Job ID = 1295551 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 23,753,963 reads read : 23,753,963 reads written : 23,753,963 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: 00:07:24 23753963 reads; of these: 23753963 (100.00%) were unpaired; of these: 3420007 (14.40%) aligned 0 times 16865688 (71.00%) aligned exactly 1 time 3468268 (14.60%) aligned >1 times 85.60% overall alignment rate Time searching: 00:07:24 Overall time: 00:07:24 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] 2656994 / 20333956 = 0.1307 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 14:33:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3663165/SRX3663165.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3663165/SRX3663165.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3663165/SRX3663165.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3663165/SRX3663165.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 14:33:16: #1 read tag files... INFO @ Mon, 03 Jun 2019 14:33:16: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 14:33:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3663165/SRX3663165.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3663165/SRX3663165.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3663165/SRX3663165.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3663165/SRX3663165.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 14:33:16: #1 read tag files... INFO @ Mon, 03 Jun 2019 14:33:16: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 14:33:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3663165/SRX3663165.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3663165/SRX3663165.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3663165/SRX3663165.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3663165/SRX3663165.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 14:33:17: #1 read tag files... INFO @ Mon, 03 Jun 2019 14:33:17: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 14:33:26: 1000000 INFO @ Mon, 03 Jun 2019 14:33:28: 1000000 INFO @ Mon, 03 Jun 2019 14:33:28: 1000000 INFO @ Mon, 03 Jun 2019 14:33:35: 2000000 INFO @ Mon, 03 Jun 2019 14:33:39: 2000000 INFO @ Mon, 03 Jun 2019 14:33:40: 2000000 INFO @ Mon, 03 Jun 2019 14:33:44: 3000000 INFO @ Mon, 03 Jun 2019 14:33:51: 3000000 INFO @ Mon, 03 Jun 2019 14:33:51: 3000000 INFO @ Mon, 03 Jun 2019 14:33:53: 4000000 INFO @ Mon, 03 Jun 2019 14:34:02: 4000000 INFO @ Mon, 03 Jun 2019 14:34:02: 4000000 INFO @ Mon, 03 Jun 2019 14:34:02: 5000000 INFO @ Mon, 03 Jun 2019 14:34:11: 6000000 INFO @ Mon, 03 Jun 2019 14:34:13: 5000000 INFO @ Mon, 03 Jun 2019 14:34:13: 5000000 INFO @ Mon, 03 Jun 2019 14:34:20: 7000000 INFO @ Mon, 03 Jun 2019 14:34:25: 6000000 INFO @ Mon, 03 Jun 2019 14:34:25: 6000000 INFO @ Mon, 03 Jun 2019 14:34:30: 8000000 INFO @ Mon, 03 Jun 2019 14:34:36: 7000000 INFO @ Mon, 03 Jun 2019 14:34:36: 7000000 INFO @ Mon, 03 Jun 2019 14:34:39: 9000000 INFO @ Mon, 03 Jun 2019 14:34:47: 8000000 INFO @ Mon, 03 Jun 2019 14:34:47: 8000000 INFO @ Mon, 03 Jun 2019 14:34:48: 10000000 INFO @ Mon, 03 Jun 2019 14:34:58: 11000000 INFO @ Mon, 03 Jun 2019 14:34:58: 9000000 INFO @ Mon, 03 Jun 2019 14:34:59: 9000000 INFO @ Mon, 03 Jun 2019 14:35:08: 12000000 INFO @ Mon, 03 Jun 2019 14:35:10: 10000000 INFO @ Mon, 03 Jun 2019 14:35:10: 10000000 INFO @ Mon, 03 Jun 2019 14:35:18: 13000000 INFO @ Mon, 03 Jun 2019 14:35:21: 11000000 INFO @ Mon, 03 Jun 2019 14:35:21: 11000000 INFO @ Mon, 03 Jun 2019 14:35:28: 14000000 INFO @ Mon, 03 Jun 2019 14:35:32: 12000000 INFO @ Mon, 03 Jun 2019 14:35:32: 12000000 INFO @ Mon, 03 Jun 2019 14:35:38: 15000000 INFO @ Mon, 03 Jun 2019 14:35:43: 13000000 INFO @ Mon, 03 Jun 2019 14:35:43: 13000000 INFO @ Mon, 03 Jun 2019 14:35:47: 16000000 INFO @ Mon, 03 Jun 2019 14:35:54: 14000000 INFO @ Mon, 03 Jun 2019 14:35:54: 14000000 INFO @ Mon, 03 Jun 2019 14:35:57: 17000000 INFO @ Mon, 03 Jun 2019 14:36:03: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 14:36:03: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 14:36:03: #1 total tags in treatment: 17676962 INFO @ Mon, 03 Jun 2019 14:36:03: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 14:36:03: #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 14:36:03: #1 tags after filtering in treatment: 17676962 INFO @ Mon, 03 Jun 2019 14:36:03: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 14:36:03: #1 finished! INFO @ Mon, 03 Jun 2019 14:36:03: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 14:36:03: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 14:36:05: #2 number of paired peaks: 114 WARNING @ Mon, 03 Jun 2019 14:36:05: Fewer paired peaks (114) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 114 pairs to build model! INFO @ Mon, 03 Jun 2019 14:36:05: start model_add_line... INFO @ Mon, 03 Jun 2019 14:36:05: start X-correlation... INFO @ Mon, 03 Jun 2019 14:36:05: end of X-cor INFO @ Mon, 03 Jun 2019 14:36:05: #2 finished! INFO @ Mon, 03 Jun 2019 14:36:05: #2 predicted fragment length is 212 bps INFO @ Mon, 03 Jun 2019 14:36:05: #2 alternative fragment length(s) may be 1,57,75,129,145,153,182,212,234,281,332,524 bps INFO @ Mon, 03 Jun 2019 14:36:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3663165/SRX3663165.20_model.r INFO @ Mon, 03 Jun 2019 14:36:05: #3 Call peaks... INFO @ Mon, 03 Jun 2019 14:36:05: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 14:36:05: 15000000 INFO @ Mon, 03 Jun 2019 14:36:06: 15000000 INFO @ Mon, 03 Jun 2019 14:36:16: 16000000 INFO @ Mon, 03 Jun 2019 14:36:16: 16000000 INFO @ Mon, 03 Jun 2019 14:36:26: 17000000 INFO @ Mon, 03 Jun 2019 14:36:27: 17000000 INFO @ Mon, 03 Jun 2019 14:36:33: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 14:36:33: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 14:36:33: #1 total tags in treatment: 17676962 INFO @ Mon, 03 Jun 2019 14:36:33: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 14:36:33: #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 14:36:34: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 14:36:34: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 14:36:34: #1 total tags in treatment: 17676962 INFO @ Mon, 03 Jun 2019 14:36:34: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 14:36:34: #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 14:36:34: #1 tags after filtering in treatment: 17676962 INFO @ Mon, 03 Jun 2019 14:36:34: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 14:36:34: #1 finished! INFO @ Mon, 03 Jun 2019 14:36:34: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 14:36:34: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 14:36:34: #1 tags after filtering in treatment: 17676962 INFO @ Mon, 03 Jun 2019 14:36:34: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 14:36:34: #1 finished! INFO @ Mon, 03 Jun 2019 14:36:34: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 14:36:34: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 14:36:35: #2 number of paired peaks: 114 WARNING @ Mon, 03 Jun 2019 14:36:35: Fewer paired peaks (114) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 114 pairs to build model! INFO @ Mon, 03 Jun 2019 14:36:35: start model_add_line... INFO @ Mon, 03 Jun 2019 14:36:35: start X-correlation... INFO @ Mon, 03 Jun 2019 14:36:35: end of X-cor INFO @ Mon, 03 Jun 2019 14:36:35: #2 finished! INFO @ Mon, 03 Jun 2019 14:36:35: #2 predicted fragment length is 212 bps INFO @ Mon, 03 Jun 2019 14:36:35: #2 alternative fragment length(s) may be 1,57,75,129,145,153,182,212,234,281,332,524 bps INFO @ Mon, 03 Jun 2019 14:36:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3663165/SRX3663165.10_model.r INFO @ Mon, 03 Jun 2019 14:36:35: #3 Call peaks... INFO @ Mon, 03 Jun 2019 14:36:35: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 14:36:36: #2 number of paired peaks: 114 WARNING @ Mon, 03 Jun 2019 14:36:36: Fewer paired peaks (114) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 114 pairs to build model! INFO @ Mon, 03 Jun 2019 14:36:36: start model_add_line... INFO @ Mon, 03 Jun 2019 14:36:36: start X-correlation... INFO @ Mon, 03 Jun 2019 14:36:36: end of X-cor INFO @ Mon, 03 Jun 2019 14:36:36: #2 finished! INFO @ Mon, 03 Jun 2019 14:36:36: #2 predicted fragment length is 212 bps INFO @ Mon, 03 Jun 2019 14:36:36: #2 alternative fragment length(s) may be 1,57,75,129,145,153,182,212,234,281,332,524 bps INFO @ Mon, 03 Jun 2019 14:36:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3663165/SRX3663165.05_model.r INFO @ Mon, 03 Jun 2019 14:36:36: #3 Call peaks... INFO @ Mon, 03 Jun 2019 14:36:36: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 14:36:52: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 14:37:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3663165/SRX3663165.20_peaks.xls INFO @ Mon, 03 Jun 2019 14:37:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3663165/SRX3663165.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 14:37:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3663165/SRX3663165.20_summits.bed INFO @ Mon, 03 Jun 2019 14:37:15: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (112 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 14:37:22: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 14:37:23: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 14:37:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3663165/SRX3663165.10_peaks.xls INFO @ Mon, 03 Jun 2019 14:37:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3663165/SRX3663165.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 14:37:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3663165/SRX3663165.10_summits.bed INFO @ Mon, 03 Jun 2019 14:37:45: Done! pass1 - making usageList (9 chroms): 0 millis pass2 - checking and writing primary data (287 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 14:37:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3663165/SRX3663165.05_peaks.xls INFO @ Mon, 03 Jun 2019 14:37:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3663165/SRX3663165.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 14:37:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3663165/SRX3663165.05_summits.bed INFO @ Mon, 03 Jun 2019 14:37:45: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (588 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。