Job ID = 10450718 sra ファイルのダウンロード中... Completed: 486756K bytes transferred in 27 seconds (144759K 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 25376516 spots for /home/okishinya/chipatlas/results/dm3/SRX3404012/SRR6303489.sra Written 25376516 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: 00:09:19 25376516 reads; of these: 25376516 (100.00%) were unpaired; of these: 677255 (2.67%) aligned 0 times 18331821 (72.24%) aligned exactly 1 time 6367440 (25.09%) aligned >1 times 97.33% overall alignment rate Time searching: 00:09:19 Overall time: 00:09:19 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] 1965299 / 24699261 = 0.0796 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 @ Wed, 07 Feb 2018 11:26:01: # Command line: callpeak -t SRX3404012.bam -f BAM -g dm -n SRX3404012.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3404012.10 # format = BAM # ChIP-seq file = ['SRX3404012.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 @ Wed, 07 Feb 2018 11:26:01: #1 read tag files... INFO @ Wed, 07 Feb 2018 11:26:01: #1 read treatment tags... INFO @ Wed, 07 Feb 2018 11:26:01: # Command line: callpeak -t SRX3404012.bam -f BAM -g dm -n SRX3404012.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3404012.05 # format = BAM # ChIP-seq file = ['SRX3404012.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 @ Wed, 07 Feb 2018 11:26:01: #1 read tag files... INFO @ Wed, 07 Feb 2018 11:26:01: #1 read treatment tags... INFO @ Wed, 07 Feb 2018 11:26:01: # Command line: callpeak -t SRX3404012.bam -f BAM -g dm -n SRX3404012.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3404012.20 # format = BAM # ChIP-seq file = ['SRX3404012.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 @ Wed, 07 Feb 2018 11:26:01: #1 read tag files... INFO @ Wed, 07 Feb 2018 11:26:01: #1 read treatment tags... INFO @ Wed, 07 Feb 2018 11:26:07: 1000000 INFO @ Wed, 07 Feb 2018 11:26:07: 1000000 INFO @ Wed, 07 Feb 2018 11:26:07: 1000000 INFO @ Wed, 07 Feb 2018 11:26:13: 2000000 INFO @ Wed, 07 Feb 2018 11:26:13: 2000000 INFO @ Wed, 07 Feb 2018 11:26:14: 2000000 INFO @ Wed, 07 Feb 2018 11:26:20: 3000000 INFO @ Wed, 07 Feb 2018 11:26:20: 3000000 INFO @ Wed, 07 Feb 2018 11:26:21: 3000000 INFO @ Wed, 07 Feb 2018 11:26:26: 4000000 INFO @ Wed, 07 Feb 2018 11:26:26: 4000000 INFO @ Wed, 07 Feb 2018 11:26:28: 4000000 INFO @ Wed, 07 Feb 2018 11:26:33: 5000000 INFO @ Wed, 07 Feb 2018 11:26:33: 5000000 INFO @ Wed, 07 Feb 2018 11:26:35: 5000000 INFO @ Wed, 07 Feb 2018 11:26:40: 6000000 INFO @ Wed, 07 Feb 2018 11:26:40: 6000000 INFO @ Wed, 07 Feb 2018 11:26:42: 6000000 INFO @ Wed, 07 Feb 2018 11:26:46: 7000000 INFO @ Wed, 07 Feb 2018 11:26:46: 7000000 INFO @ Wed, 07 Feb 2018 11:26:49: 7000000 INFO @ Wed, 07 Feb 2018 11:26:53: 8000000 INFO @ Wed, 07 Feb 2018 11:26:53: 8000000 INFO @ Wed, 07 Feb 2018 11:26:56: 8000000 INFO @ Wed, 07 Feb 2018 11:27:00: 9000000 INFO @ Wed, 07 Feb 2018 11:27:00: 9000000 INFO @ Wed, 07 Feb 2018 11:27:03: 9000000 INFO @ Wed, 07 Feb 2018 11:27:06: 10000000 INFO @ Wed, 07 Feb 2018 11:27:06: 10000000 INFO @ Wed, 07 Feb 2018 11:27:10: 10000000 INFO @ Wed, 07 Feb 2018 11:27:13: 11000000 INFO @ Wed, 07 Feb 2018 11:27:13: 11000000 INFO @ Wed, 07 Feb 2018 11:27:17: 11000000 INFO @ Wed, 07 Feb 2018 11:27:19: 12000000 INFO @ Wed, 07 Feb 2018 11:27:19: 12000000 INFO @ Wed, 07 Feb 2018 11:27:24: 12000000 INFO @ Wed, 07 Feb 2018 11:27:26: 13000000 INFO @ Wed, 07 Feb 2018 11:27:26: 13000000 INFO @ Wed, 07 Feb 2018 11:27:31: 13000000 INFO @ Wed, 07 Feb 2018 11:27:33: 14000000 INFO @ Wed, 07 Feb 2018 11:27:33: 14000000 INFO @ Wed, 07 Feb 2018 11:27:38: 14000000 INFO @ Wed, 07 Feb 2018 11:27:39: 15000000 INFO @ Wed, 07 Feb 2018 11:27:39: 15000000 INFO @ Wed, 07 Feb 2018 11:27:45: 15000000 INFO @ Wed, 07 Feb 2018 11:27:46: 16000000 INFO @ Wed, 07 Feb 2018 11:27:46: 16000000 INFO @ Wed, 07 Feb 2018 11:27:52: 16000000 INFO @ Wed, 07 Feb 2018 11:27:53: 17000000 INFO @ Wed, 07 Feb 2018 11:27:53: 17000000 INFO @ Wed, 07 Feb 2018 11:27:59: 18000000 INFO @ Wed, 07 Feb 2018 11:27:59: 18000000 INFO @ Wed, 07 Feb 2018 11:27:59: 17000000 INFO @ Wed, 07 Feb 2018 11:28:06: 19000000 INFO @ Wed, 07 Feb 2018 11:28:06: 19000000 INFO @ Wed, 07 Feb 2018 11:28:06: 18000000 INFO @ Wed, 07 Feb 2018 11:28:13: 20000000 INFO @ Wed, 07 Feb 2018 11:28:13: 20000000 INFO @ Wed, 07 Feb 2018 11:28:13: 19000000 INFO @ Wed, 07 Feb 2018 11:28:19: 21000000 INFO @ Wed, 07 Feb 2018 11:28:19: 21000000 INFO @ Wed, 07 Feb 2018 11:28:21: 20000000 INFO @ Wed, 07 Feb 2018 11:28:26: 22000000 INFO @ Wed, 07 Feb 2018 11:28:26: 22000000 INFO @ Wed, 07 Feb 2018 11:28:28: 21000000 INFO @ Wed, 07 Feb 2018 11:28:31: #1 tag size is determined as 51 bps INFO @ Wed, 07 Feb 2018 11:28:31: #1 tag size = 51 INFO @ Wed, 07 Feb 2018 11:28:31: #1 total tags in treatment: 22733962 INFO @ Wed, 07 Feb 2018 11:28:31: #1 user defined the maximum tags... INFO @ Wed, 07 Feb 2018 11:28:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 07 Feb 2018 11:28:31: #1 tag size is determined as 51 bps INFO @ Wed, 07 Feb 2018 11:28:31: #1 tag size = 51 INFO @ Wed, 07 Feb 2018 11:28:31: #1 total tags in treatment: 22733962 INFO @ Wed, 07 Feb 2018 11:28:31: #1 user defined the maximum tags... INFO @ Wed, 07 Feb 2018 11:28:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 07 Feb 2018 11:28:32: #1 tags after filtering in treatment: 22733962 INFO @ Wed, 07 Feb 2018 11:28:32: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 07 Feb 2018 11:28:32: #1 finished! INFO @ Wed, 07 Feb 2018 11:28:32: #2 Build Peak Model... INFO @ Wed, 07 Feb 2018 11:28:32: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 07 Feb 2018 11:28:32: #1 tags after filtering in treatment: 22733962 INFO @ Wed, 07 Feb 2018 11:28:32: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 07 Feb 2018 11:28:32: #1 finished! INFO @ Wed, 07 Feb 2018 11:28:32: #2 Build Peak Model... INFO @ Wed, 07 Feb 2018 11:28:32: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 07 Feb 2018 11:28:33: #2 number of paired peaks: 208 WARNING @ Wed, 07 Feb 2018 11:28:33: Fewer paired peaks (208) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 208 pairs to build model! INFO @ Wed, 07 Feb 2018 11:28:33: start model_add_line... INFO @ Wed, 07 Feb 2018 11:28:33: #2 number of paired peaks: 208 WARNING @ Wed, 07 Feb 2018 11:28:33: Fewer paired peaks (208) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 208 pairs to build model! INFO @ Wed, 07 Feb 2018 11:28:33: start model_add_line... INFO @ Wed, 07 Feb 2018 11:28:33: start X-correlation... INFO @ Wed, 07 Feb 2018 11:28:33: end of X-cor INFO @ Wed, 07 Feb 2018 11:28:33: #2 finished! INFO @ Wed, 07 Feb 2018 11:28:33: #2 predicted fragment length is 52 bps INFO @ Wed, 07 Feb 2018 11:28:33: #2 alternative fragment length(s) may be 1,52 bps INFO @ Wed, 07 Feb 2018 11:28:33: #2.2 Generate R script for model : SRX3404012.20_model.r WARNING @ Wed, 07 Feb 2018 11:28:33: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 07 Feb 2018 11:28:33: #2 You may need to consider one of the other alternative d(s): 1,52 WARNING @ Wed, 07 Feb 2018 11:28:33: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 07 Feb 2018 11:28:33: #3 Call peaks... INFO @ Wed, 07 Feb 2018 11:28:33: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 07 Feb 2018 11:28:33: start X-correlation... INFO @ Wed, 07 Feb 2018 11:28:33: end of X-cor INFO @ Wed, 07 Feb 2018 11:28:33: #2 finished! INFO @ Wed, 07 Feb 2018 11:28:33: #2 predicted fragment length is 52 bps INFO @ Wed, 07 Feb 2018 11:28:33: #2 alternative fragment length(s) may be 1,52 bps INFO @ Wed, 07 Feb 2018 11:28:33: #2.2 Generate R script for model : SRX3404012.10_model.r WARNING @ Wed, 07 Feb 2018 11:28:33: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 07 Feb 2018 11:28:33: #2 You may need to consider one of the other alternative d(s): 1,52 WARNING @ Wed, 07 Feb 2018 11:28:33: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 07 Feb 2018 11:28:33: #3 Call peaks... INFO @ Wed, 07 Feb 2018 11:28:33: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 07 Feb 2018 11:28:34: 22000000 INFO @ Wed, 07 Feb 2018 11:28:39: #1 tag size is determined as 51 bps INFO @ Wed, 07 Feb 2018 11:28:39: #1 tag size = 51 INFO @ Wed, 07 Feb 2018 11:28:39: #1 total tags in treatment: 22733962 INFO @ Wed, 07 Feb 2018 11:28:39: #1 user defined the maximum tags... INFO @ Wed, 07 Feb 2018 11:28:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 07 Feb 2018 11:28:39: #1 tags after filtering in treatment: 22733962 INFO @ Wed, 07 Feb 2018 11:28:39: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 07 Feb 2018 11:28:39: #1 finished! INFO @ Wed, 07 Feb 2018 11:28:39: #2 Build Peak Model... INFO @ Wed, 07 Feb 2018 11:28:39: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 07 Feb 2018 11:28:41: #2 number of paired peaks: 208 WARNING @ Wed, 07 Feb 2018 11:28:41: Fewer paired peaks (208) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 208 pairs to build model! INFO @ Wed, 07 Feb 2018 11:28:41: start model_add_line... INFO @ Wed, 07 Feb 2018 11:28:41: start X-correlation... INFO @ Wed, 07 Feb 2018 11:28:41: end of X-cor INFO @ Wed, 07 Feb 2018 11:28:41: #2 finished! INFO @ Wed, 07 Feb 2018 11:28:41: #2 predicted fragment length is 52 bps INFO @ Wed, 07 Feb 2018 11:28:41: #2 alternative fragment length(s) may be 1,52 bps INFO @ Wed, 07 Feb 2018 11:28:41: #2.2 Generate R script for model : SRX3404012.05_model.r WARNING @ Wed, 07 Feb 2018 11:28:41: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 07 Feb 2018 11:28:41: #2 You may need to consider one of the other alternative d(s): 1,52 WARNING @ Wed, 07 Feb 2018 11:28:41: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 07 Feb 2018 11:28:41: #3 Call peaks... INFO @ Wed, 07 Feb 2018 11:28:41: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 07 Feb 2018 11:29:17: #3 Call peaks for each chromosome... INFO @ Wed, 07 Feb 2018 11:29:19: #3 Call peaks for each chromosome... INFO @ Wed, 07 Feb 2018 11:29:25: #3 Call peaks for each chromosome... INFO @ Wed, 07 Feb 2018 11:29:42: #4 Write output xls file... SRX3404012.10_peaks.xls INFO @ Wed, 07 Feb 2018 11:29:42: #4 Write peak in narrowPeak format file... SRX3404012.10_peaks.narrowPeak INFO @ Wed, 07 Feb 2018 11:29:42: #4 Write summits bed file... SRX3404012.10_summits.bed INFO @ Wed, 07 Feb 2018 11:29:42: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1435 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 07 Feb 2018 11:29:45: #4 Write output xls file... SRX3404012.20_peaks.xls INFO @ Wed, 07 Feb 2018 11:29:45: #4 Write peak in narrowPeak format file... SRX3404012.20_peaks.narrowPeak INFO @ Wed, 07 Feb 2018 11:29:45: #4 Write summits bed file... SRX3404012.20_summits.bed INFO @ Wed, 07 Feb 2018 11:29:45: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (553 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 07 Feb 2018 11:29:47: #4 Write output xls file... SRX3404012.05_peaks.xls INFO @ Wed, 07 Feb 2018 11:29:47: #4 Write peak in narrowPeak format file... SRX3404012.05_peaks.narrowPeak INFO @ Wed, 07 Feb 2018 11:29:47: #4 Write summits bed file... SRX3404012.05_summits.bed INFO @ Wed, 07 Feb 2018 11:29:47: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2785 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。