Job ID = 1300651 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 40,700,156 reads read : 40,700,156 reads written : 40,700,156 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: 00:23:56 40700156 reads; of these: 40700156 (100.00%) were unpaired; of these: 9559171 (23.49%) aligned 0 times 12245240 (30.09%) aligned exactly 1 time 18895745 (46.43%) aligned >1 times 76.51% overall alignment rate Time searching: 00:23:57 Overall time: 00:23:57 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 16 files... [bam_rmdupse_core] 9061750 / 31140985 = 0.2910 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 20:03:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4823788/SRX4823788.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4823788/SRX4823788.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4823788/SRX4823788.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4823788/SRX4823788.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 20:03:25: #1 read tag files... INFO @ Mon, 03 Jun 2019 20:03:25: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 20:03:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4823788/SRX4823788.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4823788/SRX4823788.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4823788/SRX4823788.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4823788/SRX4823788.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 20:03:25: #1 read tag files... INFO @ Mon, 03 Jun 2019 20:03:25: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 20:03:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4823788/SRX4823788.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4823788/SRX4823788.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4823788/SRX4823788.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4823788/SRX4823788.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 20:03:25: #1 read tag files... INFO @ Mon, 03 Jun 2019 20:03:25: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 20:03:35: 1000000 INFO @ Mon, 03 Jun 2019 20:03:36: 1000000 INFO @ Mon, 03 Jun 2019 20:03:36: 1000000 INFO @ Mon, 03 Jun 2019 20:03:46: 2000000 INFO @ Mon, 03 Jun 2019 20:03:46: 2000000 INFO @ Mon, 03 Jun 2019 20:03:47: 2000000 INFO @ Mon, 03 Jun 2019 20:03:56: 3000000 INFO @ Mon, 03 Jun 2019 20:03:56: 3000000 INFO @ Mon, 03 Jun 2019 20:03:57: 3000000 INFO @ Mon, 03 Jun 2019 20:04:07: 4000000 INFO @ Mon, 03 Jun 2019 20:04:07: 4000000 INFO @ Mon, 03 Jun 2019 20:04:09: 4000000 INFO @ Mon, 03 Jun 2019 20:04:17: 5000000 INFO @ Mon, 03 Jun 2019 20:04:19: 5000000 INFO @ Mon, 03 Jun 2019 20:04:19: 5000000 INFO @ Mon, 03 Jun 2019 20:04:27: 6000000 INFO @ Mon, 03 Jun 2019 20:04:30: 6000000 INFO @ Mon, 03 Jun 2019 20:04:30: 6000000 INFO @ Mon, 03 Jun 2019 20:04:38: 7000000 INFO @ Mon, 03 Jun 2019 20:04:40: 7000000 INFO @ Mon, 03 Jun 2019 20:04:42: 7000000 INFO @ Mon, 03 Jun 2019 20:04:47: 8000000 INFO @ Mon, 03 Jun 2019 20:04:50: 8000000 INFO @ Mon, 03 Jun 2019 20:04:53: 8000000 INFO @ Mon, 03 Jun 2019 20:04:57: 9000000 INFO @ Mon, 03 Jun 2019 20:05:00: 9000000 INFO @ Mon, 03 Jun 2019 20:05:03: 9000000 INFO @ Mon, 03 Jun 2019 20:05:06: 10000000 INFO @ Mon, 03 Jun 2019 20:05:10: 10000000 INFO @ Mon, 03 Jun 2019 20:05:13: 10000000 INFO @ Mon, 03 Jun 2019 20:05:16: 11000000 INFO @ Mon, 03 Jun 2019 20:05:21: 11000000 INFO @ Mon, 03 Jun 2019 20:05:24: 11000000 INFO @ Mon, 03 Jun 2019 20:05:25: 12000000 INFO @ Mon, 03 Jun 2019 20:05:31: 12000000 INFO @ Mon, 03 Jun 2019 20:05:35: 12000000 INFO @ Mon, 03 Jun 2019 20:05:35: 13000000 INFO @ Mon, 03 Jun 2019 20:05:40: 13000000 INFO @ Mon, 03 Jun 2019 20:05:45: 14000000 INFO @ Mon, 03 Jun 2019 20:05:45: 13000000 INFO @ Mon, 03 Jun 2019 20:05:51: 14000000 INFO @ Mon, 03 Jun 2019 20:05:55: 15000000 INFO @ Mon, 03 Jun 2019 20:05:56: 14000000 INFO @ Mon, 03 Jun 2019 20:06:02: 15000000 INFO @ Mon, 03 Jun 2019 20:06:04: 16000000 INFO @ Mon, 03 Jun 2019 20:06:07: 15000000 INFO @ Mon, 03 Jun 2019 20:06:13: 16000000 INFO @ Mon, 03 Jun 2019 20:06:13: 17000000 INFO @ Mon, 03 Jun 2019 20:06:18: 16000000 INFO @ Mon, 03 Jun 2019 20:06:23: 17000000 INFO @ Mon, 03 Jun 2019 20:06:23: 18000000 INFO @ Mon, 03 Jun 2019 20:06:28: 17000000 INFO @ Mon, 03 Jun 2019 20:06:33: 19000000 INFO @ Mon, 03 Jun 2019 20:06:33: 18000000 INFO @ Mon, 03 Jun 2019 20:06:38: 18000000 INFO @ Mon, 03 Jun 2019 20:06:43: 20000000 INFO @ Mon, 03 Jun 2019 20:06:43: 19000000 INFO @ Mon, 03 Jun 2019 20:06:49: 19000000 INFO @ Mon, 03 Jun 2019 20:06:52: 21000000 INFO @ Mon, 03 Jun 2019 20:06:53: 20000000 INFO @ Mon, 03 Jun 2019 20:07:00: 20000000 INFO @ Mon, 03 Jun 2019 20:07:01: 22000000 INFO @ Mon, 03 Jun 2019 20:07:02: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 20:07:02: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 20:07:02: #1 total tags in treatment: 22079235 INFO @ Mon, 03 Jun 2019 20:07:02: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 20:07:02: #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 20:07:03: #1 tags after filtering in treatment: 22079235 INFO @ Mon, 03 Jun 2019 20:07:03: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 20:07:03: #1 finished! INFO @ Mon, 03 Jun 2019 20:07:03: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 20:07:03: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 20:07:03: 21000000 INFO @ Mon, 03 Jun 2019 20:07:05: #2 number of paired peaks: 604 WARNING @ Mon, 03 Jun 2019 20:07:05: Fewer paired peaks (604) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 604 pairs to build model! INFO @ Mon, 03 Jun 2019 20:07:05: start model_add_line... INFO @ Mon, 03 Jun 2019 20:07:06: start X-correlation... INFO @ Mon, 03 Jun 2019 20:07:06: end of X-cor INFO @ Mon, 03 Jun 2019 20:07:06: #2 finished! INFO @ Mon, 03 Jun 2019 20:07:06: #2 predicted fragment length is 2 bps INFO @ Mon, 03 Jun 2019 20:07:06: #2 alternative fragment length(s) may be 2,27 bps INFO @ Mon, 03 Jun 2019 20:07:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4823788/SRX4823788.05_model.r WARNING @ Mon, 03 Jun 2019 20:07:06: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 20:07:06: #2 You may need to consider one of the other alternative d(s): 2,27 WARNING @ Mon, 03 Jun 2019 20:07:06: #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 20:07:06: #3 Call peaks... INFO @ Mon, 03 Jun 2019 20:07:06: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 20:07:10: 21000000 INFO @ Mon, 03 Jun 2019 20:07:13: 22000000 INFO @ Mon, 03 Jun 2019 20:07:14: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 20:07:14: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 20:07:14: #1 total tags in treatment: 22079235 INFO @ Mon, 03 Jun 2019 20:07:14: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 20:07:14: #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 20:07:14: #1 tags after filtering in treatment: 22079235 INFO @ Mon, 03 Jun 2019 20:07:14: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 20:07:14: #1 finished! INFO @ Mon, 03 Jun 2019 20:07:14: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 20:07:14: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 20:07:17: #2 number of paired peaks: 604 WARNING @ Mon, 03 Jun 2019 20:07:17: Fewer paired peaks (604) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 604 pairs to build model! INFO @ Mon, 03 Jun 2019 20:07:17: start model_add_line... INFO @ Mon, 03 Jun 2019 20:07:18: start X-correlation... INFO @ Mon, 03 Jun 2019 20:07:18: end of X-cor INFO @ Mon, 03 Jun 2019 20:07:18: #2 finished! INFO @ Mon, 03 Jun 2019 20:07:18: #2 predicted fragment length is 2 bps INFO @ Mon, 03 Jun 2019 20:07:18: #2 alternative fragment length(s) may be 2,27 bps INFO @ Mon, 03 Jun 2019 20:07:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4823788/SRX4823788.10_model.r WARNING @ Mon, 03 Jun 2019 20:07:18: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 20:07:18: #2 You may need to consider one of the other alternative d(s): 2,27 WARNING @ Mon, 03 Jun 2019 20:07:18: #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 20:07:18: #3 Call peaks... INFO @ Mon, 03 Jun 2019 20:07:18: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 20:07:19: 22000000 INFO @ Mon, 03 Jun 2019 20:07:20: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 20:07:20: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 20:07:20: #1 total tags in treatment: 22079235 INFO @ Mon, 03 Jun 2019 20:07:20: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 20:07:20: #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 20:07:21: #1 tags after filtering in treatment: 22079235 INFO @ Mon, 03 Jun 2019 20:07:21: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 20:07:21: #1 finished! INFO @ Mon, 03 Jun 2019 20:07:21: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 20:07:21: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 20:07:23: #2 number of paired peaks: 604 WARNING @ Mon, 03 Jun 2019 20:07:23: Fewer paired peaks (604) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 604 pairs to build model! INFO @ Mon, 03 Jun 2019 20:07:23: start model_add_line... INFO @ Mon, 03 Jun 2019 20:07:23: start X-correlation... INFO @ Mon, 03 Jun 2019 20:07:23: end of X-cor INFO @ Mon, 03 Jun 2019 20:07:23: #2 finished! INFO @ Mon, 03 Jun 2019 20:07:23: #2 predicted fragment length is 2 bps INFO @ Mon, 03 Jun 2019 20:07:23: #2 alternative fragment length(s) may be 2,27 bps INFO @ Mon, 03 Jun 2019 20:07:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4823788/SRX4823788.20_model.r WARNING @ Mon, 03 Jun 2019 20:07:23: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 20:07:23: #2 You may need to consider one of the other alternative d(s): 2,27 WARNING @ Mon, 03 Jun 2019 20:07:23: #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 20:07:23: #3 Call peaks... INFO @ Mon, 03 Jun 2019 20:07:23: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 20:08:08: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 20:08:21: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 20:08:25: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 20:08:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4823788/SRX4823788.05_peaks.xls INFO @ Mon, 03 Jun 2019 20:08:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4823788/SRX4823788.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 20:08:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4823788/SRX4823788.05_summits.bed INFO @ Mon, 03 Jun 2019 20:08:37: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 20:08:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4823788/SRX4823788.10_peaks.xls INFO @ Mon, 03 Jun 2019 20:08:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4823788/SRX4823788.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 20:08:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4823788/SRX4823788.10_summits.bed INFO @ Mon, 03 Jun 2019 20:08:48: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 20:08:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4823788/SRX4823788.20_peaks.xls INFO @ Mon, 03 Jun 2019 20:08:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4823788/SRX4823788.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 20:08:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4823788/SRX4823788.20_summits.bed INFO @ Mon, 03 Jun 2019 20:08:52: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。