Job ID = 6983662 sra ファイルのダウンロード中... Completed: 221743K bytes transferred in 5 seconds (334716K bits/sec), in 1 file, 2 directories. % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 11636 0 11636 0 0 15916 0 --:--:-- --:--:-- --:--:-- 20965 100 35544 0 35544 0 0 39221 0 --:--:-- --:--:-- --:--:-- 48690 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 11864949 spots for /home/okishinya/chipatlas/results/dm3/SRX017472/SRR037529.sra Written 11864949 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: 00:03:24 11864949 reads; of these: 11864949 (100.00%) were unpaired; of these: 1851429 (15.60%) aligned 0 times 7513452 (63.32%) aligned exactly 1 time 2500068 (21.07%) aligned >1 times 84.40% overall alignment rate Time searching: 00:03:24 Overall time: 00:03:24 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_rmdupse_core] 1594099 / 10013520 = 0.1592 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 @ Sun, 05 Jun 2016 15:40:08: # Command line: callpeak -t SRX017472.bam -f BAM -g dm -n SRX017472.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX017472.20 # format = BAM # ChIP-seq file = ['SRX017472.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 INFO @ Sun, 05 Jun 2016 15:40:08: # Command line: callpeak -t SRX017472.bam -f BAM -g dm -n SRX017472.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX017472.10 # format = BAM # ChIP-seq file = ['SRX017472.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 INFO @ Sun, 05 Jun 2016 15:40:08: #1 read tag files... INFO @ Sun, 05 Jun 2016 15:40:08: #1 read tag files... INFO @ Sun, 05 Jun 2016 15:40:08: # Command line: callpeak -t SRX017472.bam -f BAM -g dm -n SRX017472.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX017472.05 # format = BAM # ChIP-seq file = ['SRX017472.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 INFO @ Sun, 05 Jun 2016 15:40:08: #1 read treatment tags... INFO @ Sun, 05 Jun 2016 15:40:08: #1 read treatment tags... INFO @ Sun, 05 Jun 2016 15:40:08: #1 read tag files... INFO @ Sun, 05 Jun 2016 15:40:08: #1 read treatment tags... INFO @ Sun, 05 Jun 2016 15:40:14: 1000000 INFO @ Sun, 05 Jun 2016 15:40:14: 1000000 INFO @ Sun, 05 Jun 2016 15:40:14: 1000000 INFO @ Sun, 05 Jun 2016 15:40:19: 2000000 INFO @ Sun, 05 Jun 2016 15:40:19: 2000000 INFO @ Sun, 05 Jun 2016 15:40:19: 2000000 INFO @ Sun, 05 Jun 2016 15:40:24: 3000000 INFO @ Sun, 05 Jun 2016 15:40:25: 3000000 INFO @ Sun, 05 Jun 2016 15:40:25: 3000000 INFO @ Sun, 05 Jun 2016 15:40:29: 4000000 INFO @ Sun, 05 Jun 2016 15:40:30: 4000000 INFO @ Sun, 05 Jun 2016 15:40:30: 4000000 INFO @ Sun, 05 Jun 2016 15:40:34: 5000000 INFO @ Sun, 05 Jun 2016 15:40:35: 5000000 INFO @ Sun, 05 Jun 2016 15:40:35: 5000000 INFO @ Sun, 05 Jun 2016 15:40:39: 6000000 INFO @ Sun, 05 Jun 2016 15:40:41: 6000000 INFO @ Sun, 05 Jun 2016 15:40:41: 6000000 INFO @ Sun, 05 Jun 2016 15:40:44: 7000000 INFO @ Sun, 05 Jun 2016 15:40:46: 7000000 INFO @ Sun, 05 Jun 2016 15:40:46: 7000000 INFO @ Sun, 05 Jun 2016 15:40:50: 8000000 INFO @ Sun, 05 Jun 2016 15:40:51: 8000000 INFO @ Sun, 05 Jun 2016 15:40:51: 8000000 INFO @ Sun, 05 Jun 2016 15:40:52: #1 tag size is determined as 36 bps INFO @ Sun, 05 Jun 2016 15:40:52: #1 tag size = 36 INFO @ Sun, 05 Jun 2016 15:40:52: #1 total tags in treatment: 8419421 INFO @ Sun, 05 Jun 2016 15:40:52: #1 user defined the maximum tags... INFO @ Sun, 05 Jun 2016 15:40:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 05 Jun 2016 15:40:53: #1 tags after filtering in treatment: 8419025 INFO @ Sun, 05 Jun 2016 15:40:53: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 05 Jun 2016 15:40:53: #1 finished! INFO @ Sun, 05 Jun 2016 15:40:53: #2 Build Peak Model... INFO @ Sun, 05 Jun 2016 15:40:53: #1 tag size is determined as 36 bps INFO @ Sun, 05 Jun 2016 15:40:53: #1 tag size = 36 INFO @ Sun, 05 Jun 2016 15:40:53: #1 total tags in treatment: 8419421 INFO @ Sun, 05 Jun 2016 15:40:53: #1 user defined the maximum tags... INFO @ Sun, 05 Jun 2016 15:40:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 05 Jun 2016 15:40:54: #1 tag size is determined as 36 bps INFO @ Sun, 05 Jun 2016 15:40:54: #1 tag size = 36 INFO @ Sun, 05 Jun 2016 15:40:54: #1 total tags in treatment: 8419421 INFO @ Sun, 05 Jun 2016 15:40:54: #1 user defined the maximum tags... INFO @ Sun, 05 Jun 2016 15:40:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 05 Jun 2016 15:40:55: #1 tags after filtering in treatment: 8419025 INFO @ Sun, 05 Jun 2016 15:40:55: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 05 Jun 2016 15:40:55: #1 finished! INFO @ Sun, 05 Jun 2016 15:40:55: #2 Build Peak Model... INFO @ Sun, 05 Jun 2016 15:40:55: #2 number of paired peaks: 179 WARNING @ Sun, 05 Jun 2016 15:40:55: Fewer paired peaks (179) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 179 pairs to build model! INFO @ Sun, 05 Jun 2016 15:40:55: start model_add_line... INFO @ Sun, 05 Jun 2016 15:40:55: #1 tags after filtering in treatment: 8419025 INFO @ Sun, 05 Jun 2016 15:40:55: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 05 Jun 2016 15:40:55: #1 finished! INFO @ Sun, 05 Jun 2016 15:40:55: #2 Build Peak Model... INFO @ Sun, 05 Jun 2016 15:40:56: #2 number of paired peaks: 179 WARNING @ Sun, 05 Jun 2016 15:40:56: Fewer paired peaks (179) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 179 pairs to build model! INFO @ Sun, 05 Jun 2016 15:40:56: start model_add_line... INFO @ Sun, 05 Jun 2016 15:40:56: start X-correlation... INFO @ Sun, 05 Jun 2016 15:40:56: end of X-cor INFO @ Sun, 05 Jun 2016 15:40:56: #2 finished! INFO @ Sun, 05 Jun 2016 15:40:56: #2 predicted fragment length is 44 bps INFO @ Sun, 05 Jun 2016 15:40:56: #2 alternative fragment length(s) may be 44 bps INFO @ Sun, 05 Jun 2016 15:40:56: #2.2 Generate R script for model : SRX017472.05_model.r WARNING @ Sun, 05 Jun 2016 15:40:56: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 05 Jun 2016 15:40:56: #2 You may need to consider one of the other alternative d(s): 44 WARNING @ Sun, 05 Jun 2016 15:40:56: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 05 Jun 2016 15:40:56: #3 Call peaks... INFO @ Sun, 05 Jun 2016 15:40:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 05 Jun 2016 15:40:57: #2 number of paired peaks: 179 WARNING @ Sun, 05 Jun 2016 15:40:57: Fewer paired peaks (179) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 179 pairs to build model! INFO @ Sun, 05 Jun 2016 15:40:57: start model_add_line... INFO @ Sun, 05 Jun 2016 15:40:58: start X-correlation... INFO @ Sun, 05 Jun 2016 15:40:58: end of X-cor INFO @ Sun, 05 Jun 2016 15:40:58: #2 finished! INFO @ Sun, 05 Jun 2016 15:40:58: #2 predicted fragment length is 44 bps INFO @ Sun, 05 Jun 2016 15:40:58: #2 alternative fragment length(s) may be 44 bps INFO @ Sun, 05 Jun 2016 15:40:58: #2.2 Generate R script for model : SRX017472.20_model.r WARNING @ Sun, 05 Jun 2016 15:40:58: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 05 Jun 2016 15:40:58: #2 You may need to consider one of the other alternative d(s): 44 WARNING @ Sun, 05 Jun 2016 15:40:58: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 05 Jun 2016 15:40:58: #3 Call peaks... INFO @ Sun, 05 Jun 2016 15:40:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 05 Jun 2016 15:40:58: start X-correlation... INFO @ Sun, 05 Jun 2016 15:40:58: end of X-cor INFO @ Sun, 05 Jun 2016 15:40:58: #2 finished! INFO @ Sun, 05 Jun 2016 15:40:58: #2 predicted fragment length is 44 bps INFO @ Sun, 05 Jun 2016 15:40:58: #2 alternative fragment length(s) may be 44 bps INFO @ Sun, 05 Jun 2016 15:40:58: #2.2 Generate R script for model : SRX017472.10_model.r WARNING @ Sun, 05 Jun 2016 15:40:58: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 05 Jun 2016 15:40:58: #2 You may need to consider one of the other alternative d(s): 44 WARNING @ Sun, 05 Jun 2016 15:40:58: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 05 Jun 2016 15:40:58: #3 Call peaks... INFO @ Sun, 05 Jun 2016 15:40:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 05 Jun 2016 15:41:44: #3 Call peaks for each chromosome... INFO @ Sun, 05 Jun 2016 15:41:44: #3 Call peaks for each chromosome... INFO @ Sun, 05 Jun 2016 15:41:46: #3 Call peaks for each chromosome... INFO @ Sun, 05 Jun 2016 15:42:16: #4 Write output xls file... SRX017472.10_peaks.xls INFO @ Sun, 05 Jun 2016 15:42:16: #4 Write peak in narrowPeak format file... SRX017472.10_peaks.narrowPeak INFO @ Sun, 05 Jun 2016 15:42:16: #4 Write summits bed file... SRX017472.10_summits.bed INFO @ Sun, 05 Jun 2016 15:42:16: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1410 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 05 Jun 2016 15:42:20: #4 Write output xls file... SRX017472.05_peaks.xls INFO @ Sun, 05 Jun 2016 15:42:20: #4 Write peak in narrowPeak format file... SRX017472.05_peaks.narrowPeak INFO @ Sun, 05 Jun 2016 15:42:20: #4 Write summits bed file... SRX017472.05_summits.bed INFO @ Sun, 05 Jun 2016 15:42:20: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3885 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sun, 05 Jun 2016 15:42:21: #4 Write output xls file... SRX017472.20_peaks.xls INFO @ Sun, 05 Jun 2016 15:42:21: #4 Write peak in narrowPeak format file... SRX017472.20_peaks.narrowPeak INFO @ Sun, 05 Jun 2016 15:42:21: #4 Write summits bed file... SRX017472.20_summits.bed INFO @ Sun, 05 Jun 2016 15:42:21: Done! pass1 - making usageList (10 chroms): 0 millis pass2 - checking and writing primary data (331 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。