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single-cell-genetics / cellsnp-lite

Efficient genotyping bi-allelic SNPs on single cells
https://cellsnp-lite.readthedocs.io
Apache License 2.0
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HiC-pro mapping_combine.log: Failed to open file "XXX" : File exists #130

Open leventLiu opened 4 months ago

leventLiu commented 4 months ago

Hi, When I ran HiC-pro, I found the result of allValidPairs is 0 kb. The log file shows that in mapping_combine.log, an error: [E::hts_open_format] Failed to open file "tmp/64cell-1_R1_Csav.ref.0002.bam" : File exists.

/gpfsssdpool/softwares/anaconda3/envs/hicpro/bin/samtools merge -@ 24 -n -f bowtie_results/bwt2/64cell-1/64cell-1_R1_Csav.ref.bwt2merged.bam bowtie_results/bwt2_global/64cell-1/64cell-1_R1_Csav.ref.bwt2glob.bam bowtie_results/bwt2_local/64cell-1/64cell-1_R1_Csav.ref.bwt2glob.unmap_bwt2loc.bam /gpfsssdpool/softwares/anaconda3/envs/hicpro/bin/samtools merge -@ 24 -n -f bowtie_results/bwt2/64cell-1/64cell-1_R1_Csav.ref.bwt2merged.bam bowtie_results/bwt2_global/64cell-1/64cell-1_R1_Csav.ref.bwt2glob.bam bowtie_results/bwt2_local/64cell-1/64cell-1_R1_Csav.ref.bwt2glob.unmap_bwt2loc.bam /gpfsssdpool/softwares/anaconda3/envs/hicpro/bin/samtools sort -@ 24 -m 41M -n -T tmp/64cell-1_R1_Csav.ref -o bowtie_results/bwt2/64cell-1/64cell-1_R1_Csav.ref.bwt2merged.sorted.bam bowtie_results/bwt2/64cell-1/64cell-1_R1_Csav.ref.bwt2merged.bam /gpfsssdpool/softwares/anaconda3/envs/hicpro/bin/samtools sort -@ 24 -m 41M -n -T tmp/64cell-1_R1_Csav.ref -o bowtie_results/bwt2/64cell-1/64cell-1_R1_Csav.ref.bwt2merged.sorted.bam bowtie_results/bwt2/64cell-1/64cell-1_R1_Csav.ref.bwt2merged.bam [E::hts_open_format] Failed to open file "tmp/64cell-1_R1_Csav.ref.0002.bam" : File exists [E::hts_open_format] Failed to open file "tmp/64cell-1_R1_Csav.ref.0015.bam" : File exists [E::hts_open_format] Failed to open file "tmp/64cell-1_R1_Csav.ref.0013.bam" : File exists [E::hts_open_format] Failed to open file "tmp/64cell-1_R1_Csav.ref.0003.bam" : File exists [E::hts_open_format] Failed to open file "tmp/64cell-1_R1_Csav.ref.0008.bam" : File exists [E::hts_open_format] Failed to open file "tmp/64cell-1_R1_Csav.ref.0018.bam" : File exists [E::hts_open_format] Failed to open file "tmp/64cell-1_R1_Csav.ref.0010.bam" : File exists [E::hts_open_format] Failed to open file "tmp/64cell-1_R1_Csav.ref.0000.bam" : File exists samtools sort: failed to create temporary file "tmp/64cell-1_R1_Csav.ref.0000.bam": File exists [E::hts_open_format] Failed to open file "tmp/64cell-1_R1_Csav.ref.0006.bam" : File exists [E::hts_open_format] Failed to open file "tmp/64cell-1_R1_Csav.ref.0001.bam" : File exists [E::hts_open_format] Failed to open file "tmp/64cell-1_R1_Csav.ref.0005.bam" : File exists [E::hts_open_format] Failed to open file "tmp/64cell-1_R1_Csav.ref.0011.bam" : File exists [E::hts_open_format] Failed to open file "tmp/64cell-1_R1_Csav.ref.0023.bam" : File exists

leventLiu commented 4 months ago

And I also get an error in mergeSAM.log: [E::idx_find_and_load] Could not retrieve index file for 'bowtie_results/bwt2/64cell-1/64cell-1_R2_Csav.ref.bwt2merged.bam'