Job ID = 9157787 sra ファイルのダウンロード中... Completed: 833135K bytes transferred in 9 seconds (706826K bits/sec), in 2 files, 3 directories. sra ファイルのダウンロードが完了しました。 Read layout: SINGLE fastq に変換中... Written 12102665 spots for /home/okishinya/chipatlas/results/ce10/SRX982075/SRR1956554.sra Written 12102665 spots total Written 14224137 spots for /home/okishinya/chipatlas/results/ce10/SRX982075/SRR1956555.sra Written 14224137 spots total 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: 00:07:37 26326802 reads; of these: 26326802 (100.00%) were unpaired; of these: 1469061 (5.58%) aligned 0 times 20244687 (76.90%) aligned exactly 1 time 4613054 (17.52%) aligned >1 times 94.42% overall alignment rate Time searching: 00:07:37 Overall time: 00:07:37 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 3768066 / 24857741 = 0.1516 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 @ Tue, 27 Jun 2017 13:49:14: # Command line: callpeak -t SRX982075.bam -f BAM -g ce -n SRX982075.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX982075.10 # format = BAM # ChIP-seq file = ['SRX982075.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Tue, 27 Jun 2017 13:49:14: #1 read tag files... INFO @ Tue, 27 Jun 2017 13:49:14: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 13:49:14: # Command line: callpeak -t SRX982075.bam -f BAM -g ce -n SRX982075.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX982075.20 # format = BAM # ChIP-seq file = ['SRX982075.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Tue, 27 Jun 2017 13:49:14: #1 read tag files... INFO @ Tue, 27 Jun 2017 13:49:14: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 13:49:14: # Command line: callpeak -t SRX982075.bam -f BAM -g ce -n SRX982075.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX982075.05 # format = BAM # ChIP-seq file = ['SRX982075.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Tue, 27 Jun 2017 13:49:14: #1 read tag files... INFO @ Tue, 27 Jun 2017 13:49:14: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 13:49:22: 1000000 INFO @ Tue, 27 Jun 2017 13:49:22: 1000000 INFO @ Tue, 27 Jun 2017 13:49:22: 1000000 INFO @ Tue, 27 Jun 2017 13:49:30: 2000000 INFO @ Tue, 27 Jun 2017 13:49:30: 2000000 INFO @ Tue, 27 Jun 2017 13:49:30: 2000000 INFO @ Tue, 27 Jun 2017 13:49:37: 3000000 INFO @ Tue, 27 Jun 2017 13:49:37: 3000000 INFO @ Tue, 27 Jun 2017 13:49:37: 3000000 INFO @ Tue, 27 Jun 2017 13:49:46: 4000000 INFO @ Tue, 27 Jun 2017 13:49:46: 4000000 INFO @ Tue, 27 Jun 2017 13:49:47: 4000000 INFO @ Tue, 27 Jun 2017 13:49:54: 5000000 INFO @ Tue, 27 Jun 2017 13:49:54: 5000000 INFO @ Tue, 27 Jun 2017 13:49:57: 5000000 INFO @ Tue, 27 Jun 2017 13:50:03: 6000000 INFO @ Tue, 27 Jun 2017 13:50:03: 6000000 INFO @ Tue, 27 Jun 2017 13:50:07: 6000000 INFO @ Tue, 27 Jun 2017 13:50:11: 7000000 INFO @ Tue, 27 Jun 2017 13:50:11: 7000000 INFO @ Tue, 27 Jun 2017 13:50:16: 7000000 INFO @ Tue, 27 Jun 2017 13:50:20: 8000000 INFO @ Tue, 27 Jun 2017 13:50:20: 8000000 INFO @ Tue, 27 Jun 2017 13:50:26: 8000000 INFO @ Tue, 27 Jun 2017 13:50:28: 9000000 INFO @ Tue, 27 Jun 2017 13:50:28: 9000000 INFO @ Tue, 27 Jun 2017 13:50:36: 9000000 INFO @ Tue, 27 Jun 2017 13:50:36: 10000000 INFO @ Tue, 27 Jun 2017 13:50:36: 10000000 INFO @ Tue, 27 Jun 2017 13:50:45: 11000000 INFO @ Tue, 27 Jun 2017 13:50:45: 11000000 INFO @ Tue, 27 Jun 2017 13:50:46: 10000000 INFO @ Tue, 27 Jun 2017 13:50:54: 12000000 INFO @ Tue, 27 Jun 2017 13:50:54: 12000000 INFO @ Tue, 27 Jun 2017 13:50:57: 11000000 INFO @ Tue, 27 Jun 2017 13:51:02: 13000000 INFO @ Tue, 27 Jun 2017 13:51:03: 13000000 INFO @ Tue, 27 Jun 2017 13:51:06: 12000000 INFO @ Tue, 27 Jun 2017 13:51:11: 14000000 INFO @ Tue, 27 Jun 2017 13:51:11: 14000000 INFO @ Tue, 27 Jun 2017 13:51:16: 13000000 INFO @ Tue, 27 Jun 2017 13:51:20: 15000000 INFO @ Tue, 27 Jun 2017 13:51:20: 15000000 INFO @ Tue, 27 Jun 2017 13:51:26: 14000000 INFO @ Tue, 27 Jun 2017 13:51:29: 16000000 INFO @ Tue, 27 Jun 2017 13:51:29: 16000000 INFO @ Tue, 27 Jun 2017 13:51:36: 15000000 INFO @ Tue, 27 Jun 2017 13:51:37: 17000000 INFO @ Tue, 27 Jun 2017 13:51:37: 17000000 INFO @ Tue, 27 Jun 2017 13:51:46: 18000000 INFO @ Tue, 27 Jun 2017 13:51:46: 18000000 INFO @ Tue, 27 Jun 2017 13:51:46: 16000000 INFO @ Tue, 27 Jun 2017 13:51:54: 19000000 INFO @ Tue, 27 Jun 2017 13:51:55: 19000000 INFO @ Tue, 27 Jun 2017 13:51:56: 17000000 INFO @ Tue, 27 Jun 2017 13:52:03: 20000000 INFO @ Tue, 27 Jun 2017 13:52:03: 20000000 INFO @ Tue, 27 Jun 2017 13:52:05: 18000000 INFO @ Tue, 27 Jun 2017 13:52:11: 21000000 INFO @ Tue, 27 Jun 2017 13:52:11: 21000000 INFO @ Tue, 27 Jun 2017 13:52:12: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 13:52:12: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 13:52:12: #1 total tags in treatment: 21089675 INFO @ Tue, 27 Jun 2017 13:52:12: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 13:52:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 13:52:12: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 13:52:12: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 13:52:12: #1 total tags in treatment: 21089675 INFO @ Tue, 27 Jun 2017 13:52:12: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 13:52:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 13:52:13: #1 tags after filtering in treatment: 21089675 INFO @ Tue, 27 Jun 2017 13:52:13: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 13:52:13: #1 finished! INFO @ Tue, 27 Jun 2017 13:52:13: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 13:52:13: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 13:52:13: #1 tags after filtering in treatment: 21089675 INFO @ Tue, 27 Jun 2017 13:52:13: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 13:52:13: #1 finished! INFO @ Tue, 27 Jun 2017 13:52:13: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 13:52:13: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 13:52:14: #2 number of paired peaks: 204 WARNING @ Tue, 27 Jun 2017 13:52:14: Fewer paired peaks (204) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 204 pairs to build model! INFO @ Tue, 27 Jun 2017 13:52:14: start model_add_line... INFO @ Tue, 27 Jun 2017 13:52:14: #2 number of paired peaks: 204 WARNING @ Tue, 27 Jun 2017 13:52:14: Fewer paired peaks (204) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 204 pairs to build model! INFO @ Tue, 27 Jun 2017 13:52:14: start model_add_line... INFO @ Tue, 27 Jun 2017 13:52:14: start X-correlation... INFO @ Tue, 27 Jun 2017 13:52:14: end of X-cor INFO @ Tue, 27 Jun 2017 13:52:14: #2 finished! INFO @ Tue, 27 Jun 2017 13:52:14: #2 predicted fragment length is 1 bps INFO @ Tue, 27 Jun 2017 13:52:14: #2 alternative fragment length(s) may be 1,30,588,597 bps INFO @ Tue, 27 Jun 2017 13:52:14: #2.2 Generate R script for model : SRX982075.05_model.r WARNING @ Tue, 27 Jun 2017 13:52:14: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 13:52:14: #2 You may need to consider one of the other alternative d(s): 1,30,588,597 WARNING @ Tue, 27 Jun 2017 13:52:14: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 27 Jun 2017 13:52:14: #3 Call peaks... INFO @ Tue, 27 Jun 2017 13:52:14: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 13:52:14: 19000000 INFO @ Tue, 27 Jun 2017 13:52:14: start X-correlation... INFO @ Tue, 27 Jun 2017 13:52:14: end of X-cor INFO @ Tue, 27 Jun 2017 13:52:14: #2 finished! INFO @ Tue, 27 Jun 2017 13:52:14: #2 predicted fragment length is 1 bps INFO @ Tue, 27 Jun 2017 13:52:14: #2 alternative fragment length(s) may be 1,30,588,597 bps INFO @ Tue, 27 Jun 2017 13:52:14: #2.2 Generate R script for model : SRX982075.10_model.r WARNING @ Tue, 27 Jun 2017 13:52:14: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 13:52:14: #2 You may need to consider one of the other alternative d(s): 1,30,588,597 WARNING @ Tue, 27 Jun 2017 13:52:14: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 27 Jun 2017 13:52:14: #3 Call peaks... INFO @ Tue, 27 Jun 2017 13:52:14: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 13:52:22: 20000000 INFO @ Tue, 27 Jun 2017 13:52:30: 21000000 INFO @ Tue, 27 Jun 2017 13:52:30: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 13:52:30: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 13:52:30: #1 total tags in treatment: 21089675 INFO @ Tue, 27 Jun 2017 13:52:30: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 13:52:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 13:52:31: #1 tags after filtering in treatment: 21089675 INFO @ Tue, 27 Jun 2017 13:52:31: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 13:52:31: #1 finished! INFO @ Tue, 27 Jun 2017 13:52:31: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 13:52:31: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 13:52:32: #2 number of paired peaks: 204 WARNING @ Tue, 27 Jun 2017 13:52:32: Fewer paired peaks (204) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 204 pairs to build model! INFO @ Tue, 27 Jun 2017 13:52:32: start model_add_line... INFO @ Tue, 27 Jun 2017 13:52:33: start X-correlation... INFO @ Tue, 27 Jun 2017 13:52:33: end of X-cor INFO @ Tue, 27 Jun 2017 13:52:33: #2 finished! INFO @ Tue, 27 Jun 2017 13:52:33: #2 predicted fragment length is 1 bps INFO @ Tue, 27 Jun 2017 13:52:33: #2 alternative fragment length(s) may be 1,30,588,597 bps INFO @ Tue, 27 Jun 2017 13:52:33: #2.2 Generate R script for model : SRX982075.20_model.r WARNING @ Tue, 27 Jun 2017 13:52:33: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 13:52:33: #2 You may need to consider one of the other alternative d(s): 1,30,588,597 WARNING @ Tue, 27 Jun 2017 13:52:33: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 27 Jun 2017 13:52:33: #3 Call peaks... INFO @ Tue, 27 Jun 2017 13:52:33: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 13:52:49: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 13:52:51: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 13:53:06: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 13:53:06: #4 Write output xls file... SRX982075.10_peaks.xls INFO @ Tue, 27 Jun 2017 13:53:06: #4 Write peak in narrowPeak format file... SRX982075.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 13:53:06: #4 Write summits bed file... SRX982075.10_summits.bed INFO @ Tue, 27 Jun 2017 13:53:06: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 13:53:10: #4 Write output xls file... SRX982075.05_peaks.xls INFO @ Tue, 27 Jun 2017 13:53:10: #4 Write peak in narrowPeak format file... SRX982075.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 13:53:10: #4 Write summits bed file... SRX982075.05_summits.bed INFO @ Tue, 27 Jun 2017 13:53:10: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 13:53:23: #4 Write output xls file... SRX982075.20_peaks.xls INFO @ Tue, 27 Jun 2017 13:53:23: #4 Write peak in narrowPeak format file... SRX982075.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 13:53:23: #4 Write summits bed file... SRX982075.20_summits.bed INFO @ Tue, 27 Jun 2017 13:53:23: 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。