Job ID = 2590846 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 18,734,401 reads read : 18,734,401 reads written : 18,734,401 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: 00:06:15 18734401 reads; of these: 18734401 (100.00%) were unpaired; of these: 2861988 (15.28%) aligned 0 times 11971071 (63.90%) aligned exactly 1 time 3901342 (20.82%) aligned >1 times 84.72% overall alignment rate Time searching: 00:06:15 Overall time: 00:06:15 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] 7934564 / 15872413 = 0.4999 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 23:49:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011081/SRX5011081.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011081/SRX5011081.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011081/SRX5011081.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011081/SRX5011081.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 23:49:32: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:49:32: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:49:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011081/SRX5011081.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011081/SRX5011081.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011081/SRX5011081.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011081/SRX5011081.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 23:49:33: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:49:33: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:49:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011081/SRX5011081.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011081/SRX5011081.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011081/SRX5011081.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011081/SRX5011081.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 23:49:34: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:49:34: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:49:40: 1000000 INFO @ Mon, 12 Aug 2019 23:49:40: 1000000 INFO @ Mon, 12 Aug 2019 23:49:41: 1000000 INFO @ Mon, 12 Aug 2019 23:49:47: 2000000 INFO @ Mon, 12 Aug 2019 23:49:48: 2000000 INFO @ Mon, 12 Aug 2019 23:49:48: 2000000 INFO @ Mon, 12 Aug 2019 23:49:54: 3000000 INFO @ Mon, 12 Aug 2019 23:49:55: 3000000 INFO @ Mon, 12 Aug 2019 23:49:55: 3000000 INFO @ Mon, 12 Aug 2019 23:50:02: 4000000 INFO @ Mon, 12 Aug 2019 23:50:02: 4000000 INFO @ Mon, 12 Aug 2019 23:50:03: 4000000 INFO @ Mon, 12 Aug 2019 23:50:09: 5000000 INFO @ Mon, 12 Aug 2019 23:50:09: 5000000 INFO @ Mon, 12 Aug 2019 23:50:10: 5000000 INFO @ Mon, 12 Aug 2019 23:50:17: 6000000 INFO @ Mon, 12 Aug 2019 23:50:17: 6000000 INFO @ Mon, 12 Aug 2019 23:50:18: 6000000 INFO @ Mon, 12 Aug 2019 23:50:24: 7000000 INFO @ Mon, 12 Aug 2019 23:50:24: 7000000 INFO @ Mon, 12 Aug 2019 23:50:26: 7000000 INFO @ Mon, 12 Aug 2019 23:50:31: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:50:31: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:50:31: #1 total tags in treatment: 7937849 INFO @ Mon, 12 Aug 2019 23:50:31: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:50:31: #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 23:50:31: #1 tags after filtering in treatment: 7937849 INFO @ Mon, 12 Aug 2019 23:50:31: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:50:31: #1 finished! INFO @ Mon, 12 Aug 2019 23:50:31: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:50:31: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:50:31: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:50:31: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:50:31: #1 total tags in treatment: 7937849 INFO @ Mon, 12 Aug 2019 23:50:31: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:50:31: #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 23:50:31: #1 tags after filtering in treatment: 7937849 INFO @ Mon, 12 Aug 2019 23:50:31: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:50:31: #1 finished! INFO @ Mon, 12 Aug 2019 23:50:31: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:50:31: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:50:32: #2 number of paired peaks: 2216 INFO @ Mon, 12 Aug 2019 23:50:32: start model_add_line... INFO @ Mon, 12 Aug 2019 23:50:32: start X-correlation... INFO @ Mon, 12 Aug 2019 23:50:32: end of X-cor INFO @ Mon, 12 Aug 2019 23:50:32: #2 finished! INFO @ Mon, 12 Aug 2019 23:50:32: #2 predicted fragment length is 110 bps INFO @ Mon, 12 Aug 2019 23:50:32: #2 alternative fragment length(s) may be 110 bps INFO @ Mon, 12 Aug 2019 23:50:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011081/SRX5011081.10_model.r INFO @ Mon, 12 Aug 2019 23:50:32: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:50:32: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:50:32: #2 number of paired peaks: 2216 INFO @ Mon, 12 Aug 2019 23:50:32: start model_add_line... INFO @ Mon, 12 Aug 2019 23:50:32: start X-correlation... INFO @ Mon, 12 Aug 2019 23:50:32: end of X-cor INFO @ Mon, 12 Aug 2019 23:50:32: #2 finished! INFO @ Mon, 12 Aug 2019 23:50:32: #2 predicted fragment length is 110 bps INFO @ Mon, 12 Aug 2019 23:50:32: #2 alternative fragment length(s) may be 110 bps INFO @ Mon, 12 Aug 2019 23:50:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011081/SRX5011081.20_model.r INFO @ Mon, 12 Aug 2019 23:50:32: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:50:32: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:50:34: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:50:34: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:50:34: #1 total tags in treatment: 7937849 INFO @ Mon, 12 Aug 2019 23:50:34: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:50:34: #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 23:50:34: #1 tags after filtering in treatment: 7937849 INFO @ Mon, 12 Aug 2019 23:50:34: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:50:34: #1 finished! INFO @ Mon, 12 Aug 2019 23:50:34: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:50:34: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:50:35: #2 number of paired peaks: 2216 INFO @ Mon, 12 Aug 2019 23:50:35: start model_add_line... INFO @ Mon, 12 Aug 2019 23:50:35: start X-correlation... INFO @ Mon, 12 Aug 2019 23:50:35: end of X-cor INFO @ Mon, 12 Aug 2019 23:50:35: #2 finished! INFO @ Mon, 12 Aug 2019 23:50:35: #2 predicted fragment length is 110 bps INFO @ Mon, 12 Aug 2019 23:50:35: #2 alternative fragment length(s) may be 110 bps INFO @ Mon, 12 Aug 2019 23:50:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011081/SRX5011081.05_model.r INFO @ Mon, 12 Aug 2019 23:50:35: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:50:35: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:50:56: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:50:56: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:50:59: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:51:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011081/SRX5011081.10_peaks.xls INFO @ Mon, 12 Aug 2019 23:51:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011081/SRX5011081.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:51:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011081/SRX5011081.10_summits.bed INFO @ Mon, 12 Aug 2019 23:51:07: Done! INFO @ Mon, 12 Aug 2019 23:51:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011081/SRX5011081.20_peaks.xls INFO @ Mon, 12 Aug 2019 23:51:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011081/SRX5011081.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:51:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011081/SRX5011081.20_summits.bed INFO @ Mon, 12 Aug 2019 23:51:07: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (4823 records, 4 fields): 13 millis CompletedMACS2peakCalling pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (2374 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:51:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011081/SRX5011081.05_peaks.xls INFO @ Mon, 12 Aug 2019 23:51:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011081/SRX5011081.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:51:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011081/SRX5011081.05_summits.bed INFO @ Mon, 12 Aug 2019 23:51:11: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (8110 records, 4 fields): 14 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。