Job ID = 1294848 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 17,639,345 reads read : 17,639,345 reads written : 17,639,345 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: 00:08:53 17639345 reads; of these: 17639345 (100.00%) were unpaired; of these: 1069163 (6.06%) aligned 0 times 10497276 (59.51%) aligned exactly 1 time 6072906 (34.43%) aligned >1 times 93.94% overall alignment rate Time searching: 00:08:53 Overall time: 00:08:53 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] 2794583 / 16570182 = 0.1687 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 10:45:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287942/SRX287942.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287942/SRX287942.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287942/SRX287942.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287942/SRX287942.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 10:45:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287942/SRX287942.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287942/SRX287942.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287942/SRX287942.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287942/SRX287942.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 10:45:28: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:45:28: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:45:28: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:45:28: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:45:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287942/SRX287942.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287942/SRX287942.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287942/SRX287942.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287942/SRX287942.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 10:45:28: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:45:28: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:45:36: 1000000 INFO @ Mon, 03 Jun 2019 10:45:36: 1000000 INFO @ Mon, 03 Jun 2019 10:45:38: 1000000 INFO @ Mon, 03 Jun 2019 10:45:44: 2000000 INFO @ Mon, 03 Jun 2019 10:45:44: 2000000 INFO @ Mon, 03 Jun 2019 10:45:47: 2000000 INFO @ Mon, 03 Jun 2019 10:45:53: 3000000 INFO @ Mon, 03 Jun 2019 10:45:53: 3000000 INFO @ Mon, 03 Jun 2019 10:45:57: 3000000 INFO @ Mon, 03 Jun 2019 10:46:01: 4000000 INFO @ Mon, 03 Jun 2019 10:46:01: 4000000 INFO @ Mon, 03 Jun 2019 10:46:06: 4000000 INFO @ Mon, 03 Jun 2019 10:46:08: 5000000 INFO @ Mon, 03 Jun 2019 10:46:08: 5000000 INFO @ Mon, 03 Jun 2019 10:46:15: 5000000 INFO @ Mon, 03 Jun 2019 10:46:16: 6000000 INFO @ Mon, 03 Jun 2019 10:46:16: 6000000 INFO @ Mon, 03 Jun 2019 10:46:23: 6000000 INFO @ Mon, 03 Jun 2019 10:46:24: 7000000 INFO @ Mon, 03 Jun 2019 10:46:24: 7000000 INFO @ Mon, 03 Jun 2019 10:46:31: 8000000 INFO @ Mon, 03 Jun 2019 10:46:31: 8000000 INFO @ Mon, 03 Jun 2019 10:46:33: 7000000 INFO @ Mon, 03 Jun 2019 10:46:39: 9000000 INFO @ Mon, 03 Jun 2019 10:46:39: 9000000 INFO @ Mon, 03 Jun 2019 10:46:41: 8000000 INFO @ Mon, 03 Jun 2019 10:46:47: 10000000 INFO @ Mon, 03 Jun 2019 10:46:47: 10000000 INFO @ Mon, 03 Jun 2019 10:46:50: 9000000 INFO @ Mon, 03 Jun 2019 10:46:54: 11000000 INFO @ Mon, 03 Jun 2019 10:46:55: 11000000 INFO @ Mon, 03 Jun 2019 10:46:59: 10000000 INFO @ Mon, 03 Jun 2019 10:47:02: 12000000 INFO @ Mon, 03 Jun 2019 10:47:02: 12000000 INFO @ Mon, 03 Jun 2019 10:47:08: 11000000 INFO @ Mon, 03 Jun 2019 10:47:09: 13000000 INFO @ Mon, 03 Jun 2019 10:47:10: 13000000 INFO @ Mon, 03 Jun 2019 10:47:16: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 10:47:16: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 10:47:16: #1 total tags in treatment: 13775599 INFO @ Mon, 03 Jun 2019 10:47:16: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:47:16: #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 10:47:16: #1 tags after filtering in treatment: 13775599 INFO @ Mon, 03 Jun 2019 10:47:16: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:47:16: #1 finished! INFO @ Mon, 03 Jun 2019 10:47:16: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:47:16: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:47:16: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 10:47:16: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 10:47:16: #1 total tags in treatment: 13775599 INFO @ Mon, 03 Jun 2019 10:47:16: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:47:16: #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 10:47:16: #1 tags after filtering in treatment: 13775599 INFO @ Mon, 03 Jun 2019 10:47:16: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:47:16: #1 finished! INFO @ Mon, 03 Jun 2019 10:47:16: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:47:16: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:47:17: 12000000 INFO @ Mon, 03 Jun 2019 10:47:17: #2 number of paired peaks: 406 WARNING @ Mon, 03 Jun 2019 10:47:17: 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 10:47:17: start model_add_line... INFO @ Mon, 03 Jun 2019 10:47:17: start X-correlation... INFO @ Mon, 03 Jun 2019 10:47:17: end of X-cor INFO @ Mon, 03 Jun 2019 10:47:17: #2 finished! INFO @ Mon, 03 Jun 2019 10:47:17: #2 predicted fragment length is 43 bps INFO @ Mon, 03 Jun 2019 10:47:17: #2 alternative fragment length(s) may be 43 bps INFO @ Mon, 03 Jun 2019 10:47:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287942/SRX287942.10_model.r WARNING @ Mon, 03 Jun 2019 10:47:17: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 10:47:17: #2 You may need to consider one of the other alternative d(s): 43 WARNING @ Mon, 03 Jun 2019 10:47:17: #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 10:47:17: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:47:17: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:47:18: #2 number of paired peaks: 406 WARNING @ Mon, 03 Jun 2019 10:47:18: 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 10:47:18: start model_add_line... INFO @ Mon, 03 Jun 2019 10:47:18: start X-correlation... INFO @ Mon, 03 Jun 2019 10:47:18: end of X-cor INFO @ Mon, 03 Jun 2019 10:47:18: #2 finished! INFO @ Mon, 03 Jun 2019 10:47:18: #2 predicted fragment length is 43 bps INFO @ Mon, 03 Jun 2019 10:47:18: #2 alternative fragment length(s) may be 43 bps INFO @ Mon, 03 Jun 2019 10:47:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287942/SRX287942.05_model.r WARNING @ Mon, 03 Jun 2019 10:47:18: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 10:47:18: #2 You may need to consider one of the other alternative d(s): 43 WARNING @ Mon, 03 Jun 2019 10:47:18: #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 10:47:18: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:47:18: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:47:25: 13000000 INFO @ Mon, 03 Jun 2019 10:47:32: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 10:47:32: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 10:47:32: #1 total tags in treatment: 13775599 INFO @ Mon, 03 Jun 2019 10:47:32: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:47:32: #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 10:47:33: #1 tags after filtering in treatment: 13775599 INFO @ Mon, 03 Jun 2019 10:47:33: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:47:33: #1 finished! INFO @ Mon, 03 Jun 2019 10:47:33: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:47:33: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:47:34: #2 number of paired peaks: 406 WARNING @ Mon, 03 Jun 2019 10:47:34: 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 10:47:34: start model_add_line... INFO @ Mon, 03 Jun 2019 10:47:34: start X-correlation... INFO @ Mon, 03 Jun 2019 10:47:34: end of X-cor INFO @ Mon, 03 Jun 2019 10:47:34: #2 finished! INFO @ Mon, 03 Jun 2019 10:47:34: #2 predicted fragment length is 43 bps INFO @ Mon, 03 Jun 2019 10:47:34: #2 alternative fragment length(s) may be 43 bps INFO @ Mon, 03 Jun 2019 10:47:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287942/SRX287942.20_model.r WARNING @ Mon, 03 Jun 2019 10:47:34: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 10:47:34: #2 You may need to consider one of the other alternative d(s): 43 WARNING @ Mon, 03 Jun 2019 10:47:34: #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 10:47:34: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:47:34: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:47:54: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:47:54: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:48:11: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:48:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287942/SRX287942.10_peaks.xls INFO @ Mon, 03 Jun 2019 10:48:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287942/SRX287942.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:48:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287942/SRX287942.10_summits.bed INFO @ Mon, 03 Jun 2019 10:48:13: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1930 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 10:48:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287942/SRX287942.05_peaks.xls INFO @ Mon, 03 Jun 2019 10:48:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287942/SRX287942.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:48:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287942/SRX287942.05_summits.bed INFO @ Mon, 03 Jun 2019 10:48:13: Done! pass1 - making usageList (13 chroms): 3 millis pass2 - checking and writing primary data (2261 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 10:48:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287942/SRX287942.20_peaks.xls INFO @ Mon, 03 Jun 2019 10:48:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287942/SRX287942.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:48:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287942/SRX287942.20_summits.bed INFO @ Mon, 03 Jun 2019 10:48:30: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (1514 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。