Job ID = 2002528 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 25,927,981 reads read : 25,927,981 reads written : 25,927,981 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR572177.sra.cache’: No such file or directory 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: 00:00:04 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:24:20 25927981 reads; of these: 25927981 (100.00%) were unpaired; of these: 454372 (1.75%) aligned 0 times 17224523 (66.43%) aligned exactly 1 time 8249086 (31.82%) aligned >1 times 98.25% overall alignment rate Time searching: 00:24:24 Overall time: 00:24:25 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] 627281 / 25473609 = 0.0246 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 @ Fri, 05 Jul 2019 12:23:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX530948/ERX530948.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX530948/ERX530948.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX530948/ERX530948.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX530948/ERX530948.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 @ Fri, 05 Jul 2019 12:23:23: #1 read tag files... INFO @ Fri, 05 Jul 2019 12:23:23: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 12:23:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX530948/ERX530948.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX530948/ERX530948.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX530948/ERX530948.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX530948/ERX530948.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 @ Fri, 05 Jul 2019 12:23:24: #1 read tag files... INFO @ Fri, 05 Jul 2019 12:23:24: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 12:23:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX530948/ERX530948.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX530948/ERX530948.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX530948/ERX530948.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX530948/ERX530948.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 @ Fri, 05 Jul 2019 12:23:25: #1 read tag files... INFO @ Fri, 05 Jul 2019 12:23:25: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 12:23:35: 1000000 INFO @ Fri, 05 Jul 2019 12:23:35: 1000000 INFO @ Fri, 05 Jul 2019 12:23:36: 1000000 INFO @ Fri, 05 Jul 2019 12:23:45: 2000000 INFO @ Fri, 05 Jul 2019 12:23:46: 2000000 INFO @ Fri, 05 Jul 2019 12:23:46: 2000000 INFO @ Fri, 05 Jul 2019 12:23:56: 3000000 INFO @ Fri, 05 Jul 2019 12:23:56: 3000000 INFO @ Fri, 05 Jul 2019 12:23:57: 3000000 INFO @ Fri, 05 Jul 2019 12:24:06: 4000000 INFO @ Fri, 05 Jul 2019 12:24:06: 4000000 INFO @ Fri, 05 Jul 2019 12:24:08: 4000000 INFO @ Fri, 05 Jul 2019 12:24:17: 5000000 INFO @ Fri, 05 Jul 2019 12:24:17: 5000000 INFO @ Fri, 05 Jul 2019 12:24:21: 5000000 INFO @ Fri, 05 Jul 2019 12:24:28: 6000000 INFO @ Fri, 05 Jul 2019 12:24:30: 6000000 INFO @ Fri, 05 Jul 2019 12:24:33: 6000000 INFO @ Fri, 05 Jul 2019 12:24:39: 7000000 INFO @ Fri, 05 Jul 2019 12:24:40: 7000000 INFO @ Fri, 05 Jul 2019 12:24:44: 7000000 INFO @ Fri, 05 Jul 2019 12:24:50: 8000000 INFO @ Fri, 05 Jul 2019 12:24:51: 8000000 INFO @ Fri, 05 Jul 2019 12:24:55: 8000000 INFO @ Fri, 05 Jul 2019 12:25:00: 9000000 INFO @ Fri, 05 Jul 2019 12:25:00: 9000000 INFO @ Fri, 05 Jul 2019 12:25:06: 9000000 INFO @ Fri, 05 Jul 2019 12:25:10: 10000000 INFO @ Fri, 05 Jul 2019 12:25:11: 10000000 INFO @ Fri, 05 Jul 2019 12:25:18: 10000000 INFO @ Fri, 05 Jul 2019 12:25:19: 11000000 INFO @ Fri, 05 Jul 2019 12:25:21: 11000000 INFO @ Fri, 05 Jul 2019 12:25:28: 12000000 INFO @ Fri, 05 Jul 2019 12:25:29: 11000000 INFO @ Fri, 05 Jul 2019 12:25:32: 12000000 INFO @ Fri, 05 Jul 2019 12:25:38: 13000000 INFO @ Fri, 05 Jul 2019 12:25:42: 12000000 INFO @ Fri, 05 Jul 2019 12:25:43: 13000000 INFO @ Fri, 05 Jul 2019 12:25:48: 14000000 INFO @ Fri, 05 Jul 2019 12:25:54: 13000000 INFO @ Fri, 05 Jul 2019 12:25:55: 14000000 INFO @ Fri, 05 Jul 2019 12:25:59: 15000000 INFO @ Fri, 05 Jul 2019 12:26:06: 15000000 INFO @ Fri, 05 Jul 2019 12:26:07: 14000000 INFO @ Fri, 05 Jul 2019 12:26:12: 16000000 INFO @ Fri, 05 Jul 2019 12:26:18: 16000000 INFO @ Fri, 05 Jul 2019 12:26:19: 15000000 INFO @ Fri, 05 Jul 2019 12:26:24: 17000000 INFO @ Fri, 05 Jul 2019 12:26:29: 17000000 INFO @ Fri, 05 Jul 2019 12:26:31: 16000000 INFO @ Fri, 05 Jul 2019 12:26:34: 18000000 INFO @ Fri, 05 Jul 2019 12:26:40: 18000000 INFO @ Fri, 05 Jul 2019 12:26:44: 17000000 INFO @ Fri, 05 Jul 2019 12:26:47: 19000000 INFO @ Fri, 05 Jul 2019 12:26:53: 19000000 INFO @ Fri, 05 Jul 2019 12:26:58: 18000000 INFO @ Fri, 05 Jul 2019 12:27:00: 20000000 INFO @ Fri, 05 Jul 2019 12:27:05: 20000000 INFO @ Fri, 05 Jul 2019 12:27:12: 21000000 INFO @ Fri, 05 Jul 2019 12:27:12: 19000000 INFO @ Fri, 05 Jul 2019 12:27:19: 21000000 INFO @ Fri, 05 Jul 2019 12:27:23: 22000000 INFO @ Fri, 05 Jul 2019 12:27:27: 20000000 INFO @ Fri, 05 Jul 2019 12:27:31: 22000000 INFO @ Fri, 05 Jul 2019 12:27:34: 23000000 INFO @ Fri, 05 Jul 2019 12:27:40: 21000000 INFO @ Fri, 05 Jul 2019 12:27:45: 23000000 INFO @ Fri, 05 Jul 2019 12:27:47: 24000000 INFO @ Fri, 05 Jul 2019 12:27:53: 22000000 INFO @ Fri, 05 Jul 2019 12:27:58: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 12:27:58: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 12:27:58: #1 total tags in treatment: 24846328 INFO @ Fri, 05 Jul 2019 12:27:58: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 12:27:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 12:27:58: 24000000 INFO @ Fri, 05 Jul 2019 12:27:58: #1 tags after filtering in treatment: 24846216 INFO @ Fri, 05 Jul 2019 12:27:58: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 12:27:58: #1 finished! INFO @ Fri, 05 Jul 2019 12:27:58: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 12:27:58: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 12:28:01: #2 number of paired peaks: 6262 INFO @ Fri, 05 Jul 2019 12:28:01: start model_add_line... INFO @ Fri, 05 Jul 2019 12:28:02: start X-correlation... INFO @ Fri, 05 Jul 2019 12:28:02: end of X-cor INFO @ Fri, 05 Jul 2019 12:28:02: #2 finished! INFO @ Fri, 05 Jul 2019 12:28:02: #2 predicted fragment length is 49 bps INFO @ Fri, 05 Jul 2019 12:28:02: #2 alternative fragment length(s) may be 49,212,400 bps INFO @ Fri, 05 Jul 2019 12:28:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX530948/ERX530948.20_model.r WARNING @ Fri, 05 Jul 2019 12:28:02: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 12:28:02: #2 You may need to consider one of the other alternative d(s): 49,212,400 WARNING @ Fri, 05 Jul 2019 12:28:02: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 05 Jul 2019 12:28:02: #3 Call peaks... INFO @ Fri, 05 Jul 2019 12:28:02: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 12:28:05: 23000000 INFO @ Fri, 05 Jul 2019 12:28:10: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 12:28:10: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 12:28:10: #1 total tags in treatment: 24846328 INFO @ Fri, 05 Jul 2019 12:28:10: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 12:28:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 12:28:11: #1 tags after filtering in treatment: 24846216 INFO @ Fri, 05 Jul 2019 12:28:11: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 12:28:11: #1 finished! INFO @ Fri, 05 Jul 2019 12:28:11: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 12:28:11: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 12:28:14: #2 number of paired peaks: 6262 INFO @ Fri, 05 Jul 2019 12:28:14: start model_add_line... INFO @ Fri, 05 Jul 2019 12:28:14: start X-correlation... INFO @ Fri, 05 Jul 2019 12:28:14: end of X-cor INFO @ Fri, 05 Jul 2019 12:28:14: #2 finished! INFO @ Fri, 05 Jul 2019 12:28:14: #2 predicted fragment length is 49 bps INFO @ Fri, 05 Jul 2019 12:28:14: #2 alternative fragment length(s) may be 49,212,400 bps INFO @ Fri, 05 Jul 2019 12:28:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX530948/ERX530948.10_model.r WARNING @ Fri, 05 Jul 2019 12:28:14: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 12:28:14: #2 You may need to consider one of the other alternative d(s): 49,212,400 WARNING @ Fri, 05 Jul 2019 12:28:14: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 05 Jul 2019 12:28:14: #3 Call peaks... INFO @ Fri, 05 Jul 2019 12:28:14: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 12:28:18: 24000000 INFO @ Fri, 05 Jul 2019 12:28:28: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 12:28:28: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 12:28:28: #1 total tags in treatment: 24846328 INFO @ Fri, 05 Jul 2019 12:28:28: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 12:28:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 12:28:29: #1 tags after filtering in treatment: 24846216 INFO @ Fri, 05 Jul 2019 12:28:29: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 12:28:29: #1 finished! INFO @ Fri, 05 Jul 2019 12:28:29: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 12:28:29: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 12:28:32: #2 number of paired peaks: 6262 INFO @ Fri, 05 Jul 2019 12:28:32: start model_add_line... INFO @ Fri, 05 Jul 2019 12:28:32: start X-correlation... INFO @ Fri, 05 Jul 2019 12:28:32: end of X-cor INFO @ Fri, 05 Jul 2019 12:28:32: #2 finished! INFO @ Fri, 05 Jul 2019 12:28:32: #2 predicted fragment length is 49 bps INFO @ Fri, 05 Jul 2019 12:28:32: #2 alternative fragment length(s) may be 49,212,400 bps INFO @ Fri, 05 Jul 2019 12:28:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX530948/ERX530948.05_model.r WARNING @ Fri, 05 Jul 2019 12:28:32: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 12:28:32: #2 You may need to consider one of the other alternative d(s): 49,212,400 WARNING @ Fri, 05 Jul 2019 12:28:32: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 05 Jul 2019 12:28:32: #3 Call peaks... INFO @ Fri, 05 Jul 2019 12:28:32: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 12:29:24: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 12:29:35: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 12:29:54: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 12:30:05: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX530948/ERX530948.20_peaks.xls INFO @ Fri, 05 Jul 2019 12:30:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX530948/ERX530948.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 12:30:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX530948/ERX530948.20_summits.bed INFO @ Fri, 05 Jul 2019 12:30:05: Done! pass1 - making usageList (33 chroms): 2 millis pass2 - checking and writing primary data (481 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 12:30:15: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX530948/ERX530948.10_peaks.xls INFO @ Fri, 05 Jul 2019 12:30:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX530948/ERX530948.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 12:30:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX530948/ERX530948.10_summits.bed INFO @ Fri, 05 Jul 2019 12:30:15: Done! pass1 - making usageList (41 chroms): 1 millis pass2 - checking and writing primary data (987 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 12:30:34: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX530948/ERX530948.05_peaks.xls INFO @ Fri, 05 Jul 2019 12:30:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX530948/ERX530948.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 12:30:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX530948/ERX530948.05_summits.bed INFO @ Fri, 05 Jul 2019 12:30:34: Done! pass1 - making usageList (51 chroms): 2 millis pass2 - checking and writing primary data (1693 records, 4 fields): 11 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。