Job ID = 2590857 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 22,403,332 reads read : 22,403,332 reads written : 22,403,332 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: 00:05:12 22403332 reads; of these: 22403332 (100.00%) were unpaired; of these: 11432142 (51.03%) aligned 0 times 8554831 (38.19%) aligned exactly 1 time 2416359 (10.79%) aligned >1 times 48.97% overall alignment rate Time searching: 00:05:12 Overall time: 00:05:12 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] 3540953 / 10971190 = 0.3228 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 23:53:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011091/SRX5011091.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011091/SRX5011091.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011091/SRX5011091.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011091/SRX5011091.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 23:53:00: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:53:00: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:53:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011091/SRX5011091.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011091/SRX5011091.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011091/SRX5011091.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011091/SRX5011091.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 23:53:01: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:53:01: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:53:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011091/SRX5011091.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011091/SRX5011091.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011091/SRX5011091.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011091/SRX5011091.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 23:53:02: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:53:02: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:53:08: 1000000 INFO @ Mon, 12 Aug 2019 23:53:09: 1000000 INFO @ Mon, 12 Aug 2019 23:53:11: 1000000 INFO @ Mon, 12 Aug 2019 23:53:17: 2000000 INFO @ Mon, 12 Aug 2019 23:53:18: 2000000 INFO @ Mon, 12 Aug 2019 23:53:19: 2000000 INFO @ Mon, 12 Aug 2019 23:53:25: 3000000 INFO @ Mon, 12 Aug 2019 23:53:26: 3000000 INFO @ Mon, 12 Aug 2019 23:53:28: 3000000 INFO @ Mon, 12 Aug 2019 23:53:34: 4000000 INFO @ Mon, 12 Aug 2019 23:53:35: 4000000 INFO @ Mon, 12 Aug 2019 23:53:36: 4000000 INFO @ Mon, 12 Aug 2019 23:53:42: 5000000 INFO @ Mon, 12 Aug 2019 23:53:43: 5000000 INFO @ Mon, 12 Aug 2019 23:53:44: 5000000 INFO @ Mon, 12 Aug 2019 23:53:51: 6000000 INFO @ Mon, 12 Aug 2019 23:53:51: 6000000 INFO @ Mon, 12 Aug 2019 23:53:53: 6000000 INFO @ Mon, 12 Aug 2019 23:53:59: 7000000 INFO @ Mon, 12 Aug 2019 23:53:59: 7000000 INFO @ Mon, 12 Aug 2019 23:54:01: 7000000 INFO @ Mon, 12 Aug 2019 23:54:02: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:54:02: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:54:02: #1 total tags in treatment: 7430237 INFO @ Mon, 12 Aug 2019 23:54:02: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:54:02: #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 23:54:02: #1 tags after filtering in treatment: 7430237 INFO @ Mon, 12 Aug 2019 23:54:02: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:54:02: #1 finished! INFO @ Mon, 12 Aug 2019 23:54:02: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:54:02: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:54:03: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:54:03: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:54:03: #1 total tags in treatment: 7430237 INFO @ Mon, 12 Aug 2019 23:54:03: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:54:03: #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 23:54:03: #1 tags after filtering in treatment: 7430237 INFO @ Mon, 12 Aug 2019 23:54:03: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:54:03: #1 finished! INFO @ Mon, 12 Aug 2019 23:54:03: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:54:03: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:54:03: #2 number of paired peaks: 3479 INFO @ Mon, 12 Aug 2019 23:54:03: start model_add_line... INFO @ Mon, 12 Aug 2019 23:54:04: start X-correlation... INFO @ Mon, 12 Aug 2019 23:54:04: end of X-cor INFO @ Mon, 12 Aug 2019 23:54:04: #2 finished! INFO @ Mon, 12 Aug 2019 23:54:04: #2 predicted fragment length is 182 bps INFO @ Mon, 12 Aug 2019 23:54:04: #2 alternative fragment length(s) may be 182 bps INFO @ Mon, 12 Aug 2019 23:54:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011091/SRX5011091.05_model.r INFO @ Mon, 12 Aug 2019 23:54:04: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:54:04: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:54:04: #2 number of paired peaks: 3479 INFO @ Mon, 12 Aug 2019 23:54:04: start model_add_line... INFO @ Mon, 12 Aug 2019 23:54:04: start X-correlation... INFO @ Mon, 12 Aug 2019 23:54:04: end of X-cor INFO @ Mon, 12 Aug 2019 23:54:04: #2 finished! INFO @ Mon, 12 Aug 2019 23:54:04: #2 predicted fragment length is 182 bps INFO @ Mon, 12 Aug 2019 23:54:04: #2 alternative fragment length(s) may be 182 bps INFO @ Mon, 12 Aug 2019 23:54:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011091/SRX5011091.10_model.r INFO @ Mon, 12 Aug 2019 23:54:04: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:54:04: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:54:04: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:54:04: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:54:04: #1 total tags in treatment: 7430237 INFO @ Mon, 12 Aug 2019 23:54:04: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:54:04: #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 23:54:05: #1 tags after filtering in treatment: 7430237 INFO @ Mon, 12 Aug 2019 23:54:05: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:54:05: #1 finished! INFO @ Mon, 12 Aug 2019 23:54:05: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:54:05: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:54:06: #2 number of paired peaks: 3479 INFO @ Mon, 12 Aug 2019 23:54:06: start model_add_line... INFO @ Mon, 12 Aug 2019 23:54:06: start X-correlation... INFO @ Mon, 12 Aug 2019 23:54:06: end of X-cor INFO @ Mon, 12 Aug 2019 23:54:06: #2 finished! INFO @ Mon, 12 Aug 2019 23:54:06: #2 predicted fragment length is 182 bps INFO @ Mon, 12 Aug 2019 23:54:06: #2 alternative fragment length(s) may be 182 bps INFO @ Mon, 12 Aug 2019 23:54:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011091/SRX5011091.20_model.r INFO @ Mon, 12 Aug 2019 23:54:06: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:54:06: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:54:28: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:54:28: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:54:30: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:54:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011091/SRX5011091.05_peaks.xls INFO @ Mon, 12 Aug 2019 23:54:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011091/SRX5011091.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:54:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011091/SRX5011091.05_summits.bed INFO @ Mon, 12 Aug 2019 23:54:39: Done! INFO @ Mon, 12 Aug 2019 23:54:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011091/SRX5011091.10_peaks.xls pass1 - making usageList (14 chroms): 5 millis pass2 - checking and writing primary data (10049 records, 4 fields): 15 millis INFO @ Mon, 12 Aug 2019 23:54:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011091/SRX5011091.10_peaks.narrowPeak CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:54:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011091/SRX5011091.10_summits.bed INFO @ Mon, 12 Aug 2019 23:54:40: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (6769 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:54:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011091/SRX5011091.20_peaks.xls INFO @ Mon, 12 Aug 2019 23:54:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011091/SRX5011091.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:54:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011091/SRX5011091.20_summits.bed INFO @ Mon, 12 Aug 2019 23:54:41: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (3828 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。