Job ID = 1294981 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 24,663,092 reads read : 24,663,092 reads written : 24,663,092 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: 00:09:15 24663092 reads; of these: 24663092 (100.00%) were unpaired; of these: 1802586 (7.31%) aligned 0 times 16183218 (65.62%) aligned exactly 1 time 6677288 (27.07%) aligned >1 times 92.69% overall alignment rate Time searching: 00:09:15 Overall time: 00:09:15 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 12 files... [bam_rmdupse_core] 3697284 / 22860506 = 0.1617 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 11:30:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX288038/SRX288038.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX288038/SRX288038.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX288038/SRX288038.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX288038/SRX288038.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 11:30:17: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:30:17: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:30:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX288038/SRX288038.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX288038/SRX288038.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX288038/SRX288038.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX288038/SRX288038.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 11:30:17: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:30:17: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:30:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX288038/SRX288038.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX288038/SRX288038.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX288038/SRX288038.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX288038/SRX288038.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 11:30:17: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:30:17: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:30:26: 1000000 INFO @ Mon, 03 Jun 2019 11:30:27: 1000000 INFO @ Mon, 03 Jun 2019 11:30:28: 1000000 INFO @ Mon, 03 Jun 2019 11:30:35: 2000000 INFO @ Mon, 03 Jun 2019 11:30:36: 2000000 INFO @ Mon, 03 Jun 2019 11:30:38: 2000000 INFO @ Mon, 03 Jun 2019 11:30:43: 3000000 INFO @ Mon, 03 Jun 2019 11:30:45: 3000000 INFO @ Mon, 03 Jun 2019 11:30:48: 3000000 INFO @ Mon, 03 Jun 2019 11:30:51: 4000000 INFO @ Mon, 03 Jun 2019 11:30:54: 4000000 INFO @ Mon, 03 Jun 2019 11:30:58: 4000000 INFO @ Mon, 03 Jun 2019 11:31:00: 5000000 INFO @ Mon, 03 Jun 2019 11:31:03: 5000000 INFO @ Mon, 03 Jun 2019 11:31:07: 6000000 INFO @ Mon, 03 Jun 2019 11:31:08: 5000000 INFO @ Mon, 03 Jun 2019 11:31:11: 6000000 INFO @ Mon, 03 Jun 2019 11:31:15: 7000000 INFO @ Mon, 03 Jun 2019 11:31:17: 6000000 INFO @ Mon, 03 Jun 2019 11:31:20: 7000000 INFO @ Mon, 03 Jun 2019 11:31:23: 8000000 INFO @ Mon, 03 Jun 2019 11:31:27: 7000000 INFO @ Mon, 03 Jun 2019 11:31:28: 8000000 INFO @ Mon, 03 Jun 2019 11:31:30: 9000000 INFO @ Mon, 03 Jun 2019 11:31:37: 9000000 INFO @ Mon, 03 Jun 2019 11:31:37: 8000000 INFO @ Mon, 03 Jun 2019 11:31:38: 10000000 INFO @ Mon, 03 Jun 2019 11:31:45: 11000000 INFO @ Mon, 03 Jun 2019 11:31:45: 10000000 INFO @ Mon, 03 Jun 2019 11:31:47: 9000000 INFO @ Mon, 03 Jun 2019 11:31:53: 12000000 INFO @ Mon, 03 Jun 2019 11:31:54: 11000000 INFO @ Mon, 03 Jun 2019 11:31:56: 10000000 INFO @ Mon, 03 Jun 2019 11:32:00: 13000000 INFO @ Mon, 03 Jun 2019 11:32:02: 12000000 INFO @ Mon, 03 Jun 2019 11:32:06: 11000000 INFO @ Mon, 03 Jun 2019 11:32:08: 14000000 INFO @ Mon, 03 Jun 2019 11:32:11: 13000000 INFO @ Mon, 03 Jun 2019 11:32:15: 12000000 INFO @ Mon, 03 Jun 2019 11:32:16: 15000000 INFO @ Mon, 03 Jun 2019 11:32:19: 14000000 INFO @ Mon, 03 Jun 2019 11:32:23: 16000000 INFO @ Mon, 03 Jun 2019 11:32:25: 13000000 INFO @ Mon, 03 Jun 2019 11:32:27: 15000000 INFO @ Mon, 03 Jun 2019 11:32:31: 17000000 INFO @ Mon, 03 Jun 2019 11:32:35: 14000000 INFO @ Mon, 03 Jun 2019 11:32:37: 16000000 INFO @ Mon, 03 Jun 2019 11:32:40: 18000000 INFO @ Mon, 03 Jun 2019 11:32:45: 15000000 INFO @ Mon, 03 Jun 2019 11:32:47: 17000000 INFO @ Mon, 03 Jun 2019 11:32:48: 19000000 INFO @ Mon, 03 Jun 2019 11:32:50: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 11:32:50: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 11:32:50: #1 total tags in treatment: 19163222 INFO @ Mon, 03 Jun 2019 11:32:50: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:32:50: #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 11:32:50: #1 tags after filtering in treatment: 19163222 INFO @ Mon, 03 Jun 2019 11:32:50: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:32:50: #1 finished! INFO @ Mon, 03 Jun 2019 11:32:50: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:32:50: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:32:52: #2 number of paired peaks: 406 WARNING @ Mon, 03 Jun 2019 11:32:52: Fewer paired peaks (406) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 406 pairs to build model! INFO @ Mon, 03 Jun 2019 11:32:52: start model_add_line... INFO @ Mon, 03 Jun 2019 11:32:52: start X-correlation... INFO @ Mon, 03 Jun 2019 11:32:52: end of X-cor INFO @ Mon, 03 Jun 2019 11:32:52: #2 finished! INFO @ Mon, 03 Jun 2019 11:32:52: #2 predicted fragment length is 204 bps INFO @ Mon, 03 Jun 2019 11:32:52: #2 alternative fragment length(s) may be 204 bps INFO @ Mon, 03 Jun 2019 11:32:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX288038/SRX288038.05_model.r INFO @ Mon, 03 Jun 2019 11:32:52: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:32:52: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:32:55: 16000000 INFO @ Mon, 03 Jun 2019 11:32:56: 18000000 INFO @ Mon, 03 Jun 2019 11:33:05: 19000000 INFO @ Mon, 03 Jun 2019 11:33:05: 17000000 INFO @ Mon, 03 Jun 2019 11:33:06: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 11:33:06: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 11:33:06: #1 total tags in treatment: 19163222 INFO @ Mon, 03 Jun 2019 11:33:06: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:33:06: #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 11:33:07: #1 tags after filtering in treatment: 19163222 INFO @ Mon, 03 Jun 2019 11:33:07: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:33:07: #1 finished! INFO @ Mon, 03 Jun 2019 11:33:07: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:33:07: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:33:08: #2 number of paired peaks: 406 WARNING @ Mon, 03 Jun 2019 11:33:08: Fewer paired peaks (406) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 406 pairs to build model! INFO @ Mon, 03 Jun 2019 11:33:08: start model_add_line... INFO @ Mon, 03 Jun 2019 11:33:09: start X-correlation... INFO @ Mon, 03 Jun 2019 11:33:09: end of X-cor INFO @ Mon, 03 Jun 2019 11:33:09: #2 finished! INFO @ Mon, 03 Jun 2019 11:33:09: #2 predicted fragment length is 204 bps INFO @ Mon, 03 Jun 2019 11:33:09: #2 alternative fragment length(s) may be 204 bps INFO @ Mon, 03 Jun 2019 11:33:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX288038/SRX288038.10_model.r INFO @ Mon, 03 Jun 2019 11:33:09: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:33:09: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:33:15: 18000000 INFO @ Mon, 03 Jun 2019 11:33:25: 19000000 INFO @ Mon, 03 Jun 2019 11:33:26: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 11:33:26: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 11:33:26: #1 total tags in treatment: 19163222 INFO @ Mon, 03 Jun 2019 11:33:26: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:33:26: #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 11:33:27: #1 tags after filtering in treatment: 19163222 INFO @ Mon, 03 Jun 2019 11:33:27: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:33:27: #1 finished! INFO @ Mon, 03 Jun 2019 11:33:27: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:33:27: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:33:28: #2 number of paired peaks: 406 WARNING @ Mon, 03 Jun 2019 11:33:28: Fewer paired peaks (406) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 406 pairs to build model! INFO @ Mon, 03 Jun 2019 11:33:28: start model_add_line... INFO @ Mon, 03 Jun 2019 11:33:29: start X-correlation... INFO @ Mon, 03 Jun 2019 11:33:29: end of X-cor INFO @ Mon, 03 Jun 2019 11:33:29: #2 finished! INFO @ Mon, 03 Jun 2019 11:33:29: #2 predicted fragment length is 204 bps INFO @ Mon, 03 Jun 2019 11:33:29: #2 alternative fragment length(s) may be 204 bps INFO @ Mon, 03 Jun 2019 11:33:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX288038/SRX288038.20_model.r INFO @ Mon, 03 Jun 2019 11:33:29: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:33:29: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:33:48: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:34:04: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:34:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX288038/SRX288038.05_peaks.xls INFO @ Mon, 03 Jun 2019 11:34:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX288038/SRX288038.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:34:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX288038/SRX288038.05_summits.bed INFO @ Mon, 03 Jun 2019 11:34:13: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (6097 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 11:34:24: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:34:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX288038/SRX288038.10_peaks.xls INFO @ Mon, 03 Jun 2019 11:34:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX288038/SRX288038.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:34:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX288038/SRX288038.10_summits.bed INFO @ Mon, 03 Jun 2019 11:34:30: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (3744 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 11:34:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX288038/SRX288038.20_peaks.xls INFO @ Mon, 03 Jun 2019 11:34:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX288038/SRX288038.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:34:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX288038/SRX288038.20_summits.bed INFO @ Mon, 03 Jun 2019 11:34:50: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (2047 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。