Job ID = 1294002 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 22,498,098 reads read : 22,498,098 reads written : 22,498,098 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: 00:07:28 22498098 reads; of these: 22498098 (100.00%) were unpaired; of these: 2654447 (11.80%) aligned 0 times 13830301 (61.47%) aligned exactly 1 time 6013350 (26.73%) aligned >1 times 88.20% overall alignment rate Time searching: 00:07:28 Overall time: 00:07:28 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] 1794034 / 19843651 = 0.0904 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 04:06:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX159173/SRX159173.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX159173/SRX159173.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX159173/SRX159173.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX159173/SRX159173.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 04:06:03: #1 read tag files... INFO @ Mon, 03 Jun 2019 04:06:03: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 04:06:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX159173/SRX159173.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX159173/SRX159173.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX159173/SRX159173.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX159173/SRX159173.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 04:06:03: #1 read tag files... INFO @ Mon, 03 Jun 2019 04:06:03: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 04:06:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX159173/SRX159173.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX159173/SRX159173.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX159173/SRX159173.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX159173/SRX159173.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 04:06:03: #1 read tag files... INFO @ Mon, 03 Jun 2019 04:06:03: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 04:06:09: 1000000 INFO @ Mon, 03 Jun 2019 04:06:11: 1000000 INFO @ Mon, 03 Jun 2019 04:06:11: 1000000 INFO @ Mon, 03 Jun 2019 04:06:15: 2000000 INFO @ Mon, 03 Jun 2019 04:06:19: 2000000 INFO @ Mon, 03 Jun 2019 04:06:19: 2000000 INFO @ Mon, 03 Jun 2019 04:06:22: 3000000 INFO @ Mon, 03 Jun 2019 04:06:27: 3000000 INFO @ Mon, 03 Jun 2019 04:06:27: 3000000 INFO @ Mon, 03 Jun 2019 04:06:28: 4000000 INFO @ Mon, 03 Jun 2019 04:06:34: 5000000 INFO @ Mon, 03 Jun 2019 04:06:34: 4000000 INFO @ Mon, 03 Jun 2019 04:06:35: 4000000 INFO @ Mon, 03 Jun 2019 04:06:40: 6000000 INFO @ Mon, 03 Jun 2019 04:06:42: 5000000 INFO @ Mon, 03 Jun 2019 04:06:42: 5000000 INFO @ Mon, 03 Jun 2019 04:06:46: 7000000 INFO @ Mon, 03 Jun 2019 04:06:50: 6000000 INFO @ Mon, 03 Jun 2019 04:06:50: 6000000 INFO @ Mon, 03 Jun 2019 04:06:53: 8000000 INFO @ Mon, 03 Jun 2019 04:06:58: 7000000 INFO @ Mon, 03 Jun 2019 04:06:58: 7000000 INFO @ Mon, 03 Jun 2019 04:06:59: 9000000 INFO @ Mon, 03 Jun 2019 04:07:05: 10000000 INFO @ Mon, 03 Jun 2019 04:07:06: 8000000 INFO @ Mon, 03 Jun 2019 04:07:06: 8000000 INFO @ Mon, 03 Jun 2019 04:07:12: 11000000 INFO @ Mon, 03 Jun 2019 04:07:14: 9000000 INFO @ Mon, 03 Jun 2019 04:07:14: 9000000 INFO @ Mon, 03 Jun 2019 04:07:18: 12000000 INFO @ Mon, 03 Jun 2019 04:07:22: 10000000 INFO @ Mon, 03 Jun 2019 04:07:22: 10000000 INFO @ Mon, 03 Jun 2019 04:07:24: 13000000 INFO @ Mon, 03 Jun 2019 04:07:30: 11000000 INFO @ Mon, 03 Jun 2019 04:07:30: 11000000 INFO @ Mon, 03 Jun 2019 04:07:31: 14000000 INFO @ Mon, 03 Jun 2019 04:07:37: 15000000 INFO @ Mon, 03 Jun 2019 04:07:38: 12000000 INFO @ Mon, 03 Jun 2019 04:07:38: 12000000 INFO @ Mon, 03 Jun 2019 04:07:44: 16000000 INFO @ Mon, 03 Jun 2019 04:07:46: 13000000 INFO @ Mon, 03 Jun 2019 04:07:46: 13000000 INFO @ Mon, 03 Jun 2019 04:07:50: 17000000 INFO @ Mon, 03 Jun 2019 04:07:54: 14000000 INFO @ Mon, 03 Jun 2019 04:07:54: 14000000 INFO @ Mon, 03 Jun 2019 04:07:57: 18000000 INFO @ Mon, 03 Jun 2019 04:07:57: #1 tag size is determined as 42 bps INFO @ Mon, 03 Jun 2019 04:07:57: #1 tag size = 42 INFO @ Mon, 03 Jun 2019 04:07:57: #1 total tags in treatment: 18049617 INFO @ Mon, 03 Jun 2019 04:07:57: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 04:07:57: #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 04:07:58: #1 tags after filtering in treatment: 18049617 INFO @ Mon, 03 Jun 2019 04:07:58: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 04:07:58: #1 finished! INFO @ Mon, 03 Jun 2019 04:07:58: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 04:07:58: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 04:07:59: #2 number of paired peaks: 559 WARNING @ Mon, 03 Jun 2019 04:07:59: Fewer paired peaks (559) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 559 pairs to build model! INFO @ Mon, 03 Jun 2019 04:07:59: start model_add_line... INFO @ Mon, 03 Jun 2019 04:07:59: start X-correlation... INFO @ Mon, 03 Jun 2019 04:07:59: end of X-cor INFO @ Mon, 03 Jun 2019 04:07:59: #2 finished! INFO @ Mon, 03 Jun 2019 04:07:59: #2 predicted fragment length is 45 bps INFO @ Mon, 03 Jun 2019 04:07:59: #2 alternative fragment length(s) may be 3,45 bps INFO @ Mon, 03 Jun 2019 04:07:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX159173/SRX159173.05_model.r WARNING @ Mon, 03 Jun 2019 04:07:59: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 04:07:59: #2 You may need to consider one of the other alternative d(s): 3,45 WARNING @ Mon, 03 Jun 2019 04:07:59: #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 04:07:59: #3 Call peaks... INFO @ Mon, 03 Jun 2019 04:08:00: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 04:08:02: 15000000 INFO @ Mon, 03 Jun 2019 04:08:02: 15000000 INFO @ Mon, 03 Jun 2019 04:08:10: 16000000 INFO @ Mon, 03 Jun 2019 04:08:10: 16000000 INFO @ Mon, 03 Jun 2019 04:08:17: 17000000 INFO @ Mon, 03 Jun 2019 04:08:17: 17000000 INFO @ Mon, 03 Jun 2019 04:08:25: 18000000 INFO @ Mon, 03 Jun 2019 04:08:25: 18000000 INFO @ Mon, 03 Jun 2019 04:08:26: #1 tag size is determined as 42 bps INFO @ Mon, 03 Jun 2019 04:08:26: #1 tag size = 42 INFO @ Mon, 03 Jun 2019 04:08:26: #1 total tags in treatment: 18049617 INFO @ Mon, 03 Jun 2019 04:08:26: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 04:08:26: #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 04:08:26: #1 tag size is determined as 42 bps INFO @ Mon, 03 Jun 2019 04:08:26: #1 tag size = 42 INFO @ Mon, 03 Jun 2019 04:08:26: #1 total tags in treatment: 18049617 INFO @ Mon, 03 Jun 2019 04:08:26: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 04:08:26: #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 04:08:26: #1 tags after filtering in treatment: 18049617 INFO @ Mon, 03 Jun 2019 04:08:26: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 04:08:26: #1 finished! INFO @ Mon, 03 Jun 2019 04:08:26: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 04:08:26: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 04:08:26: #1 tags after filtering in treatment: 18049617 INFO @ Mon, 03 Jun 2019 04:08:26: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 04:08:26: #1 finished! INFO @ Mon, 03 Jun 2019 04:08:26: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 04:08:26: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 04:08:28: #2 number of paired peaks: 559 WARNING @ Mon, 03 Jun 2019 04:08:28: Fewer paired peaks (559) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 559 pairs to build model! INFO @ Mon, 03 Jun 2019 04:08:28: start model_add_line... INFO @ Mon, 03 Jun 2019 04:08:28: #2 number of paired peaks: 559 WARNING @ Mon, 03 Jun 2019 04:08:28: Fewer paired peaks (559) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 559 pairs to build model! INFO @ Mon, 03 Jun 2019 04:08:28: start model_add_line... INFO @ Mon, 03 Jun 2019 04:08:28: start X-correlation... INFO @ Mon, 03 Jun 2019 04:08:28: end of X-cor INFO @ Mon, 03 Jun 2019 04:08:28: #2 finished! INFO @ Mon, 03 Jun 2019 04:08:28: #2 predicted fragment length is 45 bps INFO @ Mon, 03 Jun 2019 04:08:28: #2 alternative fragment length(s) may be 3,45 bps INFO @ Mon, 03 Jun 2019 04:08:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX159173/SRX159173.20_model.r WARNING @ Mon, 03 Jun 2019 04:08:28: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 04:08:28: #2 You may need to consider one of the other alternative d(s): 3,45 WARNING @ Mon, 03 Jun 2019 04:08:28: #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 04:08:28: #3 Call peaks... INFO @ Mon, 03 Jun 2019 04:08:28: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 04:08:28: start X-correlation... INFO @ Mon, 03 Jun 2019 04:08:28: end of X-cor INFO @ Mon, 03 Jun 2019 04:08:28: #2 finished! INFO @ Mon, 03 Jun 2019 04:08:28: #2 predicted fragment length is 45 bps INFO @ Mon, 03 Jun 2019 04:08:28: #2 alternative fragment length(s) may be 3,45 bps INFO @ Mon, 03 Jun 2019 04:08:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX159173/SRX159173.10_model.r WARNING @ Mon, 03 Jun 2019 04:08:28: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 04:08:28: #2 You may need to consider one of the other alternative d(s): 3,45 WARNING @ Mon, 03 Jun 2019 04:08:28: #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 04:08:28: #3 Call peaks... INFO @ Mon, 03 Jun 2019 04:08:28: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 04:08:46: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 04:09:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX159173/SRX159173.05_peaks.xls INFO @ Mon, 03 Jun 2019 04:09:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX159173/SRX159173.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 04:09:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX159173/SRX159173.05_summits.bed INFO @ Mon, 03 Jun 2019 04:09:10: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (3990 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 04:09:14: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 04:09:14: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 04:09:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX159173/SRX159173.10_peaks.xls INFO @ Mon, 03 Jun 2019 04:09:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX159173/SRX159173.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 04:09:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX159173/SRX159173.10_summits.bed INFO @ Mon, 03 Jun 2019 04:09:37: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2374 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 04:09:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX159173/SRX159173.20_peaks.xls INFO @ Mon, 03 Jun 2019 04:09:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX159173/SRX159173.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 04:09:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX159173/SRX159173.20_summits.bed INFO @ Mon, 03 Jun 2019 04:09:37: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (1198 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。