Job ID = 2001609 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 30,573,476 reads read : 30,573,476 reads written : 30,573,476 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: 00:00:00 Multiseed full-index search: 00:11:32 30573476 reads; of these: 30573476 (100.00%) were unpaired; of these: 843642 (2.76%) aligned 0 times 21966783 (71.85%) aligned exactly 1 time 7763051 (25.39%) aligned >1 times 97.24% overall alignment rate Time searching: 00:11:34 Overall time: 00:11:34 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] 1788488 / 29729834 = 0.0602 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 06:31:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101935/ERX101935.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101935/ERX101935.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101935/ERX101935.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101935/ERX101935.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 06:31:45: #1 read tag files... INFO @ Fri, 05 Jul 2019 06:31:45: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 06:31:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101935/ERX101935.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101935/ERX101935.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101935/ERX101935.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101935/ERX101935.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 06:31:45: #1 read tag files... INFO @ Fri, 05 Jul 2019 06:31:45: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 06:31:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101935/ERX101935.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101935/ERX101935.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101935/ERX101935.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101935/ERX101935.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 06:31:46: #1 read tag files... INFO @ Fri, 05 Jul 2019 06:31:46: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 06:31:55: 1000000 INFO @ Fri, 05 Jul 2019 06:31:55: 1000000 INFO @ Fri, 05 Jul 2019 06:31:56: 1000000 INFO @ Fri, 05 Jul 2019 06:32:04: 2000000 INFO @ Fri, 05 Jul 2019 06:32:04: 2000000 INFO @ Fri, 05 Jul 2019 06:32:06: 2000000 INFO @ Fri, 05 Jul 2019 06:32:13: 3000000 INFO @ Fri, 05 Jul 2019 06:32:14: 3000000 INFO @ Fri, 05 Jul 2019 06:32:15: 3000000 INFO @ Fri, 05 Jul 2019 06:32:23: 4000000 INFO @ Fri, 05 Jul 2019 06:32:24: 4000000 INFO @ Fri, 05 Jul 2019 06:32:25: 4000000 INFO @ Fri, 05 Jul 2019 06:32:33: 5000000 INFO @ Fri, 05 Jul 2019 06:32:33: 5000000 INFO @ Fri, 05 Jul 2019 06:32:35: 5000000 INFO @ Fri, 05 Jul 2019 06:32:42: 6000000 INFO @ Fri, 05 Jul 2019 06:32:43: 6000000 INFO @ Fri, 05 Jul 2019 06:32:45: 6000000 INFO @ Fri, 05 Jul 2019 06:32:51: 7000000 INFO @ Fri, 05 Jul 2019 06:32:53: 7000000 INFO @ Fri, 05 Jul 2019 06:32:55: 7000000 INFO @ Fri, 05 Jul 2019 06:33:00: 8000000 INFO @ Fri, 05 Jul 2019 06:33:03: 8000000 INFO @ Fri, 05 Jul 2019 06:33:05: 8000000 INFO @ Fri, 05 Jul 2019 06:33:10: 9000000 INFO @ Fri, 05 Jul 2019 06:33:13: 9000000 INFO @ Fri, 05 Jul 2019 06:33:15: 9000000 INFO @ Fri, 05 Jul 2019 06:33:19: 10000000 INFO @ Fri, 05 Jul 2019 06:33:23: 10000000 INFO @ Fri, 05 Jul 2019 06:33:25: 10000000 INFO @ Fri, 05 Jul 2019 06:33:28: 11000000 INFO @ Fri, 05 Jul 2019 06:33:33: 11000000 INFO @ Fri, 05 Jul 2019 06:33:35: 11000000 INFO @ Fri, 05 Jul 2019 06:33:38: 12000000 INFO @ Fri, 05 Jul 2019 06:33:43: 12000000 INFO @ Fri, 05 Jul 2019 06:33:44: 12000000 INFO @ Fri, 05 Jul 2019 06:33:47: 13000000 INFO @ Fri, 05 Jul 2019 06:33:53: 13000000 INFO @ Fri, 05 Jul 2019 06:33:54: 13000000 INFO @ Fri, 05 Jul 2019 06:33:56: 14000000 INFO @ Fri, 05 Jul 2019 06:34:02: 14000000 INFO @ Fri, 05 Jul 2019 06:34:04: 14000000 INFO @ Fri, 05 Jul 2019 06:34:05: 15000000 INFO @ Fri, 05 Jul 2019 06:34:12: 15000000 INFO @ Fri, 05 Jul 2019 06:34:14: 15000000 INFO @ Fri, 05 Jul 2019 06:34:15: 16000000 INFO @ Fri, 05 Jul 2019 06:34:22: 16000000 INFO @ Fri, 05 Jul 2019 06:34:23: 16000000 INFO @ Fri, 05 Jul 2019 06:34:24: 17000000 INFO @ Fri, 05 Jul 2019 06:34:32: 17000000 INFO @ Fri, 05 Jul 2019 06:34:33: 18000000 INFO @ Fri, 05 Jul 2019 06:34:34: 17000000 INFO @ Fri, 05 Jul 2019 06:34:42: 18000000 INFO @ Fri, 05 Jul 2019 06:34:42: 19000000 INFO @ Fri, 05 Jul 2019 06:34:44: 18000000 INFO @ Fri, 05 Jul 2019 06:34:51: 20000000 INFO @ Fri, 05 Jul 2019 06:34:52: 19000000 INFO @ Fri, 05 Jul 2019 06:34:54: 19000000 INFO @ Fri, 05 Jul 2019 06:35:01: 21000000 INFO @ Fri, 05 Jul 2019 06:35:02: 20000000 INFO @ Fri, 05 Jul 2019 06:35:03: 20000000 INFO @ Fri, 05 Jul 2019 06:35:10: 22000000 INFO @ Fri, 05 Jul 2019 06:35:12: 21000000 INFO @ Fri, 05 Jul 2019 06:35:13: 21000000 INFO @ Fri, 05 Jul 2019 06:35:19: 23000000 INFO @ Fri, 05 Jul 2019 06:35:22: 22000000 INFO @ Fri, 05 Jul 2019 06:35:23: 22000000 INFO @ Fri, 05 Jul 2019 06:35:28: 24000000 INFO @ Fri, 05 Jul 2019 06:35:31: 23000000 INFO @ Fri, 05 Jul 2019 06:35:33: 23000000 INFO @ Fri, 05 Jul 2019 06:35:38: 25000000 INFO @ Fri, 05 Jul 2019 06:35:41: 24000000 INFO @ Fri, 05 Jul 2019 06:35:43: 24000000 INFO @ Fri, 05 Jul 2019 06:35:47: 26000000 INFO @ Fri, 05 Jul 2019 06:35:51: 25000000 INFO @ Fri, 05 Jul 2019 06:35:52: 25000000 INFO @ Fri, 05 Jul 2019 06:35:56: 27000000 INFO @ Fri, 05 Jul 2019 06:36:00: 26000000 INFO @ Fri, 05 Jul 2019 06:36:02: 26000000 INFO @ Fri, 05 Jul 2019 06:36:06: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 06:36:06: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 06:36:06: #1 total tags in treatment: 27941346 INFO @ Fri, 05 Jul 2019 06:36:06: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 06:36:06: #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 06:36:07: #1 tags after filtering in treatment: 27941210 INFO @ Fri, 05 Jul 2019 06:36:07: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 06:36:07: #1 finished! INFO @ Fri, 05 Jul 2019 06:36:07: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 06:36:07: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 06:36:10: 27000000 INFO @ Fri, 05 Jul 2019 06:36:12: 27000000 INFO @ Fri, 05 Jul 2019 06:36:12: #2 number of paired peaks: 45632 INFO @ Fri, 05 Jul 2019 06:36:12: start model_add_line... INFO @ Fri, 05 Jul 2019 06:36:12: start X-correlation... INFO @ Fri, 05 Jul 2019 06:36:12: end of X-cor INFO @ Fri, 05 Jul 2019 06:36:12: #2 finished! INFO @ Fri, 05 Jul 2019 06:36:12: #2 predicted fragment length is 123 bps INFO @ Fri, 05 Jul 2019 06:36:12: #2 alternative fragment length(s) may be 123,296,495 bps INFO @ Fri, 05 Jul 2019 06:36:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101935/ERX101935.05_model.r INFO @ Fri, 05 Jul 2019 06:36:12: #3 Call peaks... INFO @ Fri, 05 Jul 2019 06:36:12: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 06:36:20: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 06:36:20: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 06:36:20: #1 total tags in treatment: 27941346 INFO @ Fri, 05 Jul 2019 06:36:20: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 06:36:20: #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 06:36:20: #1 tags after filtering in treatment: 27941210 INFO @ Fri, 05 Jul 2019 06:36:20: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 06:36:20: #1 finished! INFO @ Fri, 05 Jul 2019 06:36:20: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 06:36:20: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 06:36:21: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 06:36:21: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 06:36:21: #1 total tags in treatment: 27941346 INFO @ Fri, 05 Jul 2019 06:36:21: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 06:36:21: #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 06:36:22: #1 tags after filtering in treatment: 27941210 INFO @ Fri, 05 Jul 2019 06:36:22: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 06:36:22: #1 finished! INFO @ Fri, 05 Jul 2019 06:36:22: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 06:36:22: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 06:36:25: #2 number of paired peaks: 45632 INFO @ Fri, 05 Jul 2019 06:36:25: start model_add_line... INFO @ Fri, 05 Jul 2019 06:36:26: start X-correlation... INFO @ Fri, 05 Jul 2019 06:36:26: end of X-cor INFO @ Fri, 05 Jul 2019 06:36:26: #2 finished! INFO @ Fri, 05 Jul 2019 06:36:26: #2 predicted fragment length is 123 bps INFO @ Fri, 05 Jul 2019 06:36:26: #2 alternative fragment length(s) may be 123,296,495 bps INFO @ Fri, 05 Jul 2019 06:36:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101935/ERX101935.10_model.r INFO @ Fri, 05 Jul 2019 06:36:26: #3 Call peaks... INFO @ Fri, 05 Jul 2019 06:36:26: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 06:36:27: #2 number of paired peaks: 45632 INFO @ Fri, 05 Jul 2019 06:36:27: start model_add_line... INFO @ Fri, 05 Jul 2019 06:36:27: start X-correlation... INFO @ Fri, 05 Jul 2019 06:36:27: end of X-cor INFO @ Fri, 05 Jul 2019 06:36:27: #2 finished! INFO @ Fri, 05 Jul 2019 06:36:27: #2 predicted fragment length is 123 bps INFO @ Fri, 05 Jul 2019 06:36:27: #2 alternative fragment length(s) may be 123,296,495 bps INFO @ Fri, 05 Jul 2019 06:36:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101935/ERX101935.20_model.r INFO @ Fri, 05 Jul 2019 06:36:27: #3 Call peaks... INFO @ Fri, 05 Jul 2019 06:36:27: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 06:37:38: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 06:37:53: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 06:37:54: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 06:38:23: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101935/ERX101935.05_peaks.xls INFO @ Fri, 05 Jul 2019 06:38:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101935/ERX101935.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 06:38:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101935/ERX101935.05_summits.bed INFO @ Fri, 05 Jul 2019 06:38:23: Done! pass1 - making usageList (53 chroms): 2 millis pass2 - checking and writing primary data (2076 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 06:38:38: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101935/ERX101935.10_peaks.xls INFO @ Fri, 05 Jul 2019 06:38:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101935/ERX101935.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 06:38:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101935/ERX101935.10_summits.bed INFO @ Fri, 05 Jul 2019 06:38:38: Done! pass1 - making usageList (34 chroms): 1 millis pass2 - checking and writing primary data (466 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 06:38:39: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101935/ERX101935.20_peaks.xls INFO @ Fri, 05 Jul 2019 06:38:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101935/ERX101935.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 06:38:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101935/ERX101935.20_summits.bed INFO @ Fri, 05 Jul 2019 06:38:39: Done! pass1 - making usageList (25 chroms): 1 millis pass2 - checking and writing primary data (84 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。