なんか家帰ったらもろもろうまくできた（笑）
さてリードが一つもmapされないという謎の状態に苦しんでいたのであるが、帰宅して手元のmacで試したら何の問題もなかった。
$ bwa index -a bwtsw ~/bi/genome/NC_000913.fna [bwa_index] Pack FASTA... 0.21 sec [bwa_index] Construct BWT for the packed sequence... [BWTIncCreate] textLength=9279350, availableWord=11788200 [bwt_gen] Finished constructing BWT in 5 iterations. [bwa_index] 6.26 seconds elapse. [bwa_index] Update BWT... 0.12 sec [bwa_index] Pack forward-only FASTA... 0.15 sec [bwa_index] Construct SA from BWT and Occ... 1.93 sec [main] Version: 0.6.1-r104 [main] CMD: bwa index -a bwtsw /Users/tanakanorio/bi/genome/NC_000913.fna [main] Real time: 13.193 sec; CPU: 8.671 sec $ bwa aln genome/NC_000913.fna Day4/SRR022885.200k.fastq > Day4/2_mapping/SRR022885.sai [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... 3.98 sec [bwa_aln_core] write to the disk... 0.01 sec [bwa_aln_core] 50000 sequences have been processed. [main] Version: 0.6.1-r104 [main] CMD: bwa aln genome/NC_000913.fna Day4/SRR022885.200k.fastq [main] Real time: 4.152 sec; CPU: 4.128 sec $ bwa samse genome/NC_000913.fna Day4/2_mapping/SRR022885.sai Day4/SRR022885.200k.fastq > Day4/2_mapping/SRR022885.sam [bwa_aln_core] convert to sequence coordinate... 0.30 sec [bwa_aln_core] refine gapped alignments... 0.05 sec [bwa_aln_core] print alignments... 0.19 sec [bwa_aln_core] 50000 sequences have been processed. [main] Version: 0.6.1-r104 [main] CMD: bwa samse genome/NC_000913.fna Day4/2_mapping/SRR022885.sai Day4/SRR022885.200k.fastq [main] Real time: 0.787 sec; CPU: 0.707 sec $ cd Day4/2_mapping/ casbah-4:2_mapping tanakanorio$ samtools view -bS SRR022885.sam > SRR022885.bam [samopen] SAM header is present: 1 sequences. $ samtools sort SRR022885.bam SRR022885.sort $ samtools index SRR022885.sort.bam $ samtools idxstats SRR022885.sort.bam gi|49175990|ref|NC_000913.2| 4639675 30622 0 * 0 0 19378
原因究明は、来週。
