Job ID = 1294225 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 27,059,544 reads read : 27,059,544 reads written : 27,059,544 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: 00:06:39 27059544 reads; of these: 27059544 (100.00%) were unpaired; of these: 2621474 (9.69%) aligned 0 times 22374739 (82.69%) aligned exactly 1 time 2063331 (7.63%) aligned >1 times 90.31% overall alignment rate Time searching: 00:06:39 Overall time: 00:06:39 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] 11356561 / 24438070 = 0.4647 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 05:49:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX201902/SRX201902.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX201902/SRX201902.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX201902/SRX201902.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX201902/SRX201902.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 05:49:36: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:49:36: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:49:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX201902/SRX201902.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX201902/SRX201902.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX201902/SRX201902.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX201902/SRX201902.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 05:49:36: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:49:36: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:49:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX201902/SRX201902.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX201902/SRX201902.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX201902/SRX201902.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX201902/SRX201902.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 05:49:36: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:49:36: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:49:43: 1000000 INFO @ Mon, 03 Jun 2019 05:49:45: 1000000 INFO @ Mon, 03 Jun 2019 05:49:46: 1000000 INFO @ Mon, 03 Jun 2019 05:49:51: 2000000 INFO @ Mon, 03 Jun 2019 05:49:54: 2000000 INFO @ Mon, 03 Jun 2019 05:49:56: 2000000 INFO @ Mon, 03 Jun 2019 05:49:58: 3000000 INFO @ Mon, 03 Jun 2019 05:50:02: 3000000 INFO @ Mon, 03 Jun 2019 05:50:05: 4000000 INFO @ Mon, 03 Jun 2019 05:50:06: 3000000 INFO @ Mon, 03 Jun 2019 05:50:11: 4000000 INFO @ Mon, 03 Jun 2019 05:50:12: 5000000 INFO @ Mon, 03 Jun 2019 05:50:15: 4000000 INFO @ Mon, 03 Jun 2019 05:50:19: 6000000 INFO @ Mon, 03 Jun 2019 05:50:20: 5000000 INFO @ Mon, 03 Jun 2019 05:50:24: 5000000 INFO @ Mon, 03 Jun 2019 05:50:27: 7000000 INFO @ Mon, 03 Jun 2019 05:50:29: 6000000 INFO @ Mon, 03 Jun 2019 05:50:34: 8000000 INFO @ Mon, 03 Jun 2019 05:50:34: 6000000 INFO @ Mon, 03 Jun 2019 05:50:39: 7000000 INFO @ Mon, 03 Jun 2019 05:50:41: 9000000 INFO @ Mon, 03 Jun 2019 05:50:44: 7000000 INFO @ Mon, 03 Jun 2019 05:50:47: 8000000 INFO @ Mon, 03 Jun 2019 05:50:49: 10000000 INFO @ Mon, 03 Jun 2019 05:50:55: 8000000 INFO @ Mon, 03 Jun 2019 05:50:55: 9000000 INFO @ Mon, 03 Jun 2019 05:50:57: 11000000 INFO @ Mon, 03 Jun 2019 05:51:04: 10000000 INFO @ Mon, 03 Jun 2019 05:51:05: 12000000 INFO @ Mon, 03 Jun 2019 05:51:05: 9000000 INFO @ Mon, 03 Jun 2019 05:51:12: 13000000 INFO @ Mon, 03 Jun 2019 05:51:12: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 05:51:12: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 05:51:12: #1 total tags in treatment: 13081509 INFO @ Mon, 03 Jun 2019 05:51:12: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:51:12: #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 05:51:13: #1 tags after filtering in treatment: 13081509 INFO @ Mon, 03 Jun 2019 05:51:13: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:51:13: #1 finished! INFO @ Mon, 03 Jun 2019 05:51:13: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:51:13: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:51:13: 11000000 INFO @ Mon, 03 Jun 2019 05:51:15: #2 number of paired peaks: 6238 INFO @ Mon, 03 Jun 2019 05:51:15: start model_add_line... INFO @ Mon, 03 Jun 2019 05:51:15: start X-correlation... INFO @ Mon, 03 Jun 2019 05:51:15: end of X-cor INFO @ Mon, 03 Jun 2019 05:51:15: #2 finished! INFO @ Mon, 03 Jun 2019 05:51:15: #2 predicted fragment length is 203 bps INFO @ Mon, 03 Jun 2019 05:51:15: #2 alternative fragment length(s) may be 203 bps INFO @ Mon, 03 Jun 2019 05:51:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX201902/SRX201902.10_model.r INFO @ Mon, 03 Jun 2019 05:51:15: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:51:15: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:51:15: 10000000 INFO @ Mon, 03 Jun 2019 05:51:21: 12000000 INFO @ Mon, 03 Jun 2019 05:51:26: 11000000 INFO @ Mon, 03 Jun 2019 05:51:29: 13000000 INFO @ Mon, 03 Jun 2019 05:51:29: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 05:51:29: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 05:51:29: #1 total tags in treatment: 13081509 INFO @ Mon, 03 Jun 2019 05:51:29: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:51:29: #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 05:51:30: #1 tags after filtering in treatment: 13081509 INFO @ Mon, 03 Jun 2019 05:51:30: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:51:30: #1 finished! INFO @ Mon, 03 Jun 2019 05:51:30: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:51:30: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:51:32: #2 number of paired peaks: 6238 INFO @ Mon, 03 Jun 2019 05:51:32: start model_add_line... INFO @ Mon, 03 Jun 2019 05:51:32: start X-correlation... INFO @ Mon, 03 Jun 2019 05:51:32: end of X-cor INFO @ Mon, 03 Jun 2019 05:51:32: #2 finished! INFO @ Mon, 03 Jun 2019 05:51:32: #2 predicted fragment length is 203 bps INFO @ Mon, 03 Jun 2019 05:51:32: #2 alternative fragment length(s) may be 203 bps INFO @ Mon, 03 Jun 2019 05:51:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX201902/SRX201902.05_model.r INFO @ Mon, 03 Jun 2019 05:51:32: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:51:32: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:51:36: 12000000 INFO @ Mon, 03 Jun 2019 05:51:46: 13000000 INFO @ Mon, 03 Jun 2019 05:51:47: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 05:51:47: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 05:51:47: #1 total tags in treatment: 13081509 INFO @ Mon, 03 Jun 2019 05:51:47: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:51:47: #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 05:51:47: #1 tags after filtering in treatment: 13081509 INFO @ Mon, 03 Jun 2019 05:51:47: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:51:47: #1 finished! INFO @ Mon, 03 Jun 2019 05:51:47: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:51:47: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:51:49: #2 number of paired peaks: 6238 INFO @ Mon, 03 Jun 2019 05:51:49: start model_add_line... INFO @ Mon, 03 Jun 2019 05:51:49: start X-correlation... INFO @ Mon, 03 Jun 2019 05:51:49: end of X-cor INFO @ Mon, 03 Jun 2019 05:51:49: #2 finished! INFO @ Mon, 03 Jun 2019 05:51:49: #2 predicted fragment length is 203 bps INFO @ Mon, 03 Jun 2019 05:51:49: #2 alternative fragment length(s) may be 203 bps INFO @ Mon, 03 Jun 2019 05:51:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX201902/SRX201902.20_model.r INFO @ Mon, 03 Jun 2019 05:51:49: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:51:49: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:52:03: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:52:22: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:52:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX201902/SRX201902.10_peaks.xls INFO @ Mon, 03 Jun 2019 05:52:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX201902/SRX201902.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:52:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX201902/SRX201902.10_summits.bed INFO @ Mon, 03 Jun 2019 05:52:22: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (7521 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 05:52:38: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:52:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX201902/SRX201902.05_peaks.xls INFO @ Mon, 03 Jun 2019 05:52:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX201902/SRX201902.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:52:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX201902/SRX201902.05_summits.bed INFO @ Mon, 03 Jun 2019 05:52:42: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (9598 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 05:52:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX201902/SRX201902.20_peaks.xls INFO @ Mon, 03 Jun 2019 05:52:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX201902/SRX201902.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:52:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX201902/SRX201902.20_summits.bed INFO @ Mon, 03 Jun 2019 05:52:58: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (5609 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。