Job ID = 10194733 sra ファイルのダウンロード中... Completed: 716121K bytes transferred in 10 seconds (564840K bits/sec), in 1 file. Completed: 780932K bytes transferred in 11 seconds (555179K 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 13397011 spots for /home/okishinya/chipatlas/results/rn6/SRX1056329/SRR2060199.sra Written 13397011 spots total Written 14288602 spots for /home/okishinya/chipatlas/results/rn6/SRX1056329/SRR2060200.sra Written 14288602 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 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: 00:00:02 Time loading mirror index: 00:00:00 Multiseed full-index search: 01:39:13 27685613 reads; of these: 27685613 (100.00%) were unpaired; of these: 1277520 (4.61%) aligned 0 times 19499052 (70.43%) aligned exactly 1 time 6909041 (24.96%) aligned >1 times 95.39% overall alignment rate Time searching: 01:39:16 Overall time: 01:39:16 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_sort_core] merging from 12 files... [bam_rmdupse_core] 1464634 / 26408093 = 0.0555 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 00:26:43: # Command line: callpeak -t SRX1056329.bam -f BAM -g 2.15e9 -n SRX1056329.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1056329.20 # format = BAM # ChIP-seq file = ['SRX1056329.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 00:26:43: #1 read tag files... INFO @ Sat, 11 Nov 2017 00:26:43: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 00:26:43: # Command line: callpeak -t SRX1056329.bam -f BAM -g 2.15e9 -n SRX1056329.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1056329.10 # format = BAM # ChIP-seq file = ['SRX1056329.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 00:26:43: #1 read tag files... INFO @ Sat, 11 Nov 2017 00:26:43: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 00:26:43: # Command line: callpeak -t SRX1056329.bam -f BAM -g 2.15e9 -n SRX1056329.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1056329.05 # format = BAM # ChIP-seq file = ['SRX1056329.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 00:26:43: #1 read tag files... INFO @ Sat, 11 Nov 2017 00:26:43: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 00:26:57: 1000000 INFO @ Sat, 11 Nov 2017 00:26:57: 1000000 INFO @ Sat, 11 Nov 2017 00:26:59: 1000000 INFO @ Sat, 11 Nov 2017 00:27:10: 2000000 INFO @ Sat, 11 Nov 2017 00:27:11: 2000000 INFO @ Sat, 11 Nov 2017 00:27:12: 2000000 INFO @ Sat, 11 Nov 2017 00:27:22: 3000000 INFO @ Sat, 11 Nov 2017 00:27:25: 3000000 INFO @ Sat, 11 Nov 2017 00:27:25: 3000000 INFO @ Sat, 11 Nov 2017 00:27:33: 4000000 INFO @ Sat, 11 Nov 2017 00:27:38: 4000000 INFO @ Sat, 11 Nov 2017 00:27:40: 4000000 INFO @ Sat, 11 Nov 2017 00:27:45: 5000000 INFO @ Sat, 11 Nov 2017 00:27:51: 5000000 INFO @ Sat, 11 Nov 2017 00:27:55: 5000000 INFO @ Sat, 11 Nov 2017 00:27:58: 6000000 INFO @ Sat, 11 Nov 2017 00:28:05: 6000000 INFO @ Sat, 11 Nov 2017 00:28:07: 6000000 INFO @ Sat, 11 Nov 2017 00:28:09: 7000000 INFO @ Sat, 11 Nov 2017 00:28:18: 7000000 INFO @ Sat, 11 Nov 2017 00:28:20: 7000000 INFO @ Sat, 11 Nov 2017 00:28:21: 8000000 INFO @ Sat, 11 Nov 2017 00:28:30: 8000000 INFO @ Sat, 11 Nov 2017 00:28:32: 8000000 INFO @ Sat, 11 Nov 2017 00:28:32: 9000000 INFO @ Sat, 11 Nov 2017 00:28:44: 10000000 INFO @ Sat, 11 Nov 2017 00:28:45: 9000000 INFO @ Sat, 11 Nov 2017 00:28:46: 9000000 INFO @ Sat, 11 Nov 2017 00:28:55: 11000000 INFO @ Sat, 11 Nov 2017 00:28:58: 10000000 INFO @ Sat, 11 Nov 2017 00:29:00: 10000000 INFO @ Sat, 11 Nov 2017 00:29:07: 12000000 INFO @ Sat, 11 Nov 2017 00:29:10: 11000000 INFO @ Sat, 11 Nov 2017 00:29:16: 11000000 INFO @ Sat, 11 Nov 2017 00:29:19: 13000000 INFO @ Sat, 11 Nov 2017 00:29:23: 12000000 INFO @ Sat, 11 Nov 2017 00:29:30: 14000000 INFO @ Sat, 11 Nov 2017 00:29:32: 12000000 INFO @ Sat, 11 Nov 2017 00:29:36: 13000000 INFO @ Sat, 11 Nov 2017 00:29:41: 15000000 INFO @ Sat, 11 Nov 2017 00:29:48: 13000000 INFO @ Sat, 11 Nov 2017 00:29:48: 14000000 INFO @ Sat, 11 Nov 2017 00:29:52: 16000000 INFO @ Sat, 11 Nov 2017 00:30:01: 15000000 INFO @ Sat, 11 Nov 2017 00:30:01: 14000000 INFO @ Sat, 11 Nov 2017 00:30:03: 17000000 INFO @ Sat, 11 Nov 2017 00:30:14: 18000000 INFO @ Sat, 11 Nov 2017 00:30:14: 16000000 INFO @ Sat, 11 Nov 2017 00:30:15: 15000000 INFO @ Sat, 11 Nov 2017 00:30:26: 19000000 INFO @ Sat, 11 Nov 2017 00:30:27: 17000000 INFO @ Sat, 11 Nov 2017 00:30:29: 16000000 INFO @ Sat, 11 Nov 2017 00:30:37: 20000000 INFO @ Sat, 11 Nov 2017 00:30:41: 18000000 INFO @ Sat, 11 Nov 2017 00:30:43: 17000000 INFO @ Sat, 11 Nov 2017 00:30:48: 21000000 INFO @ Sat, 11 Nov 2017 00:30:54: 19000000 INFO @ Sat, 11 Nov 2017 00:30:57: 18000000 INFO @ Sat, 11 Nov 2017 00:30:59: 22000000 INFO @ Sat, 11 Nov 2017 00:31:07: 20000000 INFO @ Sat, 11 Nov 2017 00:31:11: 23000000 INFO @ Sat, 11 Nov 2017 00:31:11: 19000000 INFO @ Sat, 11 Nov 2017 00:31:20: 21000000 INFO @ Sat, 11 Nov 2017 00:31:22: 24000000 INFO @ Sat, 11 Nov 2017 00:31:25: 20000000 INFO @ Sat, 11 Nov 2017 00:31:33: 22000000 INFO @ Sat, 11 Nov 2017 00:31:34: #1 tag size is determined as 100 bps INFO @ Sat, 11 Nov 2017 00:31:34: #1 tag size = 100 INFO @ Sat, 11 Nov 2017 00:31:34: #1 total tags in treatment: 24943459 INFO @ Sat, 11 Nov 2017 00:31:34: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 00:31:34: #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 00:31:34: #1 tags after filtering in treatment: 24943333 INFO @ Sat, 11 Nov 2017 00:31:34: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 00:31:34: #1 finished! INFO @ Sat, 11 Nov 2017 00:31:34: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 00:31:34: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 00:31:37: #2 number of paired peaks: 5808 INFO @ Sat, 11 Nov 2017 00:31:37: start model_add_line... INFO @ Sat, 11 Nov 2017 00:31:38: start X-correlation... INFO @ Sat, 11 Nov 2017 00:31:38: end of X-cor INFO @ Sat, 11 Nov 2017 00:31:38: #2 finished! INFO @ Sat, 11 Nov 2017 00:31:38: #2 predicted fragment length is 98 bps INFO @ Sat, 11 Nov 2017 00:31:38: #2 alternative fragment length(s) may be 98 bps INFO @ Sat, 11 Nov 2017 00:31:38: #2.2 Generate R script for model : SRX1056329.10_model.r WARNING @ Sat, 11 Nov 2017 00:31:38: #2 Since the d (98) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Nov 2017 00:31:38: #2 You may need to consider one of the other alternative d(s): 98 WARNING @ Sat, 11 Nov 2017 00:31:38: #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 00:31:38: #3 Call peaks... INFO @ Sat, 11 Nov 2017 00:31:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 00:31:39: 21000000 INFO @ Sat, 11 Nov 2017 00:31:46: 23000000 INFO @ Sat, 11 Nov 2017 00:31:53: 22000000 INFO @ Sat, 11 Nov 2017 00:31:59: 24000000 INFO @ Sat, 11 Nov 2017 00:32:07: 23000000 INFO @ Sat, 11 Nov 2017 00:32:11: #1 tag size is determined as 100 bps INFO @ Sat, 11 Nov 2017 00:32:11: #1 tag size = 100 INFO @ Sat, 11 Nov 2017 00:32:11: #1 total tags in treatment: 24943459 INFO @ Sat, 11 Nov 2017 00:32:11: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 00:32:11: #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 00:32:13: #1 tags after filtering in treatment: 24943333 INFO @ Sat, 11 Nov 2017 00:32:13: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 00:32:13: #1 finished! INFO @ Sat, 11 Nov 2017 00:32:13: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 00:32:13: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 00:32:15: #2 number of paired peaks: 5808 INFO @ Sat, 11 Nov 2017 00:32:15: start model_add_line... INFO @ Sat, 11 Nov 2017 00:32:16: start X-correlation... INFO @ Sat, 11 Nov 2017 00:32:16: end of X-cor INFO @ Sat, 11 Nov 2017 00:32:16: #2 finished! INFO @ Sat, 11 Nov 2017 00:32:16: #2 predicted fragment length is 98 bps INFO @ Sat, 11 Nov 2017 00:32:16: #2 alternative fragment length(s) may be 98 bps INFO @ Sat, 11 Nov 2017 00:32:16: #2.2 Generate R script for model : SRX1056329.20_model.r WARNING @ Sat, 11 Nov 2017 00:32:16: #2 Since the d (98) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Nov 2017 00:32:16: #2 You may need to consider one of the other alternative d(s): 98 WARNING @ Sat, 11 Nov 2017 00:32:16: #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 00:32:16: #3 Call peaks... INFO @ Sat, 11 Nov 2017 00:32:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 00:32:20: 24000000 INFO @ Sat, 11 Nov 2017 00:32:33: #1 tag size is determined as 100 bps INFO @ Sat, 11 Nov 2017 00:32:33: #1 tag size = 100 INFO @ Sat, 11 Nov 2017 00:32:33: #1 total tags in treatment: 24943459 INFO @ Sat, 11 Nov 2017 00:32:33: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 00:32:33: #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 00:32:34: #1 tags after filtering in treatment: 24943333 INFO @ Sat, 11 Nov 2017 00:32:34: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 00:32:34: #1 finished! INFO @ Sat, 11 Nov 2017 00:32:34: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 00:32:34: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 00:32:37: #2 number of paired peaks: 5808 INFO @ Sat, 11 Nov 2017 00:32:37: start model_add_line... INFO @ Sat, 11 Nov 2017 00:32:37: start X-correlation... INFO @ Sat, 11 Nov 2017 00:32:37: end of X-cor INFO @ Sat, 11 Nov 2017 00:32:37: #2 finished! INFO @ Sat, 11 Nov 2017 00:32:37: #2 predicted fragment length is 98 bps INFO @ Sat, 11 Nov 2017 00:32:37: #2 alternative fragment length(s) may be 98 bps INFO @ Sat, 11 Nov 2017 00:32:37: #2.2 Generate R script for model : SRX1056329.05_model.r WARNING @ Sat, 11 Nov 2017 00:32:37: #2 Since the d (98) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Nov 2017 00:32:37: #2 You may need to consider one of the other alternative d(s): 98 WARNING @ Sat, 11 Nov 2017 00:32:37: #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 00:32:37: #3 Call peaks... INFO @ Sat, 11 Nov 2017 00:32:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 00:32:48: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 00:33:27: #4 Write output xls file... SRX1056329.10_peaks.xls INFO @ Sat, 11 Nov 2017 00:33:27: #4 Write peak in narrowPeak format file... SRX1056329.10_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 00:33:27: #4 Write summits bed file... SRX1056329.10_summits.bed INFO @ Sat, 11 Nov 2017 00:33:27: Done! pass1 - making usageList (45 chroms): 1 millis pass2 - checking and writing primary data (839 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 00:33:29: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 00:33:49: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 00:34:12: #4 Write output xls file... SRX1056329.20_peaks.xls INFO @ Sat, 11 Nov 2017 00:34:12: #4 Write peak in narrowPeak format file... SRX1056329.20_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 00:34:12: #4 Write summits bed file... SRX1056329.20_summits.bed INFO @ Sat, 11 Nov 2017 00:34:12: Done! pass1 - making usageList (36 chroms): 1 millis pass2 - checking and writing primary data (453 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 00:34:30: #4 Write output xls file... SRX1056329.05_peaks.xls INFO @ Sat, 11 Nov 2017 00:34:30: #4 Write peak in narrowPeak format file... SRX1056329.05_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 00:34:30: #4 Write summits bed file... SRX1056329.05_summits.bed INFO @ Sat, 11 Nov 2017 00:34:30: Done! pass1 - making usageList (59 chroms): 2 millis pass2 - checking and writing primary data (1497 records, 4 fields): 10 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。