Job ID = 1295039 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 26,699,672 reads read : 26,699,672 reads written : 26,699,672 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: 00:12:26 26699672 reads; of these: 26699672 (100.00%) were unpaired; of these: 802815 (3.01%) aligned 0 times 17531856 (65.66%) aligned exactly 1 time 8365001 (31.33%) aligned >1 times 96.99% overall alignment rate Time searching: 00:12:26 Overall time: 00:12:26 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] 3105524 / 25896857 = 0.1199 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 11:55:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX306202/SRX306202.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX306202/SRX306202.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX306202/SRX306202.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX306202/SRX306202.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 11:55:14: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:55:14: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:55:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX306202/SRX306202.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX306202/SRX306202.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX306202/SRX306202.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX306202/SRX306202.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 11:55:14: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:55:14: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:55:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX306202/SRX306202.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX306202/SRX306202.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX306202/SRX306202.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX306202/SRX306202.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 11:55:14: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:55:14: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:55:22: 1000000 INFO @ Mon, 03 Jun 2019 11:55:23: 1000000 INFO @ Mon, 03 Jun 2019 11:55:24: 1000000 INFO @ Mon, 03 Jun 2019 11:55:30: 2000000 INFO @ Mon, 03 Jun 2019 11:55:32: 2000000 INFO @ Mon, 03 Jun 2019 11:55:34: 2000000 INFO @ Mon, 03 Jun 2019 11:55:38: 3000000 INFO @ Mon, 03 Jun 2019 11:55:40: 3000000 INFO @ Mon, 03 Jun 2019 11:55:44: 3000000 INFO @ Mon, 03 Jun 2019 11:55:47: 4000000 INFO @ Mon, 03 Jun 2019 11:55:49: 4000000 INFO @ Mon, 03 Jun 2019 11:55:53: 4000000 INFO @ Mon, 03 Jun 2019 11:55:56: 5000000 INFO @ Mon, 03 Jun 2019 11:55:57: 5000000 INFO @ Mon, 03 Jun 2019 11:56:03: 5000000 INFO @ Mon, 03 Jun 2019 11:56:04: 6000000 INFO @ Mon, 03 Jun 2019 11:56:06: 6000000 INFO @ Mon, 03 Jun 2019 11:56:13: 7000000 INFO @ Mon, 03 Jun 2019 11:56:13: 6000000 INFO @ Mon, 03 Jun 2019 11:56:15: 7000000 INFO @ Mon, 03 Jun 2019 11:56:21: 8000000 INFO @ Mon, 03 Jun 2019 11:56:23: 7000000 INFO @ Mon, 03 Jun 2019 11:56:23: 8000000 INFO @ Mon, 03 Jun 2019 11:56:30: 9000000 INFO @ Mon, 03 Jun 2019 11:56:32: 9000000 INFO @ Mon, 03 Jun 2019 11:56:33: 8000000 INFO @ Mon, 03 Jun 2019 11:56:38: 10000000 INFO @ Mon, 03 Jun 2019 11:56:40: 10000000 INFO @ Mon, 03 Jun 2019 11:56:43: 9000000 INFO @ Mon, 03 Jun 2019 11:56:47: 11000000 INFO @ Mon, 03 Jun 2019 11:56:48: 11000000 INFO @ Mon, 03 Jun 2019 11:56:53: 10000000 INFO @ Mon, 03 Jun 2019 11:56:55: 12000000 INFO @ Mon, 03 Jun 2019 11:56:56: 12000000 INFO @ Mon, 03 Jun 2019 11:57:03: 11000000 INFO @ Mon, 03 Jun 2019 11:57:03: 13000000 INFO @ Mon, 03 Jun 2019 11:57:04: 13000000 INFO @ Mon, 03 Jun 2019 11:57:11: 14000000 INFO @ Mon, 03 Jun 2019 11:57:12: 14000000 INFO @ Mon, 03 Jun 2019 11:57:12: 12000000 INFO @ Mon, 03 Jun 2019 11:57:19: 15000000 INFO @ Mon, 03 Jun 2019 11:57:20: 15000000 INFO @ Mon, 03 Jun 2019 11:57:22: 13000000 INFO @ Mon, 03 Jun 2019 11:57:28: 16000000 INFO @ Mon, 03 Jun 2019 11:57:28: 16000000 INFO @ Mon, 03 Jun 2019 11:57:31: 14000000 INFO @ Mon, 03 Jun 2019 11:57:36: 17000000 INFO @ Mon, 03 Jun 2019 11:57:36: 17000000 INFO @ Mon, 03 Jun 2019 11:57:42: 15000000 INFO @ Mon, 03 Jun 2019 11:57:44: 18000000 INFO @ Mon, 03 Jun 2019 11:57:44: 18000000 INFO @ Mon, 03 Jun 2019 11:57:51: 16000000 INFO @ Mon, 03 Jun 2019 11:57:52: 19000000 INFO @ Mon, 03 Jun 2019 11:57:52: 19000000 INFO @ Mon, 03 Jun 2019 11:58:00: 20000000 INFO @ Mon, 03 Jun 2019 11:58:00: 20000000 INFO @ Mon, 03 Jun 2019 11:58:01: 17000000 INFO @ Mon, 03 Jun 2019 11:58:07: 21000000 INFO @ Mon, 03 Jun 2019 11:58:08: 21000000 INFO @ Mon, 03 Jun 2019 11:58:11: 18000000 INFO @ Mon, 03 Jun 2019 11:58:15: 22000000 INFO @ Mon, 03 Jun 2019 11:58:16: 22000000 INFO @ Mon, 03 Jun 2019 11:58:20: 19000000 INFO @ Mon, 03 Jun 2019 11:58:22: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 11:58:22: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 11:58:22: #1 total tags in treatment: 22791333 INFO @ Mon, 03 Jun 2019 11:58:22: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:58:22: #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 11:58:22: #1 tags after filtering in treatment: 22791333 INFO @ Mon, 03 Jun 2019 11:58:22: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:58:22: #1 finished! INFO @ Mon, 03 Jun 2019 11:58:22: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:58:22: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:58:23: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 11:58:23: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 11:58:23: #1 total tags in treatment: 22791333 INFO @ Mon, 03 Jun 2019 11:58:23: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:58:23: #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 11:58:23: #1 tags after filtering in treatment: 22791333 INFO @ Mon, 03 Jun 2019 11:58:23: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:58:23: #1 finished! INFO @ Mon, 03 Jun 2019 11:58:23: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:58:23: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:58:24: #2 number of paired peaks: 305 WARNING @ Mon, 03 Jun 2019 11:58:24: Fewer paired peaks (305) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 305 pairs to build model! INFO @ Mon, 03 Jun 2019 11:58:24: start model_add_line... INFO @ Mon, 03 Jun 2019 11:58:24: start X-correlation... INFO @ Mon, 03 Jun 2019 11:58:24: end of X-cor INFO @ Mon, 03 Jun 2019 11:58:24: #2 finished! INFO @ Mon, 03 Jun 2019 11:58:24: #2 predicted fragment length is 42 bps INFO @ Mon, 03 Jun 2019 11:58:24: #2 alternative fragment length(s) may be 2,42,534,552 bps INFO @ Mon, 03 Jun 2019 11:58:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX306202/SRX306202.10_model.r WARNING @ Mon, 03 Jun 2019 11:58:24: #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 11:58:24: #2 You may need to consider one of the other alternative d(s): 2,42,534,552 WARNING @ Mon, 03 Jun 2019 11:58:24: #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 11:58:24: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:58:24: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:58:25: #2 number of paired peaks: 305 WARNING @ Mon, 03 Jun 2019 11:58:25: Fewer paired peaks (305) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 305 pairs to build model! INFO @ Mon, 03 Jun 2019 11:58:25: start model_add_line... INFO @ Mon, 03 Jun 2019 11:58:26: start X-correlation... INFO @ Mon, 03 Jun 2019 11:58:26: end of X-cor INFO @ Mon, 03 Jun 2019 11:58:26: #2 finished! INFO @ Mon, 03 Jun 2019 11:58:26: #2 predicted fragment length is 42 bps INFO @ Mon, 03 Jun 2019 11:58:26: #2 alternative fragment length(s) may be 2,42,534,552 bps INFO @ Mon, 03 Jun 2019 11:58:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX306202/SRX306202.20_model.r WARNING @ Mon, 03 Jun 2019 11:58:26: #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 11:58:26: #2 You may need to consider one of the other alternative d(s): 2,42,534,552 WARNING @ Mon, 03 Jun 2019 11:58:26: #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 11:58:26: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:58:26: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:58:30: 20000000 INFO @ Mon, 03 Jun 2019 11:58:39: 21000000 INFO @ Mon, 03 Jun 2019 11:58:48: 22000000 INFO @ Mon, 03 Jun 2019 11:58:55: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 11:58:55: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 11:58:55: #1 total tags in treatment: 22791333 INFO @ Mon, 03 Jun 2019 11:58:55: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:58:55: #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 11:58:56: #1 tags after filtering in treatment: 22791333 INFO @ Mon, 03 Jun 2019 11:58:56: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:58:56: #1 finished! INFO @ Mon, 03 Jun 2019 11:58:56: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:58:56: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:58:58: #2 number of paired peaks: 305 WARNING @ Mon, 03 Jun 2019 11:58:58: Fewer paired peaks (305) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 305 pairs to build model! INFO @ Mon, 03 Jun 2019 11:58:58: start model_add_line... INFO @ Mon, 03 Jun 2019 11:58:58: start X-correlation... INFO @ Mon, 03 Jun 2019 11:58:58: end of X-cor INFO @ Mon, 03 Jun 2019 11:58:58: #2 finished! INFO @ Mon, 03 Jun 2019 11:58:58: #2 predicted fragment length is 42 bps INFO @ Mon, 03 Jun 2019 11:58:58: #2 alternative fragment length(s) may be 2,42,534,552 bps INFO @ Mon, 03 Jun 2019 11:58:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX306202/SRX306202.05_model.r WARNING @ Mon, 03 Jun 2019 11:58:58: #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 11:58:58: #2 You may need to consider one of the other alternative d(s): 2,42,534,552 WARNING @ Mon, 03 Jun 2019 11:58:58: #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 11:58:58: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:58:58: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:59:23: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:59:25: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:59:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX306202/SRX306202.10_peaks.xls INFO @ Mon, 03 Jun 2019 11:59:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX306202/SRX306202.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:59:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX306202/SRX306202.10_summits.bed INFO @ Mon, 03 Jun 2019 11:59:51: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (2282 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 11:59:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX306202/SRX306202.20_peaks.xls INFO @ Mon, 03 Jun 2019 11:59:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX306202/SRX306202.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:59:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX306202/SRX306202.20_summits.bed INFO @ Mon, 03 Jun 2019 11:59:52: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (870 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 12:00:00: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 12:00:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX306202/SRX306202.05_peaks.xls INFO @ Mon, 03 Jun 2019 12:00:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX306202/SRX306202.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 12:00:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX306202/SRX306202.05_summits.bed INFO @ Mon, 03 Jun 2019 12:00:28: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3580 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。