Job ID = 1294421 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 21,566,409 reads read : 21,566,409 reads written : 21,566,409 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: 00:09:40 21566409 reads; of these: 21566409 (100.00%) were unpaired; of these: 1035602 (4.80%) aligned 0 times 14626393 (67.82%) aligned exactly 1 time 5904414 (27.38%) aligned >1 times 95.20% overall alignment rate Time searching: 00:09:41 Overall time: 00:09:41 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] 3033804 / 20530807 = 0.1478 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 07:57:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287592/SRX287592.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287592/SRX287592.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287592/SRX287592.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287592/SRX287592.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 07:57:08: #1 read tag files... INFO @ Mon, 03 Jun 2019 07:57:08: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 07:57:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287592/SRX287592.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287592/SRX287592.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287592/SRX287592.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287592/SRX287592.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 07:57:08: #1 read tag files... INFO @ Mon, 03 Jun 2019 07:57:08: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 07:57:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287592/SRX287592.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287592/SRX287592.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287592/SRX287592.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287592/SRX287592.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 07:57:08: #1 read tag files... INFO @ Mon, 03 Jun 2019 07:57:08: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 07:57:18: 1000000 INFO @ Mon, 03 Jun 2019 07:57:22: 1000000 INFO @ Mon, 03 Jun 2019 07:57:22: 1000000 INFO @ Mon, 03 Jun 2019 07:57:28: 2000000 INFO @ Mon, 03 Jun 2019 07:57:33: 2000000 INFO @ Mon, 03 Jun 2019 07:57:34: 2000000 INFO @ Mon, 03 Jun 2019 07:57:37: 3000000 INFO @ Mon, 03 Jun 2019 07:57:42: 3000000 INFO @ Mon, 03 Jun 2019 07:57:46: 3000000 INFO @ Mon, 03 Jun 2019 07:57:47: 4000000 INFO @ Mon, 03 Jun 2019 07:57:50: 4000000 INFO @ Mon, 03 Jun 2019 07:57:56: 5000000 INFO @ Mon, 03 Jun 2019 07:57:57: 4000000 INFO @ Mon, 03 Jun 2019 07:57:59: 5000000 INFO @ Mon, 03 Jun 2019 07:58:05: 6000000 INFO @ Mon, 03 Jun 2019 07:58:07: 6000000 INFO @ Mon, 03 Jun 2019 07:58:09: 5000000 INFO @ Mon, 03 Jun 2019 07:58:15: 7000000 INFO @ Mon, 03 Jun 2019 07:58:16: 7000000 INFO @ Mon, 03 Jun 2019 07:58:20: 6000000 INFO @ Mon, 03 Jun 2019 07:58:25: 8000000 INFO @ Mon, 03 Jun 2019 07:58:25: 8000000 INFO @ Mon, 03 Jun 2019 07:58:33: 7000000 INFO @ Mon, 03 Jun 2019 07:58:33: 9000000 INFO @ Mon, 03 Jun 2019 07:58:34: 9000000 INFO @ Mon, 03 Jun 2019 07:58:42: 10000000 INFO @ Mon, 03 Jun 2019 07:58:44: 10000000 INFO @ Mon, 03 Jun 2019 07:58:45: 8000000 INFO @ Mon, 03 Jun 2019 07:58:50: 11000000 INFO @ Mon, 03 Jun 2019 07:58:53: 11000000 INFO @ Mon, 03 Jun 2019 07:58:56: 9000000 INFO @ Mon, 03 Jun 2019 07:58:59: 12000000 INFO @ Mon, 03 Jun 2019 07:59:02: 12000000 INFO @ Mon, 03 Jun 2019 07:59:07: 13000000 INFO @ Mon, 03 Jun 2019 07:59:07: 10000000 INFO @ Mon, 03 Jun 2019 07:59:11: 13000000 INFO @ Mon, 03 Jun 2019 07:59:16: 14000000 INFO @ Mon, 03 Jun 2019 07:59:19: 11000000 INFO @ Mon, 03 Jun 2019 07:59:20: 14000000 INFO @ Mon, 03 Jun 2019 07:59:26: 15000000 INFO @ Mon, 03 Jun 2019 07:59:30: 15000000 INFO @ Mon, 03 Jun 2019 07:59:31: 12000000 INFO @ Mon, 03 Jun 2019 07:59:34: 16000000 INFO @ Mon, 03 Jun 2019 07:59:39: 16000000 INFO @ Mon, 03 Jun 2019 07:59:42: 17000000 INFO @ Mon, 03 Jun 2019 07:59:43: 13000000 INFO @ Mon, 03 Jun 2019 07:59:47: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 07:59:47: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 07:59:47: #1 total tags in treatment: 17497003 INFO @ Mon, 03 Jun 2019 07:59:47: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 07:59:47: #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 07:59:47: #1 tags after filtering in treatment: 17497003 INFO @ Mon, 03 Jun 2019 07:59:47: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 07:59:47: #1 finished! INFO @ Mon, 03 Jun 2019 07:59:47: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 07:59:47: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 07:59:48: 17000000 INFO @ Mon, 03 Jun 2019 07:59:49: #2 number of paired peaks: 231 WARNING @ Mon, 03 Jun 2019 07:59:49: Fewer paired peaks (231) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 231 pairs to build model! INFO @ Mon, 03 Jun 2019 07:59:49: start model_add_line... INFO @ Mon, 03 Jun 2019 07:59:49: start X-correlation... INFO @ Mon, 03 Jun 2019 07:59:49: end of X-cor INFO @ Mon, 03 Jun 2019 07:59:49: #2 finished! INFO @ Mon, 03 Jun 2019 07:59:49: #2 predicted fragment length is 85 bps INFO @ Mon, 03 Jun 2019 07:59:49: #2 alternative fragment length(s) may be 85 bps INFO @ Mon, 03 Jun 2019 07:59:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287592/SRX287592.20_model.r WARNING @ Mon, 03 Jun 2019 07:59:49: #2 Since the d (85) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 07:59:49: #2 You may need to consider one of the other alternative d(s): 85 WARNING @ Mon, 03 Jun 2019 07:59:49: #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 07:59:49: #3 Call peaks... INFO @ Mon, 03 Jun 2019 07:59:49: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 07:59:53: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 07:59:53: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 07:59:53: #1 total tags in treatment: 17497003 INFO @ Mon, 03 Jun 2019 07:59:53: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 07:59:53: #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 07:59:53: #1 tags after filtering in treatment: 17497003 INFO @ Mon, 03 Jun 2019 07:59:53: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 07:59:53: #1 finished! INFO @ Mon, 03 Jun 2019 07:59:53: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 07:59:53: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 07:59:54: 14000000 INFO @ Mon, 03 Jun 2019 07:59:55: #2 number of paired peaks: 231 WARNING @ Mon, 03 Jun 2019 07:59:55: Fewer paired peaks (231) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 231 pairs to build model! INFO @ Mon, 03 Jun 2019 07:59:55: start model_add_line... INFO @ Mon, 03 Jun 2019 07:59:55: start X-correlation... INFO @ Mon, 03 Jun 2019 07:59:55: end of X-cor INFO @ Mon, 03 Jun 2019 07:59:55: #2 finished! INFO @ Mon, 03 Jun 2019 07:59:55: #2 predicted fragment length is 85 bps INFO @ Mon, 03 Jun 2019 07:59:55: #2 alternative fragment length(s) may be 85 bps INFO @ Mon, 03 Jun 2019 07:59:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287592/SRX287592.10_model.r WARNING @ Mon, 03 Jun 2019 07:59:55: #2 Since the d (85) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 07:59:55: #2 You may need to consider one of the other alternative d(s): 85 WARNING @ Mon, 03 Jun 2019 07:59:55: #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 07:59:55: #3 Call peaks... INFO @ Mon, 03 Jun 2019 07:59:55: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 08:00:06: 15000000 INFO @ Mon, 03 Jun 2019 08:00:17: 16000000 INFO @ Mon, 03 Jun 2019 08:00:29: 17000000 INFO @ Mon, 03 Jun 2019 08:00:34: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 08:00:34: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 08:00:34: #1 total tags in treatment: 17497003 INFO @ Mon, 03 Jun 2019 08:00:34: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 08:00:34: #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 08:00:34: #1 tags after filtering in treatment: 17497003 INFO @ Mon, 03 Jun 2019 08:00:35: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 08:00:35: #1 finished! INFO @ Mon, 03 Jun 2019 08:00:35: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 08:00:35: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 08:00:36: #2 number of paired peaks: 231 WARNING @ Mon, 03 Jun 2019 08:00:36: Fewer paired peaks (231) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 231 pairs to build model! INFO @ Mon, 03 Jun 2019 08:00:36: start model_add_line... INFO @ Mon, 03 Jun 2019 08:00:36: start X-correlation... INFO @ Mon, 03 Jun 2019 08:00:36: end of X-cor INFO @ Mon, 03 Jun 2019 08:00:36: #2 finished! INFO @ Mon, 03 Jun 2019 08:00:36: #2 predicted fragment length is 85 bps INFO @ Mon, 03 Jun 2019 08:00:36: #2 alternative fragment length(s) may be 85 bps INFO @ Mon, 03 Jun 2019 08:00:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287592/SRX287592.05_model.r WARNING @ Mon, 03 Jun 2019 08:00:36: #2 Since the d (85) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 08:00:36: #2 You may need to consider one of the other alternative d(s): 85 WARNING @ Mon, 03 Jun 2019 08:00:36: #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 08:00:36: #3 Call peaks... INFO @ Mon, 03 Jun 2019 08:00:36: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 08:00:38: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 08:00:45: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 08:01:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287592/SRX287592.20_peaks.xls INFO @ Mon, 03 Jun 2019 08:01:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287592/SRX287592.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 08:01:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287592/SRX287592.20_summits.bed INFO @ Mon, 03 Jun 2019 08:01:01: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (1176 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 08:01:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287592/SRX287592.10_peaks.xls INFO @ Mon, 03 Jun 2019 08:01:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287592/SRX287592.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 08:01:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287592/SRX287592.10_summits.bed INFO @ Mon, 03 Jun 2019 08:01:08: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1720 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 08:01:27: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 08:01:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287592/SRX287592.05_peaks.xls INFO @ Mon, 03 Jun 2019 08:01:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287592/SRX287592.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 08:01:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287592/SRX287592.05_summits.bed INFO @ Mon, 03 Jun 2019 08:01:50: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (2253 records, 4 fields): 9 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。