Job ID = 1294942 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 16,234,497 reads read : 16,234,497 reads written : 16,234,497 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: 00:05:43 16234497 reads; of these: 16234497 (100.00%) were unpaired; of these: 1313455 (8.09%) aligned 0 times 12148324 (74.83%) aligned exactly 1 time 2772718 (17.08%) aligned >1 times 91.91% overall alignment rate Time searching: 00:05:43 Overall time: 00:05:43 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] 2844346 / 14921042 = 0.1906 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 11:07:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX288006/SRX288006.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX288006/SRX288006.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX288006/SRX288006.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX288006/SRX288006.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 11:07:59: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:07:59: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:07:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX288006/SRX288006.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX288006/SRX288006.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX288006/SRX288006.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX288006/SRX288006.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 11:07:59: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:07:59: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:07:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX288006/SRX288006.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX288006/SRX288006.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX288006/SRX288006.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX288006/SRX288006.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 11:07:59: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:07:59: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:08:07: 1000000 INFO @ Mon, 03 Jun 2019 11:08:10: 1000000 INFO @ Mon, 03 Jun 2019 11:08:10: 1000000 INFO @ Mon, 03 Jun 2019 11:08:15: 2000000 INFO @ Mon, 03 Jun 2019 11:08:20: 2000000 INFO @ Mon, 03 Jun 2019 11:08:21: 2000000 INFO @ Mon, 03 Jun 2019 11:08:23: 3000000 INFO @ Mon, 03 Jun 2019 11:08:30: 3000000 INFO @ Mon, 03 Jun 2019 11:08:31: 4000000 INFO @ Mon, 03 Jun 2019 11:08:31: 3000000 INFO @ Mon, 03 Jun 2019 11:08:39: 5000000 INFO @ Mon, 03 Jun 2019 11:08:39: 4000000 INFO @ Mon, 03 Jun 2019 11:08:41: 4000000 INFO @ Mon, 03 Jun 2019 11:08:47: 6000000 INFO @ Mon, 03 Jun 2019 11:08:49: 5000000 INFO @ Mon, 03 Jun 2019 11:08:52: 5000000 INFO @ Mon, 03 Jun 2019 11:08:55: 7000000 INFO @ Mon, 03 Jun 2019 11:08:58: 6000000 INFO @ Mon, 03 Jun 2019 11:09:02: 6000000 INFO @ Mon, 03 Jun 2019 11:09:03: 8000000 INFO @ Mon, 03 Jun 2019 11:09:08: 7000000 INFO @ Mon, 03 Jun 2019 11:09:10: 9000000 INFO @ Mon, 03 Jun 2019 11:09:12: 7000000 INFO @ Mon, 03 Jun 2019 11:09:17: 8000000 INFO @ Mon, 03 Jun 2019 11:09:18: 10000000 INFO @ Mon, 03 Jun 2019 11:09:22: 8000000 INFO @ Mon, 03 Jun 2019 11:09:26: 9000000 INFO @ Mon, 03 Jun 2019 11:09:26: 11000000 INFO @ Mon, 03 Jun 2019 11:09:32: 9000000 INFO @ Mon, 03 Jun 2019 11:09:34: 12000000 INFO @ Mon, 03 Jun 2019 11:09:35: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 11:09:35: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 11:09:35: #1 total tags in treatment: 12076696 INFO @ Mon, 03 Jun 2019 11:09:35: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:09:35: #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 11:09:35: #1 tags after filtering in treatment: 12076696 INFO @ Mon, 03 Jun 2019 11:09:35: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:09:35: #1 finished! INFO @ Mon, 03 Jun 2019 11:09:35: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:09:35: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:09:36: 10000000 INFO @ Mon, 03 Jun 2019 11:09:37: #2 number of paired peaks: 4232 INFO @ Mon, 03 Jun 2019 11:09:37: start model_add_line... INFO @ Mon, 03 Jun 2019 11:09:37: start X-correlation... INFO @ Mon, 03 Jun 2019 11:09:37: end of X-cor INFO @ Mon, 03 Jun 2019 11:09:37: #2 finished! INFO @ Mon, 03 Jun 2019 11:09:37: #2 predicted fragment length is 222 bps INFO @ Mon, 03 Jun 2019 11:09:37: #2 alternative fragment length(s) may be 222 bps INFO @ Mon, 03 Jun 2019 11:09:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX288006/SRX288006.20_model.r INFO @ Mon, 03 Jun 2019 11:09:37: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:09:37: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:09:42: 10000000 INFO @ Mon, 03 Jun 2019 11:09:45: 11000000 INFO @ Mon, 03 Jun 2019 11:09:53: 11000000 INFO @ Mon, 03 Jun 2019 11:09:55: 12000000 INFO @ Mon, 03 Jun 2019 11:09:56: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 11:09:56: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 11:09:56: #1 total tags in treatment: 12076696 INFO @ Mon, 03 Jun 2019 11:09:56: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:09:56: #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 11:09:56: #1 tags after filtering in treatment: 12076696 INFO @ Mon, 03 Jun 2019 11:09:56: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:09:56: #1 finished! INFO @ Mon, 03 Jun 2019 11:09:56: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:09:56: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:09:58: #2 number of paired peaks: 4232 INFO @ Mon, 03 Jun 2019 11:09:58: start model_add_line... INFO @ Mon, 03 Jun 2019 11:09:58: start X-correlation... INFO @ Mon, 03 Jun 2019 11:09:58: end of X-cor INFO @ Mon, 03 Jun 2019 11:09:58: #2 finished! INFO @ Mon, 03 Jun 2019 11:09:58: #2 predicted fragment length is 222 bps INFO @ Mon, 03 Jun 2019 11:09:58: #2 alternative fragment length(s) may be 222 bps INFO @ Mon, 03 Jun 2019 11:09:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX288006/SRX288006.05_model.r INFO @ Mon, 03 Jun 2019 11:09:58: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:09:58: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:10:03: 12000000 INFO @ Mon, 03 Jun 2019 11:10:04: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 11:10:04: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 11:10:04: #1 total tags in treatment: 12076696 INFO @ Mon, 03 Jun 2019 11:10:04: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:10:04: #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 11:10:04: #1 tags after filtering in treatment: 12076696 INFO @ Mon, 03 Jun 2019 11:10:04: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:10:04: #1 finished! INFO @ Mon, 03 Jun 2019 11:10:04: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:10:04: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:10:05: #2 number of paired peaks: 4232 INFO @ Mon, 03 Jun 2019 11:10:05: start model_add_line... INFO @ Mon, 03 Jun 2019 11:10:06: start X-correlation... INFO @ Mon, 03 Jun 2019 11:10:06: end of X-cor INFO @ Mon, 03 Jun 2019 11:10:06: #2 finished! INFO @ Mon, 03 Jun 2019 11:10:06: #2 predicted fragment length is 222 bps INFO @ Mon, 03 Jun 2019 11:10:06: #2 alternative fragment length(s) may be 222 bps INFO @ Mon, 03 Jun 2019 11:10:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX288006/SRX288006.10_model.r INFO @ Mon, 03 Jun 2019 11:10:06: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:10:06: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:10:19: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:10:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX288006/SRX288006.20_peaks.xls INFO @ Mon, 03 Jun 2019 11:10:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX288006/SRX288006.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:10:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX288006/SRX288006.20_summits.bed INFO @ Mon, 03 Jun 2019 11:10:38: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (5344 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 11:10:39: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:10:46: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:10:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX288006/SRX288006.05_peaks.xls INFO @ Mon, 03 Jun 2019 11:10:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX288006/SRX288006.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:10:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX288006/SRX288006.05_summits.bed INFO @ Mon, 03 Jun 2019 11:10:59: Done! pass1 - making usageList (14 chroms): 5 millis pass2 - checking and writing primary data (8849 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 11:11:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX288006/SRX288006.10_peaks.xls INFO @ Mon, 03 Jun 2019 11:11:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX288006/SRX288006.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:11:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX288006/SRX288006.10_summits.bed INFO @ Mon, 03 Jun 2019 11:11:06: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (7137 records, 4 fields): 11 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。