Job ID = 2002168 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 29,433,011 reads read : 29,433,011 reads written : 29,433,011 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR458087.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: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:10:26 29433011 reads; of these: 29433011 (100.00%) were unpaired; of these: 729695 (2.48%) aligned 0 times 20191215 (68.60%) aligned exactly 1 time 8512101 (28.92%) aligned >1 times 97.52% overall alignment rate Time searching: 00:10:28 Overall time: 00:10:28 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 8 files... [bam_rmdupse_core] 1483977 / 28703316 = 0.0517 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 11:04:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX190370/ERX190370.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX190370/ERX190370.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX190370/ERX190370.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX190370/ERX190370.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 11:04:53: #1 read tag files... INFO @ Fri, 05 Jul 2019 11:04:53: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 11:04:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX190370/ERX190370.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX190370/ERX190370.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX190370/ERX190370.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX190370/ERX190370.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 11:04:54: #1 read tag files... INFO @ Fri, 05 Jul 2019 11:04:54: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 11:04:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX190370/ERX190370.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX190370/ERX190370.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX190370/ERX190370.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX190370/ERX190370.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 11:04:55: #1 read tag files... INFO @ Fri, 05 Jul 2019 11:04:55: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 11:05:01: 1000000 INFO @ Fri, 05 Jul 2019 11:05:02: 1000000 INFO @ Fri, 05 Jul 2019 11:05:02: 1000000 INFO @ Fri, 05 Jul 2019 11:05:08: 2000000 INFO @ Fri, 05 Jul 2019 11:05:08: 2000000 INFO @ Fri, 05 Jul 2019 11:05:11: 2000000 INFO @ Fri, 05 Jul 2019 11:05:15: 3000000 INFO @ Fri, 05 Jul 2019 11:05:16: 3000000 INFO @ Fri, 05 Jul 2019 11:05:19: 3000000 INFO @ Fri, 05 Jul 2019 11:05:21: 4000000 INFO @ Fri, 05 Jul 2019 11:05:24: 4000000 INFO @ Fri, 05 Jul 2019 11:05:27: 4000000 INFO @ Fri, 05 Jul 2019 11:05:27: 5000000 INFO @ Fri, 05 Jul 2019 11:05:31: 5000000 INFO @ Fri, 05 Jul 2019 11:05:34: 6000000 INFO @ Fri, 05 Jul 2019 11:05:35: 5000000 INFO @ Fri, 05 Jul 2019 11:05:39: 6000000 INFO @ Fri, 05 Jul 2019 11:05:40: 7000000 INFO @ Fri, 05 Jul 2019 11:05:43: 6000000 INFO @ Fri, 05 Jul 2019 11:05:47: 8000000 INFO @ Fri, 05 Jul 2019 11:05:47: 7000000 INFO @ Fri, 05 Jul 2019 11:05:51: 7000000 INFO @ Fri, 05 Jul 2019 11:05:53: 9000000 INFO @ Fri, 05 Jul 2019 11:05:55: 8000000 INFO @ Fri, 05 Jul 2019 11:05:59: 8000000 INFO @ Fri, 05 Jul 2019 11:06:00: 10000000 INFO @ Fri, 05 Jul 2019 11:06:03: 9000000 INFO @ Fri, 05 Jul 2019 11:06:06: 11000000 INFO @ Fri, 05 Jul 2019 11:06:08: 9000000 INFO @ Fri, 05 Jul 2019 11:06:12: 10000000 INFO @ Fri, 05 Jul 2019 11:06:12: 12000000 INFO @ Fri, 05 Jul 2019 11:06:16: 10000000 INFO @ Fri, 05 Jul 2019 11:06:19: 13000000 INFO @ Fri, 05 Jul 2019 11:06:19: 11000000 INFO @ Fri, 05 Jul 2019 11:06:24: 11000000 INFO @ Fri, 05 Jul 2019 11:06:25: 14000000 INFO @ Fri, 05 Jul 2019 11:06:27: 12000000 INFO @ Fri, 05 Jul 2019 11:06:32: 15000000 INFO @ Fri, 05 Jul 2019 11:06:32: 12000000 INFO @ Fri, 05 Jul 2019 11:06:35: 13000000 INFO @ Fri, 05 Jul 2019 11:06:38: 16000000 INFO @ Fri, 05 Jul 2019 11:06:40: 13000000 INFO @ Fri, 05 Jul 2019 11:06:43: 14000000 INFO @ Fri, 05 Jul 2019 11:06:45: 17000000 INFO @ Fri, 05 Jul 2019 11:06:48: 14000000 INFO @ Fri, 05 Jul 2019 11:06:50: 15000000 INFO @ Fri, 05 Jul 2019 11:06:52: 18000000 INFO @ Fri, 05 Jul 2019 11:06:56: 15000000 INFO @ Fri, 05 Jul 2019 11:06:58: 16000000 INFO @ Fri, 05 Jul 2019 11:06:58: 19000000 INFO @ Fri, 05 Jul 2019 11:07:05: 20000000 INFO @ Fri, 05 Jul 2019 11:07:05: 16000000 INFO @ Fri, 05 Jul 2019 11:07:06: 17000000 INFO @ Fri, 05 Jul 2019 11:07:11: 21000000 INFO @ Fri, 05 Jul 2019 11:07:13: 17000000 INFO @ Fri, 05 Jul 2019 11:07:13: 18000000 INFO @ Fri, 05 Jul 2019 11:07:17: 22000000 INFO @ Fri, 05 Jul 2019 11:07:21: 18000000 INFO @ Fri, 05 Jul 2019 11:07:21: 19000000 INFO @ Fri, 05 Jul 2019 11:07:24: 23000000 INFO @ Fri, 05 Jul 2019 11:07:29: 19000000 INFO @ Fri, 05 Jul 2019 11:07:29: 20000000 INFO @ Fri, 05 Jul 2019 11:07:30: 24000000 INFO @ Fri, 05 Jul 2019 11:07:37: 25000000 INFO @ Fri, 05 Jul 2019 11:07:37: 21000000 INFO @ Fri, 05 Jul 2019 11:07:37: 20000000 INFO @ Fri, 05 Jul 2019 11:07:43: 26000000 INFO @ Fri, 05 Jul 2019 11:07:44: 22000000 INFO @ Fri, 05 Jul 2019 11:07:45: 21000000 INFO @ Fri, 05 Jul 2019 11:07:50: 27000000 INFO @ Fri, 05 Jul 2019 11:07:51: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 11:07:51: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 11:07:51: #1 total tags in treatment: 27219339 INFO @ Fri, 05 Jul 2019 11:07:51: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 11:07:51: #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 11:07:52: #1 tags after filtering in treatment: 27219239 INFO @ Fri, 05 Jul 2019 11:07:52: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 11:07:52: #1 finished! INFO @ Fri, 05 Jul 2019 11:07:52: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 11:07:52: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 11:07:52: 23000000 INFO @ Fri, 05 Jul 2019 11:07:53: 22000000 INFO @ Fri, 05 Jul 2019 11:07:55: #2 number of paired peaks: 7834 INFO @ Fri, 05 Jul 2019 11:07:55: start model_add_line... INFO @ Fri, 05 Jul 2019 11:07:56: start X-correlation... INFO @ Fri, 05 Jul 2019 11:07:56: end of X-cor INFO @ Fri, 05 Jul 2019 11:07:56: #2 finished! INFO @ Fri, 05 Jul 2019 11:07:56: #2 predicted fragment length is 41 bps INFO @ Fri, 05 Jul 2019 11:07:56: #2 alternative fragment length(s) may be 41,80 bps INFO @ Fri, 05 Jul 2019 11:07:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX190370/ERX190370.20_model.r WARNING @ Fri, 05 Jul 2019 11:07:56: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 11:07:56: #2 You may need to consider one of the other alternative d(s): 41,80 WARNING @ Fri, 05 Jul 2019 11:07:56: #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 11:07:56: #3 Call peaks... INFO @ Fri, 05 Jul 2019 11:07:56: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 11:08:00: 24000000 INFO @ Fri, 05 Jul 2019 11:08:01: 23000000 INFO @ Fri, 05 Jul 2019 11:08:07: 25000000 INFO @ Fri, 05 Jul 2019 11:08:10: 24000000 INFO @ Fri, 05 Jul 2019 11:08:15: 26000000 INFO @ Fri, 05 Jul 2019 11:08:18: 25000000 INFO @ Fri, 05 Jul 2019 11:08:23: 27000000 INFO @ Fri, 05 Jul 2019 11:08:25: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 11:08:25: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 11:08:25: #1 total tags in treatment: 27219339 INFO @ Fri, 05 Jul 2019 11:08:25: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 11:08:25: #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 11:08:26: #1 tags after filtering in treatment: 27219239 INFO @ Fri, 05 Jul 2019 11:08:26: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 11:08:26: #1 finished! INFO @ Fri, 05 Jul 2019 11:08:26: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 11:08:26: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 11:08:26: 26000000 INFO @ Fri, 05 Jul 2019 11:08:29: #2 number of paired peaks: 7834 INFO @ Fri, 05 Jul 2019 11:08:29: start model_add_line... INFO @ Fri, 05 Jul 2019 11:08:29: start X-correlation... INFO @ Fri, 05 Jul 2019 11:08:29: end of X-cor INFO @ Fri, 05 Jul 2019 11:08:29: #2 finished! INFO @ Fri, 05 Jul 2019 11:08:29: #2 predicted fragment length is 41 bps INFO @ Fri, 05 Jul 2019 11:08:29: #2 alternative fragment length(s) may be 41,80 bps INFO @ Fri, 05 Jul 2019 11:08:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX190370/ERX190370.05_model.r WARNING @ Fri, 05 Jul 2019 11:08:30: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 11:08:30: #2 You may need to consider one of the other alternative d(s): 41,80 WARNING @ Fri, 05 Jul 2019 11:08:30: #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 11:08:30: #3 Call peaks... INFO @ Fri, 05 Jul 2019 11:08:30: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 11:08:34: 27000000 INFO @ Fri, 05 Jul 2019 11:08:36: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 11:08:36: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 11:08:36: #1 total tags in treatment: 27219339 INFO @ Fri, 05 Jul 2019 11:08:36: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 11:08:36: #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 11:08:37: #1 tags after filtering in treatment: 27219239 INFO @ Fri, 05 Jul 2019 11:08:37: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 11:08:37: #1 finished! INFO @ Fri, 05 Jul 2019 11:08:37: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 11:08:37: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 11:08:40: #2 number of paired peaks: 7834 INFO @ Fri, 05 Jul 2019 11:08:40: start model_add_line... INFO @ Fri, 05 Jul 2019 11:08:40: start X-correlation... INFO @ Fri, 05 Jul 2019 11:08:40: end of X-cor INFO @ Fri, 05 Jul 2019 11:08:40: #2 finished! INFO @ Fri, 05 Jul 2019 11:08:40: #2 predicted fragment length is 41 bps INFO @ Fri, 05 Jul 2019 11:08:40: #2 alternative fragment length(s) may be 41,80 bps INFO @ Fri, 05 Jul 2019 11:08:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX190370/ERX190370.10_model.r WARNING @ Fri, 05 Jul 2019 11:08:41: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 11:08:41: #2 You may need to consider one of the other alternative d(s): 41,80 WARNING @ Fri, 05 Jul 2019 11:08:41: #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 11:08:41: #3 Call peaks... INFO @ Fri, 05 Jul 2019 11:08:41: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 11:09:21: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 11:09:54: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 11:10:03: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX190370/ERX190370.20_peaks.xls INFO @ Fri, 05 Jul 2019 11:10:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX190370/ERX190370.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 11:10:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX190370/ERX190370.20_summits.bed INFO @ Fri, 05 Jul 2019 11:10:03: Done! pass1 - making usageList (33 chroms): 1 millis pass2 - checking and writing primary data (478 records, 4 fields): 224 millis INFO @ Fri, 05 Jul 2019 11:10:06: #3 Call peaks for each chromosome... CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 11:10:37: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX190370/ERX190370.05_peaks.xls INFO @ Fri, 05 Jul 2019 11:10:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX190370/ERX190370.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 11:10:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX190370/ERX190370.05_summits.bed INFO @ Fri, 05 Jul 2019 11:10:38: Done! pass1 - making usageList (66 chroms): 3 millis pass2 - checking and writing primary data (2555 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 11:10:49: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX190370/ERX190370.10_peaks.xls INFO @ Fri, 05 Jul 2019 11:10:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX190370/ERX190370.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 11:10:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX190370/ERX190370.10_summits.bed INFO @ Fri, 05 Jul 2019 11:10:49: Done! pass1 - making usageList (42 chroms): 2 millis pass2 - checking and writing primary data (1157 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。