Job ID = 1294140 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 35,816,233 reads read : 35,816,233 reads written : 35,816,233 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: 00:10:27 35816233 reads; of these: 35816233 (100.00%) were unpaired; of these: 1235634 (3.45%) aligned 0 times 28730932 (80.22%) aligned exactly 1 time 5849667 (16.33%) aligned >1 times 96.55% overall alignment rate Time searching: 00:10:27 Overall time: 00:10:27 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 16 files... [bam_rmdupse_core] 13162282 / 34580599 = 0.3806 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 05:23:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX193318/SRX193318.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX193318/SRX193318.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX193318/SRX193318.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX193318/SRX193318.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 05:23:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX193318/SRX193318.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX193318/SRX193318.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX193318/SRX193318.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX193318/SRX193318.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 05:23:39: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:23:39: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:23:39: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:23:39: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:23:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX193318/SRX193318.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX193318/SRX193318.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX193318/SRX193318.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX193318/SRX193318.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 05:23:39: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:23:39: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:23:49: 1000000 INFO @ Mon, 03 Jun 2019 05:23:49: 1000000 INFO @ Mon, 03 Jun 2019 05:23:49: 1000000 INFO @ Mon, 03 Jun 2019 05:23:58: 2000000 INFO @ Mon, 03 Jun 2019 05:23:58: 2000000 INFO @ Mon, 03 Jun 2019 05:23:58: 2000000 INFO @ Mon, 03 Jun 2019 05:24:07: 3000000 INFO @ Mon, 03 Jun 2019 05:24:07: 3000000 INFO @ Mon, 03 Jun 2019 05:24:07: 3000000 INFO @ Mon, 03 Jun 2019 05:24:17: 4000000 INFO @ Mon, 03 Jun 2019 05:24:17: 4000000 INFO @ Mon, 03 Jun 2019 05:24:18: 4000000 INFO @ Mon, 03 Jun 2019 05:24:27: 5000000 INFO @ Mon, 03 Jun 2019 05:24:27: 5000000 INFO @ Mon, 03 Jun 2019 05:24:28: 5000000 INFO @ Mon, 03 Jun 2019 05:24:37: 6000000 INFO @ Mon, 03 Jun 2019 05:24:37: 6000000 INFO @ Mon, 03 Jun 2019 05:24:38: 6000000 INFO @ Mon, 03 Jun 2019 05:24:47: 7000000 INFO @ Mon, 03 Jun 2019 05:24:47: 7000000 INFO @ Mon, 03 Jun 2019 05:24:48: 7000000 INFO @ Mon, 03 Jun 2019 05:24:57: 8000000 INFO @ Mon, 03 Jun 2019 05:24:57: 8000000 INFO @ Mon, 03 Jun 2019 05:24:58: 8000000 INFO @ Mon, 03 Jun 2019 05:25:07: 9000000 INFO @ Mon, 03 Jun 2019 05:25:07: 9000000 INFO @ Mon, 03 Jun 2019 05:25:08: 9000000 INFO @ Mon, 03 Jun 2019 05:25:17: 10000000 INFO @ Mon, 03 Jun 2019 05:25:17: 10000000 INFO @ Mon, 03 Jun 2019 05:25:18: 10000000 INFO @ Mon, 03 Jun 2019 05:25:27: 11000000 INFO @ Mon, 03 Jun 2019 05:25:27: 11000000 INFO @ Mon, 03 Jun 2019 05:25:28: 11000000 INFO @ Mon, 03 Jun 2019 05:25:37: 12000000 INFO @ Mon, 03 Jun 2019 05:25:37: 12000000 INFO @ Mon, 03 Jun 2019 05:25:37: 12000000 INFO @ Mon, 03 Jun 2019 05:25:47: 13000000 INFO @ Mon, 03 Jun 2019 05:25:47: 13000000 INFO @ Mon, 03 Jun 2019 05:25:48: 13000000 INFO @ Mon, 03 Jun 2019 05:25:56: 14000000 INFO @ Mon, 03 Jun 2019 05:25:56: 14000000 INFO @ Mon, 03 Jun 2019 05:25:58: 14000000 INFO @ Mon, 03 Jun 2019 05:26:05: 15000000 INFO @ Mon, 03 Jun 2019 05:26:05: 15000000 INFO @ Mon, 03 Jun 2019 05:26:08: 15000000 INFO @ Mon, 03 Jun 2019 05:26:14: 16000000 INFO @ Mon, 03 Jun 2019 05:26:14: 16000000 INFO @ Mon, 03 Jun 2019 05:26:17: 16000000 INFO @ Mon, 03 Jun 2019 05:26:23: 17000000 INFO @ Mon, 03 Jun 2019 05:26:23: 17000000 INFO @ Mon, 03 Jun 2019 05:26:26: 17000000 INFO @ Mon, 03 Jun 2019 05:26:32: 18000000 INFO @ Mon, 03 Jun 2019 05:26:32: 18000000 INFO @ Mon, 03 Jun 2019 05:26:35: 18000000 INFO @ Mon, 03 Jun 2019 05:26:41: 19000000 INFO @ Mon, 03 Jun 2019 05:26:42: 19000000 INFO @ Mon, 03 Jun 2019 05:26:44: 19000000 INFO @ Mon, 03 Jun 2019 05:26:50: 20000000 INFO @ Mon, 03 Jun 2019 05:26:50: 20000000 INFO @ Mon, 03 Jun 2019 05:26:53: 20000000 INFO @ Mon, 03 Jun 2019 05:26:59: 21000000 INFO @ Mon, 03 Jun 2019 05:26:59: 21000000 INFO @ Mon, 03 Jun 2019 05:27:02: 21000000 INFO @ Mon, 03 Jun 2019 05:27:03: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 05:27:03: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 05:27:03: #1 total tags in treatment: 21418317 INFO @ Mon, 03 Jun 2019 05:27:03: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:27:03: #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 05:27:03: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 05:27:03: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 05:27:03: #1 total tags in treatment: 21418317 INFO @ Mon, 03 Jun 2019 05:27:03: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:27:03: #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 05:27:04: #1 tags after filtering in treatment: 21418317 INFO @ Mon, 03 Jun 2019 05:27:04: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:27:04: #1 finished! INFO @ Mon, 03 Jun 2019 05:27:04: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:27:04: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:27:04: #1 tags after filtering in treatment: 21418317 INFO @ Mon, 03 Jun 2019 05:27:04: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:27:04: #1 finished! INFO @ Mon, 03 Jun 2019 05:27:04: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:27:04: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:27:05: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 05:27:05: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 05:27:05: #1 total tags in treatment: 21418317 INFO @ Mon, 03 Jun 2019 05:27:05: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:27:05: #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 05:27:06: #1 tags after filtering in treatment: 21418317 INFO @ Mon, 03 Jun 2019 05:27:06: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:27:06: #1 finished! INFO @ Mon, 03 Jun 2019 05:27:06: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:27:06: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:27:07: #2 number of paired peaks: 10656 INFO @ Mon, 03 Jun 2019 05:27:07: start model_add_line... INFO @ Mon, 03 Jun 2019 05:27:07: #2 number of paired peaks: 10656 INFO @ Mon, 03 Jun 2019 05:27:07: start model_add_line... INFO @ Mon, 03 Jun 2019 05:27:07: start X-correlation... INFO @ Mon, 03 Jun 2019 05:27:07: end of X-cor INFO @ Mon, 03 Jun 2019 05:27:07: #2 finished! INFO @ Mon, 03 Jun 2019 05:27:07: #2 predicted fragment length is 149 bps INFO @ Mon, 03 Jun 2019 05:27:07: #2 alternative fragment length(s) may be 4,149 bps INFO @ Mon, 03 Jun 2019 05:27:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX193318/SRX193318.05_model.r INFO @ Mon, 03 Jun 2019 05:27:07: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:27:07: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:27:07: start X-correlation... INFO @ Mon, 03 Jun 2019 05:27:07: end of X-cor INFO @ Mon, 03 Jun 2019 05:27:07: #2 finished! INFO @ Mon, 03 Jun 2019 05:27:07: #2 predicted fragment length is 149 bps INFO @ Mon, 03 Jun 2019 05:27:07: #2 alternative fragment length(s) may be 4,149 bps INFO @ Mon, 03 Jun 2019 05:27:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX193318/SRX193318.10_model.r INFO @ Mon, 03 Jun 2019 05:27:07: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:27:07: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:27:09: #2 number of paired peaks: 10656 INFO @ Mon, 03 Jun 2019 05:27:09: start model_add_line... INFO @ Mon, 03 Jun 2019 05:27:10: start X-correlation... INFO @ Mon, 03 Jun 2019 05:27:10: end of X-cor INFO @ Mon, 03 Jun 2019 05:27:10: #2 finished! INFO @ Mon, 03 Jun 2019 05:27:10: #2 predicted fragment length is 149 bps INFO @ Mon, 03 Jun 2019 05:27:10: #2 alternative fragment length(s) may be 4,149 bps INFO @ Mon, 03 Jun 2019 05:27:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX193318/SRX193318.20_model.r INFO @ Mon, 03 Jun 2019 05:27:10: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:27:10: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:28:15: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:28:15: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:28:17: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 03 Jun 2019 05:28:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX193318/SRX193318.05_peaks.xls INFO @ Mon, 03 Jun 2019 05:28:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX193318/SRX193318.10_peaks.xls INFO @ Mon, 03 Jun 2019 05:28:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX193318/SRX193318.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:28:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX193318/SRX193318.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:28:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX193318/SRX193318.05_summits.bed INFO @ Mon, 03 Jun 2019 05:28:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX193318/SRX193318.10_summits.bed INFO @ Mon, 03 Jun 2019 05:28:38: Done! INFO @ Mon, 03 Jun 2019 05:28:38: Done! pass1 - making usageList (14 chroms): 4 millis pass1 - making usageList (14 chroms): 4 millis pass2 - checking and writing primary data (11972 records, 4 fields): 17 millis pass2 - checking and writing primary data (14591 records, 4 fields): 21 millis CompletedMACS2peakCalling CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 05:28:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX193318/SRX193318.20_peaks.xls INFO @ Mon, 03 Jun 2019 05:28:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX193318/SRX193318.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:28:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX193318/SRX193318.20_summits.bed INFO @ Mon, 03 Jun 2019 05:28:40: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (8233 records, 4 fields): 12 millis CompletedMACS2peakCalling BigWig に変換しました。