tmp-1849043 -2 /tmp/bs_seeker2_BS-7-1_S1L003.bam-bowtie2-local-TMP-fMDSV0/Trimed_RGA_2.fa.tmp-1849043 -S /tmp/bs_seeker2_BS-7-1_S1L003.bam-bowtie2-local-TMP-fMDSV0/W_C2T_fr_m4.mapping.tmp-1849043', None) exit with an error code: 1. Please, check the log files. (ERR): bowtie2-align died with signal 6 (ABRT) (core dumped)
Hi, I am so sad that my alignment job was disturbed when already have run for half a month. Could you please tell me whether there is any way to continue running this job or not? Thank you very much!
My job is like that: bsub -J ${index} -n 4 -o %J.${index}.out -e %J.${index}.err -q smp -R "rusage[mem=80GB]" "python /public/home/chaohe/BSseeker2-2.1.1/bs_seeker2-align.py -1 ${prefix}/${index}_R1_001_val_1.fq.gz -2 ${prefix}/${index}_R2_001_val_2.fq.gz -g IWGSC_v1.fasta --aligner=bowtie2 -o ${index}.bam -f bam --bt-p 8"
And the error output is : (ERR): bowtie2-align died with signal 6 (ABRT) (core dumped) ERROR: ('/public/home/chaohe/miniconda3/envs/py2/bin/bowtie2 --local --quiet -D 50 --no-mixed --norc --sam-nohead --no-discordant -k 2 -p 8 -X 500 --fr -x /public/home/chaohe/BSseeker2-2.1.1/bs_utils/reference_genomes/IWGSC_v1.fasta_bowtie2/W_C2T -f -1 /tmp/bs_seeker2_BS-7-1_S1L003.bam-bowtie2-local-TMP-fMDSV0/Trimed_FCT_1.fa.tmp-1849043 -2 /tmp/bs_seeker2_BS-7-1_S1L003.bam-bowtie2-local-TMP-fMDSV0/Trimed_RGA_2.fa.tmp-1849043 -S /tmp/bs_seeker2_BS-7-1_S1L003.bam-bowtie2-local-TMP-fMDSV0/W_C2T_fr_m4.mapping.tmp-1849043', None) exit with an error code: 1. Please, check the log files. (ERR): bowtie2-align died with signal 6 (ABRT) (core dumped)