Job ID = 11388801 sra ファイルのダウンロード中... Completed: 233317K bytes transferred in 8 seconds (225795K bits/sec), in 1 file. Completed: 244137K bytes transferred in 9 seconds (203025K 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 10685625 spots for /home/okishinya/chipatlas/results/rn6/SRX3657370/SRR6681057.sra Written 10685625 spots for /home/okishinya/chipatlas/results/rn6/SRX3657370/SRR6681057.sra Read 11064962 spots for /home/okishinya/chipatlas/results/rn6/SRX3657370/SRR6681058.sra Written 11064962 spots for /home/okishinya/chipatlas/results/rn6/SRX3657370/SRR6681058.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 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: 00:00:01 Multiseed full-index search: 00:41:10 21750587 reads; of these: 21750587 (100.00%) were unpaired; of these: 660061 (3.03%) aligned 0 times 15117351 (69.50%) aligned exactly 1 time 5973175 (27.46%) aligned >1 times 96.97% overall alignment rate Time searching: 00:41:13 Overall time: 00:41:13 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] 882888 / 21090526 = 0.0419 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 @ Wed, 12 Dec 2018 23:38:15: # Command line: callpeak -t SRX3657370.bam -f BAM -g 2.15e9 -n SRX3657370.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3657370.10 # format = BAM # ChIP-seq file = ['SRX3657370.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 @ Wed, 12 Dec 2018 23:38:15: #1 read tag files... INFO @ Wed, 12 Dec 2018 23:38:15: #1 read treatment tags... INFO @ Wed, 12 Dec 2018 23:38:15: # Command line: callpeak -t SRX3657370.bam -f BAM -g 2.15e9 -n SRX3657370.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3657370.05 # format = BAM # ChIP-seq file = ['SRX3657370.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 @ Wed, 12 Dec 2018 23:38:15: #1 read tag files... INFO @ Wed, 12 Dec 2018 23:38:15: #1 read treatment tags... INFO @ Wed, 12 Dec 2018 23:38:15: # Command line: callpeak -t SRX3657370.bam -f BAM -g 2.15e9 -n SRX3657370.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3657370.20 # format = BAM # ChIP-seq file = ['SRX3657370.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 @ Wed, 12 Dec 2018 23:38:15: #1 read tag files... INFO @ Wed, 12 Dec 2018 23:38:15: #1 read treatment tags... INFO @ Wed, 12 Dec 2018 23:38:32: 1000000 INFO @ Wed, 12 Dec 2018 23:38:33: 1000000 INFO @ Wed, 12 Dec 2018 23:38:35: 1000000 INFO @ Wed, 12 Dec 2018 23:38:48: 2000000 INFO @ Wed, 12 Dec 2018 23:38:53: 2000000 INFO @ Wed, 12 Dec 2018 23:38:54: 2000000 INFO @ Wed, 12 Dec 2018 23:39:02: 3000000 INFO @ Wed, 12 Dec 2018 23:39:11: 3000000 INFO @ Wed, 12 Dec 2018 23:39:13: 3000000 INFO @ Wed, 12 Dec 2018 23:39:17: 4000000 INFO @ Wed, 12 Dec 2018 23:39:30: 4000000 INFO @ Wed, 12 Dec 2018 23:39:30: 4000000 INFO @ Wed, 12 Dec 2018 23:39:32: 5000000 INFO @ Wed, 12 Dec 2018 23:39:46: 5000000 INFO @ Wed, 12 Dec 2018 23:39:47: 6000000 INFO @ Wed, 12 Dec 2018 23:39:48: 5000000 INFO @ Wed, 12 Dec 2018 23:40:02: 7000000 INFO @ Wed, 12 Dec 2018 23:40:02: 6000000 INFO @ Wed, 12 Dec 2018 23:40:07: 6000000 INFO @ Wed, 12 Dec 2018 23:40:17: 8000000 INFO @ Wed, 12 Dec 2018 23:40:17: 7000000 INFO @ Wed, 12 Dec 2018 23:40:24: 7000000 INFO @ Wed, 12 Dec 2018 23:40:31: 9000000 INFO @ Wed, 12 Dec 2018 23:40:36: 8000000 INFO @ Wed, 12 Dec 2018 23:40:40: 8000000 INFO @ Wed, 12 Dec 2018 23:40:46: 10000000 INFO @ Wed, 12 Dec 2018 23:40:53: 9000000 INFO @ Wed, 12 Dec 2018 23:40:57: 9000000 INFO @ Wed, 12 Dec 2018 23:41:01: 11000000 INFO @ Wed, 12 Dec 2018 23:41:11: 10000000 INFO @ Wed, 12 Dec 2018 23:41:14: 10000000 INFO @ Wed, 12 Dec 2018 23:41:15: 12000000 INFO @ Wed, 12 Dec 2018 23:41:28: 13000000 INFO @ Wed, 12 Dec 2018 23:41:29: 11000000 INFO @ Wed, 12 Dec 2018 23:41:30: 11000000 INFO @ Wed, 12 Dec 2018 23:41:42: 14000000 INFO @ Wed, 12 Dec 2018 23:41:46: 12000000 INFO @ Wed, 12 Dec 2018 23:41:49: 12000000 INFO @ Wed, 12 Dec 2018 23:41:55: 15000000 INFO @ Wed, 12 Dec 2018 23:42:02: 13000000 INFO @ Wed, 12 Dec 2018 23:42:08: 13000000 INFO @ Wed, 12 Dec 2018 23:42:09: 16000000 INFO @ Wed, 12 Dec 2018 23:42:19: 14000000 INFO @ Wed, 12 Dec 2018 23:42:23: 17000000 INFO @ Wed, 12 Dec 2018 23:42:26: 14000000 INFO @ Wed, 12 Dec 2018 23:42:35: 15000000 INFO @ Wed, 12 Dec 2018 23:42:39: 18000000 INFO @ Wed, 12 Dec 2018 23:42:46: 15000000 INFO @ Wed, 12 Dec 2018 23:42:50: 16000000 INFO @ Wed, 12 Dec 2018 23:42:55: 19000000 INFO @ Wed, 12 Dec 2018 23:42:59: 16000000 INFO @ Wed, 12 Dec 2018 23:43:05: 17000000 INFO @ Wed, 12 Dec 2018 23:43:10: 20000000 INFO @ Wed, 12 Dec 2018 23:43:13: 17000000 INFO @ Wed, 12 Dec 2018 23:43:13: #1 tag size is determined as 50 bps INFO @ Wed, 12 Dec 2018 23:43:13: #1 tag size = 50 INFO @ Wed, 12 Dec 2018 23:43:13: #1 total tags in treatment: 20207638 INFO @ Wed, 12 Dec 2018 23:43:13: #1 user defined the maximum tags... INFO @ Wed, 12 Dec 2018 23:43:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 12 Dec 2018 23:43:14: #1 tags after filtering in treatment: 20207518 INFO @ Wed, 12 Dec 2018 23:43:14: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 12 Dec 2018 23:43:14: #1 finished! INFO @ Wed, 12 Dec 2018 23:43:14: #2 Build Peak Model... INFO @ Wed, 12 Dec 2018 23:43:14: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 12 Dec 2018 23:43:17: #2 number of paired peaks: 5886 INFO @ Wed, 12 Dec 2018 23:43:17: start model_add_line... INFO @ Wed, 12 Dec 2018 23:43:17: start X-correlation... INFO @ Wed, 12 Dec 2018 23:43:17: end of X-cor INFO @ Wed, 12 Dec 2018 23:43:17: #2 finished! INFO @ Wed, 12 Dec 2018 23:43:17: #2 predicted fragment length is 50 bps INFO @ Wed, 12 Dec 2018 23:43:17: #2 alternative fragment length(s) may be 50,228,386,407,512 bps INFO @ Wed, 12 Dec 2018 23:43:17: #2.2 Generate R script for model : SRX3657370.10_model.r WARNING @ Wed, 12 Dec 2018 23:43:17: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 12 Dec 2018 23:43:17: #2 You may need to consider one of the other alternative d(s): 50,228,386,407,512 WARNING @ Wed, 12 Dec 2018 23:43:17: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 12 Dec 2018 23:43:17: #3 Call peaks... INFO @ Wed, 12 Dec 2018 23:43:17: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 12 Dec 2018 23:43:18: 18000000 INFO @ Wed, 12 Dec 2018 23:43:27: 18000000 INFO @ Wed, 12 Dec 2018 23:43:29: 19000000 INFO @ Wed, 12 Dec 2018 23:43:41: 20000000 INFO @ Wed, 12 Dec 2018 23:43:43: #1 tag size is determined as 50 bps INFO @ Wed, 12 Dec 2018 23:43:43: #1 tag size = 50 INFO @ Wed, 12 Dec 2018 23:43:43: #1 total tags in treatment: 20207638 INFO @ Wed, 12 Dec 2018 23:43:43: #1 user defined the maximum tags... INFO @ Wed, 12 Dec 2018 23:43:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 12 Dec 2018 23:43:43: 19000000 INFO @ Wed, 12 Dec 2018 23:43:44: #1 tags after filtering in treatment: 20207518 INFO @ Wed, 12 Dec 2018 23:43:44: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 12 Dec 2018 23:43:44: #1 finished! INFO @ Wed, 12 Dec 2018 23:43:44: #2 Build Peak Model... INFO @ Wed, 12 Dec 2018 23:43:44: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 12 Dec 2018 23:43:47: #2 number of paired peaks: 5886 INFO @ Wed, 12 Dec 2018 23:43:47: start model_add_line... INFO @ Wed, 12 Dec 2018 23:43:47: start X-correlation... INFO @ Wed, 12 Dec 2018 23:43:47: end of X-cor INFO @ Wed, 12 Dec 2018 23:43:47: #2 finished! INFO @ Wed, 12 Dec 2018 23:43:47: #2 predicted fragment length is 50 bps INFO @ Wed, 12 Dec 2018 23:43:47: #2 alternative fragment length(s) may be 50,228,386,407,512 bps INFO @ Wed, 12 Dec 2018 23:43:47: #2.2 Generate R script for model : SRX3657370.20_model.r WARNING @ Wed, 12 Dec 2018 23:43:47: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 12 Dec 2018 23:43:47: #2 You may need to consider one of the other alternative d(s): 50,228,386,407,512 WARNING @ Wed, 12 Dec 2018 23:43:47: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 12 Dec 2018 23:43:47: #3 Call peaks... INFO @ Wed, 12 Dec 2018 23:43:47: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 12 Dec 2018 23:43:59: 20000000 INFO @ Wed, 12 Dec 2018 23:44:02: #1 tag size is determined as 50 bps INFO @ Wed, 12 Dec 2018 23:44:02: #1 tag size = 50 INFO @ Wed, 12 Dec 2018 23:44:02: #1 total tags in treatment: 20207638 INFO @ Wed, 12 Dec 2018 23:44:02: #1 user defined the maximum tags... INFO @ Wed, 12 Dec 2018 23:44:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 12 Dec 2018 23:44:03: #1 tags after filtering in treatment: 20207518 INFO @ Wed, 12 Dec 2018 23:44:03: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 12 Dec 2018 23:44:03: #1 finished! INFO @ Wed, 12 Dec 2018 23:44:03: #2 Build Peak Model... INFO @ Wed, 12 Dec 2018 23:44:03: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 12 Dec 2018 23:44:06: #2 number of paired peaks: 5886 INFO @ Wed, 12 Dec 2018 23:44:06: start model_add_line... INFO @ Wed, 12 Dec 2018 23:44:06: start X-correlation... INFO @ Wed, 12 Dec 2018 23:44:06: end of X-cor INFO @ Wed, 12 Dec 2018 23:44:06: #2 finished! INFO @ Wed, 12 Dec 2018 23:44:06: #2 predicted fragment length is 50 bps INFO @ Wed, 12 Dec 2018 23:44:06: #2 alternative fragment length(s) may be 50,228,386,407,512 bps INFO @ Wed, 12 Dec 2018 23:44:06: #2.2 Generate R script for model : SRX3657370.05_model.r WARNING @ Wed, 12 Dec 2018 23:44:06: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 12 Dec 2018 23:44:06: #2 You may need to consider one of the other alternative d(s): 50,228,386,407,512 WARNING @ Wed, 12 Dec 2018 23:44:06: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 12 Dec 2018 23:44:06: #3 Call peaks... INFO @ Wed, 12 Dec 2018 23:44:06: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 12 Dec 2018 23:44:18: #3 Call peaks for each chromosome... INFO @ Wed, 12 Dec 2018 23:44:50: #3 Call peaks for each chromosome... INFO @ Wed, 12 Dec 2018 23:44:53: #4 Write output xls file... SRX3657370.10_peaks.xls INFO @ Wed, 12 Dec 2018 23:44:53: #4 Write peak in narrowPeak format file... SRX3657370.10_peaks.narrowPeak INFO @ Wed, 12 Dec 2018 23:44:53: #4 Write summits bed file... SRX3657370.10_summits.bed INFO @ Wed, 12 Dec 2018 23:44:53: Done! pass1 - making usageList (38 chroms): 7 millis pass2 - checking and writing primary data (851 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Wed, 12 Dec 2018 23:45:08: #3 Call peaks for each chromosome... INFO @ Wed, 12 Dec 2018 23:45:24: #4 Write output xls file... SRX3657370.20_peaks.xls INFO @ Wed, 12 Dec 2018 23:45:24: #4 Write peak in narrowPeak format file... SRX3657370.20_peaks.narrowPeak INFO @ Wed, 12 Dec 2018 23:45:24: #4 Write summits bed file... SRX3657370.20_summits.bed INFO @ Wed, 12 Dec 2018 23:45:24: Done! pass1 - making usageList (32 chroms): 4 millis pass2 - checking and writing primary data (403 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Wed, 12 Dec 2018 23:45:43: #4 Write output xls file... SRX3657370.05_peaks.xls INFO @ Wed, 12 Dec 2018 23:45:44: #4 Write peak in narrowPeak format file... SRX3657370.05_peaks.narrowPeak INFO @ Wed, 12 Dec 2018 23:45:44: #4 Write summits bed file... SRX3657370.05_summits.bed INFO @ Wed, 12 Dec 2018 23:45:44: Done! pass1 - making usageList (47 chroms): 5 millis pass2 - checking and writing primary data (1453 records, 4 fields): 12 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。