Job ID = 1294158 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 34,789,009 reads read : 34,789,009 reads written : 34,789,009 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: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:11:12 34789009 reads; of these: 34789009 (100.00%) were unpaired; of these: 1676271 (4.82%) aligned 0 times 24444714 (70.27%) aligned exactly 1 time 8668024 (24.92%) aligned >1 times 95.18% overall alignment rate Time searching: 00:11:13 Overall time: 00:11:13 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] 5059874 / 33112738 = 0.1528 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 05:32:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX193334/SRX193334.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX193334/SRX193334.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX193334/SRX193334.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX193334/SRX193334.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 05:32:46: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:32:46: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:32:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX193334/SRX193334.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX193334/SRX193334.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX193334/SRX193334.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX193334/SRX193334.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 05:32:46: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:32:46: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:32:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX193334/SRX193334.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX193334/SRX193334.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX193334/SRX193334.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX193334/SRX193334.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 05:32:46: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:32:46: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:32:56: 1000000 INFO @ Mon, 03 Jun 2019 05:32:56: 1000000 INFO @ Mon, 03 Jun 2019 05:32:57: 1000000 INFO @ Mon, 03 Jun 2019 05:33:05: 2000000 INFO @ Mon, 03 Jun 2019 05:33:06: 2000000 INFO @ Mon, 03 Jun 2019 05:33:07: 2000000 INFO @ Mon, 03 Jun 2019 05:33:14: 3000000 INFO @ Mon, 03 Jun 2019 05:33:15: 3000000 INFO @ Mon, 03 Jun 2019 05:33:17: 3000000 INFO @ Mon, 03 Jun 2019 05:33:24: 4000000 INFO @ Mon, 03 Jun 2019 05:33:25: 4000000 INFO @ Mon, 03 Jun 2019 05:33:28: 4000000 INFO @ Mon, 03 Jun 2019 05:33:34: 5000000 INFO @ Mon, 03 Jun 2019 05:33:34: 5000000 INFO @ Mon, 03 Jun 2019 05:33:38: 5000000 INFO @ Mon, 03 Jun 2019 05:33:44: 6000000 INFO @ Mon, 03 Jun 2019 05:33:45: 6000000 INFO @ Mon, 03 Jun 2019 05:33:48: 6000000 INFO @ Mon, 03 Jun 2019 05:33:54: 7000000 INFO @ Mon, 03 Jun 2019 05:33:56: 7000000 INFO @ Mon, 03 Jun 2019 05:33:58: 7000000 INFO @ Mon, 03 Jun 2019 05:34:03: 8000000 INFO @ Mon, 03 Jun 2019 05:34:07: 8000000 INFO @ Mon, 03 Jun 2019 05:34:09: 8000000 INFO @ Mon, 03 Jun 2019 05:34:13: 9000000 INFO @ Mon, 03 Jun 2019 05:34:18: 9000000 INFO @ Mon, 03 Jun 2019 05:34:19: 9000000 INFO @ Mon, 03 Jun 2019 05:34:22: 10000000 INFO @ Mon, 03 Jun 2019 05:34:27: 10000000 INFO @ Mon, 03 Jun 2019 05:34:30: 10000000 INFO @ Mon, 03 Jun 2019 05:34:31: 11000000 INFO @ Mon, 03 Jun 2019 05:34:37: 11000000 INFO @ Mon, 03 Jun 2019 05:34:41: 12000000 INFO @ Mon, 03 Jun 2019 05:34:43: 11000000 INFO @ Mon, 03 Jun 2019 05:34:46: 12000000 INFO @ Mon, 03 Jun 2019 05:34:50: 13000000 INFO @ Mon, 03 Jun 2019 05:34:54: 12000000 INFO @ Mon, 03 Jun 2019 05:34:56: 13000000 INFO @ Mon, 03 Jun 2019 05:34:59: 14000000 INFO @ Mon, 03 Jun 2019 05:35:04: 14000000 INFO @ Mon, 03 Jun 2019 05:35:06: 13000000 INFO @ Mon, 03 Jun 2019 05:35:08: 15000000 INFO @ Mon, 03 Jun 2019 05:35:13: 15000000 INFO @ Mon, 03 Jun 2019 05:35:17: 14000000 INFO @ Mon, 03 Jun 2019 05:35:18: 16000000 INFO @ Mon, 03 Jun 2019 05:35:22: 16000000 INFO @ Mon, 03 Jun 2019 05:35:27: 17000000 INFO @ Mon, 03 Jun 2019 05:35:28: 15000000 INFO @ Mon, 03 Jun 2019 05:35:32: 17000000 INFO @ Mon, 03 Jun 2019 05:35:37: 18000000 INFO @ Mon, 03 Jun 2019 05:35:39: 16000000 INFO @ Mon, 03 Jun 2019 05:35:40: 18000000 INFO @ Mon, 03 Jun 2019 05:35:46: 19000000 INFO @ Mon, 03 Jun 2019 05:35:49: 19000000 INFO @ Mon, 03 Jun 2019 05:35:50: 17000000 INFO @ Mon, 03 Jun 2019 05:35:56: 20000000 INFO @ Mon, 03 Jun 2019 05:35:58: 20000000 INFO @ Mon, 03 Jun 2019 05:36:00: 18000000 INFO @ Mon, 03 Jun 2019 05:36:05: 21000000 INFO @ Mon, 03 Jun 2019 05:36:07: 21000000 INFO @ Mon, 03 Jun 2019 05:36:11: 19000000 INFO @ Mon, 03 Jun 2019 05:36:15: 22000000 INFO @ Mon, 03 Jun 2019 05:36:16: 22000000 INFO @ Mon, 03 Jun 2019 05:36:22: 20000000 INFO @ Mon, 03 Jun 2019 05:36:24: 23000000 INFO @ Mon, 03 Jun 2019 05:36:25: 23000000 INFO @ Mon, 03 Jun 2019 05:36:33: 21000000 INFO @ Mon, 03 Jun 2019 05:36:34: 24000000 INFO @ Mon, 03 Jun 2019 05:36:34: 24000000 INFO @ Mon, 03 Jun 2019 05:36:44: 25000000 INFO @ Mon, 03 Jun 2019 05:36:44: 22000000 INFO @ Mon, 03 Jun 2019 05:36:44: 25000000 INFO @ Mon, 03 Jun 2019 05:36:54: 26000000 INFO @ Mon, 03 Jun 2019 05:36:54: 26000000 INFO @ Mon, 03 Jun 2019 05:36:55: 23000000 INFO @ Mon, 03 Jun 2019 05:37:03: 27000000 INFO @ Mon, 03 Jun 2019 05:37:03: 27000000 INFO @ Mon, 03 Jun 2019 05:37:06: 24000000 INFO @ Mon, 03 Jun 2019 05:37:13: 28000000 INFO @ Mon, 03 Jun 2019 05:37:13: 28000000 INFO @ Mon, 03 Jun 2019 05:37:13: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 05:37:13: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 05:37:13: #1 total tags in treatment: 28052864 INFO @ Mon, 03 Jun 2019 05:37:13: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:37:13: #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 05:37:13: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 05:37:13: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 05:37:13: #1 total tags in treatment: 28052864 INFO @ Mon, 03 Jun 2019 05:37:13: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:37:13: #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 05:37:14: #1 tags after filtering in treatment: 28052864 INFO @ Mon, 03 Jun 2019 05:37:14: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:37:14: #1 finished! INFO @ Mon, 03 Jun 2019 05:37:14: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:37:14: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:37:14: #1 tags after filtering in treatment: 28052864 INFO @ Mon, 03 Jun 2019 05:37:14: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:37:14: #1 finished! INFO @ Mon, 03 Jun 2019 05:37:14: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:37:14: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:37:16: #2 number of paired peaks: 196 WARNING @ Mon, 03 Jun 2019 05:37:16: Fewer paired peaks (196) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 196 pairs to build model! INFO @ Mon, 03 Jun 2019 05:37:16: start model_add_line... INFO @ Mon, 03 Jun 2019 05:37:16: #2 number of paired peaks: 196 WARNING @ Mon, 03 Jun 2019 05:37:16: Fewer paired peaks (196) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 196 pairs to build model! INFO @ Mon, 03 Jun 2019 05:37:16: start model_add_line... INFO @ Mon, 03 Jun 2019 05:37:16: start X-correlation... INFO @ Mon, 03 Jun 2019 05:37:16: end of X-cor INFO @ Mon, 03 Jun 2019 05:37:16: #2 finished! INFO @ Mon, 03 Jun 2019 05:37:16: #2 predicted fragment length is 42 bps INFO @ Mon, 03 Jun 2019 05:37:16: #2 alternative fragment length(s) may be 3,42,588 bps INFO @ Mon, 03 Jun 2019 05:37:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX193334/SRX193334.10_model.r WARNING @ Mon, 03 Jun 2019 05:37:16: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 05:37:16: #2 You may need to consider one of the other alternative d(s): 3,42,588 WARNING @ Mon, 03 Jun 2019 05:37:16: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 05:37:16: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:37:16: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:37:17: start X-correlation... INFO @ Mon, 03 Jun 2019 05:37:17: end of X-cor INFO @ Mon, 03 Jun 2019 05:37:17: #2 finished! INFO @ Mon, 03 Jun 2019 05:37:17: #2 predicted fragment length is 42 bps INFO @ Mon, 03 Jun 2019 05:37:17: #2 alternative fragment length(s) may be 3,42,588 bps INFO @ Mon, 03 Jun 2019 05:37:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX193334/SRX193334.05_model.r WARNING @ Mon, 03 Jun 2019 05:37:17: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 05:37:17: #2 You may need to consider one of the other alternative d(s): 3,42,588 WARNING @ Mon, 03 Jun 2019 05:37:17: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 05:37:17: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:37:17: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:37:17: 25000000 INFO @ Mon, 03 Jun 2019 05:37:27: 26000000 INFO @ Mon, 03 Jun 2019 05:37:37: 27000000 INFO @ Mon, 03 Jun 2019 05:37:47: 28000000 INFO @ Mon, 03 Jun 2019 05:37:48: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 05:37:48: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 05:37:48: #1 total tags in treatment: 28052864 INFO @ Mon, 03 Jun 2019 05:37:48: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:37:48: #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 05:37:49: #1 tags after filtering in treatment: 28052864 INFO @ Mon, 03 Jun 2019 05:37:49: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:37:49: #1 finished! INFO @ Mon, 03 Jun 2019 05:37:49: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:37:49: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:37:51: #2 number of paired peaks: 196 WARNING @ Mon, 03 Jun 2019 05:37:51: Fewer paired peaks (196) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 196 pairs to build model! INFO @ Mon, 03 Jun 2019 05:37:51: start model_add_line... INFO @ Mon, 03 Jun 2019 05:37:51: start X-correlation... INFO @ Mon, 03 Jun 2019 05:37:51: end of X-cor INFO @ Mon, 03 Jun 2019 05:37:51: #2 finished! INFO @ Mon, 03 Jun 2019 05:37:51: #2 predicted fragment length is 42 bps INFO @ Mon, 03 Jun 2019 05:37:51: #2 alternative fragment length(s) may be 3,42,588 bps INFO @ Mon, 03 Jun 2019 05:37:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX193334/SRX193334.20_model.r WARNING @ Mon, 03 Jun 2019 05:37:51: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 05:37:51: #2 You may need to consider one of the other alternative d(s): 3,42,588 WARNING @ Mon, 03 Jun 2019 05:37:51: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 05:37:51: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:37:51: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:38:19: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:38:19: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:38:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX193334/SRX193334.10_peaks.xls INFO @ Mon, 03 Jun 2019 05:38:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX193334/SRX193334.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:38:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX193334/SRX193334.10_summits.bed INFO @ Mon, 03 Jun 2019 05:38:50: Done! INFO @ Mon, 03 Jun 2019 05:38:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX193334/SRX193334.05_peaks.xls INFO @ Mon, 03 Jun 2019 05:38:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX193334/SRX193334.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:38:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX193334/SRX193334.05_summits.bed pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (1176 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 05:38:50: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (4385 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 05:38:55: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:39:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX193334/SRX193334.20_peaks.xls INFO @ Mon, 03 Jun 2019 05:39:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX193334/SRX193334.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:39:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX193334/SRX193334.20_summits.bed INFO @ Mon, 03 Jun 2019 05:39:26: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (407 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。