Job ID = 1295017 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 17,539,534 reads read : 17,539,534 reads written : 17,539,534 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:06:01 17539534 reads; of these: 17539534 (100.00%) were unpaired; of these: 1046524 (5.97%) aligned 0 times 12969766 (73.95%) aligned exactly 1 time 3523244 (20.09%) aligned >1 times 94.03% overall alignment rate Time searching: 00:06:02 Overall time: 00:06:02 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] 3022004 / 16493010 = 0.1832 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 11:33:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX306191/SRX306191.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX306191/SRX306191.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX306191/SRX306191.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX306191/SRX306191.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 11:33:41: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:33:41: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:33:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX306191/SRX306191.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX306191/SRX306191.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX306191/SRX306191.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX306191/SRX306191.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 11:33:41: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:33:41: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:33:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX306191/SRX306191.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX306191/SRX306191.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX306191/SRX306191.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX306191/SRX306191.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 11:33:41: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:33:41: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:33:50: 1000000 INFO @ Mon, 03 Jun 2019 11:33:51: 1000000 INFO @ Mon, 03 Jun 2019 11:33:52: 1000000 INFO @ Mon, 03 Jun 2019 11:33:59: 2000000 INFO @ Mon, 03 Jun 2019 11:34:01: 2000000 INFO @ Mon, 03 Jun 2019 11:34:02: 2000000 INFO @ Mon, 03 Jun 2019 11:34:08: 3000000 INFO @ Mon, 03 Jun 2019 11:34:11: 3000000 INFO @ Mon, 03 Jun 2019 11:34:12: 3000000 INFO @ Mon, 03 Jun 2019 11:34:17: 4000000 INFO @ Mon, 03 Jun 2019 11:34:20: 4000000 INFO @ Mon, 03 Jun 2019 11:34:22: 4000000 INFO @ Mon, 03 Jun 2019 11:34:25: 5000000 INFO @ Mon, 03 Jun 2019 11:34:31: 5000000 INFO @ Mon, 03 Jun 2019 11:34:33: 5000000 INFO @ Mon, 03 Jun 2019 11:34:34: 6000000 INFO @ Mon, 03 Jun 2019 11:34:40: 6000000 INFO @ Mon, 03 Jun 2019 11:34:43: 6000000 INFO @ Mon, 03 Jun 2019 11:34:43: 7000000 INFO @ Mon, 03 Jun 2019 11:34:51: 7000000 INFO @ Mon, 03 Jun 2019 11:34:52: 8000000 INFO @ Mon, 03 Jun 2019 11:34:53: 7000000 INFO @ Mon, 03 Jun 2019 11:35:00: 8000000 INFO @ Mon, 03 Jun 2019 11:35:00: 9000000 INFO @ Mon, 03 Jun 2019 11:35:04: 8000000 INFO @ Mon, 03 Jun 2019 11:35:08: 10000000 INFO @ Mon, 03 Jun 2019 11:35:09: 9000000 INFO @ Mon, 03 Jun 2019 11:35:15: 9000000 INFO @ Mon, 03 Jun 2019 11:35:17: 11000000 INFO @ Mon, 03 Jun 2019 11:35:18: 10000000 INFO @ Mon, 03 Jun 2019 11:35:25: 12000000 INFO @ Mon, 03 Jun 2019 11:35:26: 10000000 INFO @ Mon, 03 Jun 2019 11:35:28: 11000000 INFO @ Mon, 03 Jun 2019 11:35:33: 13000000 INFO @ Mon, 03 Jun 2019 11:35:36: 11000000 INFO @ Mon, 03 Jun 2019 11:35:37: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 11:35:37: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 11:35:37: #1 total tags in treatment: 13471006 INFO @ Mon, 03 Jun 2019 11:35:37: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:35:37: #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 11:35:37: #1 tags after filtering in treatment: 13471006 INFO @ Mon, 03 Jun 2019 11:35:37: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:35:37: #1 finished! INFO @ Mon, 03 Jun 2019 11:35:37: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:35:37: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:35:38: 12000000 INFO @ Mon, 03 Jun 2019 11:35:39: #2 number of paired peaks: 2337 INFO @ Mon, 03 Jun 2019 11:35:39: start model_add_line... INFO @ Mon, 03 Jun 2019 11:35:39: start X-correlation... INFO @ Mon, 03 Jun 2019 11:35:39: end of X-cor INFO @ Mon, 03 Jun 2019 11:35:39: #2 finished! INFO @ Mon, 03 Jun 2019 11:35:39: #2 predicted fragment length is 172 bps INFO @ Mon, 03 Jun 2019 11:35:39: #2 alternative fragment length(s) may be 172 bps INFO @ Mon, 03 Jun 2019 11:35:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX306191/SRX306191.20_model.r INFO @ Mon, 03 Jun 2019 11:35:39: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:35:39: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:35:47: 12000000 INFO @ Mon, 03 Jun 2019 11:35:48: 13000000 INFO @ Mon, 03 Jun 2019 11:35:52: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 11:35:52: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 11:35:52: #1 total tags in treatment: 13471006 INFO @ Mon, 03 Jun 2019 11:35:52: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:35:52: #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 11:35:52: #1 tags after filtering in treatment: 13471006 INFO @ Mon, 03 Jun 2019 11:35:52: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:35:52: #1 finished! INFO @ Mon, 03 Jun 2019 11:35:52: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:35:52: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:35:54: #2 number of paired peaks: 2337 INFO @ Mon, 03 Jun 2019 11:35:54: start model_add_line... INFO @ Mon, 03 Jun 2019 11:35:54: start X-correlation... INFO @ Mon, 03 Jun 2019 11:35:54: end of X-cor INFO @ Mon, 03 Jun 2019 11:35:54: #2 finished! INFO @ Mon, 03 Jun 2019 11:35:54: #2 predicted fragment length is 172 bps INFO @ Mon, 03 Jun 2019 11:35:54: #2 alternative fragment length(s) may be 172 bps INFO @ Mon, 03 Jun 2019 11:35:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX306191/SRX306191.10_model.r INFO @ Mon, 03 Jun 2019 11:35:54: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:35:54: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:35:57: 13000000 INFO @ Mon, 03 Jun 2019 11:36:02: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 11:36:02: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 11:36:02: #1 total tags in treatment: 13471006 INFO @ Mon, 03 Jun 2019 11:36:02: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:36:02: #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 11:36:02: #1 tags after filtering in treatment: 13471006 INFO @ Mon, 03 Jun 2019 11:36:02: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:36:02: #1 finished! INFO @ Mon, 03 Jun 2019 11:36:02: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:36:02: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:36:04: #2 number of paired peaks: 2337 INFO @ Mon, 03 Jun 2019 11:36:04: start model_add_line... INFO @ Mon, 03 Jun 2019 11:36:04: start X-correlation... INFO @ Mon, 03 Jun 2019 11:36:04: end of X-cor INFO @ Mon, 03 Jun 2019 11:36:04: #2 finished! INFO @ Mon, 03 Jun 2019 11:36:04: #2 predicted fragment length is 172 bps INFO @ Mon, 03 Jun 2019 11:36:04: #2 alternative fragment length(s) may be 172 bps INFO @ Mon, 03 Jun 2019 11:36:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX306191/SRX306191.05_model.r INFO @ Mon, 03 Jun 2019 11:36:04: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:36:04: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:36:25: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:36:42: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:36:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX306191/SRX306191.20_peaks.xls INFO @ Mon, 03 Jun 2019 11:36:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX306191/SRX306191.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:36:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX306191/SRX306191.20_summits.bed INFO @ Mon, 03 Jun 2019 11:36:48: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (4439 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 11:36:51: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:37:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX306191/SRX306191.10_peaks.xls INFO @ Mon, 03 Jun 2019 11:37:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX306191/SRX306191.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:37:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX306191/SRX306191.10_summits.bed INFO @ Mon, 03 Jun 2019 11:37:07: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6645 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 11:37:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX306191/SRX306191.05_peaks.xls INFO @ Mon, 03 Jun 2019 11:37:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX306191/SRX306191.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:37:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX306191/SRX306191.05_summits.bed INFO @ Mon, 03 Jun 2019 11:37:16: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (9086 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。