Job ID = 9157202 sra ファイルのダウンロード中... Completed: 397480K bytes transferred in 6 seconds (496984K 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 13338445 spots for /home/okishinya/chipatlas/results/ce10/SRX2228915/SRR4380371.sra Written 13338445 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: 00:02:44 13338445 reads; of these: 13338445 (100.00%) were unpaired; of these: 88989 (0.67%) aligned 0 times 10992121 (82.41%) aligned exactly 1 time 2257335 (16.92%) aligned >1 times 99.33% overall alignment rate Time searching: 00:02:44 Overall time: 00:02:44 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_rmdupse_core] 2113737 / 13249456 = 0.1595 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 11:05:11: # Command line: callpeak -t SRX2228915.bam -f BAM -g ce -n SRX2228915.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2228915.20 # format = BAM # ChIP-seq file = ['SRX2228915.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 11:05:11: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:05:11: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:05:11: # Command line: callpeak -t SRX2228915.bam -f BAM -g ce -n SRX2228915.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2228915.05 # format = BAM # ChIP-seq file = ['SRX2228915.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 11:05:11: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:05:11: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:05:11: # Command line: callpeak -t SRX2228915.bam -f BAM -g ce -n SRX2228915.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2228915.10 # format = BAM # ChIP-seq file = ['SRX2228915.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 11:05:11: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:05:11: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:05:18: 1000000 INFO @ Tue, 27 Jun 2017 11:05:18: 1000000 INFO @ Tue, 27 Jun 2017 11:05:19: 1000000 INFO @ Tue, 27 Jun 2017 11:05:25: 2000000 INFO @ Tue, 27 Jun 2017 11:05:25: 2000000 INFO @ Tue, 27 Jun 2017 11:05:27: 2000000 INFO @ Tue, 27 Jun 2017 11:05:32: 3000000 INFO @ Tue, 27 Jun 2017 11:05:32: 3000000 INFO @ Tue, 27 Jun 2017 11:05:34: 3000000 INFO @ Tue, 27 Jun 2017 11:05:40: 4000000 INFO @ Tue, 27 Jun 2017 11:05:40: 4000000 INFO @ Tue, 27 Jun 2017 11:05:42: 4000000 INFO @ Tue, 27 Jun 2017 11:05:47: 5000000 INFO @ Tue, 27 Jun 2017 11:05:47: 5000000 INFO @ Tue, 27 Jun 2017 11:05:50: 5000000 INFO @ Tue, 27 Jun 2017 11:05:54: 6000000 INFO @ Tue, 27 Jun 2017 11:05:54: 6000000 INFO @ Tue, 27 Jun 2017 11:05:57: 6000000 INFO @ Tue, 27 Jun 2017 11:06:00: 7000000 INFO @ Tue, 27 Jun 2017 11:06:00: 7000000 INFO @ Tue, 27 Jun 2017 11:06:04: 7000000 INFO @ Tue, 27 Jun 2017 11:06:07: 8000000 INFO @ Tue, 27 Jun 2017 11:06:07: 8000000 INFO @ Tue, 27 Jun 2017 11:06:11: 8000000 INFO @ Tue, 27 Jun 2017 11:06:14: 9000000 INFO @ Tue, 27 Jun 2017 11:06:14: 9000000 INFO @ Tue, 27 Jun 2017 11:06:17: 9000000 INFO @ Tue, 27 Jun 2017 11:06:20: 10000000 INFO @ Tue, 27 Jun 2017 11:06:20: 10000000 INFO @ Tue, 27 Jun 2017 11:06:24: 10000000 INFO @ Tue, 27 Jun 2017 11:06:27: 11000000 INFO @ Tue, 27 Jun 2017 11:06:27: 11000000 INFO @ Tue, 27 Jun 2017 11:06:28: #1 tag size is determined as 42 bps INFO @ Tue, 27 Jun 2017 11:06:28: #1 tag size = 42 INFO @ Tue, 27 Jun 2017 11:06:28: #1 total tags in treatment: 11135719 INFO @ Tue, 27 Jun 2017 11:06:28: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:06:28: #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 11:06:28: #1 tags after filtering in treatment: 11135719 INFO @ Tue, 27 Jun 2017 11:06:28: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:06:28: #1 finished! INFO @ Tue, 27 Jun 2017 11:06:28: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:06:28: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:06:28: #1 tag size is determined as 42 bps INFO @ Tue, 27 Jun 2017 11:06:28: #1 tag size = 42 INFO @ Tue, 27 Jun 2017 11:06:28: #1 total tags in treatment: 11135719 INFO @ Tue, 27 Jun 2017 11:06:28: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:06:28: #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 11:06:29: #1 tags after filtering in treatment: 11135719 INFO @ Tue, 27 Jun 2017 11:06:29: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:06:29: #1 finished! INFO @ Tue, 27 Jun 2017 11:06:29: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:06:29: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:06:29: #2 number of paired peaks: 363 WARNING @ Tue, 27 Jun 2017 11:06:29: Fewer paired peaks (363) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 363 pairs to build model! INFO @ Tue, 27 Jun 2017 11:06:29: start model_add_line... INFO @ Tue, 27 Jun 2017 11:06:29: start X-correlation... INFO @ Tue, 27 Jun 2017 11:06:29: end of X-cor INFO @ Tue, 27 Jun 2017 11:06:29: #2 finished! INFO @ Tue, 27 Jun 2017 11:06:29: #2 predicted fragment length is 41 bps INFO @ Tue, 27 Jun 2017 11:06:29: #2 alternative fragment length(s) may be 3,41,584,587 bps INFO @ Tue, 27 Jun 2017 11:06:29: #2.2 Generate R script for model : SRX2228915.05_model.r WARNING @ Tue, 27 Jun 2017 11:06:29: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 11:06:29: #2 You may need to consider one of the other alternative d(s): 3,41,584,587 WARNING @ Tue, 27 Jun 2017 11:06:29: #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 11:06:29: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:06:29: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:06:30: #2 number of paired peaks: 363 WARNING @ Tue, 27 Jun 2017 11:06:30: Fewer paired peaks (363) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 363 pairs to build model! INFO @ Tue, 27 Jun 2017 11:06:30: start model_add_line... INFO @ Tue, 27 Jun 2017 11:06:30: start X-correlation... INFO @ Tue, 27 Jun 2017 11:06:30: end of X-cor INFO @ Tue, 27 Jun 2017 11:06:30: #2 finished! INFO @ Tue, 27 Jun 2017 11:06:30: #2 predicted fragment length is 41 bps INFO @ Tue, 27 Jun 2017 11:06:30: #2 alternative fragment length(s) may be 3,41,584,587 bps INFO @ Tue, 27 Jun 2017 11:06:30: #2.2 Generate R script for model : SRX2228915.20_model.r WARNING @ Tue, 27 Jun 2017 11:06:30: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 11:06:30: #2 You may need to consider one of the other alternative d(s): 3,41,584,587 WARNING @ Tue, 27 Jun 2017 11:06:30: #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 11:06:30: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:06:30: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:06:31: 11000000 INFO @ Tue, 27 Jun 2017 11:06:32: #1 tag size is determined as 42 bps INFO @ Tue, 27 Jun 2017 11:06:32: #1 tag size = 42 INFO @ Tue, 27 Jun 2017 11:06:32: #1 total tags in treatment: 11135719 INFO @ Tue, 27 Jun 2017 11:06:32: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:06:32: #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 11:06:33: #1 tags after filtering in treatment: 11135719 INFO @ Tue, 27 Jun 2017 11:06:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:06:33: #1 finished! INFO @ Tue, 27 Jun 2017 11:06:33: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:06:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:06:33: #2 number of paired peaks: 363 WARNING @ Tue, 27 Jun 2017 11:06:33: Fewer paired peaks (363) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 363 pairs to build model! INFO @ Tue, 27 Jun 2017 11:06:33: start model_add_line... INFO @ Tue, 27 Jun 2017 11:06:33: start X-correlation... INFO @ Tue, 27 Jun 2017 11:06:33: end of X-cor INFO @ Tue, 27 Jun 2017 11:06:33: #2 finished! INFO @ Tue, 27 Jun 2017 11:06:33: #2 predicted fragment length is 41 bps INFO @ Tue, 27 Jun 2017 11:06:33: #2 alternative fragment length(s) may be 3,41,584,587 bps INFO @ Tue, 27 Jun 2017 11:06:33: #2.2 Generate R script for model : SRX2228915.10_model.r WARNING @ Tue, 27 Jun 2017 11:06:33: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 11:06:33: #2 You may need to consider one of the other alternative d(s): 3,41,584,587 WARNING @ Tue, 27 Jun 2017 11:06:33: #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 11:06:33: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:06:33: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:06:54: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:06:54: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:06:58: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:07:06: #4 Write output xls file... SRX2228915.20_peaks.xls INFO @ Tue, 27 Jun 2017 11:07:06: #4 Write peak in narrowPeak format file... SRX2228915.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:07:06: #4 Write summits bed file... SRX2228915.20_summits.bed INFO @ Tue, 27 Jun 2017 11:07:06: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (132 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 11:07:07: #4 Write output xls file... SRX2228915.05_peaks.xls INFO @ Tue, 27 Jun 2017 11:07:07: #4 Write peak in narrowPeak format file... SRX2228915.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:07:07: #4 Write summits bed file... SRX2228915.05_summits.bed INFO @ Tue, 27 Jun 2017 11:07:07: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (950 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 11:07:10: #4 Write output xls file... SRX2228915.10_peaks.xls INFO @ Tue, 27 Jun 2017 11:07:10: #4 Write peak in narrowPeak format file... SRX2228915.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:07:10: #4 Write summits bed file... SRX2228915.10_summits.bed INFO @ Tue, 27 Jun 2017 11:07:10: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (375 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。