Job ID = 9370030 sra ファイルのダウンロード中... Completed: 1942619K bytes transferred in 116 seconds (136741K bits/sec), in 1 file, 2 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 40067033 spots for /home/okishinya/chipatlas/results/ce10/SRX2710287/SRR5418741.sra Written 40067033 spots total rm: cannot remove `[DSE]RR*.fastq': そのようなファイルやディレクトリはありません 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: 00:57:26 40067033 reads; of these: 40067033 (100.00%) were unpaired; of these: 3569930 (8.91%) aligned 0 times 18495885 (46.16%) aligned exactly 1 time 18001218 (44.93%) aligned >1 times 91.09% overall alignment rate Time searching: 00:57:26 Overall time: 00:57:26 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 16 files... [bam_rmdupse_core] 17949647 / 36497103 = 0.4918 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 @ Fri, 04 Aug 2017 13:18:40: # Command line: callpeak -t SRX2710287.bam -f BAM -g ce -n SRX2710287.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2710287.05 # format = BAM # ChIP-seq file = ['SRX2710287.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 @ Fri, 04 Aug 2017 13:18:40: #1 read tag files... INFO @ Fri, 04 Aug 2017 13:18:40: #1 read treatment tags... INFO @ Fri, 04 Aug 2017 13:18:40: # Command line: callpeak -t SRX2710287.bam -f BAM -g ce -n SRX2710287.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2710287.10 # format = BAM # ChIP-seq file = ['SRX2710287.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 @ Fri, 04 Aug 2017 13:18:40: #1 read tag files... INFO @ Fri, 04 Aug 2017 13:18:40: #1 read treatment tags... INFO @ Fri, 04 Aug 2017 13:18:40: # Command line: callpeak -t SRX2710287.bam -f BAM -g ce -n SRX2710287.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2710287.20 # format = BAM # ChIP-seq file = ['SRX2710287.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 @ Fri, 04 Aug 2017 13:18:40: #1 read tag files... INFO @ Fri, 04 Aug 2017 13:18:40: #1 read treatment tags... INFO @ Fri, 04 Aug 2017 13:18:53: 1000000 INFO @ Fri, 04 Aug 2017 13:18:53: 1000000 INFO @ Fri, 04 Aug 2017 13:18:54: 1000000 INFO @ Fri, 04 Aug 2017 13:19:06: 2000000 INFO @ Fri, 04 Aug 2017 13:19:06: 2000000 INFO @ Fri, 04 Aug 2017 13:19:09: 2000000 INFO @ Fri, 04 Aug 2017 13:19:19: 3000000 INFO @ Fri, 04 Aug 2017 13:19:20: 3000000 INFO @ Fri, 04 Aug 2017 13:19:25: 3000000 INFO @ Fri, 04 Aug 2017 13:19:31: 4000000 INFO @ Fri, 04 Aug 2017 13:19:34: 4000000 INFO @ Fri, 04 Aug 2017 13:19:37: 4000000 INFO @ Fri, 04 Aug 2017 13:19:45: 5000000 INFO @ Fri, 04 Aug 2017 13:19:47: 5000000 INFO @ Fri, 04 Aug 2017 13:19:51: 5000000 INFO @ Fri, 04 Aug 2017 13:19:58: 6000000 INFO @ Fri, 04 Aug 2017 13:20:00: 6000000 INFO @ Fri, 04 Aug 2017 13:20:02: 6000000 INFO @ Fri, 04 Aug 2017 13:20:12: 7000000 INFO @ Fri, 04 Aug 2017 13:20:13: 7000000 INFO @ Fri, 04 Aug 2017 13:20:15: 7000000 INFO @ Fri, 04 Aug 2017 13:20:28: 8000000 INFO @ Fri, 04 Aug 2017 13:20:29: 8000000 INFO @ Fri, 04 Aug 2017 13:20:34: 8000000 INFO @ Fri, 04 Aug 2017 13:20:40: 9000000 INFO @ Fri, 04 Aug 2017 13:20:42: 9000000 INFO @ Fri, 04 Aug 2017 13:20:50: 9000000 INFO @ Fri, 04 Aug 2017 13:20:54: 10000000 INFO @ Fri, 04 Aug 2017 13:20:56: 10000000 INFO @ Fri, 04 Aug 2017 13:21:05: 10000000 INFO @ Fri, 04 Aug 2017 13:21:09: 11000000 INFO @ Fri, 04 Aug 2017 13:21:12: 11000000 INFO @ Fri, 04 Aug 2017 13:21:19: 11000000 INFO @ Fri, 04 Aug 2017 13:21:24: 12000000 INFO @ Fri, 04 Aug 2017 13:21:31: 12000000 INFO @ Fri, 04 Aug 2017 13:21:37: 12000000 INFO @ Fri, 04 Aug 2017 13:21:41: 13000000 INFO @ Fri, 04 Aug 2017 13:21:46: 13000000 INFO @ Fri, 04 Aug 2017 13:21:52: 13000000 INFO @ Fri, 04 Aug 2017 13:21:58: 14000000 INFO @ Fri, 04 Aug 2017 13:22:05: 14000000 INFO @ Fri, 04 Aug 2017 13:22:09: 14000000 INFO @ Fri, 04 Aug 2017 13:22:11: 15000000 INFO @ Fri, 04 Aug 2017 13:22:25: 15000000 INFO @ Fri, 04 Aug 2017 13:22:25: 15000000 INFO @ Fri, 04 Aug 2017 13:22:27: 16000000 INFO @ Fri, 04 Aug 2017 13:22:41: 16000000 INFO @ Fri, 04 Aug 2017 13:22:43: 17000000 INFO @ Fri, 04 Aug 2017 13:22:45: 16000000 INFO @ Fri, 04 Aug 2017 13:22:52: 17000000 INFO @ Fri, 04 Aug 2017 13:22:54: 18000000 INFO @ Fri, 04 Aug 2017 13:22:59: 17000000 INFO @ Fri, 04 Aug 2017 13:23:02: #1 tag size is determined as 76 bps INFO @ Fri, 04 Aug 2017 13:23:02: #1 tag size = 76 INFO @ Fri, 04 Aug 2017 13:23:02: #1 total tags in treatment: 18547456 INFO @ Fri, 04 Aug 2017 13:23:02: #1 user defined the maximum tags... INFO @ Fri, 04 Aug 2017 13:23:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 Aug 2017 13:23:03: #1 tags after filtering in treatment: 18547456 INFO @ Fri, 04 Aug 2017 13:23:03: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 Aug 2017 13:23:03: #1 finished! INFO @ Fri, 04 Aug 2017 13:23:03: #2 Build Peak Model... INFO @ Fri, 04 Aug 2017 13:23:03: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 Aug 2017 13:23:06: #2 number of paired peaks: 1016 INFO @ Fri, 04 Aug 2017 13:23:06: start model_add_line... INFO @ Fri, 04 Aug 2017 13:23:07: start X-correlation... INFO @ Fri, 04 Aug 2017 13:23:07: end of X-cor INFO @ Fri, 04 Aug 2017 13:23:07: #2 finished! INFO @ Fri, 04 Aug 2017 13:23:07: #2 predicted fragment length is 1 bps INFO @ Fri, 04 Aug 2017 13:23:07: #2 alternative fragment length(s) may be 1,67 bps INFO @ Fri, 04 Aug 2017 13:23:07: #2.2 Generate R script for model : SRX2710287.10_model.r WARNING @ Fri, 04 Aug 2017 13:23:07: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 04 Aug 2017 13:23:07: #2 You may need to consider one of the other alternative d(s): 1,67 WARNING @ Fri, 04 Aug 2017 13:23:07: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 04 Aug 2017 13:23:07: #3 Call peaks... INFO @ Fri, 04 Aug 2017 13:23:07: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 Aug 2017 13:23:07: 18000000 INFO @ Fri, 04 Aug 2017 13:23:14: 18000000 INFO @ Fri, 04 Aug 2017 13:23:16: #1 tag size is determined as 76 bps INFO @ Fri, 04 Aug 2017 13:23:16: #1 tag size = 76 INFO @ Fri, 04 Aug 2017 13:23:16: #1 total tags in treatment: 18547456 INFO @ Fri, 04 Aug 2017 13:23:16: #1 user defined the maximum tags... INFO @ Fri, 04 Aug 2017 13:23:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 Aug 2017 13:23:16: #1 tags after filtering in treatment: 18547456 INFO @ Fri, 04 Aug 2017 13:23:16: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 Aug 2017 13:23:16: #1 finished! INFO @ Fri, 04 Aug 2017 13:23:16: #2 Build Peak Model... INFO @ Fri, 04 Aug 2017 13:23:16: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 Aug 2017 13:23:19: #2 number of paired peaks: 1016 INFO @ Fri, 04 Aug 2017 13:23:19: start model_add_line... INFO @ Fri, 04 Aug 2017 13:23:19: start X-correlation... INFO @ Fri, 04 Aug 2017 13:23:19: end of X-cor INFO @ Fri, 04 Aug 2017 13:23:19: #2 finished! INFO @ Fri, 04 Aug 2017 13:23:19: #2 predicted fragment length is 1 bps INFO @ Fri, 04 Aug 2017 13:23:19: #2 alternative fragment length(s) may be 1,67 bps INFO @ Fri, 04 Aug 2017 13:23:19: #2.2 Generate R script for model : SRX2710287.20_model.r WARNING @ Fri, 04 Aug 2017 13:23:19: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 04 Aug 2017 13:23:19: #2 You may need to consider one of the other alternative d(s): 1,67 WARNING @ Fri, 04 Aug 2017 13:23:19: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 04 Aug 2017 13:23:19: #3 Call peaks... INFO @ Fri, 04 Aug 2017 13:23:19: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 Aug 2017 13:23:24: #1 tag size is determined as 76 bps INFO @ Fri, 04 Aug 2017 13:23:24: #1 tag size = 76 INFO @ Fri, 04 Aug 2017 13:23:24: #1 total tags in treatment: 18547456 INFO @ Fri, 04 Aug 2017 13:23:24: #1 user defined the maximum tags... INFO @ Fri, 04 Aug 2017 13:23:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 Aug 2017 13:23:24: #1 tags after filtering in treatment: 18547456 INFO @ Fri, 04 Aug 2017 13:23:24: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 Aug 2017 13:23:24: #1 finished! INFO @ Fri, 04 Aug 2017 13:23:24: #2 Build Peak Model... INFO @ Fri, 04 Aug 2017 13:23:24: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 Aug 2017 13:23:26: #2 number of paired peaks: 1016 INFO @ Fri, 04 Aug 2017 13:23:26: start model_add_line... INFO @ Fri, 04 Aug 2017 13:23:26: start X-correlation... INFO @ Fri, 04 Aug 2017 13:23:26: end of X-cor INFO @ Fri, 04 Aug 2017 13:23:26: #2 finished! INFO @ Fri, 04 Aug 2017 13:23:26: #2 predicted fragment length is 1 bps INFO @ Fri, 04 Aug 2017 13:23:26: #2 alternative fragment length(s) may be 1,67 bps INFO @ Fri, 04 Aug 2017 13:23:26: #2.2 Generate R script for model : SRX2710287.05_model.r WARNING @ Fri, 04 Aug 2017 13:23:26: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 04 Aug 2017 13:23:26: #2 You may need to consider one of the other alternative d(s): 1,67 WARNING @ Fri, 04 Aug 2017 13:23:26: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 04 Aug 2017 13:23:26: #3 Call peaks... INFO @ Fri, 04 Aug 2017 13:23:26: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 Aug 2017 13:24:01: #3 Call peaks for each chromosome... INFO @ Fri, 04 Aug 2017 13:24:10: #3 Call peaks for each chromosome... INFO @ Fri, 04 Aug 2017 13:24:20: #3 Call peaks for each chromosome... INFO @ Fri, 04 Aug 2017 13:24:29: #4 Write output xls file... SRX2710287.10_peaks.xls INFO @ Fri, 04 Aug 2017 13:24:29: #4 Write peak in narrowPeak format file... SRX2710287.10_peaks.narrowPeak INFO @ Fri, 04 Aug 2017 13:24:29: #4 Write summits bed file... SRX2710287.10_summits.bed INFO @ Fri, 04 Aug 2017 13:24:29: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 04 Aug 2017 13:24:39: #4 Write output xls file... SRX2710287.20_peaks.xls INFO @ Fri, 04 Aug 2017 13:24:39: #4 Write peak in narrowPeak format file... SRX2710287.20_peaks.narrowPeak INFO @ Fri, 04 Aug 2017 13:24:39: #4 Write summits bed file... SRX2710287.20_summits.bed INFO @ Fri, 04 Aug 2017 13:24:39: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 04 Aug 2017 13:24:49: #4 Write output xls file... SRX2710287.05_peaks.xls INFO @ Fri, 04 Aug 2017 13:24:49: #4 Write peak in narrowPeak format file... SRX2710287.05_peaks.narrowPeak INFO @ Fri, 04 Aug 2017 13:24:49: #4 Write summits bed file... SRX2710287.05_summits.bed INFO @ Fri, 04 Aug 2017 13:24:49: Done! pass1 - making usageList (0 chroms): 4 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。