Job ID = 9371918 sra ファイルのダウンロード中... Completed: 492245K bytes transferred in 17 seconds (235333K 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 22611246 spots for /home/okishinya/chipatlas/results/dm3/SRX2520642/SRR5206761.sra Written 22611246 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: 00:09:04 22611246 reads; of these: 22611246 (100.00%) were unpaired; of these: 1019228 (4.51%) aligned 0 times 16103689 (71.22%) aligned exactly 1 time 5488329 (24.27%) aligned >1 times 95.49% overall alignment rate Time searching: 00:09:04 Overall time: 00:09:04 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] 1949917 / 21592018 = 0.0903 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 15:04:25: # Command line: callpeak -t SRX2520642.bam -f BAM -g dm -n SRX2520642.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2520642.05 # format = BAM # ChIP-seq file = ['SRX2520642.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 15:04:25: #1 read tag files... INFO @ Fri, 04 Aug 2017 15:04:25: #1 read treatment tags... INFO @ Fri, 04 Aug 2017 15:04:25: # Command line: callpeak -t SRX2520642.bam -f BAM -g dm -n SRX2520642.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2520642.20 # format = BAM # ChIP-seq file = ['SRX2520642.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 15:04:25: #1 read tag files... INFO @ Fri, 04 Aug 2017 15:04:25: #1 read treatment tags... INFO @ Fri, 04 Aug 2017 15:04:25: # Command line: callpeak -t SRX2520642.bam -f BAM -g dm -n SRX2520642.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2520642.10 # format = BAM # ChIP-seq file = ['SRX2520642.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 15:04:25: #1 read tag files... INFO @ Fri, 04 Aug 2017 15:04:25: #1 read treatment tags... INFO @ Fri, 04 Aug 2017 15:04:33: 1000000 INFO @ Fri, 04 Aug 2017 15:04:33: 1000000 INFO @ Fri, 04 Aug 2017 15:04:33: 1000000 INFO @ Fri, 04 Aug 2017 15:04:41: 2000000 INFO @ Fri, 04 Aug 2017 15:04:41: 2000000 INFO @ Fri, 04 Aug 2017 15:04:41: 2000000 INFO @ Fri, 04 Aug 2017 15:04:49: 3000000 INFO @ Fri, 04 Aug 2017 15:04:49: 3000000 INFO @ Fri, 04 Aug 2017 15:04:49: 3000000 INFO @ Fri, 04 Aug 2017 15:04:57: 4000000 INFO @ Fri, 04 Aug 2017 15:04:57: 4000000 INFO @ Fri, 04 Aug 2017 15:04:57: 4000000 INFO @ Fri, 04 Aug 2017 15:05:04: 5000000 INFO @ Fri, 04 Aug 2017 15:05:07: 5000000 INFO @ Fri, 04 Aug 2017 15:05:07: 5000000 INFO @ Fri, 04 Aug 2017 15:05:12: 6000000 INFO @ Fri, 04 Aug 2017 15:05:17: 6000000 INFO @ Fri, 04 Aug 2017 15:05:17: 6000000 INFO @ Fri, 04 Aug 2017 15:05:20: 7000000 INFO @ Fri, 04 Aug 2017 15:05:27: 7000000 INFO @ Fri, 04 Aug 2017 15:05:27: 7000000 INFO @ Fri, 04 Aug 2017 15:05:27: 8000000 INFO @ Fri, 04 Aug 2017 15:05:35: 9000000 INFO @ Fri, 04 Aug 2017 15:05:36: 8000000 INFO @ Fri, 04 Aug 2017 15:05:37: 8000000 INFO @ Fri, 04 Aug 2017 15:05:43: 10000000 INFO @ Fri, 04 Aug 2017 15:05:44: 9000000 INFO @ Fri, 04 Aug 2017 15:05:46: 9000000 INFO @ Fri, 04 Aug 2017 15:05:51: 11000000 INFO @ Fri, 04 Aug 2017 15:05:52: 10000000 INFO @ Fri, 04 Aug 2017 15:05:56: 10000000 INFO @ Fri, 04 Aug 2017 15:05:59: 12000000 INFO @ Fri, 04 Aug 2017 15:06:00: 11000000 INFO @ Fri, 04 Aug 2017 15:06:06: 11000000 INFO @ Fri, 04 Aug 2017 15:06:06: 13000000 INFO @ Fri, 04 Aug 2017 15:06:07: 12000000 INFO @ Fri, 04 Aug 2017 15:06:15: 12000000 INFO @ Fri, 04 Aug 2017 15:06:15: 14000000 INFO @ Fri, 04 Aug 2017 15:06:16: 13000000 INFO @ Fri, 04 Aug 2017 15:06:23: 13000000 INFO @ Fri, 04 Aug 2017 15:06:23: 15000000 INFO @ Fri, 04 Aug 2017 15:06:24: 14000000 INFO @ Fri, 04 Aug 2017 15:06:32: 14000000 INFO @ Fri, 04 Aug 2017 15:06:32: 16000000 INFO @ Fri, 04 Aug 2017 15:06:33: 15000000 INFO @ Fri, 04 Aug 2017 15:06:40: 15000000 INFO @ Fri, 04 Aug 2017 15:06:40: 17000000 INFO @ Fri, 04 Aug 2017 15:06:41: 16000000 INFO @ Fri, 04 Aug 2017 15:06:48: 16000000 INFO @ Fri, 04 Aug 2017 15:06:49: 18000000 INFO @ Fri, 04 Aug 2017 15:06:50: 17000000 INFO @ Fri, 04 Aug 2017 15:06:57: 17000000 INFO @ Fri, 04 Aug 2017 15:06:57: 19000000 INFO @ Fri, 04 Aug 2017 15:06:58: 18000000 INFO @ Fri, 04 Aug 2017 15:07:02: #1 tag size is determined as 50 bps INFO @ Fri, 04 Aug 2017 15:07:02: #1 tag size = 50 INFO @ Fri, 04 Aug 2017 15:07:02: #1 total tags in treatment: 19642101 INFO @ Fri, 04 Aug 2017 15:07:02: #1 user defined the maximum tags... INFO @ Fri, 04 Aug 2017 15:07:02: #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 15:07:03: #1 tags after filtering in treatment: 19642101 INFO @ Fri, 04 Aug 2017 15:07:03: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 Aug 2017 15:07:03: #1 finished! INFO @ Fri, 04 Aug 2017 15:07:03: #2 Build Peak Model... INFO @ Fri, 04 Aug 2017 15:07:03: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 Aug 2017 15:07:04: #2 number of paired peaks: 179 WARNING @ Fri, 04 Aug 2017 15:07:04: 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 @ Fri, 04 Aug 2017 15:07:04: start model_add_line... INFO @ Fri, 04 Aug 2017 15:07:04: start X-correlation... INFO @ Fri, 04 Aug 2017 15:07:04: end of X-cor INFO @ Fri, 04 Aug 2017 15:07:04: #2 finished! INFO @ Fri, 04 Aug 2017 15:07:04: #2 predicted fragment length is 49 bps INFO @ Fri, 04 Aug 2017 15:07:04: #2 alternative fragment length(s) may be 49 bps INFO @ Fri, 04 Aug 2017 15:07:04: #2.2 Generate R script for model : SRX2520642.10_model.r WARNING @ Fri, 04 Aug 2017 15:07:04: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 04 Aug 2017 15:07:04: #2 You may need to consider one of the other alternative d(s): 49 WARNING @ Fri, 04 Aug 2017 15:07:04: #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 15:07:04: #3 Call peaks... INFO @ Fri, 04 Aug 2017 15:07:04: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 Aug 2017 15:07:05: 18000000 INFO @ Fri, 04 Aug 2017 15:07:06: 19000000 INFO @ Fri, 04 Aug 2017 15:07:11: #1 tag size is determined as 50 bps INFO @ Fri, 04 Aug 2017 15:07:11: #1 tag size = 50 INFO @ Fri, 04 Aug 2017 15:07:11: #1 total tags in treatment: 19642101 INFO @ Fri, 04 Aug 2017 15:07:11: #1 user defined the maximum tags... INFO @ Fri, 04 Aug 2017 15:07:11: #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 15:07:11: #1 tags after filtering in treatment: 19642101 INFO @ Fri, 04 Aug 2017 15:07:11: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 Aug 2017 15:07:11: #1 finished! INFO @ Fri, 04 Aug 2017 15:07:11: #2 Build Peak Model... INFO @ Fri, 04 Aug 2017 15:07:11: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 Aug 2017 15:07:12: 19000000 INFO @ Fri, 04 Aug 2017 15:07:12: #2 number of paired peaks: 179 WARNING @ Fri, 04 Aug 2017 15:07:12: 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 @ Fri, 04 Aug 2017 15:07:12: start model_add_line... INFO @ Fri, 04 Aug 2017 15:07:13: start X-correlation... INFO @ Fri, 04 Aug 2017 15:07:13: end of X-cor INFO @ Fri, 04 Aug 2017 15:07:13: #2 finished! INFO @ Fri, 04 Aug 2017 15:07:13: #2 predicted fragment length is 49 bps INFO @ Fri, 04 Aug 2017 15:07:13: #2 alternative fragment length(s) may be 49 bps INFO @ Fri, 04 Aug 2017 15:07:13: #2.2 Generate R script for model : SRX2520642.20_model.r WARNING @ Fri, 04 Aug 2017 15:07:13: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 04 Aug 2017 15:07:13: #2 You may need to consider one of the other alternative d(s): 49 WARNING @ Fri, 04 Aug 2017 15:07:13: #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 15:07:13: #3 Call peaks... INFO @ Fri, 04 Aug 2017 15:07:13: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 Aug 2017 15:07:16: #1 tag size is determined as 50 bps INFO @ Fri, 04 Aug 2017 15:07:16: #1 tag size = 50 INFO @ Fri, 04 Aug 2017 15:07:16: #1 total tags in treatment: 19642101 INFO @ Fri, 04 Aug 2017 15:07:16: #1 user defined the maximum tags... INFO @ Fri, 04 Aug 2017 15:07:16: #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 15:07:17: #1 tags after filtering in treatment: 19642101 INFO @ Fri, 04 Aug 2017 15:07:17: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 Aug 2017 15:07:17: #1 finished! INFO @ Fri, 04 Aug 2017 15:07:17: #2 Build Peak Model... INFO @ Fri, 04 Aug 2017 15:07:17: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 Aug 2017 15:07:18: #2 number of paired peaks: 179 WARNING @ Fri, 04 Aug 2017 15:07:18: 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 @ Fri, 04 Aug 2017 15:07:18: start model_add_line... INFO @ Fri, 04 Aug 2017 15:07:18: start X-correlation... INFO @ Fri, 04 Aug 2017 15:07:18: end of X-cor INFO @ Fri, 04 Aug 2017 15:07:18: #2 finished! INFO @ Fri, 04 Aug 2017 15:07:18: #2 predicted fragment length is 49 bps INFO @ Fri, 04 Aug 2017 15:07:18: #2 alternative fragment length(s) may be 49 bps INFO @ Fri, 04 Aug 2017 15:07:18: #2.2 Generate R script for model : SRX2520642.05_model.r WARNING @ Fri, 04 Aug 2017 15:07:18: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 04 Aug 2017 15:07:18: #2 You may need to consider one of the other alternative d(s): 49 WARNING @ Fri, 04 Aug 2017 15:07:18: #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 15:07:18: #3 Call peaks... INFO @ Fri, 04 Aug 2017 15:07:18: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 Aug 2017 15:07:44: #3 Call peaks for each chromosome... INFO @ Fri, 04 Aug 2017 15:07:54: #3 Call peaks for each chromosome... INFO @ Fri, 04 Aug 2017 15:07:59: #3 Call peaks for each chromosome... INFO @ Fri, 04 Aug 2017 15:08:05: #4 Write output xls file... SRX2520642.10_peaks.xls INFO @ Fri, 04 Aug 2017 15:08:05: #4 Write peak in narrowPeak format file... SRX2520642.10_peaks.narrowPeak INFO @ Fri, 04 Aug 2017 15:08:05: #4 Write summits bed file... SRX2520642.10_summits.bed INFO @ Fri, 04 Aug 2017 15:08:05: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (1266 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 04 Aug 2017 15:08:14: #4 Write output xls file... SRX2520642.20_peaks.xls INFO @ Fri, 04 Aug 2017 15:08:14: #4 Write peak in narrowPeak format file... SRX2520642.20_peaks.narrowPeak INFO @ Fri, 04 Aug 2017 15:08:14: #4 Write summits bed file... SRX2520642.20_summits.bed INFO @ Fri, 04 Aug 2017 15:08:14: Done! pass1 - making usageList (9 chroms): 2 millis pass2 - checking and writing primary data (808 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 04 Aug 2017 15:08:22: #4 Write output xls file... SRX2520642.05_peaks.xls INFO @ Fri, 04 Aug 2017 15:08:22: #4 Write peak in narrowPeak format file... SRX2520642.05_peaks.narrowPeak INFO @ Fri, 04 Aug 2017 15:08:22: #4 Write summits bed file... SRX2520642.05_summits.bed INFO @ Fri, 04 Aug 2017 15:08:22: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (1862 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。