Job ID = 1294391 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 23,442,248 reads read : 23,442,248 reads written : 23,442,248 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘fastqDump_tmp*’: 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: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:08:39 23442248 reads; of these: 23442248 (100.00%) were unpaired; of these: 1025720 (4.38%) aligned 0 times 17415626 (74.29%) aligned exactly 1 time 5000902 (21.33%) aligned >1 times 95.62% overall alignment rate Time searching: 00:08:39 Overall time: 00:08:39 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 4061439 / 22416528 = 0.1812 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 @ Mon, 03 Jun 2019 07:32:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287568/SRX287568.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287568/SRX287568.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287568/SRX287568.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287568/SRX287568.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Mon, 03 Jun 2019 07:32:26: #1 read tag files... INFO @ Mon, 03 Jun 2019 07:32:26: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 07:32:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287568/SRX287568.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287568/SRX287568.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287568/SRX287568.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287568/SRX287568.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Mon, 03 Jun 2019 07:32:26: #1 read tag files... INFO @ Mon, 03 Jun 2019 07:32:26: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 07:32:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287568/SRX287568.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287568/SRX287568.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287568/SRX287568.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287568/SRX287568.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Mon, 03 Jun 2019 07:32:26: #1 read tag files... INFO @ Mon, 03 Jun 2019 07:32:26: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 07:32:35: 1000000 INFO @ Mon, 03 Jun 2019 07:32:36: 1000000 INFO @ Mon, 03 Jun 2019 07:32:38: 1000000 INFO @ Mon, 03 Jun 2019 07:32:43: 2000000 INFO @ Mon, 03 Jun 2019 07:32:45: 2000000 INFO @ Mon, 03 Jun 2019 07:32:49: 2000000 INFO @ Mon, 03 Jun 2019 07:32:52: 3000000 INFO @ Mon, 03 Jun 2019 07:32:54: 3000000 INFO @ Mon, 03 Jun 2019 07:33:00: 4000000 INFO @ Mon, 03 Jun 2019 07:33:00: 3000000 INFO @ Mon, 03 Jun 2019 07:33:03: 4000000 INFO @ Mon, 03 Jun 2019 07:33:09: 5000000 INFO @ Mon, 03 Jun 2019 07:33:11: 5000000 INFO @ Mon, 03 Jun 2019 07:33:12: 4000000 INFO @ Mon, 03 Jun 2019 07:33:18: 6000000 INFO @ Mon, 03 Jun 2019 07:33:21: 6000000 INFO @ Mon, 03 Jun 2019 07:33:23: 5000000 INFO @ Mon, 03 Jun 2019 07:33:26: 7000000 INFO @ Mon, 03 Jun 2019 07:33:29: 7000000 INFO @ Mon, 03 Jun 2019 07:33:34: 8000000 INFO @ Mon, 03 Jun 2019 07:33:35: 6000000 INFO @ Mon, 03 Jun 2019 07:33:38: 8000000 INFO @ Mon, 03 Jun 2019 07:33:43: 9000000 INFO @ Mon, 03 Jun 2019 07:33:46: 7000000 INFO @ Mon, 03 Jun 2019 07:33:47: 9000000 INFO @ Mon, 03 Jun 2019 07:33:51: 10000000 INFO @ Mon, 03 Jun 2019 07:33:56: 10000000 INFO @ Mon, 03 Jun 2019 07:33:57: 8000000 INFO @ Mon, 03 Jun 2019 07:33:59: 11000000 INFO @ Mon, 03 Jun 2019 07:34:05: 11000000 INFO @ Mon, 03 Jun 2019 07:34:08: 12000000 INFO @ Mon, 03 Jun 2019 07:34:08: 9000000 INFO @ Mon, 03 Jun 2019 07:34:14: 12000000 INFO @ Mon, 03 Jun 2019 07:34:16: 13000000 INFO @ Mon, 03 Jun 2019 07:34:19: 10000000 INFO @ Mon, 03 Jun 2019 07:34:23: 13000000 INFO @ Mon, 03 Jun 2019 07:34:24: 14000000 INFO @ Mon, 03 Jun 2019 07:34:30: 11000000 INFO @ Mon, 03 Jun 2019 07:34:32: 14000000 INFO @ Mon, 03 Jun 2019 07:34:34: 15000000 INFO @ Mon, 03 Jun 2019 07:34:41: 12000000 INFO @ Mon, 03 Jun 2019 07:34:41: 15000000 INFO @ Mon, 03 Jun 2019 07:34:44: 16000000 INFO @ Mon, 03 Jun 2019 07:34:50: 16000000 INFO @ Mon, 03 Jun 2019 07:34:51: 13000000 INFO @ Mon, 03 Jun 2019 07:34:55: 17000000 INFO @ Mon, 03 Jun 2019 07:34:59: 17000000 INFO @ Mon, 03 Jun 2019 07:35:02: 14000000 INFO @ Mon, 03 Jun 2019 07:35:05: 18000000 INFO @ Mon, 03 Jun 2019 07:35:09: 18000000 INFO @ Mon, 03 Jun 2019 07:35:09: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 07:35:09: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 07:35:09: #1 total tags in treatment: 18355089 INFO @ Mon, 03 Jun 2019 07:35:09: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 07:35:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 07:35:09: #1 tags after filtering in treatment: 18355089 INFO @ Mon, 03 Jun 2019 07:35:09: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 07:35:09: #1 finished! INFO @ Mon, 03 Jun 2019 07:35:09: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 07:35:09: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 07:35:11: #2 number of paired peaks: 1385 INFO @ Mon, 03 Jun 2019 07:35:11: start model_add_line... INFO @ Mon, 03 Jun 2019 07:35:11: 15000000 INFO @ Mon, 03 Jun 2019 07:35:11: start X-correlation... INFO @ Mon, 03 Jun 2019 07:35:11: end of X-cor INFO @ Mon, 03 Jun 2019 07:35:11: #2 finished! INFO @ Mon, 03 Jun 2019 07:35:11: #2 predicted fragment length is 201 bps INFO @ Mon, 03 Jun 2019 07:35:11: #2 alternative fragment length(s) may be 4,201 bps INFO @ Mon, 03 Jun 2019 07:35:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287568/SRX287568.10_model.r INFO @ Mon, 03 Jun 2019 07:35:11: #3 Call peaks... INFO @ Mon, 03 Jun 2019 07:35:11: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 07:35:12: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 07:35:12: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 07:35:12: #1 total tags in treatment: 18355089 INFO @ Mon, 03 Jun 2019 07:35:12: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 07:35:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 07:35:12: #1 tags after filtering in treatment: 18355089 INFO @ Mon, 03 Jun 2019 07:35:12: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 07:35:12: #1 finished! INFO @ Mon, 03 Jun 2019 07:35:12: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 07:35:12: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 07:35:14: #2 number of paired peaks: 1385 INFO @ Mon, 03 Jun 2019 07:35:14: start model_add_line... INFO @ Mon, 03 Jun 2019 07:35:14: start X-correlation... INFO @ Mon, 03 Jun 2019 07:35:14: end of X-cor INFO @ Mon, 03 Jun 2019 07:35:14: #2 finished! INFO @ Mon, 03 Jun 2019 07:35:14: #2 predicted fragment length is 201 bps INFO @ Mon, 03 Jun 2019 07:35:14: #2 alternative fragment length(s) may be 4,201 bps INFO @ Mon, 03 Jun 2019 07:35:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287568/SRX287568.05_model.r INFO @ Mon, 03 Jun 2019 07:35:14: #3 Call peaks... INFO @ Mon, 03 Jun 2019 07:35:14: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 07:35:21: 16000000 INFO @ Mon, 03 Jun 2019 07:35:29: 17000000 INFO @ Mon, 03 Jun 2019 07:35:37: 18000000 INFO @ Mon, 03 Jun 2019 07:35:40: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 07:35:40: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 07:35:40: #1 total tags in treatment: 18355089 INFO @ Mon, 03 Jun 2019 07:35:40: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 07:35:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 07:35:40: #1 tags after filtering in treatment: 18355089 INFO @ Mon, 03 Jun 2019 07:35:40: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 07:35:40: #1 finished! INFO @ Mon, 03 Jun 2019 07:35:40: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 07:35:40: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 07:35:42: #2 number of paired peaks: 1385 INFO @ Mon, 03 Jun 2019 07:35:42: start model_add_line... INFO @ Mon, 03 Jun 2019 07:35:42: start X-correlation... INFO @ Mon, 03 Jun 2019 07:35:42: end of X-cor INFO @ Mon, 03 Jun 2019 07:35:42: #2 finished! INFO @ Mon, 03 Jun 2019 07:35:42: #2 predicted fragment length is 201 bps INFO @ Mon, 03 Jun 2019 07:35:42: #2 alternative fragment length(s) may be 4,201 bps INFO @ Mon, 03 Jun 2019 07:35:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287568/SRX287568.20_model.r INFO @ Mon, 03 Jun 2019 07:35:42: #3 Call peaks... INFO @ Mon, 03 Jun 2019 07:35:42: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 07:36:08: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 07:36:10: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 07:36:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287568/SRX287568.10_peaks.xls INFO @ Mon, 03 Jun 2019 07:36:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287568/SRX287568.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 07:36:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287568/SRX287568.10_summits.bed INFO @ Mon, 03 Jun 2019 07:36:32: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1116 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 07:36:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287568/SRX287568.05_peaks.xls INFO @ Mon, 03 Jun 2019 07:36:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287568/SRX287568.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 07:36:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287568/SRX287568.05_summits.bed INFO @ Mon, 03 Jun 2019 07:36:34: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2134 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 07:36:40: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 07:37:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287568/SRX287568.20_peaks.xls INFO @ Mon, 03 Jun 2019 07:37:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287568/SRX287568.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 07:37:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287568/SRX287568.20_summits.bed INFO @ Mon, 03 Jun 2019 07:37:04: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (634 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。