Job ID = 1293995 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 35,921,511 reads read : 35,921,511 reads written : 35,921,511 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: 00:09:25 35921511 reads; of these: 35921511 (100.00%) were unpaired; of these: 12468451 (34.71%) aligned 0 times 18312415 (50.98%) aligned exactly 1 time 5140645 (14.31%) aligned >1 times 65.29% overall alignment rate Time searching: 00:09:25 Overall time: 00:09:25 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] 6231790 / 23453060 = 0.2657 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 04:06:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX159166/SRX159166.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX159166/SRX159166.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX159166/SRX159166.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX159166/SRX159166.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 04:06:46: #1 read tag files... INFO @ Mon, 03 Jun 2019 04:06:46: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 04:06:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX159166/SRX159166.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX159166/SRX159166.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX159166/SRX159166.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX159166/SRX159166.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 04:06:46: #1 read tag files... INFO @ Mon, 03 Jun 2019 04:06:46: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 04:06:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX159166/SRX159166.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX159166/SRX159166.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX159166/SRX159166.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX159166/SRX159166.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 04:06:46: #1 read tag files... INFO @ Mon, 03 Jun 2019 04:06:46: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 04:06:53: 1000000 INFO @ Mon, 03 Jun 2019 04:06:53: 1000000 INFO @ Mon, 03 Jun 2019 04:06:54: 1000000 INFO @ Mon, 03 Jun 2019 04:07:00: 2000000 INFO @ Mon, 03 Jun 2019 04:07:00: 2000000 INFO @ Mon, 03 Jun 2019 04:07:01: 2000000 INFO @ Mon, 03 Jun 2019 04:07:07: 3000000 INFO @ Mon, 03 Jun 2019 04:07:08: 3000000 INFO @ Mon, 03 Jun 2019 04:07:09: 3000000 INFO @ Mon, 03 Jun 2019 04:07:14: 4000000 INFO @ Mon, 03 Jun 2019 04:07:14: 4000000 INFO @ Mon, 03 Jun 2019 04:07:16: 4000000 INFO @ Mon, 03 Jun 2019 04:07:21: 5000000 INFO @ Mon, 03 Jun 2019 04:07:22: 5000000 INFO @ Mon, 03 Jun 2019 04:07:24: 5000000 INFO @ Mon, 03 Jun 2019 04:07:28: 6000000 INFO @ Mon, 03 Jun 2019 04:07:29: 6000000 INFO @ Mon, 03 Jun 2019 04:07:31: 6000000 INFO @ Mon, 03 Jun 2019 04:07:35: 7000000 INFO @ Mon, 03 Jun 2019 04:07:37: 7000000 INFO @ Mon, 03 Jun 2019 04:07:39: 7000000 INFO @ Mon, 03 Jun 2019 04:07:42: 8000000 INFO @ Mon, 03 Jun 2019 04:07:44: 8000000 INFO @ Mon, 03 Jun 2019 04:07:47: 8000000 INFO @ Mon, 03 Jun 2019 04:07:50: 9000000 INFO @ Mon, 03 Jun 2019 04:07:52: 9000000 INFO @ Mon, 03 Jun 2019 04:07:54: 9000000 INFO @ Mon, 03 Jun 2019 04:07:57: 10000000 INFO @ Mon, 03 Jun 2019 04:08:00: 10000000 INFO @ Mon, 03 Jun 2019 04:08:02: 10000000 INFO @ Mon, 03 Jun 2019 04:08:04: 11000000 INFO @ Mon, 03 Jun 2019 04:08:08: 11000000 INFO @ Mon, 03 Jun 2019 04:08:10: 11000000 INFO @ Mon, 03 Jun 2019 04:08:11: 12000000 INFO @ Mon, 03 Jun 2019 04:08:16: 12000000 INFO @ Mon, 03 Jun 2019 04:08:18: 12000000 INFO @ Mon, 03 Jun 2019 04:08:19: 13000000 INFO @ Mon, 03 Jun 2019 04:08:24: 13000000 INFO @ Mon, 03 Jun 2019 04:08:26: 14000000 INFO @ Mon, 03 Jun 2019 04:08:26: 13000000 INFO @ Mon, 03 Jun 2019 04:08:32: 14000000 INFO @ Mon, 03 Jun 2019 04:08:33: 15000000 INFO @ Mon, 03 Jun 2019 04:08:34: 14000000 INFO @ Mon, 03 Jun 2019 04:08:40: 15000000 INFO @ Mon, 03 Jun 2019 04:08:40: 16000000 INFO @ Mon, 03 Jun 2019 04:08:42: 15000000 INFO @ Mon, 03 Jun 2019 04:08:47: 17000000 INFO @ Mon, 03 Jun 2019 04:08:48: 16000000 INFO @ Mon, 03 Jun 2019 04:08:49: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 04:08:49: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 04:08:49: #1 total tags in treatment: 17221270 INFO @ Mon, 03 Jun 2019 04:08:49: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 04:08:49: #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 04:08:49: #1 tags after filtering in treatment: 17221270 INFO @ Mon, 03 Jun 2019 04:08:49: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 04:08:49: #1 finished! INFO @ Mon, 03 Jun 2019 04:08:49: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 04:08:49: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 04:08:50: 16000000 INFO @ Mon, 03 Jun 2019 04:08:51: #2 number of paired peaks: 2106 INFO @ Mon, 03 Jun 2019 04:08:51: start model_add_line... INFO @ Mon, 03 Jun 2019 04:08:51: start X-correlation... INFO @ Mon, 03 Jun 2019 04:08:52: end of X-cor INFO @ Mon, 03 Jun 2019 04:08:52: #2 finished! INFO @ Mon, 03 Jun 2019 04:08:52: #2 predicted fragment length is 150 bps INFO @ Mon, 03 Jun 2019 04:08:52: #2 alternative fragment length(s) may be 150 bps INFO @ Mon, 03 Jun 2019 04:08:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX159166/SRX159166.10_model.r INFO @ Mon, 03 Jun 2019 04:08:52: #3 Call peaks... INFO @ Mon, 03 Jun 2019 04:08:52: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 04:08:55: 17000000 INFO @ Mon, 03 Jun 2019 04:08:56: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 04:08:56: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 04:08:56: #1 total tags in treatment: 17221270 INFO @ Mon, 03 Jun 2019 04:08:56: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 04:08:56: #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 04:08:57: #1 tags after filtering in treatment: 17221270 INFO @ Mon, 03 Jun 2019 04:08:57: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 04:08:57: #1 finished! INFO @ Mon, 03 Jun 2019 04:08:57: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 04:08:57: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 04:08:57: 17000000 INFO @ Mon, 03 Jun 2019 04:08:59: #2 number of paired peaks: 2106 INFO @ Mon, 03 Jun 2019 04:08:59: start model_add_line... INFO @ Mon, 03 Jun 2019 04:08:59: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 04:08:59: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 04:08:59: #1 total tags in treatment: 17221270 INFO @ Mon, 03 Jun 2019 04:08:59: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 04:08:59: #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 04:08:59: start X-correlation... INFO @ Mon, 03 Jun 2019 04:08:59: end of X-cor INFO @ Mon, 03 Jun 2019 04:08:59: #2 finished! INFO @ Mon, 03 Jun 2019 04:08:59: #2 predicted fragment length is 150 bps INFO @ Mon, 03 Jun 2019 04:08:59: #2 alternative fragment length(s) may be 150 bps INFO @ Mon, 03 Jun 2019 04:08:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX159166/SRX159166.20_model.r INFO @ Mon, 03 Jun 2019 04:08:59: #3 Call peaks... INFO @ Mon, 03 Jun 2019 04:08:59: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 04:08:59: #1 tags after filtering in treatment: 17221270 INFO @ Mon, 03 Jun 2019 04:08:59: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 04:08:59: #1 finished! INFO @ Mon, 03 Jun 2019 04:08:59: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 04:08:59: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 04:09:01: #2 number of paired peaks: 2106 INFO @ Mon, 03 Jun 2019 04:09:01: start model_add_line... INFO @ Mon, 03 Jun 2019 04:09:01: start X-correlation... INFO @ Mon, 03 Jun 2019 04:09:01: end of X-cor INFO @ Mon, 03 Jun 2019 04:09:01: #2 finished! INFO @ Mon, 03 Jun 2019 04:09:01: #2 predicted fragment length is 150 bps INFO @ Mon, 03 Jun 2019 04:09:01: #2 alternative fragment length(s) may be 150 bps INFO @ Mon, 03 Jun 2019 04:09:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX159166/SRX159166.05_model.r INFO @ Mon, 03 Jun 2019 04:09:01: #3 Call peaks... INFO @ Mon, 03 Jun 2019 04:09:01: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 04:09:42: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 04:09:50: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 04:09:52: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 04:10:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX159166/SRX159166.10_peaks.xls INFO @ Mon, 03 Jun 2019 04:10:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX159166/SRX159166.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 04:10:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX159166/SRX159166.10_summits.bed INFO @ Mon, 03 Jun 2019 04:10:06: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (7982 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 04:10:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX159166/SRX159166.20_peaks.xls INFO @ Mon, 03 Jun 2019 04:10:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX159166/SRX159166.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 04:10:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX159166/SRX159166.20_summits.bed INFO @ Mon, 03 Jun 2019 04:10:14: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (5695 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 04:10:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX159166/SRX159166.05_peaks.xls INFO @ Mon, 03 Jun 2019 04:10:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX159166/SRX159166.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 04:10:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX159166/SRX159166.05_summits.bed INFO @ Mon, 03 Jun 2019 04:10:16: Done! pass1 - making usageList (15 chroms): 5 millis pass2 - checking and writing primary data (10603 records, 4 fields): 22 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。