Job ID = 9730471 sra ファイルのダウンロード中... Completed: 688440K bytes transferred in 41 seconds (137170K 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 30436213 spots for /home/okishinya/chipatlas/results/dm3/SRX2831144/SRR5572466.sra Written 30436213 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: 00:09:39 30436213 reads; of these: 30436213 (100.00%) were unpaired; of these: 3631128 (11.93%) aligned 0 times 20116723 (66.09%) aligned exactly 1 time 6688362 (21.98%) aligned >1 times 88.07% overall alignment rate Time searching: 00:09:39 Overall time: 00:09:39 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 12 files... [bam_rmdupse_core] 3228454 / 26805085 = 0.1204 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, 03 Sep 2017 01:12:39: # Command line: callpeak -t SRX2831144.bam -f BAM -g dm -n SRX2831144.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2831144.20 # format = BAM # ChIP-seq file = ['SRX2831144.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 @ Sun, 03 Sep 2017 01:12:39: #1 read tag files... INFO @ Sun, 03 Sep 2017 01:12:39: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 01:12:39: # Command line: callpeak -t SRX2831144.bam -f BAM -g dm -n SRX2831144.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2831144.05 # format = BAM # ChIP-seq file = ['SRX2831144.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 @ Sun, 03 Sep 2017 01:12:39: #1 read tag files... INFO @ Sun, 03 Sep 2017 01:12:39: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 01:12:39: # Command line: callpeak -t SRX2831144.bam -f BAM -g dm -n SRX2831144.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2831144.10 # format = BAM # ChIP-seq file = ['SRX2831144.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 @ Sun, 03 Sep 2017 01:12:39: #1 read tag files... INFO @ Sun, 03 Sep 2017 01:12:39: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 01:12:45: 1000000 INFO @ Sun, 03 Sep 2017 01:12:45: 1000000 INFO @ Sun, 03 Sep 2017 01:12:46: 1000000 INFO @ Sun, 03 Sep 2017 01:12:52: 2000000 INFO @ Sun, 03 Sep 2017 01:12:52: 2000000 INFO @ Sun, 03 Sep 2017 01:12:52: 2000000 INFO @ Sun, 03 Sep 2017 01:12:59: 3000000 INFO @ Sun, 03 Sep 2017 01:12:59: 3000000 INFO @ Sun, 03 Sep 2017 01:12:59: 3000000 INFO @ Sun, 03 Sep 2017 01:13:05: 4000000 INFO @ Sun, 03 Sep 2017 01:13:05: 4000000 INFO @ Sun, 03 Sep 2017 01:13:06: 4000000 INFO @ Sun, 03 Sep 2017 01:13:12: 5000000 INFO @ Sun, 03 Sep 2017 01:13:12: 5000000 INFO @ Sun, 03 Sep 2017 01:13:13: 5000000 INFO @ Sun, 03 Sep 2017 01:13:18: 6000000 INFO @ Sun, 03 Sep 2017 01:13:19: 6000000 INFO @ Sun, 03 Sep 2017 01:13:20: 6000000 INFO @ Sun, 03 Sep 2017 01:13:25: 7000000 INFO @ Sun, 03 Sep 2017 01:13:25: 7000000 INFO @ Sun, 03 Sep 2017 01:13:27: 7000000 INFO @ Sun, 03 Sep 2017 01:13:32: 8000000 INFO @ Sun, 03 Sep 2017 01:13:32: 8000000 INFO @ Sun, 03 Sep 2017 01:13:34: 8000000 INFO @ Sun, 03 Sep 2017 01:13:38: 9000000 INFO @ Sun, 03 Sep 2017 01:13:38: 9000000 INFO @ Sun, 03 Sep 2017 01:13:40: 9000000 INFO @ Sun, 03 Sep 2017 01:13:45: 10000000 INFO @ Sun, 03 Sep 2017 01:13:45: 10000000 INFO @ Sun, 03 Sep 2017 01:13:47: 10000000 INFO @ Sun, 03 Sep 2017 01:13:51: 11000000 INFO @ Sun, 03 Sep 2017 01:13:52: 11000000 INFO @ Sun, 03 Sep 2017 01:13:54: 11000000 INFO @ Sun, 03 Sep 2017 01:13:58: 12000000 INFO @ Sun, 03 Sep 2017 01:13:58: 12000000 INFO @ Sun, 03 Sep 2017 01:14:01: 12000000 INFO @ Sun, 03 Sep 2017 01:14:04: 13000000 INFO @ Sun, 03 Sep 2017 01:14:05: 13000000 INFO @ Sun, 03 Sep 2017 01:14:08: 13000000 INFO @ Sun, 03 Sep 2017 01:14:10: 14000000 INFO @ Sun, 03 Sep 2017 01:14:12: 14000000 INFO @ Sun, 03 Sep 2017 01:14:15: 14000000 INFO @ Sun, 03 Sep 2017 01:14:17: 15000000 INFO @ Sun, 03 Sep 2017 01:14:19: 15000000 INFO @ Sun, 03 Sep 2017 01:14:22: 15000000 INFO @ Sun, 03 Sep 2017 01:14:23: 16000000 INFO @ Sun, 03 Sep 2017 01:14:25: 16000000 INFO @ Sun, 03 Sep 2017 01:14:28: 16000000 INFO @ Sun, 03 Sep 2017 01:14:29: 17000000 INFO @ Sun, 03 Sep 2017 01:14:32: 17000000 INFO @ Sun, 03 Sep 2017 01:14:35: 17000000 INFO @ Sun, 03 Sep 2017 01:14:36: 18000000 INFO @ Sun, 03 Sep 2017 01:14:39: 18000000 INFO @ Sun, 03 Sep 2017 01:14:42: 18000000 INFO @ Sun, 03 Sep 2017 01:14:42: 19000000 INFO @ Sun, 03 Sep 2017 01:14:45: 19000000 INFO @ Sun, 03 Sep 2017 01:14:49: 20000000 INFO @ Sun, 03 Sep 2017 01:14:49: 19000000 INFO @ Sun, 03 Sep 2017 01:14:52: 20000000 INFO @ Sun, 03 Sep 2017 01:14:55: 21000000 INFO @ Sun, 03 Sep 2017 01:14:56: 20000000 INFO @ Sun, 03 Sep 2017 01:14:59: 21000000 INFO @ Sun, 03 Sep 2017 01:15:01: 22000000 INFO @ Sun, 03 Sep 2017 01:15:03: 21000000 INFO @ Sun, 03 Sep 2017 01:15:06: 22000000 INFO @ Sun, 03 Sep 2017 01:15:08: 23000000 INFO @ Sun, 03 Sep 2017 01:15:10: 22000000 INFO @ Sun, 03 Sep 2017 01:15:12: #1 tag size is determined as 50 bps INFO @ Sun, 03 Sep 2017 01:15:12: #1 tag size = 50 INFO @ Sun, 03 Sep 2017 01:15:12: #1 total tags in treatment: 23576631 INFO @ Sun, 03 Sep 2017 01:15:12: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 01:15:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Sep 2017 01:15:12: #1 tags after filtering in treatment: 23576631 INFO @ Sun, 03 Sep 2017 01:15:12: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Sep 2017 01:15:12: #1 finished! INFO @ Sun, 03 Sep 2017 01:15:12: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 01:15:12: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 01:15:12: 23000000 INFO @ Sun, 03 Sep 2017 01:15:14: #2 number of paired peaks: 372 WARNING @ Sun, 03 Sep 2017 01:15:14: Fewer paired peaks (372) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 372 pairs to build model! INFO @ Sun, 03 Sep 2017 01:15:14: start model_add_line... INFO @ Sun, 03 Sep 2017 01:15:14: start X-correlation... INFO @ Sun, 03 Sep 2017 01:15:14: end of X-cor INFO @ Sun, 03 Sep 2017 01:15:14: #2 finished! INFO @ Sun, 03 Sep 2017 01:15:14: #2 predicted fragment length is 37 bps INFO @ Sun, 03 Sep 2017 01:15:14: #2 alternative fragment length(s) may be 2,37 bps INFO @ Sun, 03 Sep 2017 01:15:14: #2.2 Generate R script for model : SRX2831144.10_model.r WARNING @ Sun, 03 Sep 2017 01:15:14: #2 Since the d (37) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Sep 2017 01:15:14: #2 You may need to consider one of the other alternative d(s): 2,37 WARNING @ Sun, 03 Sep 2017 01:15:14: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 03 Sep 2017 01:15:14: #3 Call peaks... INFO @ Sun, 03 Sep 2017 01:15:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Sep 2017 01:15:16: #1 tag size is determined as 50 bps INFO @ Sun, 03 Sep 2017 01:15:16: #1 tag size = 50 INFO @ Sun, 03 Sep 2017 01:15:16: #1 total tags in treatment: 23576631 INFO @ Sun, 03 Sep 2017 01:15:16: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 01:15:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Sep 2017 01:15:16: 23000000 INFO @ Sun, 03 Sep 2017 01:15:17: #1 tags after filtering in treatment: 23576631 INFO @ Sun, 03 Sep 2017 01:15:17: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Sep 2017 01:15:17: #1 finished! INFO @ Sun, 03 Sep 2017 01:15:17: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 01:15:17: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 01:15:18: #2 number of paired peaks: 372 WARNING @ Sun, 03 Sep 2017 01:15:18: Fewer paired peaks (372) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 372 pairs to build model! INFO @ Sun, 03 Sep 2017 01:15:18: start model_add_line... INFO @ Sun, 03 Sep 2017 01:15:19: start X-correlation... INFO @ Sun, 03 Sep 2017 01:15:19: end of X-cor INFO @ Sun, 03 Sep 2017 01:15:19: #2 finished! INFO @ Sun, 03 Sep 2017 01:15:19: #2 predicted fragment length is 37 bps INFO @ Sun, 03 Sep 2017 01:15:19: #2 alternative fragment length(s) may be 2,37 bps INFO @ Sun, 03 Sep 2017 01:15:19: #2.2 Generate R script for model : SRX2831144.20_model.r WARNING @ Sun, 03 Sep 2017 01:15:19: #2 Since the d (37) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Sep 2017 01:15:19: #2 You may need to consider one of the other alternative d(s): 2,37 WARNING @ Sun, 03 Sep 2017 01:15:19: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 03 Sep 2017 01:15:19: #3 Call peaks... INFO @ Sun, 03 Sep 2017 01:15:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Sep 2017 01:15:20: #1 tag size is determined as 50 bps INFO @ Sun, 03 Sep 2017 01:15:20: #1 tag size = 50 INFO @ Sun, 03 Sep 2017 01:15:20: #1 total tags in treatment: 23576631 INFO @ Sun, 03 Sep 2017 01:15:20: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 01:15:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Sep 2017 01:15:21: #1 tags after filtering in treatment: 23576631 INFO @ Sun, 03 Sep 2017 01:15:21: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Sep 2017 01:15:21: #1 finished! INFO @ Sun, 03 Sep 2017 01:15:21: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 01:15:21: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 01:15:22: #2 number of paired peaks: 372 WARNING @ Sun, 03 Sep 2017 01:15:22: Fewer paired peaks (372) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 372 pairs to build model! INFO @ Sun, 03 Sep 2017 01:15:22: start model_add_line... INFO @ Sun, 03 Sep 2017 01:15:22: start X-correlation... INFO @ Sun, 03 Sep 2017 01:15:22: end of X-cor INFO @ Sun, 03 Sep 2017 01:15:22: #2 finished! INFO @ Sun, 03 Sep 2017 01:15:22: #2 predicted fragment length is 37 bps INFO @ Sun, 03 Sep 2017 01:15:22: #2 alternative fragment length(s) may be 2,37 bps INFO @ Sun, 03 Sep 2017 01:15:22: #2.2 Generate R script for model : SRX2831144.05_model.r WARNING @ Sun, 03 Sep 2017 01:15:22: #2 Since the d (37) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Sep 2017 01:15:22: #2 You may need to consider one of the other alternative d(s): 2,37 WARNING @ Sun, 03 Sep 2017 01:15:22: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 03 Sep 2017 01:15:22: #3 Call peaks... INFO @ Sun, 03 Sep 2017 01:15:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Sep 2017 01:15:57: #3 Call peaks for each chromosome... INFO @ Sun, 03 Sep 2017 01:16:04: #3 Call peaks for each chromosome... INFO @ Sun, 03 Sep 2017 01:16:15: #3 Call peaks for each chromosome... INFO @ Sun, 03 Sep 2017 01:16:22: #4 Write output xls file... SRX2831144.10_peaks.xls INFO @ Sun, 03 Sep 2017 01:16:22: #4 Write peak in narrowPeak format file... SRX2831144.10_peaks.narrowPeak INFO @ Sun, 03 Sep 2017 01:16:22: #4 Write summits bed file... SRX2831144.10_summits.bed INFO @ Sun, 03 Sep 2017 01:16:22: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1869 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 03 Sep 2017 01:16:31: #4 Write output xls file... SRX2831144.20_peaks.xls INFO @ Sun, 03 Sep 2017 01:16:31: #4 Write peak in narrowPeak format file... SRX2831144.20_peaks.narrowPeak INFO @ Sun, 03 Sep 2017 01:16:31: #4 Write summits bed file... SRX2831144.20_summits.bed INFO @ Sun, 03 Sep 2017 01:16:31: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (706 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 03 Sep 2017 01:16:39: #4 Write output xls file... SRX2831144.05_peaks.xls INFO @ Sun, 03 Sep 2017 01:16:39: #4 Write peak in narrowPeak format file... SRX2831144.05_peaks.narrowPeak INFO @ Sun, 03 Sep 2017 01:16:39: #4 Write summits bed file... SRX2831144.05_summits.bed INFO @ Sun, 03 Sep 2017 01:16:39: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (3905 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。