Job ID = 9157259 sra ファイルのダウンロード中... Completed: 442477K bytes transferred in 5 seconds (619498K 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 10864382 spots for /home/okishinya/chipatlas/results/ce10/SRX2350741/SRR5024050.sra Written 10864382 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: 00:03:05 10864382 reads; of these: 10864382 (100.00%) were unpaired; of these: 536300 (4.94%) aligned 0 times 8994402 (82.79%) aligned exactly 1 time 1333680 (12.28%) aligned >1 times 95.06% overall alignment rate Time searching: 00:03:05 Overall time: 00:03:05 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] 646717 / 10328082 = 0.0626 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 11:18:28: # Command line: callpeak -t SRX2350741.bam -f BAM -g ce -n SRX2350741.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2350741.20 # format = BAM # ChIP-seq file = ['SRX2350741.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 11:18:28: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:18:28: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:18:28: # Command line: callpeak -t SRX2350741.bam -f BAM -g ce -n SRX2350741.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2350741.05 # format = BAM # ChIP-seq file = ['SRX2350741.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 11:18:28: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:18:28: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:18:28: # Command line: callpeak -t SRX2350741.bam -f BAM -g ce -n SRX2350741.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2350741.10 # format = BAM # ChIP-seq file = ['SRX2350741.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 11:18:28: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:18:28: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:18:35: 1000000 INFO @ Tue, 27 Jun 2017 11:18:37: 1000000 INFO @ Tue, 27 Jun 2017 11:18:37: 1000000 INFO @ Tue, 27 Jun 2017 11:18:43: 2000000 INFO @ Tue, 27 Jun 2017 11:18:46: 2000000 INFO @ Tue, 27 Jun 2017 11:18:46: 2000000 INFO @ Tue, 27 Jun 2017 11:18:51: 3000000 INFO @ Tue, 27 Jun 2017 11:18:55: 3000000 INFO @ Tue, 27 Jun 2017 11:18:55: 3000000 INFO @ Tue, 27 Jun 2017 11:18:58: 4000000 INFO @ Tue, 27 Jun 2017 11:19:03: 4000000 INFO @ Tue, 27 Jun 2017 11:19:03: 4000000 INFO @ Tue, 27 Jun 2017 11:19:06: 5000000 INFO @ Tue, 27 Jun 2017 11:19:12: 5000000 INFO @ Tue, 27 Jun 2017 11:19:12: 5000000 INFO @ Tue, 27 Jun 2017 11:19:13: 6000000 INFO @ Tue, 27 Jun 2017 11:19:20: 7000000 INFO @ Tue, 27 Jun 2017 11:19:22: 6000000 INFO @ Tue, 27 Jun 2017 11:19:22: 6000000 INFO @ Tue, 27 Jun 2017 11:19:28: 8000000 INFO @ Tue, 27 Jun 2017 11:19:31: 7000000 INFO @ Tue, 27 Jun 2017 11:19:31: 7000000 INFO @ Tue, 27 Jun 2017 11:19:36: 9000000 INFO @ Tue, 27 Jun 2017 11:19:39: 8000000 INFO @ Tue, 27 Jun 2017 11:19:39: 8000000 INFO @ Tue, 27 Jun 2017 11:19:42: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 11:19:42: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 11:19:42: #1 total tags in treatment: 9681365 INFO @ Tue, 27 Jun 2017 11:19:42: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:19:42: #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 11:19:42: #1 tags after filtering in treatment: 9681365 INFO @ Tue, 27 Jun 2017 11:19:42: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:19:42: #1 finished! INFO @ Tue, 27 Jun 2017 11:19:42: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:19:42: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:19:43: #2 number of paired peaks: 219 WARNING @ Tue, 27 Jun 2017 11:19:43: Fewer paired peaks (219) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 219 pairs to build model! INFO @ Tue, 27 Jun 2017 11:19:43: start model_add_line... INFO @ Tue, 27 Jun 2017 11:19:43: start X-correlation... INFO @ Tue, 27 Jun 2017 11:19:43: end of X-cor INFO @ Tue, 27 Jun 2017 11:19:43: #2 finished! INFO @ Tue, 27 Jun 2017 11:19:43: #2 predicted fragment length is 49 bps INFO @ Tue, 27 Jun 2017 11:19:43: #2 alternative fragment length(s) may be 3,49,558 bps INFO @ Tue, 27 Jun 2017 11:19:43: #2.2 Generate R script for model : SRX2350741.20_model.r WARNING @ Tue, 27 Jun 2017 11:19:43: #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 11:19:43: #2 You may need to consider one of the other alternative d(s): 3,49,558 WARNING @ Tue, 27 Jun 2017 11:19:43: #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 11:19:43: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:19:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:19:48: 9000000 INFO @ Tue, 27 Jun 2017 11:19:48: 9000000 INFO @ Tue, 27 Jun 2017 11:19:53: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 11:19:53: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 11:19:53: #1 total tags in treatment: 9681365 INFO @ Tue, 27 Jun 2017 11:19:53: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:19:53: #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 11:19:53: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 11:19:53: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 11:19:53: #1 total tags in treatment: 9681365 INFO @ Tue, 27 Jun 2017 11:19:53: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:19:53: #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 11:19:53: #1 tags after filtering in treatment: 9681365 INFO @ Tue, 27 Jun 2017 11:19:53: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:19:53: #1 finished! INFO @ Tue, 27 Jun 2017 11:19:53: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:19:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:19:53: #1 tags after filtering in treatment: 9681365 INFO @ Tue, 27 Jun 2017 11:19:53: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:19:53: #1 finished! INFO @ Tue, 27 Jun 2017 11:19:53: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:19:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:19:54: #2 number of paired peaks: 219 WARNING @ Tue, 27 Jun 2017 11:19:54: Fewer paired peaks (219) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 219 pairs to build model! INFO @ Tue, 27 Jun 2017 11:19:54: start model_add_line... INFO @ Tue, 27 Jun 2017 11:19:54: #2 number of paired peaks: 219 WARNING @ Tue, 27 Jun 2017 11:19:54: Fewer paired peaks (219) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 219 pairs to build model! INFO @ Tue, 27 Jun 2017 11:19:54: start model_add_line... INFO @ Tue, 27 Jun 2017 11:19:54: start X-correlation... INFO @ Tue, 27 Jun 2017 11:19:54: end of X-cor INFO @ Tue, 27 Jun 2017 11:19:54: #2 finished! INFO @ Tue, 27 Jun 2017 11:19:54: #2 predicted fragment length is 49 bps INFO @ Tue, 27 Jun 2017 11:19:54: #2 alternative fragment length(s) may be 3,49,558 bps INFO @ Tue, 27 Jun 2017 11:19:54: #2.2 Generate R script for model : SRX2350741.10_model.r WARNING @ Tue, 27 Jun 2017 11:19:54: #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 11:19:54: #2 You may need to consider one of the other alternative d(s): 3,49,558 WARNING @ Tue, 27 Jun 2017 11:19:54: #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 11:19:54: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:19:54: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:19:54: start X-correlation... INFO @ Tue, 27 Jun 2017 11:19:54: end of X-cor INFO @ Tue, 27 Jun 2017 11:19:54: #2 finished! INFO @ Tue, 27 Jun 2017 11:19:54: #2 predicted fragment length is 49 bps INFO @ Tue, 27 Jun 2017 11:19:54: #2 alternative fragment length(s) may be 3,49,558 bps INFO @ Tue, 27 Jun 2017 11:19:54: #2.2 Generate R script for model : SRX2350741.05_model.r WARNING @ Tue, 27 Jun 2017 11:19:54: #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 11:19:54: #2 You may need to consider one of the other alternative d(s): 3,49,558 WARNING @ Tue, 27 Jun 2017 11:19:54: #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 11:19:54: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:19:54: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:20:03: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:20:13: #4 Write output xls file... SRX2350741.20_peaks.xls INFO @ Tue, 27 Jun 2017 11:20:13: #4 Write peak in narrowPeak format file... SRX2350741.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:20:13: #4 Write summits bed file... SRX2350741.20_summits.bed INFO @ Tue, 27 Jun 2017 11:20:13: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (108 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 11:20:14: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:20:15: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:20:26: #4 Write output xls file... SRX2350741.10_peaks.xls INFO @ Tue, 27 Jun 2017 11:20:26: #4 Write peak in narrowPeak format file... SRX2350741.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:20:26: #4 Write summits bed file... SRX2350741.10_summits.bed INFO @ Tue, 27 Jun 2017 11:20:26: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (255 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 11:20:27: #4 Write output xls file... SRX2350741.05_peaks.xls INFO @ Tue, 27 Jun 2017 11:20:27: #4 Write peak in narrowPeak format file... SRX2350741.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:20:27: #4 Write summits bed file... SRX2350741.05_summits.bed INFO @ Tue, 27 Jun 2017 11:20:27: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (480 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。