Job ID = 2001593 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 23,896,335 reads read : 23,896,335 reads written : 23,896,335 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: 00:09:18 23896335 reads; of these: 23896335 (100.00%) were unpaired; of these: 505177 (2.11%) aligned 0 times 17979694 (75.24%) aligned exactly 1 time 5411464 (22.65%) aligned >1 times 97.89% overall alignment rate Time searching: 00:09:19 Overall time: 00:09:19 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] 1421419 / 23391158 = 0.0608 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 05:56:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101923/ERX101923.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101923/ERX101923.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101923/ERX101923.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101923/ERX101923.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 05:56:04: #1 read tag files... INFO @ Fri, 05 Jul 2019 05:56:04: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 05:56:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101923/ERX101923.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101923/ERX101923.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101923/ERX101923.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101923/ERX101923.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 05:56:05: #1 read tag files... INFO @ Fri, 05 Jul 2019 05:56:05: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 05:56:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101923/ERX101923.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101923/ERX101923.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101923/ERX101923.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101923/ERX101923.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 05:56:06: #1 read tag files... INFO @ Fri, 05 Jul 2019 05:56:06: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 05:56:13: 1000000 INFO @ Fri, 05 Jul 2019 05:56:13: 1000000 INFO @ Fri, 05 Jul 2019 05:56:15: 1000000 INFO @ Fri, 05 Jul 2019 05:56:19: 2000000 INFO @ Fri, 05 Jul 2019 05:56:22: 2000000 INFO @ Fri, 05 Jul 2019 05:56:23: 2000000 INFO @ Fri, 05 Jul 2019 05:56:26: 3000000 INFO @ Fri, 05 Jul 2019 05:56:30: 3000000 INFO @ Fri, 05 Jul 2019 05:56:31: 3000000 INFO @ Fri, 05 Jul 2019 05:56:32: 4000000 INFO @ Fri, 05 Jul 2019 05:56:38: 4000000 INFO @ Fri, 05 Jul 2019 05:56:39: 4000000 INFO @ Fri, 05 Jul 2019 05:56:39: 5000000 INFO @ Fri, 05 Jul 2019 05:56:46: 6000000 INFO @ Fri, 05 Jul 2019 05:56:46: 5000000 INFO @ Fri, 05 Jul 2019 05:56:47: 5000000 INFO @ Fri, 05 Jul 2019 05:56:52: 7000000 INFO @ Fri, 05 Jul 2019 05:56:54: 6000000 INFO @ Fri, 05 Jul 2019 05:56:55: 6000000 INFO @ Fri, 05 Jul 2019 05:56:59: 8000000 INFO @ Fri, 05 Jul 2019 05:57:03: 7000000 INFO @ Fri, 05 Jul 2019 05:57:03: 7000000 INFO @ Fri, 05 Jul 2019 05:57:05: 9000000 INFO @ Fri, 05 Jul 2019 05:57:11: 8000000 INFO @ Fri, 05 Jul 2019 05:57:12: 8000000 INFO @ Fri, 05 Jul 2019 05:57:12: 10000000 INFO @ Fri, 05 Jul 2019 05:57:18: 11000000 INFO @ Fri, 05 Jul 2019 05:57:19: 9000000 INFO @ Fri, 05 Jul 2019 05:57:20: 9000000 INFO @ Fri, 05 Jul 2019 05:57:25: 12000000 INFO @ Fri, 05 Jul 2019 05:57:27: 10000000 INFO @ Fri, 05 Jul 2019 05:57:28: 10000000 INFO @ Fri, 05 Jul 2019 05:57:31: 13000000 INFO @ Fri, 05 Jul 2019 05:57:35: 11000000 INFO @ Fri, 05 Jul 2019 05:57:36: 11000000 INFO @ Fri, 05 Jul 2019 05:57:38: 14000000 INFO @ Fri, 05 Jul 2019 05:57:42: 12000000 INFO @ Fri, 05 Jul 2019 05:57:45: 15000000 INFO @ Fri, 05 Jul 2019 05:57:45: 12000000 INFO @ Fri, 05 Jul 2019 05:57:50: 13000000 INFO @ Fri, 05 Jul 2019 05:57:51: 16000000 INFO @ Fri, 05 Jul 2019 05:57:53: 13000000 INFO @ Fri, 05 Jul 2019 05:57:58: 17000000 INFO @ Fri, 05 Jul 2019 05:57:58: 14000000 INFO @ Fri, 05 Jul 2019 05:58:01: 14000000 INFO @ Fri, 05 Jul 2019 05:58:04: 18000000 INFO @ Fri, 05 Jul 2019 05:58:06: 15000000 INFO @ Fri, 05 Jul 2019 05:58:09: 15000000 INFO @ Fri, 05 Jul 2019 05:58:11: 19000000 INFO @ Fri, 05 Jul 2019 05:58:15: 16000000 INFO @ Fri, 05 Jul 2019 05:58:17: 16000000 INFO @ Fri, 05 Jul 2019 05:58:18: 20000000 INFO @ Fri, 05 Jul 2019 05:58:22: 17000000 INFO @ Fri, 05 Jul 2019 05:58:24: 21000000 INFO @ Fri, 05 Jul 2019 05:58:26: 17000000 INFO @ Fri, 05 Jul 2019 05:58:30: 18000000 INFO @ Fri, 05 Jul 2019 05:58:31: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 05:58:31: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 05:58:31: #1 total tags in treatment: 21969739 INFO @ Fri, 05 Jul 2019 05:58:31: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 05:58:31: #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 05:58:32: #1 tags after filtering in treatment: 21969588 INFO @ Fri, 05 Jul 2019 05:58:32: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 05:58:32: #1 finished! INFO @ Fri, 05 Jul 2019 05:58:32: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 05:58:32: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 05:58:34: 18000000 INFO @ Fri, 05 Jul 2019 05:58:37: #2 number of paired peaks: 65189 INFO @ Fri, 05 Jul 2019 05:58:37: start model_add_line... INFO @ Fri, 05 Jul 2019 05:58:37: start X-correlation... INFO @ Fri, 05 Jul 2019 05:58:37: end of X-cor INFO @ Fri, 05 Jul 2019 05:58:37: #2 finished! INFO @ Fri, 05 Jul 2019 05:58:37: #2 predicted fragment length is 130 bps INFO @ Fri, 05 Jul 2019 05:58:37: #2 alternative fragment length(s) may be 1,130,294,497 bps INFO @ Fri, 05 Jul 2019 05:58:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101923/ERX101923.10_model.r INFO @ Fri, 05 Jul 2019 05:58:37: #3 Call peaks... INFO @ Fri, 05 Jul 2019 05:58:37: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 05:58:39: 19000000 INFO @ Fri, 05 Jul 2019 05:58:42: 19000000 INFO @ Fri, 05 Jul 2019 05:58:46: 20000000 INFO @ Fri, 05 Jul 2019 05:58:50: 20000000 INFO @ Fri, 05 Jul 2019 05:58:54: 21000000 INFO @ Fri, 05 Jul 2019 05:58:57: 21000000 INFO @ Fri, 05 Jul 2019 05:59:02: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 05:59:02: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 05:59:02: #1 total tags in treatment: 21969739 INFO @ Fri, 05 Jul 2019 05:59:02: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 05:59:02: #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 05:59:03: #1 tags after filtering in treatment: 21969588 INFO @ Fri, 05 Jul 2019 05:59:03: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 05:59:03: #1 finished! INFO @ Fri, 05 Jul 2019 05:59:03: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 05:59:03: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 05:59:06: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 05:59:06: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 05:59:06: #1 total tags in treatment: 21969739 INFO @ Fri, 05 Jul 2019 05:59:06: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 05:59:06: #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 05:59:06: #1 tags after filtering in treatment: 21969588 INFO @ Fri, 05 Jul 2019 05:59:06: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 05:59:06: #1 finished! INFO @ Fri, 05 Jul 2019 05:59:06: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 05:59:06: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 05:59:08: #2 number of paired peaks: 65189 INFO @ Fri, 05 Jul 2019 05:59:08: start model_add_line... INFO @ Fri, 05 Jul 2019 05:59:09: start X-correlation... INFO @ Fri, 05 Jul 2019 05:59:09: end of X-cor INFO @ Fri, 05 Jul 2019 05:59:09: #2 finished! INFO @ Fri, 05 Jul 2019 05:59:09: #2 predicted fragment length is 130 bps INFO @ Fri, 05 Jul 2019 05:59:09: #2 alternative fragment length(s) may be 1,130,294,497 bps INFO @ Fri, 05 Jul 2019 05:59:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101923/ERX101923.20_model.r INFO @ Fri, 05 Jul 2019 05:59:09: #3 Call peaks... INFO @ Fri, 05 Jul 2019 05:59:09: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 05:59:12: #2 number of paired peaks: 65189 INFO @ Fri, 05 Jul 2019 05:59:12: start model_add_line... INFO @ Fri, 05 Jul 2019 05:59:12: start X-correlation... INFO @ Fri, 05 Jul 2019 05:59:12: end of X-cor INFO @ Fri, 05 Jul 2019 05:59:12: #2 finished! INFO @ Fri, 05 Jul 2019 05:59:12: #2 predicted fragment length is 130 bps INFO @ Fri, 05 Jul 2019 05:59:12: #2 alternative fragment length(s) may be 1,130,294,497 bps INFO @ Fri, 05 Jul 2019 05:59:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101923/ERX101923.05_model.r INFO @ Fri, 05 Jul 2019 05:59:12: #3 Call peaks... INFO @ Fri, 05 Jul 2019 05:59:12: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 05:59:50: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 06:00:23: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 06:00:27: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 06:00:28: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101923/ERX101923.10_peaks.xls INFO @ Fri, 05 Jul 2019 06:00:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101923/ERX101923.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 06:00:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101923/ERX101923.10_summits.bed INFO @ Fri, 05 Jul 2019 06:00:28: Done! pass1 - making usageList (38 chroms): 2 millis pass2 - checking and writing primary data (533 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 06:01:03: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101923/ERX101923.20_peaks.xls INFO @ Fri, 05 Jul 2019 06:01:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101923/ERX101923.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 06:01:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101923/ERX101923.20_summits.bed INFO @ Fri, 05 Jul 2019 06:01:03: Done! pass1 - making usageList (25 chroms): 1 millis pass2 - checking and writing primary data (74 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 06:01:05: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101923/ERX101923.05_peaks.xls INFO @ Fri, 05 Jul 2019 06:01:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101923/ERX101923.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 06:01:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101923/ERX101923.05_summits.bed INFO @ Fri, 05 Jul 2019 06:01:05: Done! pass1 - making usageList (59 chroms): 1 millis pass2 - checking and writing primary data (2707 records, 4 fields): 13 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。