Job ID = 1294110 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 9,135,726 reads read : 9,135,726 reads written : 9,135,726 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: 00:03:45 9135726 reads; of these: 9135726 (100.00%) were unpaired; of these: 288372 (3.16%) aligned 0 times 5186275 (56.77%) aligned exactly 1 time 3661079 (40.07%) aligned >1 times 96.84% overall alignment rate Time searching: 00:03:45 Overall time: 00:03:45 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] 2657940 / 8847354 = 0.3004 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 04:59:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX187080/SRX187080.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX187080/SRX187080.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX187080/SRX187080.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX187080/SRX187080.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 04:59:07: #1 read tag files... INFO @ Mon, 03 Jun 2019 04:59:07: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 04:59:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX187080/SRX187080.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX187080/SRX187080.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX187080/SRX187080.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX187080/SRX187080.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 04:59:07: #1 read tag files... INFO @ Mon, 03 Jun 2019 04:59:07: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 04:59:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX187080/SRX187080.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX187080/SRX187080.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX187080/SRX187080.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX187080/SRX187080.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 04:59:07: #1 read tag files... INFO @ Mon, 03 Jun 2019 04:59:07: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 04:59:14: 1000000 INFO @ Mon, 03 Jun 2019 04:59:16: 1000000 INFO @ Mon, 03 Jun 2019 04:59:16: 1000000 INFO @ Mon, 03 Jun 2019 04:59:21: 2000000 INFO @ Mon, 03 Jun 2019 04:59:24: 2000000 INFO @ Mon, 03 Jun 2019 04:59:25: 2000000 INFO @ Mon, 03 Jun 2019 04:59:29: 3000000 INFO @ Mon, 03 Jun 2019 04:59:33: 3000000 INFO @ Mon, 03 Jun 2019 04:59:34: 3000000 INFO @ Mon, 03 Jun 2019 04:59:37: 4000000 INFO @ Mon, 03 Jun 2019 04:59:41: 4000000 INFO @ Mon, 03 Jun 2019 04:59:43: 4000000 INFO @ Mon, 03 Jun 2019 04:59:44: 5000000 INFO @ Mon, 03 Jun 2019 04:59:49: 5000000 INFO @ Mon, 03 Jun 2019 04:59:51: 6000000 INFO @ Mon, 03 Jun 2019 04:59:52: 5000000 INFO @ Mon, 03 Jun 2019 04:59:52: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 04:59:52: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 04:59:52: #1 total tags in treatment: 6189414 INFO @ Mon, 03 Jun 2019 04:59:52: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 04:59:52: #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 04:59:52: #1 tags after filtering in treatment: 6189414 INFO @ Mon, 03 Jun 2019 04:59:52: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 04:59:52: #1 finished! INFO @ Mon, 03 Jun 2019 04:59:52: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 04:59:52: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 04:59:53: #2 number of paired peaks: 1881 INFO @ Mon, 03 Jun 2019 04:59:53: start model_add_line... INFO @ Mon, 03 Jun 2019 04:59:53: start X-correlation... INFO @ Mon, 03 Jun 2019 04:59:53: end of X-cor INFO @ Mon, 03 Jun 2019 04:59:53: #2 finished! INFO @ Mon, 03 Jun 2019 04:59:53: #2 predicted fragment length is 86 bps INFO @ Mon, 03 Jun 2019 04:59:53: #2 alternative fragment length(s) may be 86 bps INFO @ Mon, 03 Jun 2019 04:59:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX187080/SRX187080.20_model.r INFO @ Mon, 03 Jun 2019 04:59:53: #3 Call peaks... INFO @ Mon, 03 Jun 2019 04:59:53: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 04:59:58: 6000000 INFO @ Mon, 03 Jun 2019 04:59:59: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 04:59:59: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 04:59:59: #1 total tags in treatment: 6189414 INFO @ Mon, 03 Jun 2019 04:59:59: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 04:59:59: #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 04:59:59: #1 tags after filtering in treatment: 6189414 INFO @ Mon, 03 Jun 2019 04:59:59: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 04:59:59: #1 finished! INFO @ Mon, 03 Jun 2019 04:59:59: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 04:59:59: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:00:00: #2 number of paired peaks: 1881 INFO @ Mon, 03 Jun 2019 05:00:00: start model_add_line... INFO @ Mon, 03 Jun 2019 05:00:00: 6000000 INFO @ Mon, 03 Jun 2019 05:00:00: start X-correlation... INFO @ Mon, 03 Jun 2019 05:00:00: end of X-cor INFO @ Mon, 03 Jun 2019 05:00:00: #2 finished! INFO @ Mon, 03 Jun 2019 05:00:00: #2 predicted fragment length is 86 bps INFO @ Mon, 03 Jun 2019 05:00:00: #2 alternative fragment length(s) may be 86 bps INFO @ Mon, 03 Jun 2019 05:00:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX187080/SRX187080.05_model.r INFO @ Mon, 03 Jun 2019 05:00:00: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:00:00: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:00:02: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 05:00:02: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 05:00:02: #1 total tags in treatment: 6189414 INFO @ Mon, 03 Jun 2019 05:00:02: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:00:02: #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 05:00:02: #1 tags after filtering in treatment: 6189414 INFO @ Mon, 03 Jun 2019 05:00:02: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:00:02: #1 finished! INFO @ Mon, 03 Jun 2019 05:00:02: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:00:02: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:00:02: #2 number of paired peaks: 1881 INFO @ Mon, 03 Jun 2019 05:00:02: start model_add_line... INFO @ Mon, 03 Jun 2019 05:00:03: start X-correlation... INFO @ Mon, 03 Jun 2019 05:00:03: end of X-cor INFO @ Mon, 03 Jun 2019 05:00:03: #2 finished! INFO @ Mon, 03 Jun 2019 05:00:03: #2 predicted fragment length is 86 bps INFO @ Mon, 03 Jun 2019 05:00:03: #2 alternative fragment length(s) may be 86 bps INFO @ Mon, 03 Jun 2019 05:00:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX187080/SRX187080.10_model.r INFO @ Mon, 03 Jun 2019 05:00:03: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:00:03: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:00:12: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:00:19: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:00:21: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:00:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX187080/SRX187080.20_peaks.xls INFO @ Mon, 03 Jun 2019 05:00:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX187080/SRX187080.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:00:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX187080/SRX187080.20_summits.bed INFO @ Mon, 03 Jun 2019 05:00:22: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (1458 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 05:00:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX187080/SRX187080.05_peaks.xls INFO @ Mon, 03 Jun 2019 05:00:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX187080/SRX187080.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:00:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX187080/SRX187080.05_summits.bed INFO @ Mon, 03 Jun 2019 05:00:29: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (10362 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 05:00:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX187080/SRX187080.10_peaks.xls INFO @ Mon, 03 Jun 2019 05:00:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX187080/SRX187080.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:00:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX187080/SRX187080.10_summits.bed INFO @ Mon, 03 Jun 2019 05:00:31: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4382 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。