Job ID = 2002175 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 26,257,639 reads read : 26,257,639 reads written : 26,257,639 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: 00:00:02 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:12:13 26257639 reads; of these: 26257639 (100.00%) were unpaired; of these: 908586 (3.46%) aligned 0 times 18476507 (70.37%) aligned exactly 1 time 6872546 (26.17%) aligned >1 times 96.54% overall alignment rate Time searching: 00:12:16 Overall time: 00:12:16 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] 2339691 / 25349053 = 0.0923 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 11:30:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX210257/ERX210257.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX210257/ERX210257.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX210257/ERX210257.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX210257/ERX210257.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 11:30:44: #1 read tag files... INFO @ Fri, 05 Jul 2019 11:30:44: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 11:30:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX210257/ERX210257.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX210257/ERX210257.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX210257/ERX210257.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX210257/ERX210257.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 11:30:45: #1 read tag files... INFO @ Fri, 05 Jul 2019 11:30:45: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 11:30:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX210257/ERX210257.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX210257/ERX210257.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX210257/ERX210257.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX210257/ERX210257.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 11:30:46: #1 read tag files... INFO @ Fri, 05 Jul 2019 11:30:46: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 11:30:51: 1000000 INFO @ Fri, 05 Jul 2019 11:30:53: 1000000 INFO @ Fri, 05 Jul 2019 11:30:54: 1000000 INFO @ Fri, 05 Jul 2019 11:30:58: 2000000 INFO @ Fri, 05 Jul 2019 11:31:01: 2000000 INFO @ Fri, 05 Jul 2019 11:31:01: 2000000 INFO @ Fri, 05 Jul 2019 11:31:05: 3000000 INFO @ Fri, 05 Jul 2019 11:31:09: 3000000 INFO @ Fri, 05 Jul 2019 11:31:09: 3000000 INFO @ Fri, 05 Jul 2019 11:31:12: 4000000 INFO @ Fri, 05 Jul 2019 11:31:16: 4000000 INFO @ Fri, 05 Jul 2019 11:31:16: 4000000 INFO @ Fri, 05 Jul 2019 11:31:18: 5000000 INFO @ Fri, 05 Jul 2019 11:31:24: 5000000 INFO @ Fri, 05 Jul 2019 11:31:24: 5000000 INFO @ Fri, 05 Jul 2019 11:31:25: 6000000 INFO @ Fri, 05 Jul 2019 11:31:31: 6000000 INFO @ Fri, 05 Jul 2019 11:31:31: 6000000 INFO @ Fri, 05 Jul 2019 11:31:32: 7000000 INFO @ Fri, 05 Jul 2019 11:31:39: 8000000 INFO @ Fri, 05 Jul 2019 11:31:39: 7000000 INFO @ Fri, 05 Jul 2019 11:31:39: 7000000 INFO @ Fri, 05 Jul 2019 11:31:45: 9000000 INFO @ Fri, 05 Jul 2019 11:31:46: 8000000 INFO @ Fri, 05 Jul 2019 11:31:46: 8000000 INFO @ Fri, 05 Jul 2019 11:31:52: 10000000 INFO @ Fri, 05 Jul 2019 11:31:54: 9000000 INFO @ Fri, 05 Jul 2019 11:31:54: 9000000 INFO @ Fri, 05 Jul 2019 11:31:59: 11000000 INFO @ Fri, 05 Jul 2019 11:32:02: 10000000 INFO @ Fri, 05 Jul 2019 11:32:02: 10000000 INFO @ Fri, 05 Jul 2019 11:32:06: 12000000 INFO @ Fri, 05 Jul 2019 11:32:09: 11000000 INFO @ Fri, 05 Jul 2019 11:32:09: 11000000 INFO @ Fri, 05 Jul 2019 11:32:12: 13000000 INFO @ Fri, 05 Jul 2019 11:32:17: 12000000 INFO @ Fri, 05 Jul 2019 11:32:17: 12000000 INFO @ Fri, 05 Jul 2019 11:32:19: 14000000 INFO @ Fri, 05 Jul 2019 11:32:24: 13000000 INFO @ Fri, 05 Jul 2019 11:32:26: 13000000 INFO @ Fri, 05 Jul 2019 11:32:26: 15000000 INFO @ Fri, 05 Jul 2019 11:32:32: 14000000 INFO @ Fri, 05 Jul 2019 11:32:33: 16000000 INFO @ Fri, 05 Jul 2019 11:32:35: 14000000 INFO @ Fri, 05 Jul 2019 11:32:39: 15000000 INFO @ Fri, 05 Jul 2019 11:32:40: 17000000 INFO @ Fri, 05 Jul 2019 11:32:44: 15000000 INFO @ Fri, 05 Jul 2019 11:32:47: 18000000 INFO @ Fri, 05 Jul 2019 11:32:47: 16000000 INFO @ Fri, 05 Jul 2019 11:32:52: 16000000 INFO @ Fri, 05 Jul 2019 11:32:54: 19000000 INFO @ Fri, 05 Jul 2019 11:32:54: 17000000 INFO @ Fri, 05 Jul 2019 11:33:00: 20000000 INFO @ Fri, 05 Jul 2019 11:33:01: 17000000 INFO @ Fri, 05 Jul 2019 11:33:01: 18000000 INFO @ Fri, 05 Jul 2019 11:33:07: 21000000 INFO @ Fri, 05 Jul 2019 11:33:09: 19000000 INFO @ Fri, 05 Jul 2019 11:33:09: 18000000 INFO @ Fri, 05 Jul 2019 11:33:14: 22000000 INFO @ Fri, 05 Jul 2019 11:33:16: 20000000 INFO @ Fri, 05 Jul 2019 11:33:18: 19000000 INFO @ Fri, 05 Jul 2019 11:33:21: 23000000 INFO @ Fri, 05 Jul 2019 11:33:21: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 11:33:21: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 11:33:21: #1 total tags in treatment: 23009362 INFO @ Fri, 05 Jul 2019 11:33:21: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 11:33:21: #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 11:33:22: #1 tags after filtering in treatment: 23009240 INFO @ Fri, 05 Jul 2019 11:33:22: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 11:33:22: #1 finished! INFO @ Fri, 05 Jul 2019 11:33:22: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 11:33:22: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 11:33:24: 21000000 INFO @ Fri, 05 Jul 2019 11:33:26: #2 number of paired peaks: 31413 INFO @ Fri, 05 Jul 2019 11:33:26: start model_add_line... INFO @ Fri, 05 Jul 2019 11:33:26: start X-correlation... INFO @ Fri, 05 Jul 2019 11:33:26: end of X-cor INFO @ Fri, 05 Jul 2019 11:33:26: #2 finished! INFO @ Fri, 05 Jul 2019 11:33:26: #2 predicted fragment length is 134 bps INFO @ Fri, 05 Jul 2019 11:33:26: #2 alternative fragment length(s) may be 134 bps INFO @ Fri, 05 Jul 2019 11:33:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX210257/ERX210257.05_model.r INFO @ Fri, 05 Jul 2019 11:33:26: #3 Call peaks... INFO @ Fri, 05 Jul 2019 11:33:26: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 11:33:26: 20000000 INFO @ Fri, 05 Jul 2019 11:33:31: 22000000 INFO @ Fri, 05 Jul 2019 11:33:35: 21000000 INFO @ Fri, 05 Jul 2019 11:33:38: 23000000 INFO @ Fri, 05 Jul 2019 11:33:39: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 11:33:39: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 11:33:39: #1 total tags in treatment: 23009362 INFO @ Fri, 05 Jul 2019 11:33:39: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 11:33:39: #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 11:33:40: #1 tags after filtering in treatment: 23009240 INFO @ Fri, 05 Jul 2019 11:33:40: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 11:33:40: #1 finished! INFO @ Fri, 05 Jul 2019 11:33:40: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 11:33:40: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 11:33:43: 22000000 INFO @ Fri, 05 Jul 2019 11:33:43: #2 number of paired peaks: 31413 INFO @ Fri, 05 Jul 2019 11:33:43: start model_add_line... INFO @ Fri, 05 Jul 2019 11:33:44: start X-correlation... INFO @ Fri, 05 Jul 2019 11:33:44: end of X-cor INFO @ Fri, 05 Jul 2019 11:33:44: #2 finished! INFO @ Fri, 05 Jul 2019 11:33:44: #2 predicted fragment length is 134 bps INFO @ Fri, 05 Jul 2019 11:33:44: #2 alternative fragment length(s) may be 134 bps INFO @ Fri, 05 Jul 2019 11:33:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX210257/ERX210257.10_model.r INFO @ Fri, 05 Jul 2019 11:33:44: #3 Call peaks... INFO @ Fri, 05 Jul 2019 11:33:44: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 11:33:51: 23000000 INFO @ Fri, 05 Jul 2019 11:33:52: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 11:33:52: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 11:33:52: #1 total tags in treatment: 23009362 INFO @ Fri, 05 Jul 2019 11:33:52: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 11:33:52: #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 11:33:52: #1 tags after filtering in treatment: 23009240 INFO @ Fri, 05 Jul 2019 11:33:52: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 11:33:52: #1 finished! INFO @ Fri, 05 Jul 2019 11:33:52: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 11:33:52: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 11:33:56: #2 number of paired peaks: 31413 INFO @ Fri, 05 Jul 2019 11:33:56: start model_add_line... INFO @ Fri, 05 Jul 2019 11:33:57: start X-correlation... INFO @ Fri, 05 Jul 2019 11:33:57: end of X-cor INFO @ Fri, 05 Jul 2019 11:33:57: #2 finished! INFO @ Fri, 05 Jul 2019 11:33:57: #2 predicted fragment length is 134 bps INFO @ Fri, 05 Jul 2019 11:33:57: #2 alternative fragment length(s) may be 134 bps INFO @ Fri, 05 Jul 2019 11:33:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX210257/ERX210257.20_model.r INFO @ Fri, 05 Jul 2019 11:33:57: #3 Call peaks... INFO @ Fri, 05 Jul 2019 11:33:57: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 11:34:39: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 11:34:56: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 11:35:09: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 11:35:16: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX210257/ERX210257.05_peaks.xls INFO @ Fri, 05 Jul 2019 11:35:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX210257/ERX210257.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 11:35:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX210257/ERX210257.05_summits.bed INFO @ Fri, 05 Jul 2019 11:35:17: Done! pass1 - making usageList (110 chroms): 7 millis pass2 - checking and writing primary data (28923 records, 4 fields): 41 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 11:35:33: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX210257/ERX210257.10_peaks.xls INFO @ Fri, 05 Jul 2019 11:35:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX210257/ERX210257.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 11:35:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX210257/ERX210257.10_summits.bed INFO @ Fri, 05 Jul 2019 11:35:34: Done! pass1 - making usageList (90 chroms): 5 millis pass2 - checking and writing primary data (19531 records, 4 fields): 94 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 11:35:45: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX210257/ERX210257.20_peaks.xls INFO @ Fri, 05 Jul 2019 11:35:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX210257/ERX210257.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 11:35:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX210257/ERX210257.20_summits.bed INFO @ Fri, 05 Jul 2019 11:35:46: Done! pass1 - making usageList (63 chroms): 5 millis pass2 - checking and writing primary data (11487 records, 4 fields): 18 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。