Job ID = 1294971 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 15,741,291 reads read : 15,741,291 reads written : 15,741,291 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: 00:06:01 15741291 reads; of these: 15741291 (100.00%) were unpaired; of these: 1408321 (8.95%) aligned 0 times 10656196 (67.70%) aligned exactly 1 time 3676774 (23.36%) aligned >1 times 91.05% overall alignment rate Time searching: 00:06:01 Overall time: 00:06:01 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] 1823664 / 14332970 = 0.1272 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 11:17:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX288030/SRX288030.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX288030/SRX288030.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX288030/SRX288030.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX288030/SRX288030.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 11:17:42: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:17:42: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:17:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX288030/SRX288030.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX288030/SRX288030.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX288030/SRX288030.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX288030/SRX288030.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 11:17:42: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:17:42: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:17:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX288030/SRX288030.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX288030/SRX288030.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX288030/SRX288030.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX288030/SRX288030.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 11:17:42: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:17:42: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:17:50: 1000000 INFO @ Mon, 03 Jun 2019 11:17:51: 1000000 INFO @ Mon, 03 Jun 2019 11:17:51: 1000000 INFO @ Mon, 03 Jun 2019 11:17:57: 2000000 INFO @ Mon, 03 Jun 2019 11:17:58: 2000000 INFO @ Mon, 03 Jun 2019 11:17:59: 2000000 INFO @ Mon, 03 Jun 2019 11:18:04: 3000000 INFO @ Mon, 03 Jun 2019 11:18:06: 3000000 INFO @ Mon, 03 Jun 2019 11:18:07: 3000000 INFO @ Mon, 03 Jun 2019 11:18:11: 4000000 INFO @ Mon, 03 Jun 2019 11:18:13: 4000000 INFO @ Mon, 03 Jun 2019 11:18:15: 4000000 INFO @ Mon, 03 Jun 2019 11:18:18: 5000000 INFO @ Mon, 03 Jun 2019 11:18:21: 5000000 INFO @ Mon, 03 Jun 2019 11:18:23: 5000000 INFO @ Mon, 03 Jun 2019 11:18:25: 6000000 INFO @ Mon, 03 Jun 2019 11:18:28: 6000000 INFO @ Mon, 03 Jun 2019 11:18:31: 6000000 INFO @ Mon, 03 Jun 2019 11:18:32: 7000000 INFO @ Mon, 03 Jun 2019 11:18:36: 7000000 INFO @ Mon, 03 Jun 2019 11:18:39: 8000000 INFO @ Mon, 03 Jun 2019 11:18:39: 7000000 INFO @ Mon, 03 Jun 2019 11:18:43: 8000000 INFO @ Mon, 03 Jun 2019 11:18:46: 9000000 INFO @ Mon, 03 Jun 2019 11:18:48: 8000000 INFO @ Mon, 03 Jun 2019 11:18:50: 9000000 INFO @ Mon, 03 Jun 2019 11:18:53: 10000000 INFO @ Mon, 03 Jun 2019 11:18:56: 9000000 INFO @ Mon, 03 Jun 2019 11:18:58: 10000000 INFO @ Mon, 03 Jun 2019 11:19:01: 11000000 INFO @ Mon, 03 Jun 2019 11:19:04: 10000000 INFO @ Mon, 03 Jun 2019 11:19:05: 11000000 INFO @ Mon, 03 Jun 2019 11:19:08: 12000000 INFO @ Mon, 03 Jun 2019 11:19:12: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 11:19:12: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 11:19:12: #1 total tags in treatment: 12509306 INFO @ Mon, 03 Jun 2019 11:19:12: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:19:12: #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 11:19:12: #1 tags after filtering in treatment: 12509306 INFO @ Mon, 03 Jun 2019 11:19:12: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:19:12: #1 finished! INFO @ Mon, 03 Jun 2019 11:19:12: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:19:12: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:19:12: 12000000 INFO @ Mon, 03 Jun 2019 11:19:13: 11000000 INFO @ Mon, 03 Jun 2019 11:19:13: #2 number of paired peaks: 1484 INFO @ Mon, 03 Jun 2019 11:19:13: start model_add_line... INFO @ Mon, 03 Jun 2019 11:19:13: start X-correlation... INFO @ Mon, 03 Jun 2019 11:19:13: end of X-cor INFO @ Mon, 03 Jun 2019 11:19:13: #2 finished! INFO @ Mon, 03 Jun 2019 11:19:13: #2 predicted fragment length is 211 bps INFO @ Mon, 03 Jun 2019 11:19:13: #2 alternative fragment length(s) may be 211 bps INFO @ Mon, 03 Jun 2019 11:19:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX288030/SRX288030.20_model.r INFO @ Mon, 03 Jun 2019 11:19:13: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:19:13: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:19:16: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 11:19:16: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 11:19:16: #1 total tags in treatment: 12509306 INFO @ Mon, 03 Jun 2019 11:19:16: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:19:16: #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 11:19:16: #1 tags after filtering in treatment: 12509306 INFO @ Mon, 03 Jun 2019 11:19:16: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:19:16: #1 finished! INFO @ Mon, 03 Jun 2019 11:19:16: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:19:16: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:19:17: #2 number of paired peaks: 1484 INFO @ Mon, 03 Jun 2019 11:19:17: start model_add_line... INFO @ Mon, 03 Jun 2019 11:19:18: start X-correlation... INFO @ Mon, 03 Jun 2019 11:19:18: end of X-cor INFO @ Mon, 03 Jun 2019 11:19:18: #2 finished! INFO @ Mon, 03 Jun 2019 11:19:18: #2 predicted fragment length is 211 bps INFO @ Mon, 03 Jun 2019 11:19:18: #2 alternative fragment length(s) may be 211 bps INFO @ Mon, 03 Jun 2019 11:19:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX288030/SRX288030.05_model.r INFO @ Mon, 03 Jun 2019 11:19:18: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:19:18: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:19:20: 12000000 INFO @ Mon, 03 Jun 2019 11:19:25: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 11:19:25: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 11:19:25: #1 total tags in treatment: 12509306 INFO @ Mon, 03 Jun 2019 11:19:25: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:19:25: #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 11:19:25: #1 tags after filtering in treatment: 12509306 INFO @ Mon, 03 Jun 2019 11:19:25: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:19:25: #1 finished! INFO @ Mon, 03 Jun 2019 11:19:25: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:19:25: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:19:26: #2 number of paired peaks: 1484 INFO @ Mon, 03 Jun 2019 11:19:26: start model_add_line... INFO @ Mon, 03 Jun 2019 11:19:26: start X-correlation... INFO @ Mon, 03 Jun 2019 11:19:26: end of X-cor INFO @ Mon, 03 Jun 2019 11:19:26: #2 finished! INFO @ Mon, 03 Jun 2019 11:19:26: #2 predicted fragment length is 211 bps INFO @ Mon, 03 Jun 2019 11:19:26: #2 alternative fragment length(s) may be 211 bps INFO @ Mon, 03 Jun 2019 11:19:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX288030/SRX288030.10_model.r INFO @ Mon, 03 Jun 2019 11:19:26: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:19:26: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:19:53: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:19:58: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:20:06: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:20:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX288030/SRX288030.20_peaks.xls INFO @ Mon, 03 Jun 2019 11:20:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX288030/SRX288030.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:20:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX288030/SRX288030.20_summits.bed INFO @ Mon, 03 Jun 2019 11:20:11: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3039 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 11:20:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX288030/SRX288030.05_peaks.xls INFO @ Mon, 03 Jun 2019 11:20:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX288030/SRX288030.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:20:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX288030/SRX288030.05_summits.bed INFO @ Mon, 03 Jun 2019 11:20:17: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (6272 records, 4 fields): 38 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 11:20:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX288030/SRX288030.10_peaks.xls INFO @ Mon, 03 Jun 2019 11:20:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX288030/SRX288030.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:20:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX288030/SRX288030.10_summits.bed INFO @ Mon, 03 Jun 2019 11:20:25: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (4653 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。