Job ID = 2002144 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 26,725,265 reads read : 26,725,265 reads written : 26,725,265 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: 00:00:09 Time loading forward index: 00:00:06 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:09:35 26725265 reads; of these: 26725265 (100.00%) were unpaired; of these: 638713 (2.39%) aligned 0 times 20145076 (75.38%) aligned exactly 1 time 5941476 (22.23%) aligned >1 times 97.61% overall alignment rate Time searching: 00:09:51 Overall time: 00:09:51 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] 2011241 / 26086552 = 0.0771 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 10:44:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX102044/ERX102044.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX102044/ERX102044.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX102044/ERX102044.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX102044/ERX102044.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 10:44:30: #1 read tag files... INFO @ Fri, 05 Jul 2019 10:44:30: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 10:44:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX102044/ERX102044.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX102044/ERX102044.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX102044/ERX102044.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX102044/ERX102044.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 10:44:31: #1 read tag files... INFO @ Fri, 05 Jul 2019 10:44:31: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 10:44:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX102044/ERX102044.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX102044/ERX102044.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX102044/ERX102044.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX102044/ERX102044.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 10:44:32: #1 read tag files... INFO @ Fri, 05 Jul 2019 10:44:32: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 10:44:35: 1000000 INFO @ Fri, 05 Jul 2019 10:44:36: 1000000 INFO @ Fri, 05 Jul 2019 10:44:37: 1000000 INFO @ Fri, 05 Jul 2019 10:44:40: 2000000 INFO @ Fri, 05 Jul 2019 10:44:41: 2000000 INFO @ Fri, 05 Jul 2019 10:44:42: 2000000 INFO @ Fri, 05 Jul 2019 10:44:45: 3000000 INFO @ Fri, 05 Jul 2019 10:44:45: 3000000 INFO @ Fri, 05 Jul 2019 10:44:47: 3000000 INFO @ Fri, 05 Jul 2019 10:44:50: 4000000 INFO @ Fri, 05 Jul 2019 10:44:50: 4000000 INFO @ Fri, 05 Jul 2019 10:44:52: 4000000 INFO @ Fri, 05 Jul 2019 10:44:55: 5000000 INFO @ Fri, 05 Jul 2019 10:44:55: 5000000 INFO @ Fri, 05 Jul 2019 10:44:57: 5000000 INFO @ Fri, 05 Jul 2019 10:45:00: 6000000 INFO @ Fri, 05 Jul 2019 10:45:00: 6000000 INFO @ Fri, 05 Jul 2019 10:45:01: 6000000 INFO @ Fri, 05 Jul 2019 10:45:04: 7000000 INFO @ Fri, 05 Jul 2019 10:45:04: 7000000 INFO @ Fri, 05 Jul 2019 10:45:06: 7000000 INFO @ Fri, 05 Jul 2019 10:45:09: 8000000 INFO @ Fri, 05 Jul 2019 10:45:09: 8000000 INFO @ Fri, 05 Jul 2019 10:45:11: 8000000 INFO @ Fri, 05 Jul 2019 10:45:14: 9000000 INFO @ Fri, 05 Jul 2019 10:45:14: 9000000 INFO @ Fri, 05 Jul 2019 10:45:16: 9000000 INFO @ Fri, 05 Jul 2019 10:45:18: 10000000 INFO @ Fri, 05 Jul 2019 10:45:19: 10000000 INFO @ Fri, 05 Jul 2019 10:45:21: 10000000 INFO @ Fri, 05 Jul 2019 10:45:23: 11000000 INFO @ Fri, 05 Jul 2019 10:45:23: 11000000 INFO @ Fri, 05 Jul 2019 10:45:26: 11000000 INFO @ Fri, 05 Jul 2019 10:45:28: 12000000 INFO @ Fri, 05 Jul 2019 10:45:28: 12000000 INFO @ Fri, 05 Jul 2019 10:45:31: 12000000 INFO @ Fri, 05 Jul 2019 10:45:33: 13000000 INFO @ Fri, 05 Jul 2019 10:45:33: 13000000 INFO @ Fri, 05 Jul 2019 10:45:36: 13000000 INFO @ Fri, 05 Jul 2019 10:45:38: 14000000 INFO @ Fri, 05 Jul 2019 10:45:38: 14000000 INFO @ Fri, 05 Jul 2019 10:45:40: 14000000 INFO @ Fri, 05 Jul 2019 10:45:42: 15000000 INFO @ Fri, 05 Jul 2019 10:45:43: 15000000 INFO @ Fri, 05 Jul 2019 10:45:45: 15000000 INFO @ Fri, 05 Jul 2019 10:45:47: 16000000 INFO @ Fri, 05 Jul 2019 10:45:48: 16000000 INFO @ Fri, 05 Jul 2019 10:45:50: 16000000 INFO @ Fri, 05 Jul 2019 10:45:52: 17000000 INFO @ Fri, 05 Jul 2019 10:45:53: 17000000 INFO @ Fri, 05 Jul 2019 10:45:55: 17000000 INFO @ Fri, 05 Jul 2019 10:45:57: 18000000 INFO @ Fri, 05 Jul 2019 10:45:58: 18000000 INFO @ Fri, 05 Jul 2019 10:46:00: 18000000 INFO @ Fri, 05 Jul 2019 10:46:02: 19000000 INFO @ Fri, 05 Jul 2019 10:46:03: 19000000 INFO @ Fri, 05 Jul 2019 10:46:05: 19000000 INFO @ Fri, 05 Jul 2019 10:46:07: 20000000 INFO @ Fri, 05 Jul 2019 10:46:08: 20000000 INFO @ Fri, 05 Jul 2019 10:46:10: 20000000 INFO @ Fri, 05 Jul 2019 10:46:12: 21000000 INFO @ Fri, 05 Jul 2019 10:46:13: 21000000 INFO @ Fri, 05 Jul 2019 10:46:15: 21000000 INFO @ Fri, 05 Jul 2019 10:46:17: 22000000 INFO @ Fri, 05 Jul 2019 10:46:18: 22000000 INFO @ Fri, 05 Jul 2019 10:46:20: 22000000 INFO @ Fri, 05 Jul 2019 10:46:22: 23000000 INFO @ Fri, 05 Jul 2019 10:46:23: 23000000 INFO @ Fri, 05 Jul 2019 10:46:25: 23000000 INFO @ Fri, 05 Jul 2019 10:46:27: 24000000 INFO @ Fri, 05 Jul 2019 10:46:28: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 10:46:28: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 10:46:28: #1 total tags in treatment: 24075311 INFO @ Fri, 05 Jul 2019 10:46:28: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 10:46:28: #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 10:46:28: 24000000 INFO @ Fri, 05 Jul 2019 10:46:29: #1 tags after filtering in treatment: 24075128 INFO @ Fri, 05 Jul 2019 10:46:29: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 10:46:29: #1 finished! INFO @ Fri, 05 Jul 2019 10:46:29: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 10:46:29: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 10:46:29: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 10:46:29: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 10:46:29: #1 total tags in treatment: 24075311 INFO @ Fri, 05 Jul 2019 10:46:29: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 10:46:29: #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 10:46:29: #1 tags after filtering in treatment: 24075128 INFO @ Fri, 05 Jul 2019 10:46:29: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 10:46:29: #1 finished! INFO @ Fri, 05 Jul 2019 10:46:29: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 10:46:29: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 10:46:30: 24000000 INFO @ Fri, 05 Jul 2019 10:46:31: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 10:46:31: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 10:46:31: #1 total tags in treatment: 24075311 INFO @ Fri, 05 Jul 2019 10:46:31: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 10:46:31: #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 10:46:32: #1 tags after filtering in treatment: 24075128 INFO @ Fri, 05 Jul 2019 10:46:32: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 10:46:32: #1 finished! INFO @ Fri, 05 Jul 2019 10:46:32: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 10:46:32: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 10:46:32: #2 number of paired peaks: 65768 INFO @ Fri, 05 Jul 2019 10:46:32: start model_add_line... INFO @ Fri, 05 Jul 2019 10:46:33: start X-correlation... INFO @ Fri, 05 Jul 2019 10:46:33: end of X-cor INFO @ Fri, 05 Jul 2019 10:46:33: #2 finished! INFO @ Fri, 05 Jul 2019 10:46:33: #2 predicted fragment length is 127 bps INFO @ Fri, 05 Jul 2019 10:46:33: #2 alternative fragment length(s) may be 1,127,294,502 bps INFO @ Fri, 05 Jul 2019 10:46:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX102044/ERX102044.10_model.r INFO @ Fri, 05 Jul 2019 10:46:33: #3 Call peaks... INFO @ Fri, 05 Jul 2019 10:46:33: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 10:46:33: #2 number of paired peaks: 65768 INFO @ Fri, 05 Jul 2019 10:46:33: start model_add_line... INFO @ Fri, 05 Jul 2019 10:46:33: start X-correlation... INFO @ Fri, 05 Jul 2019 10:46:33: end of X-cor INFO @ Fri, 05 Jul 2019 10:46:33: #2 finished! INFO @ Fri, 05 Jul 2019 10:46:33: #2 predicted fragment length is 127 bps INFO @ Fri, 05 Jul 2019 10:46:33: #2 alternative fragment length(s) may be 1,127,294,502 bps INFO @ Fri, 05 Jul 2019 10:46:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX102044/ERX102044.05_model.r INFO @ Fri, 05 Jul 2019 10:46:33: #3 Call peaks... INFO @ Fri, 05 Jul 2019 10:46:33: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 10:46:35: #2 number of paired peaks: 65768 INFO @ Fri, 05 Jul 2019 10:46:35: start model_add_line... INFO @ Fri, 05 Jul 2019 10:46:36: start X-correlation... INFO @ Fri, 05 Jul 2019 10:46:36: end of X-cor INFO @ Fri, 05 Jul 2019 10:46:36: #2 finished! INFO @ Fri, 05 Jul 2019 10:46:36: #2 predicted fragment length is 127 bps INFO @ Fri, 05 Jul 2019 10:46:36: #2 alternative fragment length(s) may be 1,127,294,502 bps INFO @ Fri, 05 Jul 2019 10:46:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX102044/ERX102044.20_model.r INFO @ Fri, 05 Jul 2019 10:46:36: #3 Call peaks... INFO @ Fri, 05 Jul 2019 10:46:36: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 10:47:21: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 10:47:21: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 10:47:24: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 10:47:49: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX102044/ERX102044.10_peaks.xls INFO @ Fri, 05 Jul 2019 10:47:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX102044/ERX102044.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 10:47:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX102044/ERX102044.10_summits.bed INFO @ Fri, 05 Jul 2019 10:47:49: Done! pass1 - making usageList (41 chroms): 1 millis pass2 - checking and writing primary data (869 records, 4 fields): 5 millis INFO @ Fri, 05 Jul 2019 10:47:50: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX102044/ERX102044.05_peaks.xls INFO @ Fri, 05 Jul 2019 10:47:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX102044/ERX102044.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 10:47:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX102044/ERX102044.05_summits.bed INFO @ Fri, 05 Jul 2019 10:47:50: Done! pass1 - making usageList (67 chroms): 1 millis pass2 - checking and writing primary data (4471 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 10:47:52: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX102044/ERX102044.20_peaks.xls INFO @ Fri, 05 Jul 2019 10:47:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX102044/ERX102044.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 10:47:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX102044/ERX102044.20_summits.bed INFO @ Fri, 05 Jul 2019 10:47:52: Done! pass1 - making usageList (27 chroms): 1 millis pass2 - checking and writing primary data (94 records, 4 fields): 2 millis CompletedMACS2peakCalling CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。