Job ID = 10320343 sra ファイルのダウンロード中... Completed: 405478K bytes transferred in 7 seconds (450719K bits/sec), in 1 file. 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 18955656 spots for /home/okishinya/chipatlas/results/dm3/SRX3270980/SRR6159391.sra Written 18955656 spots total rm: cannot remove `[DSE]RX*': そのようなファイルやディレクトリはありません 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: 00:08:15 18955656 reads; of these: 18955656 (100.00%) were unpaired; of these: 1292020 (6.82%) aligned 0 times 11534735 (60.85%) aligned exactly 1 time 6128901 (32.33%) aligned >1 times 93.18% overall alignment rate Time searching: 00:08:15 Overall time: 00:08:15 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 8 files... [bam_rmdupse_core] 2224069 / 17663636 = 0.1259 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 @ Thu, 11 Jan 2018 02:19:14: # Command line: callpeak -t SRX3270980.bam -f BAM -g dm -n SRX3270980.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3270980.10 # format = BAM # ChIP-seq file = ['SRX3270980.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 @ Thu, 11 Jan 2018 02:19:14: #1 read tag files... INFO @ Thu, 11 Jan 2018 02:19:14: #1 read treatment tags... INFO @ Thu, 11 Jan 2018 02:19:14: # Command line: callpeak -t SRX3270980.bam -f BAM -g dm -n SRX3270980.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3270980.05 # format = BAM # ChIP-seq file = ['SRX3270980.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 @ Thu, 11 Jan 2018 02:19:14: #1 read tag files... INFO @ Thu, 11 Jan 2018 02:19:14: #1 read treatment tags... INFO @ Thu, 11 Jan 2018 02:19:14: # Command line: callpeak -t SRX3270980.bam -f BAM -g dm -n SRX3270980.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3270980.20 # format = BAM # ChIP-seq file = ['SRX3270980.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 @ Thu, 11 Jan 2018 02:19:14: #1 read tag files... INFO @ Thu, 11 Jan 2018 02:19:14: #1 read treatment tags... INFO @ Thu, 11 Jan 2018 02:19:20: 1000000 INFO @ Thu, 11 Jan 2018 02:19:21: 1000000 INFO @ Thu, 11 Jan 2018 02:19:21: 1000000 INFO @ Thu, 11 Jan 2018 02:19:27: 2000000 INFO @ Thu, 11 Jan 2018 02:19:27: 2000000 INFO @ Thu, 11 Jan 2018 02:19:27: 2000000 INFO @ Thu, 11 Jan 2018 02:19:33: 3000000 INFO @ Thu, 11 Jan 2018 02:19:34: 3000000 INFO @ Thu, 11 Jan 2018 02:19:34: 3000000 INFO @ Thu, 11 Jan 2018 02:19:40: 4000000 INFO @ Thu, 11 Jan 2018 02:19:41: 4000000 INFO @ Thu, 11 Jan 2018 02:19:41: 4000000 INFO @ Thu, 11 Jan 2018 02:19:46: 5000000 INFO @ Thu, 11 Jan 2018 02:19:47: 5000000 INFO @ Thu, 11 Jan 2018 02:19:47: 5000000 INFO @ Thu, 11 Jan 2018 02:19:52: 6000000 INFO @ Thu, 11 Jan 2018 02:19:54: 6000000 INFO @ Thu, 11 Jan 2018 02:19:54: 6000000 INFO @ Thu, 11 Jan 2018 02:19:59: 7000000 INFO @ Thu, 11 Jan 2018 02:20:00: 7000000 INFO @ Thu, 11 Jan 2018 02:20:00: 7000000 INFO @ Thu, 11 Jan 2018 02:20:05: 8000000 INFO @ Thu, 11 Jan 2018 02:20:07: 8000000 INFO @ Thu, 11 Jan 2018 02:20:07: 8000000 INFO @ Thu, 11 Jan 2018 02:20:11: 9000000 INFO @ Thu, 11 Jan 2018 02:20:14: 9000000 INFO @ Thu, 11 Jan 2018 02:20:14: 9000000 INFO @ Thu, 11 Jan 2018 02:20:18: 10000000 INFO @ Thu, 11 Jan 2018 02:20:20: 10000000 INFO @ Thu, 11 Jan 2018 02:20:20: 10000000 INFO @ Thu, 11 Jan 2018 02:20:24: 11000000 INFO @ Thu, 11 Jan 2018 02:20:27: 11000000 INFO @ Thu, 11 Jan 2018 02:20:27: 11000000 INFO @ Thu, 11 Jan 2018 02:20:30: 12000000 INFO @ Thu, 11 Jan 2018 02:20:34: 12000000 INFO @ Thu, 11 Jan 2018 02:20:34: 12000000 INFO @ Thu, 11 Jan 2018 02:20:37: 13000000 INFO @ Thu, 11 Jan 2018 02:20:40: 13000000 INFO @ Thu, 11 Jan 2018 02:20:40: 13000000 INFO @ Thu, 11 Jan 2018 02:20:43: 14000000 INFO @ Thu, 11 Jan 2018 02:20:47: 14000000 INFO @ Thu, 11 Jan 2018 02:20:47: 14000000 INFO @ Thu, 11 Jan 2018 02:20:49: 15000000 INFO @ Thu, 11 Jan 2018 02:20:52: #1 tag size is determined as 51 bps INFO @ Thu, 11 Jan 2018 02:20:52: #1 tag size = 51 INFO @ Thu, 11 Jan 2018 02:20:52: #1 total tags in treatment: 15439567 INFO @ Thu, 11 Jan 2018 02:20:52: #1 user defined the maximum tags... INFO @ Thu, 11 Jan 2018 02:20:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 11 Jan 2018 02:20:53: #1 tags after filtering in treatment: 15439567 INFO @ Thu, 11 Jan 2018 02:20:53: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 11 Jan 2018 02:20:53: #1 finished! INFO @ Thu, 11 Jan 2018 02:20:53: #2 Build Peak Model... INFO @ Thu, 11 Jan 2018 02:20:53: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 11 Jan 2018 02:20:53: 15000000 INFO @ Thu, 11 Jan 2018 02:20:53: 15000000 INFO @ Thu, 11 Jan 2018 02:20:54: #2 number of paired peaks: 219 WARNING @ Thu, 11 Jan 2018 02:20:54: 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 @ Thu, 11 Jan 2018 02:20:54: start model_add_line... INFO @ Thu, 11 Jan 2018 02:20:54: start X-correlation... INFO @ Thu, 11 Jan 2018 02:20:54: end of X-cor INFO @ Thu, 11 Jan 2018 02:20:54: #2 finished! INFO @ Thu, 11 Jan 2018 02:20:54: #2 predicted fragment length is 47 bps INFO @ Thu, 11 Jan 2018 02:20:54: #2 alternative fragment length(s) may be 47 bps INFO @ Thu, 11 Jan 2018 02:20:54: #2.2 Generate R script for model : SRX3270980.10_model.r WARNING @ Thu, 11 Jan 2018 02:20:54: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 11 Jan 2018 02:20:54: #2 You may need to consider one of the other alternative d(s): 47 WARNING @ Thu, 11 Jan 2018 02:20:54: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 11 Jan 2018 02:20:54: #3 Call peaks... INFO @ Thu, 11 Jan 2018 02:20:54: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 11 Jan 2018 02:20:56: #1 tag size is determined as 51 bps INFO @ Thu, 11 Jan 2018 02:20:56: #1 tag size = 51 INFO @ Thu, 11 Jan 2018 02:20:56: #1 total tags in treatment: 15439567 INFO @ Thu, 11 Jan 2018 02:20:56: #1 user defined the maximum tags... INFO @ Thu, 11 Jan 2018 02:20:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 11 Jan 2018 02:20:56: #1 tag size is determined as 51 bps INFO @ Thu, 11 Jan 2018 02:20:56: #1 tag size = 51 INFO @ Thu, 11 Jan 2018 02:20:56: #1 total tags in treatment: 15439567 INFO @ Thu, 11 Jan 2018 02:20:56: #1 user defined the maximum tags... INFO @ Thu, 11 Jan 2018 02:20:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 11 Jan 2018 02:20:57: #1 tags after filtering in treatment: 15439567 INFO @ Thu, 11 Jan 2018 02:20:57: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 11 Jan 2018 02:20:57: #1 finished! INFO @ Thu, 11 Jan 2018 02:20:57: #2 Build Peak Model... INFO @ Thu, 11 Jan 2018 02:20:57: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 11 Jan 2018 02:20:57: #1 tags after filtering in treatment: 15439567 INFO @ Thu, 11 Jan 2018 02:20:57: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 11 Jan 2018 02:20:57: #1 finished! INFO @ Thu, 11 Jan 2018 02:20:57: #2 Build Peak Model... INFO @ Thu, 11 Jan 2018 02:20:57: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 11 Jan 2018 02:20:58: #2 number of paired peaks: 219 WARNING @ Thu, 11 Jan 2018 02:20:58: 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 @ Thu, 11 Jan 2018 02:20:58: start model_add_line... INFO @ Thu, 11 Jan 2018 02:20:58: #2 number of paired peaks: 219 WARNING @ Thu, 11 Jan 2018 02:20:58: 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 @ Thu, 11 Jan 2018 02:20:58: start model_add_line... INFO @ Thu, 11 Jan 2018 02:20:58: start X-correlation... INFO @ Thu, 11 Jan 2018 02:20:58: end of X-cor INFO @ Thu, 11 Jan 2018 02:20:58: #2 finished! INFO @ Thu, 11 Jan 2018 02:20:58: #2 predicted fragment length is 47 bps INFO @ Thu, 11 Jan 2018 02:20:58: #2 alternative fragment length(s) may be 47 bps INFO @ Thu, 11 Jan 2018 02:20:58: #2.2 Generate R script for model : SRX3270980.20_model.r WARNING @ Thu, 11 Jan 2018 02:20:58: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 11 Jan 2018 02:20:58: #2 You may need to consider one of the other alternative d(s): 47 WARNING @ Thu, 11 Jan 2018 02:20:58: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 11 Jan 2018 02:20:58: #3 Call peaks... INFO @ Thu, 11 Jan 2018 02:20:58: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 11 Jan 2018 02:20:58: start X-correlation... INFO @ Thu, 11 Jan 2018 02:20:58: end of X-cor INFO @ Thu, 11 Jan 2018 02:20:58: #2 finished! INFO @ Thu, 11 Jan 2018 02:20:58: #2 predicted fragment length is 47 bps INFO @ Thu, 11 Jan 2018 02:20:58: #2 alternative fragment length(s) may be 47 bps INFO @ Thu, 11 Jan 2018 02:20:58: #2.2 Generate R script for model : SRX3270980.05_model.r WARNING @ Thu, 11 Jan 2018 02:20:58: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 11 Jan 2018 02:20:58: #2 You may need to consider one of the other alternative d(s): 47 WARNING @ Thu, 11 Jan 2018 02:20:58: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 11 Jan 2018 02:20:58: #3 Call peaks... INFO @ Thu, 11 Jan 2018 02:20:58: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 11 Jan 2018 02:21:28: #3 Call peaks for each chromosome... INFO @ Thu, 11 Jan 2018 02:21:28: #3 Call peaks for each chromosome... INFO @ Thu, 11 Jan 2018 02:21:29: #3 Call peaks for each chromosome... INFO @ Thu, 11 Jan 2018 02:21:47: #4 Write output xls file... SRX3270980.20_peaks.xls INFO @ Thu, 11 Jan 2018 02:21:47: #4 Write peak in narrowPeak format file... SRX3270980.20_peaks.narrowPeak INFO @ Thu, 11 Jan 2018 02:21:47: #4 Write summits bed file... SRX3270980.20_summits.bed INFO @ Thu, 11 Jan 2018 02:21:47: Done! pass1 - making usageList (11 chroms): 0 millis pass2 - checking and writing primary data (1087 records, 4 fields): 107 millis CompletedMACS2peakCalling INFO @ Thu, 11 Jan 2018 02:21:47: #4 Write output xls file... SRX3270980.05_peaks.xls INFO @ Thu, 11 Jan 2018 02:21:47: #4 Write peak in narrowPeak format file... SRX3270980.05_peaks.narrowPeak INFO @ Thu, 11 Jan 2018 02:21:47: #4 Write summits bed file... SRX3270980.05_summits.bed INFO @ Thu, 11 Jan 2018 02:21:47: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2666 records, 4 fields): 5 millis INFO @ Thu, 11 Jan 2018 02:21:47: #4 Write output xls file... SRX3270980.10_peaks.xls CompletedMACS2peakCalling INFO @ Thu, 11 Jan 2018 02:21:47: #4 Write peak in narrowPeak format file... SRX3270980.10_peaks.narrowPeak INFO @ Thu, 11 Jan 2018 02:21:47: #4 Write summits bed file... SRX3270980.10_summits.bed INFO @ Thu, 11 Jan 2018 02:21:47: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1872 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。