Job ID = 1294221 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 49,307,721 reads read : 49,307,721 reads written : 49,307,721 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: 00:14:27 49307721 reads; of these: 49307721 (100.00%) were unpaired; of these: 1741549 (3.53%) aligned 0 times 38070361 (77.21%) aligned exactly 1 time 9495811 (19.26%) aligned >1 times 96.47% overall alignment rate Time searching: 00:14:27 Overall time: 00:14:27 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 20 files... [bam_rmdupse_core] 27649663 / 47566172 = 0.5813 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 06:01:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX201898/SRX201898.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX201898/SRX201898.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX201898/SRX201898.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX201898/SRX201898.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 06:01:56: #1 read tag files... INFO @ Mon, 03 Jun 2019 06:01:56: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 06:01:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX201898/SRX201898.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX201898/SRX201898.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX201898/SRX201898.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX201898/SRX201898.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 06:01:56: #1 read tag files... INFO @ Mon, 03 Jun 2019 06:01:56: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 06:01:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX201898/SRX201898.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX201898/SRX201898.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX201898/SRX201898.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX201898/SRX201898.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 06:01:56: #1 read tag files... INFO @ Mon, 03 Jun 2019 06:01:56: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 06:02:04: 1000000 INFO @ Mon, 03 Jun 2019 06:02:04: 1000000 INFO @ Mon, 03 Jun 2019 06:02:06: 1000000 INFO @ Mon, 03 Jun 2019 06:02:11: 2000000 INFO @ Mon, 03 Jun 2019 06:02:11: 2000000 INFO @ Mon, 03 Jun 2019 06:02:15: 2000000 INFO @ Mon, 03 Jun 2019 06:02:17: 3000000 INFO @ Mon, 03 Jun 2019 06:02:18: 3000000 INFO @ Mon, 03 Jun 2019 06:02:24: 3000000 INFO @ Mon, 03 Jun 2019 06:02:24: 4000000 INFO @ Mon, 03 Jun 2019 06:02:25: 4000000 INFO @ Mon, 03 Jun 2019 06:02:31: 5000000 INFO @ Mon, 03 Jun 2019 06:02:32: 5000000 INFO @ Mon, 03 Jun 2019 06:02:32: 4000000 INFO @ Mon, 03 Jun 2019 06:02:38: 6000000 INFO @ Mon, 03 Jun 2019 06:02:39: 6000000 INFO @ Mon, 03 Jun 2019 06:02:41: 5000000 INFO @ Mon, 03 Jun 2019 06:02:45: 7000000 INFO @ Mon, 03 Jun 2019 06:02:46: 7000000 INFO @ Mon, 03 Jun 2019 06:02:50: 6000000 INFO @ Mon, 03 Jun 2019 06:02:52: 8000000 INFO @ Mon, 03 Jun 2019 06:02:54: 8000000 INFO @ Mon, 03 Jun 2019 06:02:59: 9000000 INFO @ Mon, 03 Jun 2019 06:03:00: 7000000 INFO @ Mon, 03 Jun 2019 06:03:01: 9000000 INFO @ Mon, 03 Jun 2019 06:03:06: 10000000 INFO @ Mon, 03 Jun 2019 06:03:09: 10000000 INFO @ Mon, 03 Jun 2019 06:03:09: 8000000 INFO @ Mon, 03 Jun 2019 06:03:13: 11000000 INFO @ Mon, 03 Jun 2019 06:03:16: 11000000 INFO @ Mon, 03 Jun 2019 06:03:19: 9000000 INFO @ Mon, 03 Jun 2019 06:03:20: 12000000 INFO @ Mon, 03 Jun 2019 06:03:23: 12000000 INFO @ Mon, 03 Jun 2019 06:03:27: 13000000 INFO @ Mon, 03 Jun 2019 06:03:28: 10000000 INFO @ Mon, 03 Jun 2019 06:03:31: 13000000 INFO @ Mon, 03 Jun 2019 06:03:34: 14000000 INFO @ Mon, 03 Jun 2019 06:03:37: 11000000 INFO @ Mon, 03 Jun 2019 06:03:38: 14000000 INFO @ Mon, 03 Jun 2019 06:03:40: 15000000 INFO @ Mon, 03 Jun 2019 06:03:45: 15000000 INFO @ Mon, 03 Jun 2019 06:03:47: 12000000 INFO @ Mon, 03 Jun 2019 06:03:47: 16000000 INFO @ Mon, 03 Jun 2019 06:03:53: 16000000 INFO @ Mon, 03 Jun 2019 06:03:54: 17000000 INFO @ Mon, 03 Jun 2019 06:03:56: 13000000 INFO @ Mon, 03 Jun 2019 06:04:00: 17000000 INFO @ Mon, 03 Jun 2019 06:04:01: 18000000 INFO @ Mon, 03 Jun 2019 06:04:05: 14000000 INFO @ Mon, 03 Jun 2019 06:04:07: 18000000 INFO @ Mon, 03 Jun 2019 06:04:08: 19000000 INFO @ Mon, 03 Jun 2019 06:04:14: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 06:04:14: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 06:04:14: #1 total tags in treatment: 19916509 INFO @ Mon, 03 Jun 2019 06:04:14: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 06:04:14: #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 06:04:14: 15000000 INFO @ Mon, 03 Jun 2019 06:04:14: 19000000 INFO @ Mon, 03 Jun 2019 06:04:15: #1 tags after filtering in treatment: 19916509 INFO @ Mon, 03 Jun 2019 06:04:15: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 06:04:15: #1 finished! INFO @ Mon, 03 Jun 2019 06:04:15: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 06:04:15: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 06:04:17: #2 number of paired peaks: 5660 INFO @ Mon, 03 Jun 2019 06:04:17: start model_add_line... INFO @ Mon, 03 Jun 2019 06:04:18: start X-correlation... INFO @ Mon, 03 Jun 2019 06:04:18: end of X-cor INFO @ Mon, 03 Jun 2019 06:04:18: #2 finished! INFO @ Mon, 03 Jun 2019 06:04:18: #2 predicted fragment length is 205 bps INFO @ Mon, 03 Jun 2019 06:04:18: #2 alternative fragment length(s) may be 205 bps INFO @ Mon, 03 Jun 2019 06:04:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX201898/SRX201898.10_model.r INFO @ Mon, 03 Jun 2019 06:04:18: #3 Call peaks... INFO @ Mon, 03 Jun 2019 06:04:18: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 06:04:21: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 06:04:21: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 06:04:21: #1 total tags in treatment: 19916509 INFO @ Mon, 03 Jun 2019 06:04:21: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 06:04:21: #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 06:04:22: #1 tags after filtering in treatment: 19916509 INFO @ Mon, 03 Jun 2019 06:04:22: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 06:04:22: #1 finished! INFO @ Mon, 03 Jun 2019 06:04:22: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 06:04:22: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 06:04:23: 16000000 INFO @ Mon, 03 Jun 2019 06:04:24: #2 number of paired peaks: 5660 INFO @ Mon, 03 Jun 2019 06:04:24: start model_add_line... INFO @ Mon, 03 Jun 2019 06:04:24: start X-correlation... INFO @ Mon, 03 Jun 2019 06:04:24: end of X-cor INFO @ Mon, 03 Jun 2019 06:04:24: #2 finished! INFO @ Mon, 03 Jun 2019 06:04:24: #2 predicted fragment length is 205 bps INFO @ Mon, 03 Jun 2019 06:04:24: #2 alternative fragment length(s) may be 205 bps INFO @ Mon, 03 Jun 2019 06:04:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX201898/SRX201898.20_model.r INFO @ Mon, 03 Jun 2019 06:04:24: #3 Call peaks... INFO @ Mon, 03 Jun 2019 06:04:24: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 06:04:32: 17000000 INFO @ Mon, 03 Jun 2019 06:04:41: 18000000 INFO @ Mon, 03 Jun 2019 06:04:50: 19000000 INFO @ Mon, 03 Jun 2019 06:04:58: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 06:04:58: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 06:04:58: #1 total tags in treatment: 19916509 INFO @ Mon, 03 Jun 2019 06:04:58: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 06:04:58: #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 06:04:58: #1 tags after filtering in treatment: 19916509 INFO @ Mon, 03 Jun 2019 06:04:58: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 06:04:58: #1 finished! INFO @ Mon, 03 Jun 2019 06:04:58: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 06:04:58: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 06:05:01: #2 number of paired peaks: 5660 INFO @ Mon, 03 Jun 2019 06:05:01: start model_add_line... INFO @ Mon, 03 Jun 2019 06:05:01: start X-correlation... INFO @ Mon, 03 Jun 2019 06:05:01: end of X-cor INFO @ Mon, 03 Jun 2019 06:05:01: #2 finished! INFO @ Mon, 03 Jun 2019 06:05:01: #2 predicted fragment length is 205 bps INFO @ Mon, 03 Jun 2019 06:05:01: #2 alternative fragment length(s) may be 205 bps INFO @ Mon, 03 Jun 2019 06:05:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX201898/SRX201898.05_model.r INFO @ Mon, 03 Jun 2019 06:05:01: #3 Call peaks... INFO @ Mon, 03 Jun 2019 06:05:01: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 06:05:27: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 06:05:35: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 06:05:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX201898/SRX201898.10_peaks.xls INFO @ Mon, 03 Jun 2019 06:05:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX201898/SRX201898.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 06:05:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX201898/SRX201898.10_summits.bed INFO @ Mon, 03 Jun 2019 06:05:52: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (10058 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 06:06:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX201898/SRX201898.20_peaks.xls INFO @ Mon, 03 Jun 2019 06:06:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX201898/SRX201898.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 06:06:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX201898/SRX201898.20_summits.bed INFO @ Mon, 03 Jun 2019 06:06:00: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (8237 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 06:06:12: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 06:06:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX201898/SRX201898.05_peaks.xls INFO @ Mon, 03 Jun 2019 06:06:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX201898/SRX201898.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 06:06:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX201898/SRX201898.05_summits.bed INFO @ Mon, 03 Jun 2019 06:06:37: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (11820 records, 4 fields): 17 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。