Job ID = 9157200 sra ファイルのダウンロード中... Completed: 541293K bytes transferred in 6 seconds (691592K 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 16440500 spots for /home/okishinya/chipatlas/results/ce10/SRX2228913/SRR4380369.sra Written 16440500 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: 00:04:23 16440500 reads; of these: 16440500 (100.00%) were unpaired; of these: 138387 (0.84%) aligned 0 times 13512933 (82.19%) aligned exactly 1 time 2789180 (16.97%) aligned >1 times 99.16% overall alignment rate Time searching: 00:04:23 Overall time: 00:04:24 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 8 files... [bam_rmdupse_core] 1797168 / 16302113 = 0.1102 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 11:07:48: # Command line: callpeak -t SRX2228913.bam -f BAM -g ce -n SRX2228913.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2228913.20 # format = BAM # ChIP-seq file = ['SRX2228913.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 11:07:48: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:07:48: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:07:48: # Command line: callpeak -t SRX2228913.bam -f BAM -g ce -n SRX2228913.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2228913.10 # format = BAM # ChIP-seq file = ['SRX2228913.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 11:07:48: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:07:48: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:07:48: # Command line: callpeak -t SRX2228913.bam -f BAM -g ce -n SRX2228913.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2228913.05 # format = BAM # ChIP-seq file = ['SRX2228913.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 11:07:48: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:07:48: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:07:56: 1000000 INFO @ Tue, 27 Jun 2017 11:07:56: 1000000 INFO @ Tue, 27 Jun 2017 11:07:56: 1000000 INFO @ Tue, 27 Jun 2017 11:08:04: 2000000 INFO @ Tue, 27 Jun 2017 11:08:04: 2000000 INFO @ Tue, 27 Jun 2017 11:08:04: 2000000 INFO @ Tue, 27 Jun 2017 11:08:11: 3000000 INFO @ Tue, 27 Jun 2017 11:08:12: 3000000 INFO @ Tue, 27 Jun 2017 11:08:12: 3000000 INFO @ Tue, 27 Jun 2017 11:08:18: 4000000 INFO @ Tue, 27 Jun 2017 11:08:18: 4000000 INFO @ Tue, 27 Jun 2017 11:08:19: 4000000 INFO @ Tue, 27 Jun 2017 11:08:25: 5000000 INFO @ Tue, 27 Jun 2017 11:08:26: 5000000 INFO @ Tue, 27 Jun 2017 11:08:27: 5000000 INFO @ Tue, 27 Jun 2017 11:08:31: 6000000 INFO @ Tue, 27 Jun 2017 11:08:33: 6000000 INFO @ Tue, 27 Jun 2017 11:08:34: 6000000 INFO @ Tue, 27 Jun 2017 11:08:38: 7000000 INFO @ Tue, 27 Jun 2017 11:08:40: 7000000 INFO @ Tue, 27 Jun 2017 11:08:42: 7000000 INFO @ Tue, 27 Jun 2017 11:08:44: 8000000 INFO @ Tue, 27 Jun 2017 11:08:47: 8000000 INFO @ Tue, 27 Jun 2017 11:08:50: 8000000 INFO @ Tue, 27 Jun 2017 11:08:52: 9000000 INFO @ Tue, 27 Jun 2017 11:08:55: 9000000 INFO @ Tue, 27 Jun 2017 11:08:58: 9000000 INFO @ Tue, 27 Jun 2017 11:09:00: 10000000 INFO @ Tue, 27 Jun 2017 11:09:03: 10000000 INFO @ Tue, 27 Jun 2017 11:09:06: 10000000 INFO @ Tue, 27 Jun 2017 11:09:09: 11000000 INFO @ Tue, 27 Jun 2017 11:09:11: 11000000 INFO @ Tue, 27 Jun 2017 11:09:15: 11000000 INFO @ Tue, 27 Jun 2017 11:09:18: 12000000 INFO @ Tue, 27 Jun 2017 11:09:19: 12000000 INFO @ Tue, 27 Jun 2017 11:09:23: 12000000 INFO @ Tue, 27 Jun 2017 11:09:26: 13000000 INFO @ Tue, 27 Jun 2017 11:09:27: 13000000 INFO @ Tue, 27 Jun 2017 11:09:32: 13000000 INFO @ Tue, 27 Jun 2017 11:09:35: 14000000 INFO @ Tue, 27 Jun 2017 11:09:35: 14000000 INFO @ Tue, 27 Jun 2017 11:09:39: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 11:09:39: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 11:09:39: #1 total tags in treatment: 14504945 INFO @ Tue, 27 Jun 2017 11:09:39: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:09:39: #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 11:09:39: #1 tags after filtering in treatment: 14504945 INFO @ Tue, 27 Jun 2017 11:09:39: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:09:39: #1 finished! INFO @ Tue, 27 Jun 2017 11:09:39: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:09:39: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:09:39: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 11:09:39: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 11:09:39: #1 total tags in treatment: 14504945 INFO @ Tue, 27 Jun 2017 11:09:39: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:09:39: #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 11:09:40: #1 tags after filtering in treatment: 14504945 INFO @ Tue, 27 Jun 2017 11:09:40: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:09:40: #1 finished! INFO @ Tue, 27 Jun 2017 11:09:40: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:09:40: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:09:40: 14000000 INFO @ Tue, 27 Jun 2017 11:09:40: #2 number of paired peaks: 339 WARNING @ Tue, 27 Jun 2017 11:09:40: Fewer paired peaks (339) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 339 pairs to build model! INFO @ Tue, 27 Jun 2017 11:09:40: start model_add_line... INFO @ Tue, 27 Jun 2017 11:09:40: start X-correlation... INFO @ Tue, 27 Jun 2017 11:09:40: end of X-cor INFO @ Tue, 27 Jun 2017 11:09:40: #2 finished! INFO @ Tue, 27 Jun 2017 11:09:40: #2 predicted fragment length is 46 bps INFO @ Tue, 27 Jun 2017 11:09:40: #2 alternative fragment length(s) may be 2,46 bps INFO @ Tue, 27 Jun 2017 11:09:40: #2.2 Generate R script for model : SRX2228913.20_model.r WARNING @ Tue, 27 Jun 2017 11:09:40: #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 11:09:40: #2 You may need to consider one of the other alternative d(s): 2,46 WARNING @ Tue, 27 Jun 2017 11:09:40: #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 11:09:40: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:09:40: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:09:41: #2 number of paired peaks: 339 WARNING @ Tue, 27 Jun 2017 11:09:41: Fewer paired peaks (339) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 339 pairs to build model! INFO @ Tue, 27 Jun 2017 11:09:41: start model_add_line... INFO @ Tue, 27 Jun 2017 11:09:41: start X-correlation... INFO @ Tue, 27 Jun 2017 11:09:41: end of X-cor INFO @ Tue, 27 Jun 2017 11:09:41: #2 finished! INFO @ Tue, 27 Jun 2017 11:09:41: #2 predicted fragment length is 46 bps INFO @ Tue, 27 Jun 2017 11:09:41: #2 alternative fragment length(s) may be 2,46 bps INFO @ Tue, 27 Jun 2017 11:09:41: #2.2 Generate R script for model : SRX2228913.05_model.r WARNING @ Tue, 27 Jun 2017 11:09:41: #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 11:09:41: #2 You may need to consider one of the other alternative d(s): 2,46 WARNING @ Tue, 27 Jun 2017 11:09:41: #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 11:09:41: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:09:41: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:09:44: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 11:09:44: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 11:09:44: #1 total tags in treatment: 14504945 INFO @ Tue, 27 Jun 2017 11:09:44: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:09:44: #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 11:09:44: #1 tags after filtering in treatment: 14504945 INFO @ Tue, 27 Jun 2017 11:09:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:09:44: #1 finished! INFO @ Tue, 27 Jun 2017 11:09:44: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:09:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:09:45: #2 number of paired peaks: 339 WARNING @ Tue, 27 Jun 2017 11:09:45: Fewer paired peaks (339) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 339 pairs to build model! INFO @ Tue, 27 Jun 2017 11:09:45: start model_add_line... INFO @ Tue, 27 Jun 2017 11:09:45: start X-correlation... INFO @ Tue, 27 Jun 2017 11:09:45: end of X-cor INFO @ Tue, 27 Jun 2017 11:09:45: #2 finished! INFO @ Tue, 27 Jun 2017 11:09:45: #2 predicted fragment length is 46 bps INFO @ Tue, 27 Jun 2017 11:09:45: #2 alternative fragment length(s) may be 2,46 bps INFO @ Tue, 27 Jun 2017 11:09:45: #2.2 Generate R script for model : SRX2228913.10_model.r WARNING @ Tue, 27 Jun 2017 11:09:45: #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 11:09:45: #2 You may need to consider one of the other alternative d(s): 2,46 WARNING @ Tue, 27 Jun 2017 11:09:45: #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 11:09:45: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:09:45: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:10:09: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:10:11: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:10:13: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:10:25: #4 Write output xls file... SRX2228913.05_peaks.xls INFO @ Tue, 27 Jun 2017 11:10:25: #4 Write peak in narrowPeak format file... SRX2228913.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:10:25: #4 Write summits bed file... SRX2228913.05_summits.bed INFO @ Tue, 27 Jun 2017 11:10:25: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (705 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 11:10:25: #4 Write output xls file... SRX2228913.20_peaks.xls INFO @ Tue, 27 Jun 2017 11:10:25: #4 Write peak in narrowPeak format file... SRX2228913.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:10:25: #4 Write summits bed file... SRX2228913.20_summits.bed INFO @ Tue, 27 Jun 2017 11:10:25: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (183 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 11:10:29: #4 Write output xls file... SRX2228913.10_peaks.xls INFO @ Tue, 27 Jun 2017 11:10:29: #4 Write peak in narrowPeak format file... SRX2228913.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:10:29: #4 Write summits bed file... SRX2228913.10_summits.bed INFO @ Tue, 27 Jun 2017 11:10:29: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (507 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。