Job ID = 2001683 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 25,222,518 reads read : 25,222,518 reads written : 25,222,518 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: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:10:04 25222518 reads; of these: 25222518 (100.00%) were unpaired; of these: 583418 (2.31%) aligned 0 times 19038926 (75.48%) aligned exactly 1 time 5600174 (22.20%) aligned >1 times 97.69% overall alignment rate Time searching: 00:10:07 Overall time: 00:10:07 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] 1764540 / 24639100 = 0.0716 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 08:55:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101997/ERX101997.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101997/ERX101997.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101997/ERX101997.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101997/ERX101997.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 08:55:43: #1 read tag files... INFO @ Fri, 05 Jul 2019 08:55:43: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 08:55:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101997/ERX101997.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101997/ERX101997.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101997/ERX101997.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101997/ERX101997.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 08:55:44: #1 read tag files... INFO @ Fri, 05 Jul 2019 08:55:44: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 08:55:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101997/ERX101997.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101997/ERX101997.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101997/ERX101997.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101997/ERX101997.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 08:55:45: #1 read tag files... INFO @ Fri, 05 Jul 2019 08:55:45: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 08:55:51: 1000000 INFO @ Fri, 05 Jul 2019 08:55:52: 1000000 INFO @ Fri, 05 Jul 2019 08:55:55: 1000000 INFO @ Fri, 05 Jul 2019 08:55:58: 2000000 INFO @ Fri, 05 Jul 2019 08:56:00: 2000000 INFO @ Fri, 05 Jul 2019 08:56:04: 2000000 INFO @ Fri, 05 Jul 2019 08:56:05: 3000000 INFO @ Fri, 05 Jul 2019 08:56:08: 3000000 INFO @ Fri, 05 Jul 2019 08:56:12: 4000000 INFO @ Fri, 05 Jul 2019 08:56:13: 3000000 INFO @ Fri, 05 Jul 2019 08:56:15: 4000000 INFO @ Fri, 05 Jul 2019 08:56:19: 5000000 INFO @ Fri, 05 Jul 2019 08:56:22: 4000000 INFO @ Fri, 05 Jul 2019 08:56:23: 5000000 INFO @ Fri, 05 Jul 2019 08:56:26: 6000000 INFO @ Fri, 05 Jul 2019 08:56:30: 6000000 INFO @ Fri, 05 Jul 2019 08:56:32: 5000000 INFO @ Fri, 05 Jul 2019 08:56:33: 7000000 INFO @ Fri, 05 Jul 2019 08:56:38: 7000000 INFO @ Fri, 05 Jul 2019 08:56:40: 8000000 INFO @ Fri, 05 Jul 2019 08:56:41: 6000000 INFO @ Fri, 05 Jul 2019 08:56:45: 8000000 INFO @ Fri, 05 Jul 2019 08:56:47: 9000000 INFO @ Fri, 05 Jul 2019 08:56:50: 7000000 INFO @ Fri, 05 Jul 2019 08:56:53: 9000000 INFO @ Fri, 05 Jul 2019 08:56:54: 10000000 INFO @ Fri, 05 Jul 2019 08:57:00: 8000000 INFO @ Fri, 05 Jul 2019 08:57:00: 10000000 INFO @ Fri, 05 Jul 2019 08:57:01: 11000000 INFO @ Fri, 05 Jul 2019 08:57:08: 11000000 INFO @ Fri, 05 Jul 2019 08:57:08: 12000000 INFO @ Fri, 05 Jul 2019 08:57:09: 9000000 INFO @ Fri, 05 Jul 2019 08:57:16: 12000000 INFO @ Fri, 05 Jul 2019 08:57:16: 13000000 INFO @ Fri, 05 Jul 2019 08:57:18: 10000000 INFO @ Fri, 05 Jul 2019 08:57:23: 14000000 INFO @ Fri, 05 Jul 2019 08:57:23: 13000000 INFO @ Fri, 05 Jul 2019 08:57:27: 11000000 INFO @ Fri, 05 Jul 2019 08:57:30: 15000000 INFO @ Fri, 05 Jul 2019 08:57:31: 14000000 INFO @ Fri, 05 Jul 2019 08:57:37: 16000000 INFO @ Fri, 05 Jul 2019 08:57:37: 12000000 INFO @ Fri, 05 Jul 2019 08:57:39: 15000000 INFO @ Fri, 05 Jul 2019 08:57:43: 17000000 INFO @ Fri, 05 Jul 2019 08:57:46: 16000000 INFO @ Fri, 05 Jul 2019 08:57:46: 13000000 INFO @ Fri, 05 Jul 2019 08:57:50: 18000000 INFO @ Fri, 05 Jul 2019 08:57:54: 17000000 INFO @ Fri, 05 Jul 2019 08:57:55: 14000000 INFO @ Fri, 05 Jul 2019 08:57:57: 19000000 INFO @ Fri, 05 Jul 2019 08:58:01: 18000000 INFO @ Fri, 05 Jul 2019 08:58:04: 20000000 INFO @ Fri, 05 Jul 2019 08:58:05: 15000000 INFO @ Fri, 05 Jul 2019 08:58:09: 19000000 INFO @ Fri, 05 Jul 2019 08:58:11: 21000000 INFO @ Fri, 05 Jul 2019 08:58:14: 16000000 INFO @ Fri, 05 Jul 2019 08:58:16: 20000000 INFO @ Fri, 05 Jul 2019 08:58:18: 22000000 INFO @ Fri, 05 Jul 2019 08:58:23: 17000000 INFO @ Fri, 05 Jul 2019 08:58:23: 21000000 INFO @ Fri, 05 Jul 2019 08:58:24: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 08:58:24: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 08:58:24: #1 total tags in treatment: 22874560 INFO @ Fri, 05 Jul 2019 08:58:24: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 08:58:24: #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 08:58:25: #1 tags after filtering in treatment: 22874407 INFO @ Fri, 05 Jul 2019 08:58:25: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 08:58:25: #1 finished! INFO @ Fri, 05 Jul 2019 08:58:25: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 08:58:25: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 08:58:30: #2 number of paired peaks: 68334 INFO @ Fri, 05 Jul 2019 08:58:30: start model_add_line... INFO @ Fri, 05 Jul 2019 08:58:30: start X-correlation... INFO @ Fri, 05 Jul 2019 08:58:30: end of X-cor INFO @ Fri, 05 Jul 2019 08:58:30: #2 finished! INFO @ Fri, 05 Jul 2019 08:58:30: #2 predicted fragment length is 134 bps INFO @ Fri, 05 Jul 2019 08:58:30: #2 alternative fragment length(s) may be 2,134,291,506 bps INFO @ Fri, 05 Jul 2019 08:58:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101997/ERX101997.05_model.r INFO @ Fri, 05 Jul 2019 08:58:30: #3 Call peaks... INFO @ Fri, 05 Jul 2019 08:58:30: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 08:58:31: 22000000 INFO @ Fri, 05 Jul 2019 08:58:32: 18000000 INFO @ Fri, 05 Jul 2019 08:58:38: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 08:58:38: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 08:58:38: #1 total tags in treatment: 22874560 INFO @ Fri, 05 Jul 2019 08:58:38: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 08:58:38: #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 08:58:39: #1 tags after filtering in treatment: 22874407 INFO @ Fri, 05 Jul 2019 08:58:39: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 08:58:39: #1 finished! INFO @ Fri, 05 Jul 2019 08:58:39: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 08:58:39: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 08:58:41: 19000000 INFO @ Fri, 05 Jul 2019 08:58:44: #2 number of paired peaks: 68334 INFO @ Fri, 05 Jul 2019 08:58:44: start model_add_line... INFO @ Fri, 05 Jul 2019 08:58:44: start X-correlation... INFO @ Fri, 05 Jul 2019 08:58:44: end of X-cor INFO @ Fri, 05 Jul 2019 08:58:44: #2 finished! INFO @ Fri, 05 Jul 2019 08:58:44: #2 predicted fragment length is 134 bps INFO @ Fri, 05 Jul 2019 08:58:44: #2 alternative fragment length(s) may be 2,134,291,506 bps INFO @ Fri, 05 Jul 2019 08:58:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101997/ERX101997.10_model.r INFO @ Fri, 05 Jul 2019 08:58:44: #3 Call peaks... INFO @ Fri, 05 Jul 2019 08:58:44: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 08:58:49: 20000000 INFO @ Fri, 05 Jul 2019 08:58:58: 21000000 INFO @ Fri, 05 Jul 2019 08:59:07: 22000000 INFO @ Fri, 05 Jul 2019 08:59:15: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 08:59:15: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 08:59:15: #1 total tags in treatment: 22874560 INFO @ Fri, 05 Jul 2019 08:59:15: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 08:59:15: #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 08:59:15: #1 tags after filtering in treatment: 22874407 INFO @ Fri, 05 Jul 2019 08:59:15: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 08:59:15: #1 finished! INFO @ Fri, 05 Jul 2019 08:59:15: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 08:59:15: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 08:59:20: #2 number of paired peaks: 68334 INFO @ Fri, 05 Jul 2019 08:59:20: start model_add_line... INFO @ Fri, 05 Jul 2019 08:59:21: start X-correlation... INFO @ Fri, 05 Jul 2019 08:59:21: end of X-cor INFO @ Fri, 05 Jul 2019 08:59:21: #2 finished! INFO @ Fri, 05 Jul 2019 08:59:21: #2 predicted fragment length is 134 bps INFO @ Fri, 05 Jul 2019 08:59:21: #2 alternative fragment length(s) may be 2,134,291,506 bps INFO @ Fri, 05 Jul 2019 08:59:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101997/ERX101997.20_model.r INFO @ Fri, 05 Jul 2019 08:59:21: #3 Call peaks... INFO @ Fri, 05 Jul 2019 08:59:21: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 08:59:44: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 08:59:56: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 09:00:20: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101997/ERX101997.05_peaks.xls INFO @ Fri, 05 Jul 2019 09:00:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101997/ERX101997.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 09:00:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101997/ERX101997.05_summits.bed INFO @ Fri, 05 Jul 2019 09:00:20: Done! pass1 - making usageList (72 chroms): 2 millis pass2 - checking and writing primary data (4999 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 09:00:33: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101997/ERX101997.10_peaks.xls INFO @ Fri, 05 Jul 2019 09:00:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101997/ERX101997.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 09:00:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101997/ERX101997.10_summits.bed INFO @ Fri, 05 Jul 2019 09:00:33: Done! pass1 - making usageList (41 chroms): 2 millis pass2 - checking and writing primary data (1006 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 09:00:35: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 09:01:12: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101997/ERX101997.20_peaks.xls INFO @ Fri, 05 Jul 2019 09:01:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101997/ERX101997.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 09:01:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101997/ERX101997.20_summits.bed INFO @ Fri, 05 Jul 2019 09:01:12: Done! pass1 - making usageList (27 chroms): 2 millis pass2 - checking and writing primary data (124 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。