Job ID = 9157284 sra ファイルのダウンロード中... Completed: 434836K bytes transferred in 18 seconds (191816K 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 8854069 spots for /home/okishinya/chipatlas/results/ce10/SRX2761380/SRR5476954.sra Written 8854069 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: 00:02:30 8854069 reads; of these: 8854069 (100.00%) were unpaired; of these: 537837 (6.07%) aligned 0 times 6308158 (71.25%) aligned exactly 1 time 2008074 (22.68%) aligned >1 times 93.93% overall alignment rate Time searching: 00:02:30 Overall time: 00:02:30 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] 1507447 / 8316232 = 0.1813 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 11:24:07: # Command line: callpeak -t SRX2761380.bam -f BAM -g ce -n SRX2761380.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2761380.20 # format = BAM # ChIP-seq file = ['SRX2761380.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 11:24:07: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:24:07: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:24:07: # Command line: callpeak -t SRX2761380.bam -f BAM -g ce -n SRX2761380.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2761380.10 # format = BAM # ChIP-seq file = ['SRX2761380.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 11:24:07: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:24:07: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:24:07: # Command line: callpeak -t SRX2761380.bam -f BAM -g ce -n SRX2761380.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2761380.05 # format = BAM # ChIP-seq file = ['SRX2761380.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 11:24:07: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:24:07: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:24:16: 1000000 INFO @ Tue, 27 Jun 2017 11:24:16: 1000000 INFO @ Tue, 27 Jun 2017 11:24:18: 1000000 INFO @ Tue, 27 Jun 2017 11:24:25: 2000000 INFO @ Tue, 27 Jun 2017 11:24:25: 2000000 INFO @ Tue, 27 Jun 2017 11:24:29: 2000000 INFO @ Tue, 27 Jun 2017 11:24:34: 3000000 INFO @ Tue, 27 Jun 2017 11:24:34: 3000000 INFO @ Tue, 27 Jun 2017 11:24:41: 3000000 INFO @ Tue, 27 Jun 2017 11:24:43: 4000000 INFO @ Tue, 27 Jun 2017 11:24:46: 4000000 INFO @ Tue, 27 Jun 2017 11:24:51: 5000000 INFO @ Tue, 27 Jun 2017 11:24:53: 4000000 INFO @ Tue, 27 Jun 2017 11:24:58: 5000000 INFO @ Tue, 27 Jun 2017 11:25:00: 6000000 INFO @ Tue, 27 Jun 2017 11:25:05: 5000000 INFO @ Tue, 27 Jun 2017 11:25:07: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 11:25:07: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 11:25:07: #1 total tags in treatment: 6808785 INFO @ Tue, 27 Jun 2017 11:25:07: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:25:07: #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 11:25:07: #1 tags after filtering in treatment: 6808785 INFO @ Tue, 27 Jun 2017 11:25:07: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:25:07: #1 finished! INFO @ Tue, 27 Jun 2017 11:25:07: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:25:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:25:08: #2 number of paired peaks: 631 WARNING @ Tue, 27 Jun 2017 11:25:08: Fewer paired peaks (631) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 631 pairs to build model! INFO @ Tue, 27 Jun 2017 11:25:08: start model_add_line... INFO @ Tue, 27 Jun 2017 11:25:08: start X-correlation... INFO @ Tue, 27 Jun 2017 11:25:08: end of X-cor INFO @ Tue, 27 Jun 2017 11:25:08: #2 finished! INFO @ Tue, 27 Jun 2017 11:25:08: #2 predicted fragment length is 52 bps INFO @ Tue, 27 Jun 2017 11:25:08: #2 alternative fragment length(s) may be 4,52 bps INFO @ Tue, 27 Jun 2017 11:25:08: #2.2 Generate R script for model : SRX2761380.20_model.r WARNING @ Tue, 27 Jun 2017 11:25:08: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 11:25:08: #2 You may need to consider one of the other alternative d(s): 4,52 WARNING @ Tue, 27 Jun 2017 11:25:08: #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 11:25:08: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:25:08: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:25:10: 6000000 INFO @ Tue, 27 Jun 2017 11:25:18: 6000000 INFO @ Tue, 27 Jun 2017 11:25:20: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 11:25:20: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 11:25:20: #1 total tags in treatment: 6808785 INFO @ Tue, 27 Jun 2017 11:25:20: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:25:20: #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 11:25:20: #1 tags after filtering in treatment: 6808785 INFO @ Tue, 27 Jun 2017 11:25:20: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:25:20: #1 finished! INFO @ Tue, 27 Jun 2017 11:25:20: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:25:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:25:21: #2 number of paired peaks: 631 WARNING @ Tue, 27 Jun 2017 11:25:21: Fewer paired peaks (631) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 631 pairs to build model! INFO @ Tue, 27 Jun 2017 11:25:21: start model_add_line... INFO @ Tue, 27 Jun 2017 11:25:21: start X-correlation... INFO @ Tue, 27 Jun 2017 11:25:21: end of X-cor INFO @ Tue, 27 Jun 2017 11:25:21: #2 finished! INFO @ Tue, 27 Jun 2017 11:25:21: #2 predicted fragment length is 52 bps INFO @ Tue, 27 Jun 2017 11:25:21: #2 alternative fragment length(s) may be 4,52 bps INFO @ Tue, 27 Jun 2017 11:25:21: #2.2 Generate R script for model : SRX2761380.05_model.r WARNING @ Tue, 27 Jun 2017 11:25:21: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 11:25:21: #2 You may need to consider one of the other alternative d(s): 4,52 WARNING @ Tue, 27 Jun 2017 11:25:21: #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 11:25:21: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:25:21: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:25:24: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:25:27: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 11:25:27: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 11:25:27: #1 total tags in treatment: 6808785 INFO @ Tue, 27 Jun 2017 11:25:27: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:25:27: #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 11:25:27: #1 tags after filtering in treatment: 6808785 INFO @ Tue, 27 Jun 2017 11:25:27: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:25:27: #1 finished! INFO @ Tue, 27 Jun 2017 11:25:27: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:25:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:25:27: #2 number of paired peaks: 631 WARNING @ Tue, 27 Jun 2017 11:25:27: Fewer paired peaks (631) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 631 pairs to build model! INFO @ Tue, 27 Jun 2017 11:25:27: start model_add_line... INFO @ Tue, 27 Jun 2017 11:25:27: start X-correlation... INFO @ Tue, 27 Jun 2017 11:25:27: end of X-cor INFO @ Tue, 27 Jun 2017 11:25:27: #2 finished! INFO @ Tue, 27 Jun 2017 11:25:27: #2 predicted fragment length is 52 bps INFO @ Tue, 27 Jun 2017 11:25:27: #2 alternative fragment length(s) may be 4,52 bps INFO @ Tue, 27 Jun 2017 11:25:27: #2.2 Generate R script for model : SRX2761380.10_model.r WARNING @ Tue, 27 Jun 2017 11:25:28: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 11:25:28: #2 You may need to consider one of the other alternative d(s): 4,52 WARNING @ Tue, 27 Jun 2017 11:25:28: #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 11:25:28: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:25:28: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:25:33: #4 Write output xls file... SRX2761380.20_peaks.xls INFO @ Tue, 27 Jun 2017 11:25:33: #4 Write peak in narrowPeak format file... SRX2761380.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:25:33: #4 Write summits bed file... SRX2761380.20_summits.bed INFO @ Tue, 27 Jun 2017 11:25:33: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (189 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 11:25:38: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:25:44: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:25:47: #4 Write output xls file... SRX2761380.05_peaks.xls INFO @ Tue, 27 Jun 2017 11:25:47: #4 Write peak in narrowPeak format file... SRX2761380.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:25:47: #4 Write summits bed file... SRX2761380.05_summits.bed INFO @ Tue, 27 Jun 2017 11:25:47: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (803 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 11:25:53: #4 Write output xls file... SRX2761380.10_peaks.xls INFO @ Tue, 27 Jun 2017 11:25:53: #4 Write peak in narrowPeak format file... SRX2761380.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:25:53: #4 Write summits bed file... SRX2761380.10_summits.bed INFO @ Tue, 27 Jun 2017 11:25:53: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (453 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。