ChIA-PET2报错系列——第六、七步报错

bwa_wrap hg19.fa OUTdir3/index-1_2.valid.fastq 1 OUTdir3/index-1_2.valid.sam 1
Running BWA on trimmed reads ...
bwa aln -t 1 hg19.fa OUTdir3/index-1_2.valid.fastq > OUTdir3/index-1_2.valid.fastq.sai; bwa samse hg19.fa OUTdir3/index-1_2.valid.fastq.sai OUTdir3/index-1_2.valid.fastq > OUTdir3/index-1_2.valid.sam
[bwa_aln] 17bp reads: max_diff = 2
[bwa_aln] 38bp reads: max_diff = 3
[bwa_aln] 64bp reads: max_diff = 4
[bwa_aln] 93bp reads: max_diff = 5
[bwa_aln] 124bp reads: max_diff = 6
[bwa_aln] 157bp reads: max_diff = 7
[bwa_aln] 190bp reads: max_diff = 8
[bwa_aln] 225bp reads: max_diff = 9
[bwa_aln_core] calculate SA coordinate... 132.92 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 133.00 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 134.00 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 786432 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 133.15 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 1048576 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 133.14 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 1310720 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 133.33 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 1572864 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 132.99 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 1835008 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 132.78 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 2097152 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 132.75 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 2359296 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 132.82 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 2621440 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 132.75 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 2883584 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 132.86 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 3145728 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 132.73 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 3407872 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 132.80 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 3670016 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 132.90 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 3932160 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 134.70 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 4194304 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 133.03 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 4456448 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 132.57 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 4718592 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 130.67 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 4980736 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 129.26 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 5242880 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 132.53 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 5505024 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 131.80 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 5767168 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 132.16 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 6029312 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 132.12 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 6291456 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 132.35 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 6553600 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 132.43 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 6815744 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 132.03 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 7077888 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 132.60 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 7340032 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 132.06 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 7602176 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 131.83 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 7864320 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 131.73 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 8126464 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 132.47 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 8388608 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 133.34 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 8650752 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 133.10 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 8912896 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 132.90 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 9175040 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 132.75 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 9437184 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 132.83 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 9699328 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 132.76 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 9961472 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 133.33 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 10223616 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 133.20 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 10485760 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 132.89 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 10747904 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 133.05 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 11010048 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 133.07 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 11272192 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 132.86 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 11534336 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 133.40 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 11796480 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 133.50 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 12058624 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 132.63 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 12320768 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 132.46 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 12582912 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 132.51 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 12845056 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 132.70 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 13107200 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 132.49 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 13369344 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 132.08 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 13631488 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 132.20 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 13893632 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 132.31 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 14155776 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 131.84 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 14417920 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 133.03 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 14680064 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 133.24 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 14942208 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 133.19 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 15204352 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 133.64 sec
[bwa_aln_core] write to the disk... 0.05 sec
[bwa_aln_core] 15466496 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 133.06 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core]