Job ID = 9157254 sra ファイルのダウンロード中... Completed: 510939K bytes transferred in 5 seconds (697924K 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 12272558 spots for /home/okishinya/chipatlas/results/ce10/SRX2350738/SRR5024047.sra Written 12272558 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: 00:03:26 12272558 reads; of these: 12272558 (100.00%) were unpaired; of these: 215304 (1.75%) aligned 0 times 10421170 (84.91%) aligned exactly 1 time 1636084 (13.33%) aligned >1 times 98.25% overall alignment rate Time searching: 00:03:26 Overall time: 00:03:26 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] 1787262 / 12057254 = 0.1482 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 11:18:25: # Command line: callpeak -t SRX2350738.bam -f BAM -g ce -n SRX2350738.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2350738.10 # format = BAM # ChIP-seq file = ['SRX2350738.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 11:18:25: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:18:25: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:18:25: # Command line: callpeak -t SRX2350738.bam -f BAM -g ce -n SRX2350738.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2350738.05 # format = BAM # ChIP-seq file = ['SRX2350738.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 11:18:25: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:18:25: # Command line: callpeak -t SRX2350738.bam -f BAM -g ce -n SRX2350738.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2350738.20 # format = BAM # ChIP-seq file = ['SRX2350738.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 11:18:25: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:18:25: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:18:25: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:18:32: 1000000 INFO @ Tue, 27 Jun 2017 11:18:32: 1000000 INFO @ Tue, 27 Jun 2017 11:18:33: 1000000 INFO @ Tue, 27 Jun 2017 11:18:40: 2000000 INFO @ Tue, 27 Jun 2017 11:18:41: 2000000 INFO @ Tue, 27 Jun 2017 11:18:41: 2000000 INFO @ Tue, 27 Jun 2017 11:18:48: 3000000 INFO @ Tue, 27 Jun 2017 11:18:49: 3000000 INFO @ Tue, 27 Jun 2017 11:18:49: 3000000 INFO @ Tue, 27 Jun 2017 11:18:56: 4000000 INFO @ Tue, 27 Jun 2017 11:18:57: 4000000 INFO @ Tue, 27 Jun 2017 11:18:57: 4000000 INFO @ Tue, 27 Jun 2017 11:19:04: 5000000 INFO @ Tue, 27 Jun 2017 11:19:05: 5000000 INFO @ Tue, 27 Jun 2017 11:19:05: 5000000 INFO @ Tue, 27 Jun 2017 11:19:11: 6000000 INFO @ Tue, 27 Jun 2017 11:19:13: 6000000 INFO @ Tue, 27 Jun 2017 11:19:14: 6000000 INFO @ Tue, 27 Jun 2017 11:19:19: 7000000 INFO @ Tue, 27 Jun 2017 11:19:21: 7000000 INFO @ Tue, 27 Jun 2017 11:19:22: 7000000 INFO @ Tue, 27 Jun 2017 11:19:27: 8000000 INFO @ Tue, 27 Jun 2017 11:19:30: 8000000 INFO @ Tue, 27 Jun 2017 11:19:30: 8000000 INFO @ Tue, 27 Jun 2017 11:19:34: 9000000 INFO @ Tue, 27 Jun 2017 11:19:38: 9000000 INFO @ Tue, 27 Jun 2017 11:19:39: 9000000 INFO @ Tue, 27 Jun 2017 11:19:42: 10000000 INFO @ Tue, 27 Jun 2017 11:19:44: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 11:19:44: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 11:19:44: #1 total tags in treatment: 10269992 INFO @ Tue, 27 Jun 2017 11:19:44: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:19:44: #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 11:19:44: #1 tags after filtering in treatment: 10269992 INFO @ Tue, 27 Jun 2017 11:19:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:19:44: #1 finished! INFO @ Tue, 27 Jun 2017 11:19:44: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:19:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:19:45: #2 number of paired peaks: 165 WARNING @ Tue, 27 Jun 2017 11:19:45: Fewer paired peaks (165) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 165 pairs to build model! INFO @ Tue, 27 Jun 2017 11:19:45: start model_add_line... INFO @ Tue, 27 Jun 2017 11:19:45: start X-correlation... INFO @ Tue, 27 Jun 2017 11:19:45: end of X-cor INFO @ Tue, 27 Jun 2017 11:19:45: #2 finished! INFO @ Tue, 27 Jun 2017 11:19:45: #2 predicted fragment length is 51 bps INFO @ Tue, 27 Jun 2017 11:19:45: #2 alternative fragment length(s) may be 3,51,513 bps INFO @ Tue, 27 Jun 2017 11:19:45: #2.2 Generate R script for model : SRX2350738.10_model.r WARNING @ Tue, 27 Jun 2017 11:19:45: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 11:19:45: #2 You may need to consider one of the other alternative d(s): 3,51,513 WARNING @ Tue, 27 Jun 2017 11:19:45: #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 11:19:45: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:19:45: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:19:46: 10000000 INFO @ Tue, 27 Jun 2017 11:19:47: 10000000 INFO @ Tue, 27 Jun 2017 11:19:48: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 11:19:48: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 11:19:48: #1 total tags in treatment: 10269992 INFO @ Tue, 27 Jun 2017 11:19:48: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:19:48: #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 11:19:49: #1 tags after filtering in treatment: 10269992 INFO @ Tue, 27 Jun 2017 11:19:49: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:19:49: #1 finished! INFO @ Tue, 27 Jun 2017 11:19:49: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:19:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:19:49: #2 number of paired peaks: 165 WARNING @ Tue, 27 Jun 2017 11:19:49: Fewer paired peaks (165) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 165 pairs to build model! INFO @ Tue, 27 Jun 2017 11:19:49: start model_add_line... INFO @ Tue, 27 Jun 2017 11:19:49: start X-correlation... INFO @ Tue, 27 Jun 2017 11:19:49: end of X-cor INFO @ Tue, 27 Jun 2017 11:19:49: #2 finished! INFO @ Tue, 27 Jun 2017 11:19:49: #2 predicted fragment length is 51 bps INFO @ Tue, 27 Jun 2017 11:19:49: #2 alternative fragment length(s) may be 3,51,513 bps INFO @ Tue, 27 Jun 2017 11:19:49: #2.2 Generate R script for model : SRX2350738.05_model.r WARNING @ Tue, 27 Jun 2017 11:19:50: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 11:19:50: #2 You may need to consider one of the other alternative d(s): 3,51,513 WARNING @ Tue, 27 Jun 2017 11:19:50: #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 11:19:50: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:19:50: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:19:50: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 11:19:50: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 11:19:50: #1 total tags in treatment: 10269992 INFO @ Tue, 27 Jun 2017 11:19:50: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:19:50: #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 11:19:50: #1 tags after filtering in treatment: 10269992 INFO @ Tue, 27 Jun 2017 11:19:50: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:19:50: #1 finished! INFO @ Tue, 27 Jun 2017 11:19:50: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:19:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:19:50: #2 number of paired peaks: 165 WARNING @ Tue, 27 Jun 2017 11:19:50: Fewer paired peaks (165) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 165 pairs to build model! INFO @ Tue, 27 Jun 2017 11:19:50: start model_add_line... INFO @ Tue, 27 Jun 2017 11:19:51: start X-correlation... INFO @ Tue, 27 Jun 2017 11:19:51: end of X-cor INFO @ Tue, 27 Jun 2017 11:19:51: #2 finished! INFO @ Tue, 27 Jun 2017 11:19:51: #2 predicted fragment length is 51 bps INFO @ Tue, 27 Jun 2017 11:19:51: #2 alternative fragment length(s) may be 3,51,513 bps INFO @ Tue, 27 Jun 2017 11:19:51: #2.2 Generate R script for model : SRX2350738.20_model.r WARNING @ Tue, 27 Jun 2017 11:19:51: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 11:19:51: #2 You may need to consider one of the other alternative d(s): 3,51,513 WARNING @ Tue, 27 Jun 2017 11:19:51: #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 11:19:51: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:19:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:20:05: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:20:13: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:20:13: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:20:18: #4 Write output xls file... SRX2350738.10_peaks.xls INFO @ Tue, 27 Jun 2017 11:20:18: #4 Write peak in narrowPeak format file... SRX2350738.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:20:18: #4 Write summits bed file... SRX2350738.10_summits.bed INFO @ Tue, 27 Jun 2017 11:20:18: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (231 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 11:20:24: #4 Write output xls file... SRX2350738.20_peaks.xls INFO @ Tue, 27 Jun 2017 11:20:24: #4 Write peak in narrowPeak format file... SRX2350738.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:20:24: #4 Write summits bed file... SRX2350738.20_summits.bed INFO @ Tue, 27 Jun 2017 11:20:24: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (98 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 11:20:25: #4 Write output xls file... SRX2350738.05_peaks.xls INFO @ Tue, 27 Jun 2017 11:20:25: #4 Write peak in narrowPeak format file... SRX2350738.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:20:25: #4 Write summits bed file... SRX2350738.05_summits.bed INFO @ Tue, 27 Jun 2017 11:20:25: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (465 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。