Job ID = 9371940 sra ファイルのダウンロード中... Completed: 2121689K bytes transferred in 94 seconds (184151K 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 70730310 spots for /home/okishinya/chipatlas/results/dm3/SRX2692974/SRR5398173.sra Written 70730310 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 02:45:59 70730310 reads; of these: 70730310 (100.00%) were unpaired; of these: 13432824 (18.99%) aligned 0 times 20669416 (29.22%) aligned exactly 1 time 36628070 (51.79%) aligned >1 times 81.01% overall alignment rate Time searching: 02:46:00 Overall time: 02:46:00 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 24 files... [bam_rmdupse_core] 30353379 / 57297486 = 0.5298 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 @ Fri, 04 Aug 2017 18:11:42: # Command line: callpeak -t SRX2692974.bam -f BAM -g dm -n SRX2692974.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2692974.10 # format = BAM # ChIP-seq file = ['SRX2692974.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 @ Fri, 04 Aug 2017 18:11:42: #1 read tag files... INFO @ Fri, 04 Aug 2017 18:11:42: #1 read treatment tags... INFO @ Fri, 04 Aug 2017 18:11:42: # Command line: callpeak -t SRX2692974.bam -f BAM -g dm -n SRX2692974.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2692974.20 # format = BAM # ChIP-seq file = ['SRX2692974.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 @ Fri, 04 Aug 2017 18:11:42: #1 read tag files... INFO @ Fri, 04 Aug 2017 18:11:42: #1 read treatment tags... INFO @ Fri, 04 Aug 2017 18:11:42: # Command line: callpeak -t SRX2692974.bam -f BAM -g dm -n SRX2692974.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2692974.05 # format = BAM # ChIP-seq file = ['SRX2692974.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 @ Fri, 04 Aug 2017 18:11:42: #1 read tag files... INFO @ Fri, 04 Aug 2017 18:11:42: #1 read treatment tags... INFO @ Fri, 04 Aug 2017 18:12:01: 1000000 INFO @ Fri, 04 Aug 2017 18:12:01: 1000000 INFO @ Fri, 04 Aug 2017 18:12:05: 1000000 INFO @ Fri, 04 Aug 2017 18:12:20: 2000000 INFO @ Fri, 04 Aug 2017 18:12:24: 2000000 INFO @ Fri, 04 Aug 2017 18:12:25: 2000000 INFO @ Fri, 04 Aug 2017 18:12:42: 3000000 INFO @ Fri, 04 Aug 2017 18:12:44: 3000000 INFO @ Fri, 04 Aug 2017 18:12:48: 3000000 INFO @ Fri, 04 Aug 2017 18:13:04: 4000000 INFO @ Fri, 04 Aug 2017 18:13:05: 4000000 INFO @ Fri, 04 Aug 2017 18:13:11: 4000000 INFO @ Fri, 04 Aug 2017 18:13:21: 5000000 INFO @ Fri, 04 Aug 2017 18:13:29: 5000000 INFO @ Fri, 04 Aug 2017 18:13:33: 5000000 INFO @ Fri, 04 Aug 2017 18:13:36: 6000000 INFO @ Fri, 04 Aug 2017 18:13:49: 6000000 INFO @ Fri, 04 Aug 2017 18:13:50: 6000000 INFO @ Fri, 04 Aug 2017 18:13:54: 7000000 INFO @ Fri, 04 Aug 2017 18:14:07: 7000000 INFO @ Fri, 04 Aug 2017 18:14:09: 7000000 INFO @ Fri, 04 Aug 2017 18:14:12: 8000000 INFO @ Fri, 04 Aug 2017 18:14:24: 8000000 INFO @ Fri, 04 Aug 2017 18:14:24: 8000000 INFO @ Fri, 04 Aug 2017 18:14:29: 9000000 INFO @ Fri, 04 Aug 2017 18:14:38: 9000000 INFO @ Fri, 04 Aug 2017 18:14:41: 9000000 INFO @ Fri, 04 Aug 2017 18:14:46: 10000000 INFO @ Fri, 04 Aug 2017 18:14:55: 10000000 INFO @ Fri, 04 Aug 2017 18:14:56: 10000000 INFO @ Fri, 04 Aug 2017 18:15:03: 11000000 INFO @ Fri, 04 Aug 2017 18:15:09: 11000000 INFO @ Fri, 04 Aug 2017 18:15:11: 11000000 INFO @ Fri, 04 Aug 2017 18:15:19: 12000000 INFO @ Fri, 04 Aug 2017 18:15:22: 12000000 INFO @ Fri, 04 Aug 2017 18:15:24: 12000000 INFO @ Fri, 04 Aug 2017 18:15:34: 13000000 INFO @ Fri, 04 Aug 2017 18:15:35: 13000000 INFO @ Fri, 04 Aug 2017 18:15:39: 13000000 INFO @ Fri, 04 Aug 2017 18:15:46: 14000000 INFO @ Fri, 04 Aug 2017 18:15:51: 14000000 INFO @ Fri, 04 Aug 2017 18:15:53: 14000000 INFO @ Fri, 04 Aug 2017 18:15:59: 15000000 INFO @ Fri, 04 Aug 2017 18:16:06: 15000000 INFO @ Fri, 04 Aug 2017 18:16:07: 15000000 INFO @ Fri, 04 Aug 2017 18:16:11: 16000000 INFO @ Fri, 04 Aug 2017 18:16:19: 16000000 INFO @ Fri, 04 Aug 2017 18:16:22: 17000000 INFO @ Fri, 04 Aug 2017 18:16:22: 16000000 INFO @ Fri, 04 Aug 2017 18:16:33: 17000000 INFO @ Fri, 04 Aug 2017 18:16:33: 18000000 INFO @ Fri, 04 Aug 2017 18:16:37: 17000000 INFO @ Fri, 04 Aug 2017 18:16:47: 19000000 INFO @ Fri, 04 Aug 2017 18:16:47: 18000000 INFO @ Fri, 04 Aug 2017 18:16:51: 18000000 INFO @ Fri, 04 Aug 2017 18:17:03: 19000000 INFO @ Fri, 04 Aug 2017 18:17:04: 19000000 INFO @ Fri, 04 Aug 2017 18:17:09: 20000000 INFO @ Fri, 04 Aug 2017 18:17:21: 20000000 INFO @ Fri, 04 Aug 2017 18:17:23: 20000000 INFO @ Fri, 04 Aug 2017 18:17:30: 21000000 INFO @ Fri, 04 Aug 2017 18:17:38: 21000000 INFO @ Fri, 04 Aug 2017 18:17:44: 21000000 INFO @ Fri, 04 Aug 2017 18:17:51: 22000000 INFO @ Fri, 04 Aug 2017 18:17:54: 22000000 INFO @ Fri, 04 Aug 2017 18:18:05: 22000000 INFO @ Fri, 04 Aug 2017 18:18:08: 23000000 INFO @ Fri, 04 Aug 2017 18:18:08: 23000000 INFO @ Fri, 04 Aug 2017 18:18:18: 24000000 INFO @ Fri, 04 Aug 2017 18:18:22: 23000000 INFO @ Fri, 04 Aug 2017 18:18:27: 24000000 INFO @ Fri, 04 Aug 2017 18:18:29: 25000000 INFO @ Fri, 04 Aug 2017 18:18:40: 26000000 INFO @ Fri, 04 Aug 2017 18:18:41: 24000000 INFO @ Fri, 04 Aug 2017 18:18:46: 25000000 INFO @ Fri, 04 Aug 2017 18:18:51: #1 tag size is determined as 75 bps INFO @ Fri, 04 Aug 2017 18:18:51: #1 tag size = 75 INFO @ Fri, 04 Aug 2017 18:18:51: #1 total tags in treatment: 26944107 INFO @ Fri, 04 Aug 2017 18:18:51: #1 user defined the maximum tags... INFO @ Fri, 04 Aug 2017 18:18:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 Aug 2017 18:18:52: #1 tags after filtering in treatment: 26944107 INFO @ Fri, 04 Aug 2017 18:18:52: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 Aug 2017 18:18:52: #1 finished! INFO @ Fri, 04 Aug 2017 18:18:52: #2 Build Peak Model... INFO @ Fri, 04 Aug 2017 18:18:52: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 Aug 2017 18:18:55: #2 number of paired peaks: 352 WARNING @ Fri, 04 Aug 2017 18:18:55: Fewer paired peaks (352) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 352 pairs to build model! INFO @ Fri, 04 Aug 2017 18:18:55: start model_add_line... INFO @ Fri, 04 Aug 2017 18:18:55: start X-correlation... INFO @ Fri, 04 Aug 2017 18:18:55: end of X-cor INFO @ Fri, 04 Aug 2017 18:18:55: #2 finished! INFO @ Fri, 04 Aug 2017 18:18:55: #2 predicted fragment length is 47 bps INFO @ Fri, 04 Aug 2017 18:18:55: #2 alternative fragment length(s) may be 47 bps INFO @ Fri, 04 Aug 2017 18:18:55: #2.2 Generate R script for model : SRX2692974.20_model.r WARNING @ Fri, 04 Aug 2017 18:18:55: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 04 Aug 2017 18:18:55: #2 You may need to consider one of the other alternative d(s): 47 WARNING @ Fri, 04 Aug 2017 18:18:55: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 04 Aug 2017 18:18:55: #3 Call peaks... INFO @ Fri, 04 Aug 2017 18:18:55: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 Aug 2017 18:18:55: 26000000 INFO @ Fri, 04 Aug 2017 18:18:57: 25000000 INFO @ Fri, 04 Aug 2017 18:19:06: #1 tag size is determined as 75 bps INFO @ Fri, 04 Aug 2017 18:19:06: #1 tag size = 75 INFO @ Fri, 04 Aug 2017 18:19:06: #1 total tags in treatment: 26944107 INFO @ Fri, 04 Aug 2017 18:19:06: #1 user defined the maximum tags... INFO @ Fri, 04 Aug 2017 18:19:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 Aug 2017 18:19:07: #1 tags after filtering in treatment: 26944107 INFO @ Fri, 04 Aug 2017 18:19:07: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 Aug 2017 18:19:07: #1 finished! INFO @ Fri, 04 Aug 2017 18:19:07: #2 Build Peak Model... INFO @ Fri, 04 Aug 2017 18:19:07: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 Aug 2017 18:19:09: #2 number of paired peaks: 352 WARNING @ Fri, 04 Aug 2017 18:19:09: Fewer paired peaks (352) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 352 pairs to build model! INFO @ Fri, 04 Aug 2017 18:19:09: start model_add_line... INFO @ Fri, 04 Aug 2017 18:19:09: 26000000 INFO @ Fri, 04 Aug 2017 18:19:10: start X-correlation... INFO @ Fri, 04 Aug 2017 18:19:10: end of X-cor INFO @ Fri, 04 Aug 2017 18:19:10: #2 finished! INFO @ Fri, 04 Aug 2017 18:19:10: #2 predicted fragment length is 47 bps INFO @ Fri, 04 Aug 2017 18:19:10: #2 alternative fragment length(s) may be 47 bps INFO @ Fri, 04 Aug 2017 18:19:10: #2.2 Generate R script for model : SRX2692974.10_model.r WARNING @ Fri, 04 Aug 2017 18:19:10: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 04 Aug 2017 18:19:10: #2 You may need to consider one of the other alternative d(s): 47 WARNING @ Fri, 04 Aug 2017 18:19:10: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 04 Aug 2017 18:19:10: #3 Call peaks... INFO @ Fri, 04 Aug 2017 18:19:10: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 Aug 2017 18:19:21: #1 tag size is determined as 75 bps INFO @ Fri, 04 Aug 2017 18:19:21: #1 tag size = 75 INFO @ Fri, 04 Aug 2017 18:19:21: #1 total tags in treatment: 26944107 INFO @ Fri, 04 Aug 2017 18:19:21: #1 user defined the maximum tags... INFO @ Fri, 04 Aug 2017 18:19:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 Aug 2017 18:19:22: #1 tags after filtering in treatment: 26944107 INFO @ Fri, 04 Aug 2017 18:19:22: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 Aug 2017 18:19:22: #1 finished! INFO @ Fri, 04 Aug 2017 18:19:22: #2 Build Peak Model... INFO @ Fri, 04 Aug 2017 18:19:22: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 Aug 2017 18:19:24: #2 number of paired peaks: 352 WARNING @ Fri, 04 Aug 2017 18:19:24: Fewer paired peaks (352) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 352 pairs to build model! INFO @ Fri, 04 Aug 2017 18:19:24: start model_add_line... INFO @ Fri, 04 Aug 2017 18:19:25: start X-correlation... INFO @ Fri, 04 Aug 2017 18:19:25: end of X-cor INFO @ Fri, 04 Aug 2017 18:19:25: #2 finished! INFO @ Fri, 04 Aug 2017 18:19:25: #2 predicted fragment length is 47 bps INFO @ Fri, 04 Aug 2017 18:19:25: #2 alternative fragment length(s) may be 47 bps INFO @ Fri, 04 Aug 2017 18:19:25: #2.2 Generate R script for model : SRX2692974.05_model.r WARNING @ Fri, 04 Aug 2017 18:19:25: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 04 Aug 2017 18:19:25: #2 You may need to consider one of the other alternative d(s): 47 WARNING @ Fri, 04 Aug 2017 18:19:25: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 04 Aug 2017 18:19:25: #3 Call peaks... INFO @ Fri, 04 Aug 2017 18:19:25: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 Aug 2017 18:20:15: #3 Call peaks for each chromosome... INFO @ Fri, 04 Aug 2017 18:20:26: #3 Call peaks for each chromosome... INFO @ Fri, 04 Aug 2017 18:20:40: #3 Call peaks for each chromosome... INFO @ Fri, 04 Aug 2017 18:21:05: #4 Write output xls file... SRX2692974.20_peaks.xls INFO @ Fri, 04 Aug 2017 18:21:05: #4 Write peak in narrowPeak format file... SRX2692974.20_peaks.narrowPeak INFO @ Fri, 04 Aug 2017 18:21:05: #4 Write summits bed file... SRX2692974.20_summits.bed INFO @ Fri, 04 Aug 2017 18:21:05: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (3955 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Fri, 04 Aug 2017 18:21:17: #4 Write output xls file... SRX2692974.10_peaks.xls INFO @ Fri, 04 Aug 2017 18:21:17: #4 Write peak in narrowPeak format file... SRX2692974.10_peaks.narrowPeak INFO @ Fri, 04 Aug 2017 18:21:17: #4 Write summits bed file... SRX2692974.10_summits.bed INFO @ Fri, 04 Aug 2017 18:21:17: Done! pass1 - making usageList (15 chroms): 5 millis pass2 - checking and writing primary data (10110 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Fri, 04 Aug 2017 18:21:24: #4 Write output xls file... SRX2692974.05_peaks.xls INFO @ Fri, 04 Aug 2017 18:21:25: #4 Write peak in narrowPeak format file... SRX2692974.05_peaks.narrowPeak INFO @ Fri, 04 Aug 2017 18:21:25: #4 Write summits bed file... SRX2692974.05_summits.bed INFO @ Fri, 04 Aug 2017 18:21:25: Done! pass1 - making usageList (15 chroms): 7 millis pass2 - checking and writing primary data (13851 records, 4 fields): 38 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。