Job ID = 9157398 sra ファイルのダウンロード中... Completed: 648211K bytes transferred in 9 seconds (552961K 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 23727403 spots for /home/okishinya/chipatlas/results/ce10/SRX1936239/SRR3879846.sra Written 23727403 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: 00:06:07 23727403 reads; of these: 23727403 (100.00%) were unpaired; of these: 789319 (3.33%) aligned 0 times 19504915 (82.20%) aligned exactly 1 time 3433169 (14.47%) aligned >1 times 96.67% overall alignment rate Time searching: 00:06:07 Overall time: 00:06:07 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] 3214869 / 22938084 = 0.1402 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 11:53:27: # Command line: callpeak -t SRX1936239.bam -f BAM -g ce -n SRX1936239.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1936239.20 # format = BAM # ChIP-seq file = ['SRX1936239.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 11:53:27: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:53:27: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:53:27: # Command line: callpeak -t SRX1936239.bam -f BAM -g ce -n SRX1936239.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1936239.10 # format = BAM # ChIP-seq file = ['SRX1936239.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 11:53:27: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:53:27: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:53:27: # Command line: callpeak -t SRX1936239.bam -f BAM -g ce -n SRX1936239.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1936239.05 # format = BAM # ChIP-seq file = ['SRX1936239.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 11:53:27: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:53:27: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:53:34: 1000000 INFO @ Tue, 27 Jun 2017 11:53:35: 1000000 INFO @ Tue, 27 Jun 2017 11:53:36: 1000000 INFO @ Tue, 27 Jun 2017 11:53:41: 2000000 INFO @ Tue, 27 Jun 2017 11:53:43: 2000000 INFO @ Tue, 27 Jun 2017 11:53:45: 2000000 INFO @ Tue, 27 Jun 2017 11:53:48: 3000000 INFO @ Tue, 27 Jun 2017 11:53:52: 3000000 INFO @ Tue, 27 Jun 2017 11:53:55: 3000000 INFO @ Tue, 27 Jun 2017 11:53:55: 4000000 INFO @ Tue, 27 Jun 2017 11:54:00: 4000000 INFO @ Tue, 27 Jun 2017 11:54:03: 5000000 INFO @ Tue, 27 Jun 2017 11:54:05: 4000000 INFO @ Tue, 27 Jun 2017 11:54:09: 5000000 INFO @ Tue, 27 Jun 2017 11:54:10: 6000000 INFO @ Tue, 27 Jun 2017 11:54:14: 5000000 INFO @ Tue, 27 Jun 2017 11:54:17: 7000000 INFO @ Tue, 27 Jun 2017 11:54:17: 6000000 INFO @ Tue, 27 Jun 2017 11:54:24: 6000000 INFO @ Tue, 27 Jun 2017 11:54:24: 8000000 INFO @ Tue, 27 Jun 2017 11:54:26: 7000000 INFO @ Tue, 27 Jun 2017 11:54:31: 9000000 INFO @ Tue, 27 Jun 2017 11:54:33: 7000000 INFO @ Tue, 27 Jun 2017 11:54:34: 8000000 INFO @ Tue, 27 Jun 2017 11:54:39: 10000000 INFO @ Tue, 27 Jun 2017 11:54:43: 9000000 INFO @ Tue, 27 Jun 2017 11:54:43: 8000000 INFO @ Tue, 27 Jun 2017 11:54:46: 11000000 INFO @ Tue, 27 Jun 2017 11:54:51: 10000000 INFO @ Tue, 27 Jun 2017 11:54:52: 12000000 INFO @ Tue, 27 Jun 2017 11:54:52: 9000000 INFO @ Tue, 27 Jun 2017 11:54:58: 13000000 INFO @ Tue, 27 Jun 2017 11:55:00: 11000000 INFO @ Tue, 27 Jun 2017 11:55:01: 10000000 INFO @ Tue, 27 Jun 2017 11:55:04: 14000000 INFO @ Tue, 27 Jun 2017 11:55:07: 12000000 INFO @ Tue, 27 Jun 2017 11:55:09: 11000000 INFO @ Tue, 27 Jun 2017 11:55:11: 15000000 INFO @ Tue, 27 Jun 2017 11:55:14: 13000000 INFO @ Tue, 27 Jun 2017 11:55:17: 16000000 INFO @ Tue, 27 Jun 2017 11:55:17: 12000000 INFO @ Tue, 27 Jun 2017 11:55:22: 14000000 INFO @ Tue, 27 Jun 2017 11:55:23: 17000000 INFO @ Tue, 27 Jun 2017 11:55:25: 13000000 INFO @ Tue, 27 Jun 2017 11:55:29: 18000000 INFO @ Tue, 27 Jun 2017 11:55:29: 15000000 INFO @ Tue, 27 Jun 2017 11:55:33: 14000000 INFO @ Tue, 27 Jun 2017 11:55:35: 19000000 INFO @ Tue, 27 Jun 2017 11:55:36: 16000000 INFO @ Tue, 27 Jun 2017 11:55:40: #1 tag size is determined as 52 bps INFO @ Tue, 27 Jun 2017 11:55:40: #1 tag size = 52 INFO @ Tue, 27 Jun 2017 11:55:40: #1 total tags in treatment: 19723215 INFO @ Tue, 27 Jun 2017 11:55:40: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:55:40: #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 11:55:40: 15000000 INFO @ Tue, 27 Jun 2017 11:55:40: #1 tags after filtering in treatment: 19723215 INFO @ Tue, 27 Jun 2017 11:55:40: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:55:40: #1 finished! INFO @ Tue, 27 Jun 2017 11:55:40: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:55:40: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:55:42: #2 number of paired peaks: 134 WARNING @ Tue, 27 Jun 2017 11:55:42: Fewer paired peaks (134) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 134 pairs to build model! INFO @ Tue, 27 Jun 2017 11:55:42: start model_add_line... INFO @ Tue, 27 Jun 2017 11:55:42: start X-correlation... INFO @ Tue, 27 Jun 2017 11:55:42: end of X-cor INFO @ Tue, 27 Jun 2017 11:55:42: #2 finished! INFO @ Tue, 27 Jun 2017 11:55:42: #2 predicted fragment length is 46 bps INFO @ Tue, 27 Jun 2017 11:55:42: #2 alternative fragment length(s) may be 2,46,494 bps INFO @ Tue, 27 Jun 2017 11:55:42: #2.2 Generate R script for model : SRX1936239.10_model.r WARNING @ Tue, 27 Jun 2017 11:55:42: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 11:55:42: #2 You may need to consider one of the other alternative d(s): 2,46,494 WARNING @ Tue, 27 Jun 2017 11:55:42: #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 11:55:42: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:55:42: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:55:44: 17000000 INFO @ Tue, 27 Jun 2017 11:55:48: 16000000 INFO @ Tue, 27 Jun 2017 11:55:51: 18000000 INFO @ Tue, 27 Jun 2017 11:55:55: 17000000 INFO @ Tue, 27 Jun 2017 11:55:58: 19000000 INFO @ Tue, 27 Jun 2017 11:56:03: 18000000 INFO @ Tue, 27 Jun 2017 11:56:03: #1 tag size is determined as 52 bps INFO @ Tue, 27 Jun 2017 11:56:03: #1 tag size = 52 INFO @ Tue, 27 Jun 2017 11:56:03: #1 total tags in treatment: 19723215 INFO @ Tue, 27 Jun 2017 11:56:03: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:56:03: #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 11:56:04: #1 tags after filtering in treatment: 19723215 INFO @ Tue, 27 Jun 2017 11:56:04: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:56:04: #1 finished! INFO @ Tue, 27 Jun 2017 11:56:04: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:56:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:56:06: #2 number of paired peaks: 134 WARNING @ Tue, 27 Jun 2017 11:56:06: Fewer paired peaks (134) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 134 pairs to build model! INFO @ Tue, 27 Jun 2017 11:56:06: start model_add_line... INFO @ Tue, 27 Jun 2017 11:56:06: start X-correlation... INFO @ Tue, 27 Jun 2017 11:56:06: end of X-cor INFO @ Tue, 27 Jun 2017 11:56:06: #2 finished! INFO @ Tue, 27 Jun 2017 11:56:06: #2 predicted fragment length is 46 bps INFO @ Tue, 27 Jun 2017 11:56:06: #2 alternative fragment length(s) may be 2,46,494 bps INFO @ Tue, 27 Jun 2017 11:56:06: #2.2 Generate R script for model : SRX1936239.05_model.r WARNING @ Tue, 27 Jun 2017 11:56:06: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 11:56:06: #2 You may need to consider one of the other alternative d(s): 2,46,494 WARNING @ Tue, 27 Jun 2017 11:56:06: #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 11:56:06: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:56:06: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:56:10: 19000000 INFO @ Tue, 27 Jun 2017 11:56:15: #1 tag size is determined as 52 bps INFO @ Tue, 27 Jun 2017 11:56:15: #1 tag size = 52 INFO @ Tue, 27 Jun 2017 11:56:15: #1 total tags in treatment: 19723215 INFO @ Tue, 27 Jun 2017 11:56:15: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:56:15: #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 11:56:15: #1 tags after filtering in treatment: 19723215 INFO @ Tue, 27 Jun 2017 11:56:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:56:15: #1 finished! INFO @ Tue, 27 Jun 2017 11:56:15: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:56:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:56:16: #2 number of paired peaks: 134 WARNING @ Tue, 27 Jun 2017 11:56:16: Fewer paired peaks (134) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 134 pairs to build model! INFO @ Tue, 27 Jun 2017 11:56:16: start model_add_line... INFO @ Tue, 27 Jun 2017 11:56:17: start X-correlation... INFO @ Tue, 27 Jun 2017 11:56:17: end of X-cor INFO @ Tue, 27 Jun 2017 11:56:17: #2 finished! INFO @ Tue, 27 Jun 2017 11:56:17: #2 predicted fragment length is 46 bps INFO @ Tue, 27 Jun 2017 11:56:17: #2 alternative fragment length(s) may be 2,46,494 bps INFO @ Tue, 27 Jun 2017 11:56:17: #2.2 Generate R script for model : SRX1936239.20_model.r WARNING @ Tue, 27 Jun 2017 11:56:17: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 11:56:17: #2 You may need to consider one of the other alternative d(s): 2,46,494 WARNING @ Tue, 27 Jun 2017 11:56:17: #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 11:56:17: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:56:17: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:56:18: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:56:36: #4 Write output xls file... SRX1936239.10_peaks.xls INFO @ Tue, 27 Jun 2017 11:56:36: #4 Write peak in narrowPeak format file... SRX1936239.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:56:36: #4 Write summits bed file... SRX1936239.10_summits.bed INFO @ Tue, 27 Jun 2017 11:56:36: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (381 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 11:56:44: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:56:54: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:57:03: #4 Write output xls file... SRX1936239.05_peaks.xls INFO @ Tue, 27 Jun 2017 11:57:03: #4 Write peak in narrowPeak format file... SRX1936239.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:57:03: #4 Write summits bed file... SRX1936239.05_summits.bed INFO @ Tue, 27 Jun 2017 11:57:03: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (636 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 11:57:13: #4 Write output xls file... SRX1936239.20_peaks.xls INFO @ Tue, 27 Jun 2017 11:57:13: #4 Write peak in narrowPeak format file... SRX1936239.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:57:13: #4 Write summits bed file... SRX1936239.20_summits.bed INFO @ Tue, 27 Jun 2017 11:57:13: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (134 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。