Job ID = 11171313 sra ファイルのダウンロード中... Completed: 547322K bytes transferred in 11 seconds (375666K 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... Read 12207576 spots for /home/okishinya/chipatlas/results/dm3/SRX3511946/SRR6418931.sra Written 12207576 spots for /home/okishinya/chipatlas/results/dm3/SRX3511946/SRR6418931.sra 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: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:05:43 12207576 reads; of these: 12207576 (100.00%) were unpaired; of these: 2789738 (22.85%) aligned 0 times 7562072 (61.95%) aligned exactly 1 time 1855766 (15.20%) aligned >1 times 77.15% overall alignment rate Time searching: 00:05:43 Overall time: 00:05:43 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_rmdupse_core] 675434 / 9417838 = 0.0717 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, 08 Sep 2018 13:50:36: # Command line: callpeak -t SRX3511946.bam -f BAM -g dm -n SRX3511946.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3511946.10 # format = BAM # ChIP-seq file = ['SRX3511946.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 08 Sep 2018 13:50:36: #1 read tag files... INFO @ Sat, 08 Sep 2018 13:50:36: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 13:50:36: # Command line: callpeak -t SRX3511946.bam -f BAM -g dm -n SRX3511946.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3511946.05 # format = BAM # ChIP-seq file = ['SRX3511946.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 08 Sep 2018 13:50:36: #1 read tag files... INFO @ Sat, 08 Sep 2018 13:50:36: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 13:50:36: # Command line: callpeak -t SRX3511946.bam -f BAM -g dm -n SRX3511946.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3511946.20 # format = BAM # ChIP-seq file = ['SRX3511946.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 08 Sep 2018 13:50:36: #1 read tag files... INFO @ Sat, 08 Sep 2018 13:50:36: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 13:50:44: 1000000 INFO @ Sat, 08 Sep 2018 13:50:44: 1000000 INFO @ Sat, 08 Sep 2018 13:50:44: 1000000 INFO @ Sat, 08 Sep 2018 13:50:51: 2000000 INFO @ Sat, 08 Sep 2018 13:50:51: 2000000 INFO @ Sat, 08 Sep 2018 13:50:51: 2000000 INFO @ Sat, 08 Sep 2018 13:50:59: 3000000 INFO @ Sat, 08 Sep 2018 13:50:59: 3000000 INFO @ Sat, 08 Sep 2018 13:50:59: 3000000 INFO @ Sat, 08 Sep 2018 13:51:06: 4000000 INFO @ Sat, 08 Sep 2018 13:51:06: 4000000 INFO @ Sat, 08 Sep 2018 13:51:06: 4000000 INFO @ Sat, 08 Sep 2018 13:51:14: 5000000 INFO @ Sat, 08 Sep 2018 13:51:14: 5000000 INFO @ Sat, 08 Sep 2018 13:51:14: 5000000 INFO @ Sat, 08 Sep 2018 13:51:21: 6000000 INFO @ Sat, 08 Sep 2018 13:51:21: 6000000 INFO @ Sat, 08 Sep 2018 13:51:21: 6000000 INFO @ Sat, 08 Sep 2018 13:51:28: 7000000 INFO @ Sat, 08 Sep 2018 13:51:28: 7000000 INFO @ Sat, 08 Sep 2018 13:51:29: 7000000 INFO @ Sat, 08 Sep 2018 13:51:36: 8000000 INFO @ Sat, 08 Sep 2018 13:51:36: 8000000 INFO @ Sat, 08 Sep 2018 13:51:36: 8000000 INFO @ Sat, 08 Sep 2018 13:51:41: #1 tag size is determined as 100 bps INFO @ Sat, 08 Sep 2018 13:51:41: #1 tag size = 100 INFO @ Sat, 08 Sep 2018 13:51:41: #1 total tags in treatment: 8742404 INFO @ Sat, 08 Sep 2018 13:51:41: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 13:51:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 13:51:41: #1 tags after filtering in treatment: 8742404 INFO @ Sat, 08 Sep 2018 13:51:41: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 13:51:41: #1 finished! INFO @ Sat, 08 Sep 2018 13:51:41: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 13:51:41: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 13:51:41: #1 tag size is determined as 100 bps INFO @ Sat, 08 Sep 2018 13:51:41: #1 tag size = 100 INFO @ Sat, 08 Sep 2018 13:51:41: #1 total tags in treatment: 8742404 INFO @ Sat, 08 Sep 2018 13:51:41: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 13:51:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 13:51:42: #1 tags after filtering in treatment: 8742404 INFO @ Sat, 08 Sep 2018 13:51:42: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 13:51:42: #1 finished! INFO @ Sat, 08 Sep 2018 13:51:42: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 13:51:42: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 13:51:42: #1 tag size is determined as 100 bps INFO @ Sat, 08 Sep 2018 13:51:42: #1 tag size = 100 INFO @ Sat, 08 Sep 2018 13:51:42: #1 total tags in treatment: 8742404 INFO @ Sat, 08 Sep 2018 13:51:42: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 13:51:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 13:51:42: #1 tags after filtering in treatment: 8742404 INFO @ Sat, 08 Sep 2018 13:51:42: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 13:51:42: #1 finished! INFO @ Sat, 08 Sep 2018 13:51:42: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 13:51:42: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 13:51:42: #2 number of paired peaks: 1923 INFO @ Sat, 08 Sep 2018 13:51:42: start model_add_line... INFO @ Sat, 08 Sep 2018 13:51:42: start X-correlation... INFO @ Sat, 08 Sep 2018 13:51:42: #2 number of paired peaks: 1923 INFO @ Sat, 08 Sep 2018 13:51:42: start model_add_line... INFO @ Sat, 08 Sep 2018 13:51:42: start X-correlation... INFO @ Sat, 08 Sep 2018 13:51:42: end of X-cor INFO @ Sat, 08 Sep 2018 13:51:42: end of X-cor INFO @ Sat, 08 Sep 2018 13:51:42: #2 finished! INFO @ Sat, 08 Sep 2018 13:51:42: #2 finished! INFO @ Sat, 08 Sep 2018 13:51:42: #2 predicted fragment length is 186 bps INFO @ Sat, 08 Sep 2018 13:51:42: #2 predicted fragment length is 186 bps INFO @ Sat, 08 Sep 2018 13:51:42: #2 alternative fragment length(s) may be 4,186 bps INFO @ Sat, 08 Sep 2018 13:51:42: #2 alternative fragment length(s) may be 4,186 bps INFO @ Sat, 08 Sep 2018 13:51:42: #2.2 Generate R script for model : SRX3511946.10_model.r INFO @ Sat, 08 Sep 2018 13:51:42: #2.2 Generate R script for model : SRX3511946.20_model.r WARNING @ Sat, 08 Sep 2018 13:51:43: #2 Since the d (186) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 13:51:43: #2 You may need to consider one of the other alternative d(s): 4,186 WARNING @ Sat, 08 Sep 2018 13:51:43: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Sep 2018 13:51:43: #3 Call peaks... WARNING @ Sat, 08 Sep 2018 13:51:43: #2 Since the d (186) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 13:51:43: #2 You may need to consider one of the other alternative d(s): 4,186 WARNING @ Sat, 08 Sep 2018 13:51:43: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Sep 2018 13:51:43: #3 Call peaks... INFO @ Sat, 08 Sep 2018 13:51:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 13:51:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 13:51:43: #2 number of paired peaks: 1923 INFO @ Sat, 08 Sep 2018 13:51:43: start model_add_line... INFO @ Sat, 08 Sep 2018 13:51:43: start X-correlation... INFO @ Sat, 08 Sep 2018 13:51:43: end of X-cor INFO @ Sat, 08 Sep 2018 13:51:43: #2 finished! INFO @ Sat, 08 Sep 2018 13:51:43: #2 predicted fragment length is 186 bps INFO @ Sat, 08 Sep 2018 13:51:43: #2 alternative fragment length(s) may be 4,186 bps INFO @ Sat, 08 Sep 2018 13:51:43: #2.2 Generate R script for model : SRX3511946.05_model.r WARNING @ Sat, 08 Sep 2018 13:51:43: #2 Since the d (186) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 13:51:43: #2 You may need to consider one of the other alternative d(s): 4,186 WARNING @ Sat, 08 Sep 2018 13:51:43: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Sep 2018 13:51:43: #3 Call peaks... INFO @ Sat, 08 Sep 2018 13:51:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 13:52:03: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 13:52:04: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 13:52:05: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 13:52:14: #4 Write output xls file... SRX3511946.10_peaks.xls INFO @ Sat, 08 Sep 2018 13:52:14: #4 Write peak in narrowPeak format file... SRX3511946.10_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 13:52:14: #4 Write summits bed file... SRX3511946.10_summits.bed INFO @ Sat, 08 Sep 2018 13:52:14: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (383 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 13:52:15: #4 Write output xls file... SRX3511946.20_peaks.xls INFO @ Sat, 08 Sep 2018 13:52:15: #4 Write peak in narrowPeak format file... SRX3511946.20_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 13:52:15: #4 Write summits bed file... SRX3511946.20_summits.bed INFO @ Sat, 08 Sep 2018 13:52:15: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (161 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 13:52:16: #4 Write output xls file... SRX3511946.05_peaks.xls INFO @ Sat, 08 Sep 2018 13:52:16: #4 Write peak in narrowPeak format file... SRX3511946.05_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 13:52:16: #4 Write summits bed file... SRX3511946.05_summits.bed INFO @ Sat, 08 Sep 2018 13:52:16: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (940 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。