Job ID = 1295531 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 25,757,883 reads read : 25,757,883 reads written : 25,757,883 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: 00:07:27 25757883 reads; of these: 25757883 (100.00%) were unpaired; of these: 6954497 (27.00%) aligned 0 times 14230907 (55.25%) aligned exactly 1 time 4572479 (17.75%) aligned >1 times 73.00% overall alignment rate Time searching: 00:07:27 Overall time: 00:07:27 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 8 files... [bam_rmdupse_core] 11038666 / 18803386 = 0.5871 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 14:23:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX365700/SRX365700.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX365700/SRX365700.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX365700/SRX365700.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX365700/SRX365700.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 14:23:48: #1 read tag files... INFO @ Mon, 03 Jun 2019 14:23:48: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 14:23:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX365700/SRX365700.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX365700/SRX365700.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX365700/SRX365700.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX365700/SRX365700.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 14:23:48: #1 read tag files... INFO @ Mon, 03 Jun 2019 14:23:48: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 14:23:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX365700/SRX365700.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX365700/SRX365700.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX365700/SRX365700.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX365700/SRX365700.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 14:23:48: #1 read tag files... INFO @ Mon, 03 Jun 2019 14:23:48: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 14:23:56: 1000000 INFO @ Mon, 03 Jun 2019 14:23:57: 1000000 INFO @ Mon, 03 Jun 2019 14:23:58: 1000000 INFO @ Mon, 03 Jun 2019 14:24:04: 2000000 INFO @ Mon, 03 Jun 2019 14:24:05: 2000000 INFO @ Mon, 03 Jun 2019 14:24:08: 2000000 INFO @ Mon, 03 Jun 2019 14:24:11: 3000000 INFO @ Mon, 03 Jun 2019 14:24:13: 3000000 INFO @ Mon, 03 Jun 2019 14:24:17: 3000000 INFO @ Mon, 03 Jun 2019 14:24:18: 4000000 INFO @ Mon, 03 Jun 2019 14:24:21: 4000000 INFO @ Mon, 03 Jun 2019 14:24:25: 5000000 INFO @ Mon, 03 Jun 2019 14:24:26: 4000000 INFO @ Mon, 03 Jun 2019 14:24:28: 5000000 INFO @ Mon, 03 Jun 2019 14:24:33: 6000000 INFO @ Mon, 03 Jun 2019 14:24:35: 5000000 INFO @ Mon, 03 Jun 2019 14:24:36: 6000000 INFO @ Mon, 03 Jun 2019 14:24:40: 7000000 INFO @ Mon, 03 Jun 2019 14:24:44: 6000000 INFO @ Mon, 03 Jun 2019 14:24:44: 7000000 INFO @ Mon, 03 Jun 2019 14:24:46: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 14:24:46: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 14:24:46: #1 total tags in treatment: 7764720 INFO @ Mon, 03 Jun 2019 14:24:46: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 14:24:46: #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 14:24:46: #1 tags after filtering in treatment: 7764720 INFO @ Mon, 03 Jun 2019 14:24:46: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 14:24:46: #1 finished! INFO @ Mon, 03 Jun 2019 14:24:46: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 14:24:46: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 14:24:47: #2 number of paired peaks: 1312 INFO @ Mon, 03 Jun 2019 14:24:47: start model_add_line... INFO @ Mon, 03 Jun 2019 14:24:47: start X-correlation... INFO @ Mon, 03 Jun 2019 14:24:47: end of X-cor INFO @ Mon, 03 Jun 2019 14:24:47: #2 finished! INFO @ Mon, 03 Jun 2019 14:24:47: #2 predicted fragment length is 128 bps INFO @ Mon, 03 Jun 2019 14:24:47: #2 alternative fragment length(s) may be 128 bps INFO @ Mon, 03 Jun 2019 14:24:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX365700/SRX365700.05_model.r INFO @ Mon, 03 Jun 2019 14:24:47: #3 Call peaks... INFO @ Mon, 03 Jun 2019 14:24:47: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 14:24:50: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 14:24:50: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 14:24:50: #1 total tags in treatment: 7764720 INFO @ Mon, 03 Jun 2019 14:24:50: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 14:24:50: #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 14:24:50: #1 tags after filtering in treatment: 7764720 INFO @ Mon, 03 Jun 2019 14:24:50: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 14:24:50: #1 finished! INFO @ Mon, 03 Jun 2019 14:24:50: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 14:24:50: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 14:24:51: #2 number of paired peaks: 1312 INFO @ Mon, 03 Jun 2019 14:24:51: start model_add_line... INFO @ Mon, 03 Jun 2019 14:24:51: start X-correlation... INFO @ Mon, 03 Jun 2019 14:24:51: end of X-cor INFO @ Mon, 03 Jun 2019 14:24:51: #2 finished! INFO @ Mon, 03 Jun 2019 14:24:51: #2 predicted fragment length is 128 bps INFO @ Mon, 03 Jun 2019 14:24:51: #2 alternative fragment length(s) may be 128 bps INFO @ Mon, 03 Jun 2019 14:24:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX365700/SRX365700.20_model.r INFO @ Mon, 03 Jun 2019 14:24:51: #3 Call peaks... INFO @ Mon, 03 Jun 2019 14:24:51: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 14:24:53: 7000000 INFO @ Mon, 03 Jun 2019 14:25:00: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 14:25:00: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 14:25:00: #1 total tags in treatment: 7764720 INFO @ Mon, 03 Jun 2019 14:25:00: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 14:25:00: #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 14:25:00: #1 tags after filtering in treatment: 7764720 INFO @ Mon, 03 Jun 2019 14:25:00: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 14:25:00: #1 finished! INFO @ Mon, 03 Jun 2019 14:25:00: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 14:25:00: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 14:25:01: #2 number of paired peaks: 1312 INFO @ Mon, 03 Jun 2019 14:25:01: start model_add_line... INFO @ Mon, 03 Jun 2019 14:25:01: start X-correlation... INFO @ Mon, 03 Jun 2019 14:25:01: end of X-cor INFO @ Mon, 03 Jun 2019 14:25:01: #2 finished! INFO @ Mon, 03 Jun 2019 14:25:01: #2 predicted fragment length is 128 bps INFO @ Mon, 03 Jun 2019 14:25:01: #2 alternative fragment length(s) may be 128 bps INFO @ Mon, 03 Jun 2019 14:25:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX365700/SRX365700.10_model.r INFO @ Mon, 03 Jun 2019 14:25:01: #3 Call peaks... INFO @ Mon, 03 Jun 2019 14:25:01: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 14:25:10: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 14:25:15: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 14:25:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX365700/SRX365700.05_peaks.xls INFO @ Mon, 03 Jun 2019 14:25:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX365700/SRX365700.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 14:25:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX365700/SRX365700.05_summits.bed INFO @ Mon, 03 Jun 2019 14:25:22: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (6433 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 14:25:24: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 14:25:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX365700/SRX365700.20_peaks.xls INFO @ Mon, 03 Jun 2019 14:25:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX365700/SRX365700.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 14:25:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX365700/SRX365700.20_summits.bed INFO @ Mon, 03 Jun 2019 14:25:26: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1656 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 14:25:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX365700/SRX365700.10_peaks.xls INFO @ Mon, 03 Jun 2019 14:25:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX365700/SRX365700.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 14:25:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX365700/SRX365700.10_summits.bed INFO @ Mon, 03 Jun 2019 14:25:36: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (3286 records, 4 fields): 10 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。