Job ID = 1295217 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 21,559,305 reads read : 21,559,305 reads written : 21,559,305 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: 00:08:24 21559305 reads; of these: 21559305 (100.00%) were unpaired; of these: 1335820 (6.20%) aligned 0 times 15428623 (71.56%) aligned exactly 1 time 4794862 (22.24%) aligned >1 times 93.80% overall alignment rate Time searching: 00:08:24 Overall time: 00:08:24 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] 1891127 / 20223485 = 0.0935 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 13:06:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX331390/SRX331390.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX331390/SRX331390.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX331390/SRX331390.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX331390/SRX331390.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 13:06:27: #1 read tag files... INFO @ Mon, 03 Jun 2019 13:06:27: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 13:06:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX331390/SRX331390.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX331390/SRX331390.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX331390/SRX331390.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX331390/SRX331390.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 13:06:27: #1 read tag files... INFO @ Mon, 03 Jun 2019 13:06:27: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 13:06:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX331390/SRX331390.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX331390/SRX331390.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX331390/SRX331390.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX331390/SRX331390.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 13:06:27: #1 read tag files... INFO @ Mon, 03 Jun 2019 13:06:27: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 13:06:35: 1000000 INFO @ Mon, 03 Jun 2019 13:06:37: 1000000 INFO @ Mon, 03 Jun 2019 13:06:39: 1000000 INFO @ Mon, 03 Jun 2019 13:06:45: 2000000 INFO @ Mon, 03 Jun 2019 13:06:49: 2000000 INFO @ Mon, 03 Jun 2019 13:06:52: 2000000 INFO @ Mon, 03 Jun 2019 13:06:55: 3000000 INFO @ Mon, 03 Jun 2019 13:06:59: 3000000 INFO @ Mon, 03 Jun 2019 13:07:04: 4000000 INFO @ Mon, 03 Jun 2019 13:07:05: 3000000 INFO @ Mon, 03 Jun 2019 13:07:10: 4000000 INFO @ Mon, 03 Jun 2019 13:07:13: 5000000 INFO @ Mon, 03 Jun 2019 13:07:17: 4000000 INFO @ Mon, 03 Jun 2019 13:07:20: 5000000 INFO @ Mon, 03 Jun 2019 13:07:22: 6000000 INFO @ Mon, 03 Jun 2019 13:07:29: 5000000 INFO @ Mon, 03 Jun 2019 13:07:30: 7000000 INFO @ Mon, 03 Jun 2019 13:07:30: 6000000 INFO @ Mon, 03 Jun 2019 13:07:39: 8000000 INFO @ Mon, 03 Jun 2019 13:07:41: 6000000 INFO @ Mon, 03 Jun 2019 13:07:41: 7000000 INFO @ Mon, 03 Jun 2019 13:07:48: 9000000 INFO @ Mon, 03 Jun 2019 13:07:52: 8000000 INFO @ Mon, 03 Jun 2019 13:07:53: 7000000 INFO @ Mon, 03 Jun 2019 13:07:59: 10000000 INFO @ Mon, 03 Jun 2019 13:08:02: 9000000 INFO @ Mon, 03 Jun 2019 13:08:05: 8000000 INFO @ Mon, 03 Jun 2019 13:08:07: 11000000 INFO @ Mon, 03 Jun 2019 13:08:11: 10000000 INFO @ Mon, 03 Jun 2019 13:08:16: 12000000 INFO @ Mon, 03 Jun 2019 13:08:17: 9000000 INFO @ Mon, 03 Jun 2019 13:08:21: 11000000 INFO @ Mon, 03 Jun 2019 13:08:25: 13000000 INFO @ Mon, 03 Jun 2019 13:08:29: 10000000 INFO @ Mon, 03 Jun 2019 13:08:31: 12000000 INFO @ Mon, 03 Jun 2019 13:08:34: 14000000 INFO @ Mon, 03 Jun 2019 13:08:40: 13000000 INFO @ Mon, 03 Jun 2019 13:08:40: 11000000 INFO @ Mon, 03 Jun 2019 13:08:43: 15000000 INFO @ Mon, 03 Jun 2019 13:08:50: 14000000 INFO @ Mon, 03 Jun 2019 13:08:52: 16000000 INFO @ Mon, 03 Jun 2019 13:08:52: 12000000 INFO @ Mon, 03 Jun 2019 13:09:01: 15000000 INFO @ Mon, 03 Jun 2019 13:09:02: 17000000 INFO @ Mon, 03 Jun 2019 13:09:04: 13000000 INFO @ Mon, 03 Jun 2019 13:09:11: 16000000 INFO @ Mon, 03 Jun 2019 13:09:11: 18000000 INFO @ Mon, 03 Jun 2019 13:09:14: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 13:09:14: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 13:09:14: #1 total tags in treatment: 18332358 INFO @ Mon, 03 Jun 2019 13:09:14: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 13:09:14: #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 13:09:14: #1 tags after filtering in treatment: 18332358 INFO @ Mon, 03 Jun 2019 13:09:14: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 13:09:14: #1 finished! INFO @ Mon, 03 Jun 2019 13:09:14: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 13:09:14: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 13:09:16: #2 number of paired peaks: 155 WARNING @ Mon, 03 Jun 2019 13:09:16: Fewer paired peaks (155) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 155 pairs to build model! INFO @ Mon, 03 Jun 2019 13:09:16: start model_add_line... INFO @ Mon, 03 Jun 2019 13:09:16: start X-correlation... INFO @ Mon, 03 Jun 2019 13:09:16: end of X-cor INFO @ Mon, 03 Jun 2019 13:09:16: #2 finished! INFO @ Mon, 03 Jun 2019 13:09:16: #2 predicted fragment length is 44 bps INFO @ Mon, 03 Jun 2019 13:09:16: #2 alternative fragment length(s) may be 44 bps INFO @ Mon, 03 Jun 2019 13:09:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX331390/SRX331390.10_model.r WARNING @ Mon, 03 Jun 2019 13:09:16: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 13:09:16: #2 You may need to consider one of the other alternative d(s): 44 WARNING @ Mon, 03 Jun 2019 13:09:16: #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 13:09:16: #3 Call peaks... INFO @ Mon, 03 Jun 2019 13:09:16: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 13:09:17: 14000000 INFO @ Mon, 03 Jun 2019 13:09:21: 17000000 INFO @ Mon, 03 Jun 2019 13:09:29: 15000000 INFO @ Mon, 03 Jun 2019 13:09:30: 18000000 INFO @ Mon, 03 Jun 2019 13:09:34: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 13:09:34: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 13:09:34: #1 total tags in treatment: 18332358 INFO @ Mon, 03 Jun 2019 13:09:34: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 13:09:34: #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 13:09:34: #1 tags after filtering in treatment: 18332358 INFO @ Mon, 03 Jun 2019 13:09:34: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 13:09:34: #1 finished! INFO @ Mon, 03 Jun 2019 13:09:34: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 13:09:34: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 13:09:36: #2 number of paired peaks: 155 WARNING @ Mon, 03 Jun 2019 13:09:36: Fewer paired peaks (155) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 155 pairs to build model! INFO @ Mon, 03 Jun 2019 13:09:36: start model_add_line... INFO @ Mon, 03 Jun 2019 13:09:36: start X-correlation... INFO @ Mon, 03 Jun 2019 13:09:36: end of X-cor INFO @ Mon, 03 Jun 2019 13:09:36: #2 finished! INFO @ Mon, 03 Jun 2019 13:09:36: #2 predicted fragment length is 44 bps INFO @ Mon, 03 Jun 2019 13:09:36: #2 alternative fragment length(s) may be 44 bps INFO @ Mon, 03 Jun 2019 13:09:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX331390/SRX331390.20_model.r WARNING @ Mon, 03 Jun 2019 13:09:36: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 13:09:36: #2 You may need to consider one of the other alternative d(s): 44 WARNING @ Mon, 03 Jun 2019 13:09:36: #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 13:09:36: #3 Call peaks... INFO @ Mon, 03 Jun 2019 13:09:36: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 13:09:40: 16000000 INFO @ Mon, 03 Jun 2019 13:09:50: 17000000 INFO @ Mon, 03 Jun 2019 13:10:01: 18000000 INFO @ Mon, 03 Jun 2019 13:10:03: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 13:10:05: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 13:10:05: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 13:10:05: #1 total tags in treatment: 18332358 INFO @ Mon, 03 Jun 2019 13:10:05: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 13:10:05: #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 13:10:05: #1 tags after filtering in treatment: 18332358 INFO @ Mon, 03 Jun 2019 13:10:05: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 13:10:05: #1 finished! INFO @ Mon, 03 Jun 2019 13:10:05: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 13:10:05: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 13:10:07: #2 number of paired peaks: 155 WARNING @ Mon, 03 Jun 2019 13:10:07: Fewer paired peaks (155) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 155 pairs to build model! INFO @ Mon, 03 Jun 2019 13:10:07: start model_add_line... INFO @ Mon, 03 Jun 2019 13:10:07: start X-correlation... INFO @ Mon, 03 Jun 2019 13:10:07: end of X-cor INFO @ Mon, 03 Jun 2019 13:10:07: #2 finished! INFO @ Mon, 03 Jun 2019 13:10:07: #2 predicted fragment length is 44 bps INFO @ Mon, 03 Jun 2019 13:10:07: #2 alternative fragment length(s) may be 44 bps INFO @ Mon, 03 Jun 2019 13:10:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX331390/SRX331390.05_model.r WARNING @ Mon, 03 Jun 2019 13:10:07: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 13:10:07: #2 You may need to consider one of the other alternative d(s): 44 WARNING @ Mon, 03 Jun 2019 13:10:07: #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 13:10:07: #3 Call peaks... INFO @ Mon, 03 Jun 2019 13:10:07: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 13:10:22: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 13:10:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX331390/SRX331390.10_peaks.xls INFO @ Mon, 03 Jun 2019 13:10:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX331390/SRX331390.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 13:10:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX331390/SRX331390.10_summits.bed INFO @ Mon, 03 Jun 2019 13:10:25: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1621 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 13:10:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX331390/SRX331390.20_peaks.xls INFO @ Mon, 03 Jun 2019 13:10:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX331390/SRX331390.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 13:10:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX331390/SRX331390.20_summits.bed INFO @ Mon, 03 Jun 2019 13:10:44: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1088 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 13:10:53: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 13:11:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX331390/SRX331390.05_peaks.xls INFO @ Mon, 03 Jun 2019 13:11:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX331390/SRX331390.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 13:11:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX331390/SRX331390.05_summits.bed INFO @ Mon, 03 Jun 2019 13:11:16: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2006 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。