Job ID = 1298499 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 34,352,807 reads read : 34,352,807 reads written : 34,352,807 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: 00:09:50 34352807 reads; of these: 34352807 (100.00%) were unpaired; of these: 1551179 (4.52%) aligned 0 times 28583525 (83.21%) aligned exactly 1 time 4218103 (12.28%) aligned >1 times 95.48% overall alignment rate Time searching: 00:09:51 Overall time: 00:09:51 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] 11993664 / 32801628 = 0.3656 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 17:57:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX467037/SRX467037.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX467037/SRX467037.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX467037/SRX467037.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX467037/SRX467037.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 17:57:00: #1 read tag files... INFO @ Mon, 03 Jun 2019 17:57:00: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 17:57:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX467037/SRX467037.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX467037/SRX467037.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX467037/SRX467037.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX467037/SRX467037.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 17:57:00: #1 read tag files... INFO @ Mon, 03 Jun 2019 17:57:00: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 17:57:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX467037/SRX467037.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX467037/SRX467037.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX467037/SRX467037.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX467037/SRX467037.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 17:57:00: #1 read tag files... INFO @ Mon, 03 Jun 2019 17:57:00: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 17:57:08: 1000000 INFO @ Mon, 03 Jun 2019 17:57:09: 1000000 INFO @ Mon, 03 Jun 2019 17:57:11: 1000000 INFO @ Mon, 03 Jun 2019 17:57:15: 2000000 INFO @ Mon, 03 Jun 2019 17:57:17: 2000000 INFO @ Mon, 03 Jun 2019 17:57:21: 2000000 INFO @ Mon, 03 Jun 2019 17:57:23: 3000000 INFO @ Mon, 03 Jun 2019 17:57:26: 3000000 INFO @ Mon, 03 Jun 2019 17:57:31: 4000000 INFO @ Mon, 03 Jun 2019 17:57:31: 3000000 INFO @ Mon, 03 Jun 2019 17:57:34: 4000000 INFO @ Mon, 03 Jun 2019 17:57:38: 5000000 INFO @ Mon, 03 Jun 2019 17:57:41: 4000000 INFO @ Mon, 03 Jun 2019 17:57:42: 5000000 INFO @ Mon, 03 Jun 2019 17:57:46: 6000000 INFO @ Mon, 03 Jun 2019 17:57:51: 6000000 INFO @ Mon, 03 Jun 2019 17:57:51: 5000000 INFO @ Mon, 03 Jun 2019 17:57:53: 7000000 INFO @ Mon, 03 Jun 2019 17:57:59: 7000000 INFO @ Mon, 03 Jun 2019 17:58:01: 8000000 INFO @ Mon, 03 Jun 2019 17:58:01: 6000000 INFO @ Mon, 03 Jun 2019 17:58:08: 8000000 INFO @ Mon, 03 Jun 2019 17:58:08: 9000000 INFO @ Mon, 03 Jun 2019 17:58:11: 7000000 INFO @ Mon, 03 Jun 2019 17:58:16: 10000000 INFO @ Mon, 03 Jun 2019 17:58:16: 9000000 INFO @ Mon, 03 Jun 2019 17:58:21: 8000000 INFO @ Mon, 03 Jun 2019 17:58:23: 11000000 INFO @ Mon, 03 Jun 2019 17:58:24: 10000000 INFO @ Mon, 03 Jun 2019 17:58:31: 12000000 INFO @ Mon, 03 Jun 2019 17:58:31: 9000000 INFO @ Mon, 03 Jun 2019 17:58:33: 11000000 INFO @ Mon, 03 Jun 2019 17:58:38: 13000000 INFO @ Mon, 03 Jun 2019 17:58:41: 12000000 INFO @ Mon, 03 Jun 2019 17:58:41: 10000000 INFO @ Mon, 03 Jun 2019 17:58:46: 14000000 INFO @ Mon, 03 Jun 2019 17:58:49: 13000000 INFO @ Mon, 03 Jun 2019 17:58:51: 11000000 INFO @ Mon, 03 Jun 2019 17:58:53: 15000000 INFO @ Mon, 03 Jun 2019 17:58:57: 14000000 INFO @ Mon, 03 Jun 2019 17:59:01: 16000000 INFO @ Mon, 03 Jun 2019 17:59:01: 12000000 INFO @ Mon, 03 Jun 2019 17:59:06: 15000000 INFO @ Mon, 03 Jun 2019 17:59:08: 17000000 INFO @ Mon, 03 Jun 2019 17:59:11: 13000000 INFO @ Mon, 03 Jun 2019 17:59:14: 16000000 INFO @ Mon, 03 Jun 2019 17:59:16: 18000000 INFO @ Mon, 03 Jun 2019 17:59:21: 14000000 INFO @ Mon, 03 Jun 2019 17:59:23: 17000000 INFO @ Mon, 03 Jun 2019 17:59:24: 19000000 INFO @ Mon, 03 Jun 2019 17:59:31: 15000000 INFO @ Mon, 03 Jun 2019 17:59:31: 20000000 INFO @ Mon, 03 Jun 2019 17:59:31: 18000000 INFO @ Mon, 03 Jun 2019 17:59:37: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 17:59:37: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 17:59:37: #1 total tags in treatment: 20807964 INFO @ Mon, 03 Jun 2019 17:59:37: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 17:59:37: #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 17:59:38: #1 tags after filtering in treatment: 20807964 INFO @ Mon, 03 Jun 2019 17:59:38: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 17:59:38: #1 finished! INFO @ Mon, 03 Jun 2019 17:59:38: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 17:59:38: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 17:59:40: 19000000 INFO @ Mon, 03 Jun 2019 17:59:40: #2 number of paired peaks: 200 WARNING @ Mon, 03 Jun 2019 17:59:40: Fewer paired peaks (200) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 200 pairs to build model! INFO @ Mon, 03 Jun 2019 17:59:40: start model_add_line... INFO @ Mon, 03 Jun 2019 17:59:40: start X-correlation... INFO @ Mon, 03 Jun 2019 17:59:40: end of X-cor INFO @ Mon, 03 Jun 2019 17:59:40: #2 finished! INFO @ Mon, 03 Jun 2019 17:59:40: #2 predicted fragment length is 4 bps INFO @ Mon, 03 Jun 2019 17:59:40: #2 alternative fragment length(s) may be 4,10 bps INFO @ Mon, 03 Jun 2019 17:59:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX467037/SRX467037.05_model.r WARNING @ Mon, 03 Jun 2019 17:59:40: #2 Since the d (4) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 17:59:40: #2 You may need to consider one of the other alternative d(s): 4,10 WARNING @ Mon, 03 Jun 2019 17:59:40: #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 17:59:40: #3 Call peaks... INFO @ Mon, 03 Jun 2019 17:59:40: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 17:59:41: 16000000 INFO @ Mon, 03 Jun 2019 17:59:48: 20000000 INFO @ Mon, 03 Jun 2019 17:59:51: 17000000 INFO @ Mon, 03 Jun 2019 17:59:54: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 17:59:54: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 17:59:54: #1 total tags in treatment: 20807964 INFO @ Mon, 03 Jun 2019 17:59:54: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 17:59:54: #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 17:59:55: #1 tags after filtering in treatment: 20807964 INFO @ Mon, 03 Jun 2019 17:59:55: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 17:59:55: #1 finished! INFO @ Mon, 03 Jun 2019 17:59:55: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 17:59:55: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 17:59:57: #2 number of paired peaks: 200 WARNING @ Mon, 03 Jun 2019 17:59:57: Fewer paired peaks (200) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 200 pairs to build model! INFO @ Mon, 03 Jun 2019 17:59:57: start model_add_line... INFO @ Mon, 03 Jun 2019 17:59:57: start X-correlation... INFO @ Mon, 03 Jun 2019 17:59:57: end of X-cor INFO @ Mon, 03 Jun 2019 17:59:57: #2 finished! INFO @ Mon, 03 Jun 2019 17:59:57: #2 predicted fragment length is 4 bps INFO @ Mon, 03 Jun 2019 17:59:57: #2 alternative fragment length(s) may be 4,10 bps INFO @ Mon, 03 Jun 2019 17:59:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX467037/SRX467037.10_model.r WARNING @ Mon, 03 Jun 2019 17:59:57: #2 Since the d (4) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 17:59:57: #2 You may need to consider one of the other alternative d(s): 4,10 WARNING @ Mon, 03 Jun 2019 17:59:57: #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 17:59:57: #3 Call peaks... INFO @ Mon, 03 Jun 2019 17:59:57: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 18:00:01: 18000000 INFO @ Mon, 03 Jun 2019 18:00:11: 19000000 INFO @ Mon, 03 Jun 2019 18:00:20: 20000000 INFO @ Mon, 03 Jun 2019 18:00:28: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 18:00:28: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 18:00:28: #1 total tags in treatment: 20807964 INFO @ Mon, 03 Jun 2019 18:00:28: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 18:00:28: #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 18:00:28: #1 tags after filtering in treatment: 20807964 INFO @ Mon, 03 Jun 2019 18:00:28: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 18:00:28: #1 finished! INFO @ Mon, 03 Jun 2019 18:00:28: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 18:00:28: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 18:00:29: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 18:00:30: #2 number of paired peaks: 200 WARNING @ Mon, 03 Jun 2019 18:00:30: Fewer paired peaks (200) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 200 pairs to build model! INFO @ Mon, 03 Jun 2019 18:00:30: start model_add_line... INFO @ Mon, 03 Jun 2019 18:00:30: start X-correlation... INFO @ Mon, 03 Jun 2019 18:00:30: end of X-cor INFO @ Mon, 03 Jun 2019 18:00:30: #2 finished! INFO @ Mon, 03 Jun 2019 18:00:30: #2 predicted fragment length is 4 bps INFO @ Mon, 03 Jun 2019 18:00:30: #2 alternative fragment length(s) may be 4,10 bps INFO @ Mon, 03 Jun 2019 18:00:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX467037/SRX467037.20_model.r WARNING @ Mon, 03 Jun 2019 18:00:30: #2 Since the d (4) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 18:00:30: #2 You may need to consider one of the other alternative d(s): 4,10 WARNING @ Mon, 03 Jun 2019 18:00:30: #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 18:00:30: #3 Call peaks... INFO @ Mon, 03 Jun 2019 18:00:30: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 18:00:46: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 18:00:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX467037/SRX467037.05_peaks.xls INFO @ Mon, 03 Jun 2019 18:00:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX467037/SRX467037.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 18:00:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX467037/SRX467037.05_summits.bed INFO @ Mon, 03 Jun 2019 18:00:53: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 18:01:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX467037/SRX467037.10_peaks.xls INFO @ Mon, 03 Jun 2019 18:01:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX467037/SRX467037.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 18:01:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX467037/SRX467037.10_summits.bed INFO @ Mon, 03 Jun 2019 18:01:10: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 18:01:19: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 18:01:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX467037/SRX467037.20_peaks.xls INFO @ Mon, 03 Jun 2019 18:01:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX467037/SRX467037.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 18:01:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX467037/SRX467037.20_summits.bed INFO @ Mon, 03 Jun 2019 18:01:43: Done! pass1 - making usageList (0 chroms): 1 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。