make: *** [bowtie_pairing] Error 1
pengfei liu
Run HiC-Pro 3.1.0
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Tue Feb 15 18:46:29 MET 2022
Bowtie2 alignment step1 ...
Logs: logs/sample1/mapping_step1.log
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Wed Feb 16 04:33:44 MET 2022
Bowtie2 alignment step2 ...
Logs: logs/sample1/mapping_step2.log
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Wed Feb 16 07:17:10 MET 2022
Combine R1/R2 alignment files ...
Logs: logs/sample1/mapping_combine.log
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Wed Feb 16 07:36:53 MET 2022
Mapping statistics for R1 and R2 tags ...
Logs: logs/sample1/mapping_stats.log
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Wed Feb 16 07:52:27 MET 2022
Pairing of R1 and R2 tags ...
Logs: logs/sample1/mergeSAM.log
/ebio/abt5_projects/3D_genome_of_brown_algae/data/hicpro/bin/../scripts//Makefile:141: recipe for target 'bowtie_pairing' failed
make: *** [bowtie_pairing] Error 1
(END)
First, i checked there are same rows reads number in my input R1 and R2 reads, then I checked bwt2merged.bam file:[$]~> wc -l clean_R1_Ectov5.2.bwt2merged.bam
144279729 clean_R1_Ectov5.2.bwt2merged.bam
[$]~> wc -l clean_R2_Ectov5.2.bwt2merged.bam
152525525 clean_R2_Ectov5.2.bwt2merged.bam
the raws number is different between clean_R1_Ectov5.2.bwt2merged.bam and clean_R2_Ectov5.2.bwt2merged.bam files, i think this is ok, how do you think about it?
i checked the mapping_combine.log:
[$]~> less mapping_combine.log
/ebio/abt5_projects/3D_genome_of_brown_algae/envs/hic/bin/samtools merge -@ 10 -n -f bowtie_results/bwt2/sample1/clean_R1_Ectov5.2.bwt2merged.bam bowtie_results/bwt2_global/sample1/clean_R1_Ectov5.2.bwt2glob.bam bowtie_results/bwt2_local/sample1/clean_R1_Ectov5.2.bwt2glob.unmap_bwt2loc.bam
/ebio/abt5_projects/3D_genome_of_brown_algae/envs/hic/bin/samtools merge -@ 10 -n -f bowtie_results/bwt2/sample1/clean_R2_Ectov5.2.bwt2merged.bam bowtie_results/bwt2_global/sample1/clean_R2_Ectov5.2.bwt2glob.bam bowtie_results/bwt2_local/sample1/clean_R2_Ectov5.2.bwt2glob.unmap_bwt2loc.bam
/ebio/abt5_projects/3D_genome_of_brown_algae/envs/hic/bin/samtools sort -@ 10 -m 76M -n -T tmp/clean_R1_Ectov5.2 -o bowtie_results/bwt2/sample1/clean_R1_Ectov5.2.bwt2merged.sorted.bam bowtie_results/bwt2/sample1/clean_R1_Ectov5.2.bwt2merged.bam
/ebio/abt5_projects/3D_genome_of_brown_algae/envs/hic/bin/samtools sort -@ 10 -m 76M -n -T tmp/clean_R2_Ectov5.2 -o bowtie_results/bwt2/sample1/clean_R2_Ectov5.2.bwt2merged.sorted.bam bowtie_results/bwt2/sample1/clean_R2_Ectov5.2.bwt2merged.bam
[bam_sort_core] merging from 2390 files and 10 in-memory blocks...
[E::hts_open_format] Failed to open file "tmp/clean_R1_Ectov5.2.1020.bam" : Too many open files
samtools sort: fail to open "tmp/clean_R1_Ectov5.2.1020.bam": Too many open files
[bam_sort_core] merging from 2390 files and 10 in-memory blocks...
[E::hts_open_format] Failed to open file "tmp/clean_R2_Ectov5.2.1020.bam" : Too many open files
samtools sort: fail to open "tmp/clean_R2_Ectov5.2.1020.bam": Too many open files
mapping_combine.log (END)
there are errors that failed to open bam files, do you have any solutions for my problems?
Thanks in advance!
Pengfei