Job ID = 9158407 sra ファイルのダウンロード中... Completed: 233811K bytes transferred in 4 seconds (407561K 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 23573799 spots for /home/okishinya/chipatlas/results/dm3/SRX1167504/SRR2192591.sra Written 23573799 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: 00:07:09 23573799 reads; of these: 23573799 (100.00%) were unpaired; of these: 583171 (2.47%) aligned 0 times 18271838 (77.51%) aligned exactly 1 time 4718790 (20.02%) aligned >1 times 97.53% overall alignment rate Time searching: 00:07:09 Overall time: 00:07:09 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 11561615 / 22990628 = 0.5029 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 16:55:05: # Command line: callpeak -t SRX1167504.bam -f BAM -g dm -n SRX1167504.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1167504.10 # format = BAM # ChIP-seq file = ['SRX1167504.bam'] # control file = None # effective genome size = 1.20e+08 # 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 16:55:05: #1 read tag files... INFO @ Tue, 27 Jun 2017 16:55:05: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 16:55:05: # Command line: callpeak -t SRX1167504.bam -f BAM -g dm -n SRX1167504.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1167504.20 # format = BAM # ChIP-seq file = ['SRX1167504.bam'] # control file = None # effective genome size = 1.20e+08 # 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 16:55:05: #1 read tag files... INFO @ Tue, 27 Jun 2017 16:55:05: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 16:55:05: # Command line: callpeak -t SRX1167504.bam -f BAM -g dm -n SRX1167504.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1167504.05 # format = BAM # ChIP-seq file = ['SRX1167504.bam'] # control file = None # effective genome size = 1.20e+08 # 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 16:55:05: #1 read tag files... INFO @ Tue, 27 Jun 2017 16:55:05: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 16:55:11: 1000000 INFO @ Tue, 27 Jun 2017 16:55:11: 1000000 INFO @ Tue, 27 Jun 2017 16:55:11: 1000000 INFO @ Tue, 27 Jun 2017 16:55:17: 2000000 INFO @ Tue, 27 Jun 2017 16:55:17: 2000000 INFO @ Tue, 27 Jun 2017 16:55:17: 2000000 INFO @ Tue, 27 Jun 2017 16:55:22: 3000000 INFO @ Tue, 27 Jun 2017 16:55:22: 3000000 INFO @ Tue, 27 Jun 2017 16:55:23: 3000000 INFO @ Tue, 27 Jun 2017 16:55:28: 4000000 INFO @ Tue, 27 Jun 2017 16:55:28: 4000000 INFO @ Tue, 27 Jun 2017 16:55:28: 4000000 INFO @ Tue, 27 Jun 2017 16:55:34: 5000000 INFO @ Tue, 27 Jun 2017 16:55:34: 5000000 INFO @ Tue, 27 Jun 2017 16:55:34: 5000000 INFO @ Tue, 27 Jun 2017 16:55:39: 6000000 INFO @ Tue, 27 Jun 2017 16:55:39: 6000000 INFO @ Tue, 27 Jun 2017 16:55:40: 6000000 INFO @ Tue, 27 Jun 2017 16:55:45: 7000000 INFO @ Tue, 27 Jun 2017 16:55:45: 7000000 INFO @ Tue, 27 Jun 2017 16:55:45: 7000000 INFO @ Tue, 27 Jun 2017 16:55:50: 8000000 INFO @ Tue, 27 Jun 2017 16:55:51: 8000000 INFO @ Tue, 27 Jun 2017 16:55:51: 8000000 INFO @ Tue, 27 Jun 2017 16:55:56: 9000000 INFO @ Tue, 27 Jun 2017 16:55:57: 9000000 INFO @ Tue, 27 Jun 2017 16:55:57: 9000000 INFO @ Tue, 27 Jun 2017 16:56:02: 10000000 INFO @ Tue, 27 Jun 2017 16:56:02: 10000000 INFO @ Tue, 27 Jun 2017 16:56:03: 10000000 INFO @ Tue, 27 Jun 2017 16:56:07: 11000000 INFO @ Tue, 27 Jun 2017 16:56:08: 11000000 INFO @ Tue, 27 Jun 2017 16:56:09: 11000000 INFO @ Tue, 27 Jun 2017 16:56:10: #1 tag size is determined as 50 bps INFO @ Tue, 27 Jun 2017 16:56:10: #1 tag size = 50 INFO @ Tue, 27 Jun 2017 16:56:10: #1 total tags in treatment: 11429013 INFO @ Tue, 27 Jun 2017 16:56:10: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 16:56:10: #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 16:56:10: #1 tags after filtering in treatment: 11429013 INFO @ Tue, 27 Jun 2017 16:56:10: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 16:56:10: #1 finished! INFO @ Tue, 27 Jun 2017 16:56:10: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 16:56:10: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 16:56:11: #1 tag size is determined as 50 bps INFO @ Tue, 27 Jun 2017 16:56:11: #1 tag size = 50 INFO @ Tue, 27 Jun 2017 16:56:11: #1 total tags in treatment: 11429013 INFO @ Tue, 27 Jun 2017 16:56:11: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 16:56:11: #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 16:56:11: #2 number of paired peaks: 199 WARNING @ Tue, 27 Jun 2017 16:56:11: Fewer paired peaks (199) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 199 pairs to build model! INFO @ Tue, 27 Jun 2017 16:56:11: start model_add_line... INFO @ Tue, 27 Jun 2017 16:56:11: #1 tags after filtering in treatment: 11429013 INFO @ Tue, 27 Jun 2017 16:56:11: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 16:56:11: #1 finished! INFO @ Tue, 27 Jun 2017 16:56:11: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 16:56:11: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 16:56:11: start X-correlation... INFO @ Tue, 27 Jun 2017 16:56:11: end of X-cor INFO @ Tue, 27 Jun 2017 16:56:11: #2 finished! INFO @ Tue, 27 Jun 2017 16:56:11: #2 predicted fragment length is 49 bps INFO @ Tue, 27 Jun 2017 16:56:11: #2 alternative fragment length(s) may be 49 bps INFO @ Tue, 27 Jun 2017 16:56:11: #2.2 Generate R script for model : SRX1167504.05_model.r WARNING @ Tue, 27 Jun 2017 16:56:11: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 16:56:11: #2 You may need to consider one of the other alternative d(s): 49 WARNING @ Tue, 27 Jun 2017 16:56:11: #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 16:56:11: #3 Call peaks... INFO @ Tue, 27 Jun 2017 16:56:11: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 16:56:11: #1 tag size is determined as 50 bps INFO @ Tue, 27 Jun 2017 16:56:11: #1 tag size = 50 INFO @ Tue, 27 Jun 2017 16:56:11: #1 total tags in treatment: 11429013 INFO @ Tue, 27 Jun 2017 16:56:11: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 16:56:11: #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 16:56:11: #1 tags after filtering in treatment: 11429013 INFO @ Tue, 27 Jun 2017 16:56:11: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 16:56:11: #1 finished! INFO @ Tue, 27 Jun 2017 16:56:11: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 16:56:11: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 16:56:12: #2 number of paired peaks: 199 WARNING @ Tue, 27 Jun 2017 16:56:12: Fewer paired peaks (199) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 199 pairs to build model! INFO @ Tue, 27 Jun 2017 16:56:12: start model_add_line... INFO @ Tue, 27 Jun 2017 16:56:12: start X-correlation... INFO @ Tue, 27 Jun 2017 16:56:12: end of X-cor INFO @ Tue, 27 Jun 2017 16:56:12: #2 finished! INFO @ Tue, 27 Jun 2017 16:56:12: #2 predicted fragment length is 49 bps INFO @ Tue, 27 Jun 2017 16:56:12: #2 alternative fragment length(s) may be 49 bps INFO @ Tue, 27 Jun 2017 16:56:12: #2.2 Generate R script for model : SRX1167504.10_model.r WARNING @ Tue, 27 Jun 2017 16:56:12: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 16:56:12: #2 You may need to consider one of the other alternative d(s): 49 WARNING @ Tue, 27 Jun 2017 16:56:12: #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 16:56:12: #3 Call peaks... INFO @ Tue, 27 Jun 2017 16:56:12: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 16:56:12: #2 number of paired peaks: 199 WARNING @ Tue, 27 Jun 2017 16:56:12: Fewer paired peaks (199) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 199 pairs to build model! INFO @ Tue, 27 Jun 2017 16:56:12: start model_add_line... INFO @ Tue, 27 Jun 2017 16:56:12: start X-correlation... INFO @ Tue, 27 Jun 2017 16:56:12: end of X-cor INFO @ Tue, 27 Jun 2017 16:56:12: #2 finished! INFO @ Tue, 27 Jun 2017 16:56:12: #2 predicted fragment length is 49 bps INFO @ Tue, 27 Jun 2017 16:56:12: #2 alternative fragment length(s) may be 49 bps INFO @ Tue, 27 Jun 2017 16:56:12: #2.2 Generate R script for model : SRX1167504.20_model.r WARNING @ Tue, 27 Jun 2017 16:56:12: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 16:56:12: #2 You may need to consider one of the other alternative d(s): 49 WARNING @ Tue, 27 Jun 2017 16:56:12: #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 16:56:12: #3 Call peaks... INFO @ Tue, 27 Jun 2017 16:56:12: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 16:56:35: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 16:56:36: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 16:56:37: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 16:56:48: #4 Write output xls file... SRX1167504.05_peaks.xls INFO @ Tue, 27 Jun 2017 16:56:48: #4 Write peak in narrowPeak format file... SRX1167504.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 16:56:48: #4 Write summits bed file... SRX1167504.05_summits.bed INFO @ Tue, 27 Jun 2017 16:56:48: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1687 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 16:56:49: #4 Write output xls file... SRX1167504.10_peaks.xls INFO @ Tue, 27 Jun 2017 16:56:49: #4 Write peak in narrowPeak format file... SRX1167504.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 16:56:49: #4 Write summits bed file... SRX1167504.10_summits.bed INFO @ Tue, 27 Jun 2017 16:56:49: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (1146 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 16:56:50: #4 Write output xls file... SRX1167504.20_peaks.xls INFO @ Tue, 27 Jun 2017 16:56:50: #4 Write peak in narrowPeak format file... SRX1167504.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 16:56:50: #4 Write summits bed file... SRX1167504.20_summits.bed INFO @ Tue, 27 Jun 2017 16:56:50: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (723 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。