Job ID = 2001171 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 24,626,142 reads read : 24,626,142 reads written : 24,626,142 rm: cannot remove ‘[DSE]RR*’: 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:05:34 24626142 reads; of these: 24626142 (100.00%) were unpaired; of these: 517795 (2.10%) aligned 0 times 21229568 (86.21%) aligned exactly 1 time 2878779 (11.69%) aligned >1 times 97.90% overall alignment rate Time searching: 00:05:35 Overall time: 00:05:35 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] 10790364 / 24108347 = 0.4476 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 04:17:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101859/ERX101859.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101859/ERX101859.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101859/ERX101859.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101859/ERX101859.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 04:17:55: #1 read tag files... INFO @ Fri, 05 Jul 2019 04:17:55: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 04:17:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101859/ERX101859.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101859/ERX101859.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101859/ERX101859.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101859/ERX101859.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 04:17:56: #1 read tag files... INFO @ Fri, 05 Jul 2019 04:17:56: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 04:17:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101859/ERX101859.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101859/ERX101859.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101859/ERX101859.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101859/ERX101859.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 04:17:57: #1 read tag files... INFO @ Fri, 05 Jul 2019 04:17:57: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 04:18:05: 1000000 INFO @ Fri, 05 Jul 2019 04:18:06: 1000000 INFO @ Fri, 05 Jul 2019 04:18:07: 1000000 INFO @ Fri, 05 Jul 2019 04:18:16: 2000000 INFO @ Fri, 05 Jul 2019 04:18:16: 2000000 INFO @ Fri, 05 Jul 2019 04:18:18: 2000000 INFO @ Fri, 05 Jul 2019 04:18:25: 3000000 INFO @ Fri, 05 Jul 2019 04:18:26: 3000000 INFO @ Fri, 05 Jul 2019 04:18:28: 3000000 INFO @ Fri, 05 Jul 2019 04:18:34: 4000000 INFO @ Fri, 05 Jul 2019 04:18:37: 4000000 INFO @ Fri, 05 Jul 2019 04:18:39: 4000000 INFO @ Fri, 05 Jul 2019 04:18:43: 5000000 INFO @ Fri, 05 Jul 2019 04:18:47: 5000000 INFO @ Fri, 05 Jul 2019 04:18:49: 5000000 INFO @ Fri, 05 Jul 2019 04:18:52: 6000000 INFO @ Fri, 05 Jul 2019 04:18:58: 6000000 INFO @ Fri, 05 Jul 2019 04:18:59: 6000000 INFO @ Fri, 05 Jul 2019 04:19:00: 7000000 INFO @ Fri, 05 Jul 2019 04:19:09: 8000000 INFO @ Fri, 05 Jul 2019 04:19:09: 7000000 INFO @ Fri, 05 Jul 2019 04:19:10: 7000000 INFO @ Fri, 05 Jul 2019 04:19:17: 9000000 INFO @ Fri, 05 Jul 2019 04:19:20: 8000000 INFO @ Fri, 05 Jul 2019 04:19:21: 8000000 INFO @ Fri, 05 Jul 2019 04:19:26: 10000000 INFO @ Fri, 05 Jul 2019 04:19:31: 9000000 INFO @ Fri, 05 Jul 2019 04:19:31: 9000000 INFO @ Fri, 05 Jul 2019 04:19:34: 11000000 INFO @ Fri, 05 Jul 2019 04:19:42: 10000000 INFO @ Fri, 05 Jul 2019 04:19:42: 10000000 INFO @ Fri, 05 Jul 2019 04:19:43: 12000000 INFO @ Fri, 05 Jul 2019 04:19:52: 13000000 INFO @ Fri, 05 Jul 2019 04:19:53: 11000000 INFO @ Fri, 05 Jul 2019 04:19:53: 11000000 INFO @ Fri, 05 Jul 2019 04:19:54: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 04:19:54: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 04:19:54: #1 total tags in treatment: 13317983 INFO @ Fri, 05 Jul 2019 04:19:54: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 04:19:54: #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 04:19:55: #1 tags after filtering in treatment: 13317716 INFO @ Fri, 05 Jul 2019 04:19:55: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 04:19:55: #1 finished! INFO @ Fri, 05 Jul 2019 04:19:55: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 04:19:55: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 04:19:59: #2 number of paired peaks: 56939 INFO @ Fri, 05 Jul 2019 04:19:59: start model_add_line... INFO @ Fri, 05 Jul 2019 04:19:59: start X-correlation... INFO @ Fri, 05 Jul 2019 04:19:59: end of X-cor INFO @ Fri, 05 Jul 2019 04:19:59: #2 finished! INFO @ Fri, 05 Jul 2019 04:19:59: #2 predicted fragment length is 135 bps INFO @ Fri, 05 Jul 2019 04:19:59: #2 alternative fragment length(s) may be 4,135 bps INFO @ Fri, 05 Jul 2019 04:19:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101859/ERX101859.10_model.r INFO @ Fri, 05 Jul 2019 04:19:59: #3 Call peaks... INFO @ Fri, 05 Jul 2019 04:19:59: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 04:20:03: 12000000 INFO @ Fri, 05 Jul 2019 04:20:03: 12000000 INFO @ Fri, 05 Jul 2019 04:20:13: 13000000 INFO @ Fri, 05 Jul 2019 04:20:13: 13000000 INFO @ Fri, 05 Jul 2019 04:20:16: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 04:20:16: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 04:20:16: #1 total tags in treatment: 13317983 INFO @ Fri, 05 Jul 2019 04:20:16: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 04:20:16: #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 04:20:16: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 04:20:16: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 04:20:16: #1 total tags in treatment: 13317983 INFO @ Fri, 05 Jul 2019 04:20:16: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 04:20:16: #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 04:20:16: #1 tags after filtering in treatment: 13317716 INFO @ Fri, 05 Jul 2019 04:20:16: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 04:20:16: #1 finished! INFO @ Fri, 05 Jul 2019 04:20:16: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 04:20:16: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 04:20:17: #1 tags after filtering in treatment: 13317716 INFO @ Fri, 05 Jul 2019 04:20:17: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 04:20:17: #1 finished! INFO @ Fri, 05 Jul 2019 04:20:17: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 04:20:17: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 04:20:20: #2 number of paired peaks: 56939 INFO @ Fri, 05 Jul 2019 04:20:20: start model_add_line... INFO @ Fri, 05 Jul 2019 04:20:21: start X-correlation... INFO @ Fri, 05 Jul 2019 04:20:21: end of X-cor INFO @ Fri, 05 Jul 2019 04:20:21: #2 finished! INFO @ Fri, 05 Jul 2019 04:20:21: #2 predicted fragment length is 135 bps INFO @ Fri, 05 Jul 2019 04:20:21: #2 alternative fragment length(s) may be 4,135 bps INFO @ Fri, 05 Jul 2019 04:20:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101859/ERX101859.20_model.r INFO @ Fri, 05 Jul 2019 04:20:21: #3 Call peaks... INFO @ Fri, 05 Jul 2019 04:20:21: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 04:20:21: #2 number of paired peaks: 56939 INFO @ Fri, 05 Jul 2019 04:20:21: start model_add_line... INFO @ Fri, 05 Jul 2019 04:20:21: start X-correlation... INFO @ Fri, 05 Jul 2019 04:20:21: end of X-cor INFO @ Fri, 05 Jul 2019 04:20:21: #2 finished! INFO @ Fri, 05 Jul 2019 04:20:21: #2 predicted fragment length is 135 bps INFO @ Fri, 05 Jul 2019 04:20:21: #2 alternative fragment length(s) may be 4,135 bps INFO @ Fri, 05 Jul 2019 04:20:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101859/ERX101859.05_model.r INFO @ Fri, 05 Jul 2019 04:20:21: #3 Call peaks... INFO @ Fri, 05 Jul 2019 04:20:21: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 04:20:41: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 04:21:03: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 04:21:04: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 04:21:06: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101859/ERX101859.10_peaks.xls INFO @ Fri, 05 Jul 2019 04:21:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101859/ERX101859.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 04:21:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101859/ERX101859.10_summits.bed INFO @ Fri, 05 Jul 2019 04:21:07: Done! pass1 - making usageList (105 chroms): 7 millis pass2 - checking and writing primary data (31805 records, 4 fields): 43 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 04:21:25: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101859/ERX101859.20_peaks.xls INFO @ Fri, 05 Jul 2019 04:21:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101859/ERX101859.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 04:21:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101859/ERX101859.20_summits.bed INFO @ Fri, 05 Jul 2019 04:21:25: Done! pass1 - making usageList (79 chroms): 4 millis pass2 - checking and writing primary data (18052 records, 4 fields): 26 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 04:21:28: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101859/ERX101859.05_peaks.xls INFO @ Fri, 05 Jul 2019 04:21:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101859/ERX101859.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 04:21:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101859/ERX101859.05_summits.bed INFO @ Fri, 05 Jul 2019 04:21:29: Done! pass1 - making usageList (133 chroms): 9 millis pass2 - checking and writing primary data (42763 records, 4 fields): 58 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。