linshengnan09

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R1: @A00511:346:HLNVMDSXY:1:1101:1054:1000 1:N:0:CAAGTCTA+GCCTTAAT ANTCCCGGAAAGTGCTGAGGTTTGGGCCCCTGAGACGAGAGACGTCAGGATAGACTGGGTTAGCCCCGGTTGGTTTTCAATTTATGAATCATCCTTCAAGTTTG + F#FFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFF R2: @A00511:346:HLNVMDSXY:1:1101:1054:1000 2:N:0:CAAGTCTA+GCCTTAAT GACTTTGACGTTCGAGCGTGGCATTGGTATGTGGACTGGTGGTATGTTGGTTTGCGGTTTGGTTTGGAAAGATCGATCAAACGCCAGACGGAAGGCATGACTTG + FFFFF::FFFFFFFFFF,FFFFFFFFFFFFFFFFF,FF,FFF,FFFFFFFFF:,FFF,FFFFFFFFFF:FFF:FFFFFFFFFFFFFFFFFFF,:FFF:FFF:FF

I remember running with the same data before and there was no problem. Later, I ran again and there reported an error , and then I installed the latest version,...

How can I sharing with you these two files ? The file is too big, shall I split it up and send it by mail？

ok, Could you give me your email address？

ok，I have sent the file to you via weTransfer, please check.

Sorry, the size of the complete file is 30G, so I converted the file to bam again, and send to you.

It should be the sorting step , the bam files cannot be sorted, but how to solve this problem？ I had change the 1.12 samtools version to 1.11, still did...

I check the mapping_combine.log: ~/01_bin/samtools merge -@ 36 -n -f bowtie_results/bwt2/sample1/XB_R2_merged_canu_asm.fasta.bwt2merged.bam bowtie_results/bwt2_global/sample1/XB_R2_merged_canu_asm.fasta.bwt2glob.bam bowtie_results/bwt2_local/sample1/XB_R2_merged_canu_asm.fasta.bwt2glob.unmap_bwt2loc.bam ~/01_bin/samtools merge -@ 36 -n -f bowtie_results/bwt2/sample1/XB_R1_merged_canu_asm.fasta.bwt2merged.bam bowtie_results/bwt2_global/sample1/XB_R1_merged_canu_asm.fasta.bwt2glob.bam bowtie_results/bwt2_local/sample1/XB_R1_merged_canu_asm.fasta.bwt2glob.unmap_bwt2loc.bam ~/01_bin/samtools sort -@ 36 -m 21M -n -T...

Is the parameter in the bowtie_combine.sh script ? bowtie_combine.sh： ## Set a default for legacy config files that do not have SORT_RAM set if [[ "${SORT_RAM}" == "" ]]; then...