Job ID = 2590314 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 22,039,295 reads read : 22,039,295 reads written : 22,039,295 rm: cannot remove ‘[DSE]RR*’: 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: 00:06:43 22039295 reads; of these: 22039295 (100.00%) were unpaired; of these: 3408509 (15.47%) aligned 0 times 14780332 (67.06%) aligned exactly 1 time 3850454 (17.47%) aligned >1 times 84.53% overall alignment rate Time searching: 00:06:43 Overall time: 00:06:43 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] 6801670 / 18630786 = 0.3651 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, 12 Aug 2019 21:01:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX331420/SRX331420.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX331420/SRX331420.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX331420/SRX331420.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX331420/SRX331420.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, 12 Aug 2019 21:01:15: #1 read tag files... INFO @ Mon, 12 Aug 2019 21:01:15: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 21:01:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX331420/SRX331420.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX331420/SRX331420.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX331420/SRX331420.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX331420/SRX331420.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, 12 Aug 2019 21:01:16: #1 read tag files... INFO @ Mon, 12 Aug 2019 21:01:16: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 21:01:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX331420/SRX331420.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX331420/SRX331420.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX331420/SRX331420.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX331420/SRX331420.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, 12 Aug 2019 21:01:17: #1 read tag files... INFO @ Mon, 12 Aug 2019 21:01:17: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 21:01:25: 1000000 INFO @ Mon, 12 Aug 2019 21:01:26: 1000000 INFO @ Mon, 12 Aug 2019 21:01:27: 1000000 INFO @ Mon, 12 Aug 2019 21:01:34: 2000000 INFO @ Mon, 12 Aug 2019 21:01:35: 2000000 INFO @ Mon, 12 Aug 2019 21:01:36: 2000000 INFO @ Mon, 12 Aug 2019 21:01:43: 3000000 INFO @ Mon, 12 Aug 2019 21:01:44: 3000000 INFO @ Mon, 12 Aug 2019 21:01:46: 3000000 INFO @ Mon, 12 Aug 2019 21:01:53: 4000000 INFO @ Mon, 12 Aug 2019 21:01:53: 4000000 INFO @ Mon, 12 Aug 2019 21:01:55: 4000000 INFO @ Mon, 12 Aug 2019 21:02:01: 5000000 INFO @ Mon, 12 Aug 2019 21:02:02: 5000000 INFO @ Mon, 12 Aug 2019 21:02:04: 5000000 INFO @ Mon, 12 Aug 2019 21:02:09: 6000000 INFO @ Mon, 12 Aug 2019 21:02:11: 6000000 INFO @ Mon, 12 Aug 2019 21:02:13: 6000000 INFO @ Mon, 12 Aug 2019 21:02:18: 7000000 INFO @ Mon, 12 Aug 2019 21:02:21: 7000000 INFO @ Mon, 12 Aug 2019 21:02:22: 7000000 INFO @ Mon, 12 Aug 2019 21:02:26: 8000000 INFO @ Mon, 12 Aug 2019 21:02:30: 8000000 INFO @ Mon, 12 Aug 2019 21:02:32: 8000000 INFO @ Mon, 12 Aug 2019 21:02:34: 9000000 INFO @ Mon, 12 Aug 2019 21:02:39: 9000000 INFO @ Mon, 12 Aug 2019 21:02:41: 9000000 INFO @ Mon, 12 Aug 2019 21:02:42: 10000000 INFO @ Mon, 12 Aug 2019 21:02:48: 10000000 INFO @ Mon, 12 Aug 2019 21:02:50: 11000000 INFO @ Mon, 12 Aug 2019 21:02:50: 10000000 INFO @ Mon, 12 Aug 2019 21:02:57: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 21:02:57: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 21:02:57: #1 total tags in treatment: 11829116 INFO @ Mon, 12 Aug 2019 21:02:57: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 21:02:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 21:02:57: #1 tags after filtering in treatment: 11829116 INFO @ Mon, 12 Aug 2019 21:02:57: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 21:02:57: #1 finished! INFO @ Mon, 12 Aug 2019 21:02:57: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 21:02:57: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 21:02:57: 11000000 INFO @ Mon, 12 Aug 2019 21:02:59: #2 number of paired peaks: 10038 INFO @ Mon, 12 Aug 2019 21:02:59: start model_add_line... INFO @ Mon, 12 Aug 2019 21:02:59: 11000000 INFO @ Mon, 12 Aug 2019 21:02:59: start X-correlation... INFO @ Mon, 12 Aug 2019 21:02:59: end of X-cor INFO @ Mon, 12 Aug 2019 21:02:59: #2 finished! INFO @ Mon, 12 Aug 2019 21:02:59: #2 predicted fragment length is 263 bps INFO @ Mon, 12 Aug 2019 21:02:59: #2 alternative fragment length(s) may be 263 bps INFO @ Mon, 12 Aug 2019 21:02:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX331420/SRX331420.10_model.r INFO @ Mon, 12 Aug 2019 21:02:59: #3 Call peaks... INFO @ Mon, 12 Aug 2019 21:02:59: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 21:03:05: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 21:03:05: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 21:03:05: #1 total tags in treatment: 11829116 INFO @ Mon, 12 Aug 2019 21:03:05: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 21:03:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 21:03:05: #1 tags after filtering in treatment: 11829116 INFO @ Mon, 12 Aug 2019 21:03:05: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 21:03:05: #1 finished! INFO @ Mon, 12 Aug 2019 21:03:05: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 21:03:05: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 21:03:07: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 21:03:07: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 21:03:07: #1 total tags in treatment: 11829116 INFO @ Mon, 12 Aug 2019 21:03:07: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 21:03:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 21:03:07: #1 tags after filtering in treatment: 11829116 INFO @ Mon, 12 Aug 2019 21:03:07: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 21:03:07: #1 finished! INFO @ Mon, 12 Aug 2019 21:03:07: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 21:03:07: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 21:03:07: #2 number of paired peaks: 10038 INFO @ Mon, 12 Aug 2019 21:03:07: start model_add_line... INFO @ Mon, 12 Aug 2019 21:03:07: start X-correlation... INFO @ Mon, 12 Aug 2019 21:03:07: end of X-cor INFO @ Mon, 12 Aug 2019 21:03:07: #2 finished! INFO @ Mon, 12 Aug 2019 21:03:07: #2 predicted fragment length is 263 bps INFO @ Mon, 12 Aug 2019 21:03:07: #2 alternative fragment length(s) may be 263 bps INFO @ Mon, 12 Aug 2019 21:03:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX331420/SRX331420.05_model.r INFO @ Mon, 12 Aug 2019 21:03:07: #3 Call peaks... INFO @ Mon, 12 Aug 2019 21:03:07: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 21:03:09: #2 number of paired peaks: 10038 INFO @ Mon, 12 Aug 2019 21:03:09: start model_add_line... INFO @ Mon, 12 Aug 2019 21:03:09: start X-correlation... INFO @ Mon, 12 Aug 2019 21:03:09: end of X-cor INFO @ Mon, 12 Aug 2019 21:03:09: #2 finished! INFO @ Mon, 12 Aug 2019 21:03:09: #2 predicted fragment length is 263 bps INFO @ Mon, 12 Aug 2019 21:03:09: #2 alternative fragment length(s) may be 263 bps INFO @ Mon, 12 Aug 2019 21:03:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX331420/SRX331420.20_model.r INFO @ Mon, 12 Aug 2019 21:03:09: #3 Call peaks... INFO @ Mon, 12 Aug 2019 21:03:09: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 21:03:54: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 21:04:00: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 21:04:02: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 12 Aug 2019 21:04:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX331420/SRX331420.10_peaks.xls INFO @ Mon, 12 Aug 2019 21:04:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX331420/SRX331420.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 21:04:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX331420/SRX331420.10_summits.bed INFO @ Mon, 12 Aug 2019 21:04:14: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (7960 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 21:04:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX331420/SRX331420.05_peaks.xls INFO @ Mon, 12 Aug 2019 21:04:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX331420/SRX331420.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 21:04:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX331420/SRX331420.05_summits.bed INFO @ Mon, 12 Aug 2019 21:04:18: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (8885 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 21:04:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX331420/SRX331420.20_peaks.xls INFO @ Mon, 12 Aug 2019 21:04:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX331420/SRX331420.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 21:04:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX331420/SRX331420.20_summits.bed INFO @ Mon, 12 Aug 2019 21:04:20: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6837 records, 4 fields): 11 millis CompletedMACS2peakCalling BigWig に変換しました。