Job ID = 1293665 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 22,856,531 reads read : 22,856,531 reads written : 22,856,531 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: 00:06:56 22856531 reads; of these: 22856531 (100.00%) were unpaired; of these: 735047 (3.22%) aligned 0 times 17270498 (75.56%) aligned exactly 1 time 4850986 (21.22%) aligned >1 times 96.78% overall alignment rate Time searching: 00:06:56 Overall time: 00:06:56 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] 5834599 / 22121484 = 0.2638 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 01:42:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX104977/SRX104977.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX104977/SRX104977.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX104977/SRX104977.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX104977/SRX104977.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 01:42:47: #1 read tag files... INFO @ Mon, 03 Jun 2019 01:42:47: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 01:42:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX104977/SRX104977.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX104977/SRX104977.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX104977/SRX104977.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX104977/SRX104977.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 01:42:47: #1 read tag files... INFO @ Mon, 03 Jun 2019 01:42:47: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 01:42:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX104977/SRX104977.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX104977/SRX104977.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX104977/SRX104977.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX104977/SRX104977.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 01:42:47: #1 read tag files... INFO @ Mon, 03 Jun 2019 01:42:47: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 01:42:53: 1000000 INFO @ Mon, 03 Jun 2019 01:42:54: 1000000 INFO @ Mon, 03 Jun 2019 01:42:54: 1000000 INFO @ Mon, 03 Jun 2019 01:42:59: 2000000 INFO @ Mon, 03 Jun 2019 01:43:01: 2000000 INFO @ Mon, 03 Jun 2019 01:43:01: 2000000 INFO @ Mon, 03 Jun 2019 01:43:06: 3000000 INFO @ Mon, 03 Jun 2019 01:43:08: 3000000 INFO @ Mon, 03 Jun 2019 01:43:08: 3000000 INFO @ Mon, 03 Jun 2019 01:43:12: 4000000 INFO @ Mon, 03 Jun 2019 01:43:15: 4000000 INFO @ Mon, 03 Jun 2019 01:43:15: 4000000 INFO @ Mon, 03 Jun 2019 01:43:18: 5000000 INFO @ Mon, 03 Jun 2019 01:43:21: 5000000 INFO @ Mon, 03 Jun 2019 01:43:22: 5000000 INFO @ Mon, 03 Jun 2019 01:43:24: 6000000 INFO @ Mon, 03 Jun 2019 01:43:28: 6000000 INFO @ Mon, 03 Jun 2019 01:43:29: 6000000 INFO @ Mon, 03 Jun 2019 01:43:30: 7000000 INFO @ Mon, 03 Jun 2019 01:43:35: 7000000 INFO @ Mon, 03 Jun 2019 01:43:36: 7000000 INFO @ Mon, 03 Jun 2019 01:43:37: 8000000 INFO @ Mon, 03 Jun 2019 01:43:41: 8000000 INFO @ Mon, 03 Jun 2019 01:43:43: 8000000 INFO @ Mon, 03 Jun 2019 01:43:43: 9000000 INFO @ Mon, 03 Jun 2019 01:43:48: 9000000 INFO @ Mon, 03 Jun 2019 01:43:49: 10000000 INFO @ Mon, 03 Jun 2019 01:43:49: 9000000 INFO @ Mon, 03 Jun 2019 01:43:54: 10000000 INFO @ Mon, 03 Jun 2019 01:43:55: 11000000 INFO @ Mon, 03 Jun 2019 01:43:56: 10000000 INFO @ Mon, 03 Jun 2019 01:44:01: 11000000 INFO @ Mon, 03 Jun 2019 01:44:01: 12000000 INFO @ Mon, 03 Jun 2019 01:44:03: 11000000 INFO @ Mon, 03 Jun 2019 01:44:07: 13000000 INFO @ Mon, 03 Jun 2019 01:44:08: 12000000 INFO @ Mon, 03 Jun 2019 01:44:10: 12000000 INFO @ Mon, 03 Jun 2019 01:44:14: 14000000 INFO @ Mon, 03 Jun 2019 01:44:15: 13000000 INFO @ Mon, 03 Jun 2019 01:44:17: 13000000 INFO @ Mon, 03 Jun 2019 01:44:20: 15000000 INFO @ Mon, 03 Jun 2019 01:44:21: 14000000 INFO @ Mon, 03 Jun 2019 01:44:24: 14000000 INFO @ Mon, 03 Jun 2019 01:44:26: 16000000 INFO @ Mon, 03 Jun 2019 01:44:28: 15000000 INFO @ Mon, 03 Jun 2019 01:44:28: #1 tag size is determined as 40 bps INFO @ Mon, 03 Jun 2019 01:44:28: #1 tag size = 40 INFO @ Mon, 03 Jun 2019 01:44:28: #1 total tags in treatment: 16286885 INFO @ Mon, 03 Jun 2019 01:44:28: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 01:44:28: #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 01:44:28: #1 tags after filtering in treatment: 16286885 INFO @ Mon, 03 Jun 2019 01:44:28: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 01:44:28: #1 finished! INFO @ Mon, 03 Jun 2019 01:44:28: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 01:44:28: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 01:44:30: #2 number of paired peaks: 1226 INFO @ Mon, 03 Jun 2019 01:44:30: start model_add_line... INFO @ Mon, 03 Jun 2019 01:44:30: start X-correlation... INFO @ Mon, 03 Jun 2019 01:44:30: end of X-cor INFO @ Mon, 03 Jun 2019 01:44:30: #2 finished! INFO @ Mon, 03 Jun 2019 01:44:30: #2 predicted fragment length is 130 bps INFO @ Mon, 03 Jun 2019 01:44:30: #2 alternative fragment length(s) may be 130 bps INFO @ Mon, 03 Jun 2019 01:44:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX104977/SRX104977.05_model.r INFO @ Mon, 03 Jun 2019 01:44:30: #3 Call peaks... INFO @ Mon, 03 Jun 2019 01:44:30: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 01:44:30: 15000000 INFO @ Mon, 03 Jun 2019 01:44:34: 16000000 INFO @ Mon, 03 Jun 2019 01:44:37: #1 tag size is determined as 40 bps INFO @ Mon, 03 Jun 2019 01:44:37: #1 tag size = 40 INFO @ Mon, 03 Jun 2019 01:44:37: #1 total tags in treatment: 16286885 INFO @ Mon, 03 Jun 2019 01:44:37: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 01:44:37: #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 01:44:37: #1 tags after filtering in treatment: 16286885 INFO @ Mon, 03 Jun 2019 01:44:37: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 01:44:37: #1 finished! INFO @ Mon, 03 Jun 2019 01:44:37: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 01:44:37: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 01:44:37: 16000000 INFO @ Mon, 03 Jun 2019 01:44:38: #2 number of paired peaks: 1226 INFO @ Mon, 03 Jun 2019 01:44:38: start model_add_line... INFO @ Mon, 03 Jun 2019 01:44:39: start X-correlation... INFO @ Mon, 03 Jun 2019 01:44:39: end of X-cor INFO @ Mon, 03 Jun 2019 01:44:39: #2 finished! INFO @ Mon, 03 Jun 2019 01:44:39: #2 predicted fragment length is 130 bps INFO @ Mon, 03 Jun 2019 01:44:39: #2 alternative fragment length(s) may be 130 bps INFO @ Mon, 03 Jun 2019 01:44:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX104977/SRX104977.20_model.r INFO @ Mon, 03 Jun 2019 01:44:39: #3 Call peaks... INFO @ Mon, 03 Jun 2019 01:44:39: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 01:44:39: #1 tag size is determined as 40 bps INFO @ Mon, 03 Jun 2019 01:44:39: #1 tag size = 40 INFO @ Mon, 03 Jun 2019 01:44:39: #1 total tags in treatment: 16286885 INFO @ Mon, 03 Jun 2019 01:44:39: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 01:44:39: #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 01:44:40: #1 tags after filtering in treatment: 16286885 INFO @ Mon, 03 Jun 2019 01:44:40: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 01:44:40: #1 finished! INFO @ Mon, 03 Jun 2019 01:44:40: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 01:44:40: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 01:44:41: #2 number of paired peaks: 1226 INFO @ Mon, 03 Jun 2019 01:44:41: start model_add_line... INFO @ Mon, 03 Jun 2019 01:44:41: start X-correlation... INFO @ Mon, 03 Jun 2019 01:44:41: end of X-cor INFO @ Mon, 03 Jun 2019 01:44:41: #2 finished! INFO @ Mon, 03 Jun 2019 01:44:41: #2 predicted fragment length is 130 bps INFO @ Mon, 03 Jun 2019 01:44:41: #2 alternative fragment length(s) may be 130 bps INFO @ Mon, 03 Jun 2019 01:44:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX104977/SRX104977.10_model.r INFO @ Mon, 03 Jun 2019 01:44:41: #3 Call peaks... INFO @ Mon, 03 Jun 2019 01:44:41: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 01:45:16: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 01:45:24: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 01:45:28: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 01:45:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX104977/SRX104977.05_peaks.xls INFO @ Mon, 03 Jun 2019 01:45:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX104977/SRX104977.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 01:45:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX104977/SRX104977.05_summits.bed INFO @ Mon, 03 Jun 2019 01:45:38: Done! pass1 - making usageList (14 chroms): 4 millis pass2 - checking and writing primary data (9194 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 01:45:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX104977/SRX104977.20_peaks.xls INFO @ Mon, 03 Jun 2019 01:45:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX104977/SRX104977.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 01:45:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX104977/SRX104977.20_summits.bed INFO @ Mon, 03 Jun 2019 01:45:46: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (522 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 01:45:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX104977/SRX104977.10_peaks.xls INFO @ Mon, 03 Jun 2019 01:45:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX104977/SRX104977.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 01:45:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX104977/SRX104977.10_summits.bed INFO @ Mon, 03 Jun 2019 01:45:49: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (2820 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。