Job ID = 2590272 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 6,073,606 reads read : 6,073,606 reads written : 6,073,606 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR504794.sra.cache’: 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: 00:01:42 6073606 reads; of these: 6073606 (100.00%) were unpaired; of these: 330237 (5.44%) aligned 0 times 4371630 (71.98%) aligned exactly 1 time 1371739 (22.59%) aligned >1 times 94.56% overall alignment rate Time searching: 00:01:42 Overall time: 00:01:42 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_rmdupse_core] 634879 / 5743369 = 0.1105 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 20:24:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX151960/SRX151960.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX151960/SRX151960.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX151960/SRX151960.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX151960/SRX151960.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 20:24:21: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:24:21: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:24:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX151960/SRX151960.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX151960/SRX151960.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX151960/SRX151960.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX151960/SRX151960.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 20:24:22: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:24:22: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:24:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX151960/SRX151960.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX151960/SRX151960.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX151960/SRX151960.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX151960/SRX151960.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 20:24:23: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:24:23: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:24:29: 1000000 INFO @ Mon, 12 Aug 2019 20:24:30: 1000000 INFO @ Mon, 12 Aug 2019 20:24:30: 1000000 INFO @ Mon, 12 Aug 2019 20:24:36: 2000000 INFO @ Mon, 12 Aug 2019 20:24:38: 2000000 INFO @ Mon, 12 Aug 2019 20:24:39: 2000000 INFO @ Mon, 12 Aug 2019 20:24:43: 3000000 INFO @ Mon, 12 Aug 2019 20:24:46: 3000000 INFO @ Mon, 12 Aug 2019 20:24:47: 3000000 INFO @ Mon, 12 Aug 2019 20:24:50: 4000000 INFO @ Mon, 12 Aug 2019 20:24:55: 4000000 INFO @ Mon, 12 Aug 2019 20:24:56: 4000000 INFO @ Mon, 12 Aug 2019 20:24:56: 5000000 INFO @ Mon, 12 Aug 2019 20:24:57: #1 tag size is determined as 30 bps INFO @ Mon, 12 Aug 2019 20:24:57: #1 tag size = 30 INFO @ Mon, 12 Aug 2019 20:24:57: #1 total tags in treatment: 5108490 INFO @ Mon, 12 Aug 2019 20:24:57: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:24:57: #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 20:24:57: #1 tags after filtering in treatment: 5108490 INFO @ Mon, 12 Aug 2019 20:24:57: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:24:57: #1 finished! INFO @ Mon, 12 Aug 2019 20:24:57: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:24:57: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:24:58: #2 number of paired peaks: 4001 INFO @ Mon, 12 Aug 2019 20:24:58: start model_add_line... INFO @ Mon, 12 Aug 2019 20:24:58: start X-correlation... INFO @ Mon, 12 Aug 2019 20:24:58: end of X-cor INFO @ Mon, 12 Aug 2019 20:24:58: #2 finished! INFO @ Mon, 12 Aug 2019 20:24:58: #2 predicted fragment length is 122 bps INFO @ Mon, 12 Aug 2019 20:24:58: #2 alternative fragment length(s) may be 122 bps INFO @ Mon, 12 Aug 2019 20:24:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX151960/SRX151960.20_model.r INFO @ Mon, 12 Aug 2019 20:24:58: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:24:58: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:25:03: 5000000 INFO @ Mon, 12 Aug 2019 20:25:04: 5000000 INFO @ Mon, 12 Aug 2019 20:25:04: #1 tag size is determined as 30 bps INFO @ Mon, 12 Aug 2019 20:25:04: #1 tag size = 30 INFO @ Mon, 12 Aug 2019 20:25:04: #1 total tags in treatment: 5108490 INFO @ Mon, 12 Aug 2019 20:25:04: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:25:04: #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 20:25:04: #1 tags after filtering in treatment: 5108490 INFO @ Mon, 12 Aug 2019 20:25:04: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:25:04: #1 finished! INFO @ Mon, 12 Aug 2019 20:25:04: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:25:04: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:25:05: #1 tag size is determined as 30 bps INFO @ Mon, 12 Aug 2019 20:25:05: #1 tag size = 30 INFO @ Mon, 12 Aug 2019 20:25:05: #1 total tags in treatment: 5108490 INFO @ Mon, 12 Aug 2019 20:25:05: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:25:05: #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 20:25:05: #2 number of paired peaks: 4001 INFO @ Mon, 12 Aug 2019 20:25:05: start model_add_line... INFO @ Mon, 12 Aug 2019 20:25:05: #1 tags after filtering in treatment: 5108490 INFO @ Mon, 12 Aug 2019 20:25:05: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:25:05: #1 finished! INFO @ Mon, 12 Aug 2019 20:25:05: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:25:05: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:25:05: start X-correlation... INFO @ Mon, 12 Aug 2019 20:25:05: end of X-cor INFO @ Mon, 12 Aug 2019 20:25:05: #2 finished! INFO @ Mon, 12 Aug 2019 20:25:05: #2 predicted fragment length is 122 bps INFO @ Mon, 12 Aug 2019 20:25:05: #2 alternative fragment length(s) may be 122 bps INFO @ Mon, 12 Aug 2019 20:25:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX151960/SRX151960.05_model.r INFO @ Mon, 12 Aug 2019 20:25:05: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:25:05: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:25:05: #2 number of paired peaks: 4001 INFO @ Mon, 12 Aug 2019 20:25:05: start model_add_line... INFO @ Mon, 12 Aug 2019 20:25:06: start X-correlation... INFO @ Mon, 12 Aug 2019 20:25:06: end of X-cor INFO @ Mon, 12 Aug 2019 20:25:06: #2 finished! INFO @ Mon, 12 Aug 2019 20:25:06: #2 predicted fragment length is 122 bps INFO @ Mon, 12 Aug 2019 20:25:06: #2 alternative fragment length(s) may be 122 bps INFO @ Mon, 12 Aug 2019 20:25:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX151960/SRX151960.10_model.r INFO @ Mon, 12 Aug 2019 20:25:06: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:25:06: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:25:15: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:25:22: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:25:23: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:25:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX151960/SRX151960.20_peaks.xls INFO @ Mon, 12 Aug 2019 20:25:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX151960/SRX151960.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:25:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX151960/SRX151960.20_summits.bed INFO @ Mon, 12 Aug 2019 20:25:24: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (3331 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 20:25:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX151960/SRX151960.05_peaks.xls INFO @ Mon, 12 Aug 2019 20:25:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX151960/SRX151960.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:25:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX151960/SRX151960.05_summits.bed INFO @ Mon, 12 Aug 2019 20:25:31: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (7142 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 20:25:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX151960/SRX151960.10_peaks.xls INFO @ Mon, 12 Aug 2019 20:25:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX151960/SRX151960.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:25:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX151960/SRX151960.10_summits.bed INFO @ Mon, 12 Aug 2019 20:25:32: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (5213 records, 4 fields): 10 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。