Job ID = 10195019 sra ファイルのダウンロード中... Completed: 214899K bytes transferred in 5 seconds (335975K bits/sec), in 1 file. sra ファイルのダウンロードが完了しました。 Read layout: SINGLE fastq に変換中... Written 7087739 spots for /home/okishinya/chipatlas/results/rn6/SRX913488/SRR1870918.sra Written 7087739 spots total rm: cannot remove `[DSE]RX*': そのようなファイルやディレクトリはありません rm: cannot remove `[DSE]RR*.fastq': そのようなファイルやディレクトリはありません fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:01 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:04:19 7087739 reads; of these: 7087739 (100.00%) were unpaired; of these: 455425 (6.43%) aligned 0 times 4547475 (64.16%) aligned exactly 1 time 2084839 (29.41%) aligned >1 times 93.57% overall alignment rate Time searching: 00:04:21 Overall time: 00:04:21 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 953 sequences. [bam_rmdupse_core] 259809 / 6632314 = 0.0392 in library ' ' BAM に変換しました。 Bed ファイルを作成中... BedGraph に変換中... INFO @ Sat, 11 Nov 2017 06:16:19: # Command line: callpeak -t SRX913488.bam -f BAM -g 2.15e9 -n SRX913488.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX913488.20 # format = BAM # ChIP-seq file = ['SRX913488.bam'] # control file = None # effective genome size = 2.15e+09 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sat, 11 Nov 2017 06:16:19: #1 read tag files... INFO @ Sat, 11 Nov 2017 06:16:19: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 06:16:19: # Command line: callpeak -t SRX913488.bam -f BAM -g 2.15e9 -n SRX913488.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX913488.05 # format = BAM # ChIP-seq file = ['SRX913488.bam'] # control file = None # effective genome size = 2.15e+09 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sat, 11 Nov 2017 06:16:19: #1 read tag files... INFO @ Sat, 11 Nov 2017 06:16:19: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 06:16:19: # Command line: callpeak -t SRX913488.bam -f BAM -g 2.15e9 -n SRX913488.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX913488.10 # format = BAM # ChIP-seq file = ['SRX913488.bam'] # control file = None # effective genome size = 2.15e+09 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sat, 11 Nov 2017 06:16:19: #1 read tag files... INFO @ Sat, 11 Nov 2017 06:16:19: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 06:16:26: 1000000 INFO @ Sat, 11 Nov 2017 06:16:26: 1000000 INFO @ Sat, 11 Nov 2017 06:16:27: 1000000 INFO @ Sat, 11 Nov 2017 06:16:33: 2000000 INFO @ Sat, 11 Nov 2017 06:16:34: 2000000 INFO @ Sat, 11 Nov 2017 06:16:34: 2000000 INFO @ Sat, 11 Nov 2017 06:16:40: 3000000 INFO @ Sat, 11 Nov 2017 06:16:41: 3000000 INFO @ Sat, 11 Nov 2017 06:16:41: 3000000 INFO @ Sat, 11 Nov 2017 06:16:48: 4000000 INFO @ Sat, 11 Nov 2017 06:16:48: 4000000 INFO @ Sat, 11 Nov 2017 06:16:48: 4000000 INFO @ Sat, 11 Nov 2017 06:16:55: 5000000 INFO @ Sat, 11 Nov 2017 06:16:55: 5000000 INFO @ Sat, 11 Nov 2017 06:16:56: 5000000 INFO @ Sat, 11 Nov 2017 06:17:02: 6000000 INFO @ Sat, 11 Nov 2017 06:17:02: 6000000 INFO @ Sat, 11 Nov 2017 06:17:03: 6000000 INFO @ Sat, 11 Nov 2017 06:17:05: #1 tag size is determined as 47 bps INFO @ Sat, 11 Nov 2017 06:17:05: #1 tag size = 47 INFO @ Sat, 11 Nov 2017 06:17:05: #1 total tags in treatment: 6372505 INFO @ Sat, 11 Nov 2017 06:17:05: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 06:17:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Nov 2017 06:17:05: #1 tag size is determined as 47 bps INFO @ Sat, 11 Nov 2017 06:17:05: #1 tag size = 47 INFO @ Sat, 11 Nov 2017 06:17:05: #1 total tags in treatment: 6372505 INFO @ Sat, 11 Nov 2017 06:17:05: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 06:17:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Nov 2017 06:17:05: #1 tags after filtering in treatment: 6372240 INFO @ Sat, 11 Nov 2017 06:17:05: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 06:17:05: #1 finished! INFO @ Sat, 11 Nov 2017 06:17:05: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 06:17:05: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 06:17:05: #1 tags after filtering in treatment: 6372240 INFO @ Sat, 11 Nov 2017 06:17:05: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 06:17:05: #1 finished! INFO @ Sat, 11 Nov 2017 06:17:05: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 06:17:05: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 06:17:06: #1 tag size is determined as 47 bps INFO @ Sat, 11 Nov 2017 06:17:06: #1 tag size = 47 INFO @ Sat, 11 Nov 2017 06:17:06: #1 total tags in treatment: 6372505 INFO @ Sat, 11 Nov 2017 06:17:06: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 06:17:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Nov 2017 06:17:06: #1 tags after filtering in treatment: 6372240 INFO @ Sat, 11 Nov 2017 06:17:06: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 06:17:06: #1 finished! INFO @ Sat, 11 Nov 2017 06:17:06: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 06:17:06: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 06:17:08: #2 number of paired peaks: 13362 INFO @ Sat, 11 Nov 2017 06:17:08: start model_add_line... INFO @ Sat, 11 Nov 2017 06:17:08: start X-correlation... INFO @ Sat, 11 Nov 2017 06:17:08: end of X-cor INFO @ Sat, 11 Nov 2017 06:17:08: #2 finished! INFO @ Sat, 11 Nov 2017 06:17:08: #2 predicted fragment length is 50 bps INFO @ Sat, 11 Nov 2017 06:17:08: #2 alternative fragment length(s) may be 50,136,187,230 bps INFO @ Sat, 11 Nov 2017 06:17:08: #2.2 Generate R script for model : SRX913488.05_model.r WARNING @ Sat, 11 Nov 2017 06:17:08: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Nov 2017 06:17:08: #2 You may need to consider one of the other alternative d(s): 50,136,187,230 WARNING @ Sat, 11 Nov 2017 06:17:08: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Nov 2017 06:17:08: #3 Call peaks... INFO @ Sat, 11 Nov 2017 06:17:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 06:17:08: #2 number of paired peaks: 13362 INFO @ Sat, 11 Nov 2017 06:17:08: start model_add_line... INFO @ Sat, 11 Nov 2017 06:17:08: start X-correlation... INFO @ Sat, 11 Nov 2017 06:17:08: end of X-cor INFO @ Sat, 11 Nov 2017 06:17:08: #2 finished! INFO @ Sat, 11 Nov 2017 06:17:08: #2 predicted fragment length is 50 bps INFO @ Sat, 11 Nov 2017 06:17:08: #2 alternative fragment length(s) may be 50,136,187,230 bps INFO @ Sat, 11 Nov 2017 06:17:08: #2.2 Generate R script for model : SRX913488.10_model.r WARNING @ Sat, 11 Nov 2017 06:17:08: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Nov 2017 06:17:08: #2 You may need to consider one of the other alternative d(s): 50,136,187,230 WARNING @ Sat, 11 Nov 2017 06:17:08: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Nov 2017 06:17:08: #3 Call peaks... INFO @ Sat, 11 Nov 2017 06:17:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 06:17:09: #2 number of paired peaks: 13362 INFO @ Sat, 11 Nov 2017 06:17:09: start model_add_line... INFO @ Sat, 11 Nov 2017 06:17:09: start X-correlation... INFO @ Sat, 11 Nov 2017 06:17:09: end of X-cor INFO @ Sat, 11 Nov 2017 06:17:09: #2 finished! INFO @ Sat, 11 Nov 2017 06:17:09: #2 predicted fragment length is 50 bps INFO @ Sat, 11 Nov 2017 06:17:09: #2 alternative fragment length(s) may be 50,136,187,230 bps INFO @ Sat, 11 Nov 2017 06:17:09: #2.2 Generate R script for model : SRX913488.20_model.r WARNING @ Sat, 11 Nov 2017 06:17:09: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Nov 2017 06:17:09: #2 You may need to consider one of the other alternative d(s): 50,136,187,230 WARNING @ Sat, 11 Nov 2017 06:17:09: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Nov 2017 06:17:09: #3 Call peaks... INFO @ Sat, 11 Nov 2017 06:17:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 06:17:23: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 06:17:23: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 06:17:25: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 06:17:31: #4 Write output xls file... SRX913488.05_peaks.xls INFO @ Sat, 11 Nov 2017 06:17:31: #4 Write peak in narrowPeak format file... SRX913488.05_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 06:17:31: #4 Write summits bed file... SRX913488.05_summits.bed INFO @ Sat, 11 Nov 2017 06:17:31: Done! pass1 - making usageList (34 chroms): 1 millis pass2 - checking and writing primary data (586 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 06:17:33: #4 Write output xls file... SRX913488.10_peaks.xls INFO @ Sat, 11 Nov 2017 06:17:33: #4 Write peak in narrowPeak format file... SRX913488.10_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 06:17:33: #4 Write summits bed file... SRX913488.10_summits.bed INFO @ Sat, 11 Nov 2017 06:17:33: Done! pass1 - making usageList (24 chroms): 1 millis pass2 - checking and writing primary data (301 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 06:17:33: #4 Write output xls file... SRX913488.20_peaks.xls INFO @ Sat, 11 Nov 2017 06:17:33: #4 Write peak in narrowPeak format file... SRX913488.20_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 06:17:33: #4 Write summits bed file... SRX913488.20_summits.bed INFO @ Sat, 11 Nov 2017 06:17:33: Done! pass1 - making usageList (24 chroms): 1 millis pass2 - checking and writing primary data (106 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。