Job ID = 9371434 sra ファイルのダウンロード中... Completed: 402559K bytes transferred in 7 seconds (433148K 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 15204899 spots for /home/okishinya/chipatlas/results/dm3/SRX2520644/SRR5206763.sra Written 15204899 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: 00:12:19 15204899 reads; of these: 15204899 (100.00%) were unpaired; of these: 280803 (1.85%) aligned 0 times 10358026 (68.12%) aligned exactly 1 time 4566070 (30.03%) aligned >1 times 98.15% overall alignment rate Time searching: 00:12:19 Overall time: 00:12:19 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 8 files... [bam_rmdupse_core] 3176374 / 14924096 = 0.2128 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 14:56:26: # Command line: callpeak -t SRX2520644.bam -f BAM -g dm -n SRX2520644.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2520644.20 # format = BAM # ChIP-seq file = ['SRX2520644.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 14:56:26: #1 read tag files... INFO @ Fri, 04 Aug 2017 14:56:26: #1 read treatment tags... INFO @ Fri, 04 Aug 2017 14:56:26: # Command line: callpeak -t SRX2520644.bam -f BAM -g dm -n SRX2520644.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2520644.05 # format = BAM # ChIP-seq file = ['SRX2520644.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 14:56:26: #1 read tag files... INFO @ Fri, 04 Aug 2017 14:56:26: #1 read treatment tags... INFO @ Fri, 04 Aug 2017 14:56:26: # Command line: callpeak -t SRX2520644.bam -f BAM -g dm -n SRX2520644.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2520644.10 # format = BAM # ChIP-seq file = ['SRX2520644.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 14:56:26: #1 read tag files... INFO @ Fri, 04 Aug 2017 14:56:26: #1 read treatment tags... INFO @ Fri, 04 Aug 2017 14:56:36: 1000000 INFO @ Fri, 04 Aug 2017 14:56:39: 1000000 INFO @ Fri, 04 Aug 2017 14:56:41: 1000000 INFO @ Fri, 04 Aug 2017 14:56:48: 2000000 INFO @ Fri, 04 Aug 2017 14:56:50: 2000000 INFO @ Fri, 04 Aug 2017 14:56:56: 2000000 INFO @ Fri, 04 Aug 2017 14:57:03: 3000000 INFO @ Fri, 04 Aug 2017 14:57:04: 3000000 INFO @ Fri, 04 Aug 2017 14:57:09: 3000000 INFO @ Fri, 04 Aug 2017 14:57:14: 4000000 INFO @ Fri, 04 Aug 2017 14:57:17: 4000000 INFO @ Fri, 04 Aug 2017 14:57:23: 4000000 INFO @ Fri, 04 Aug 2017 14:57:30: 5000000 INFO @ Fri, 04 Aug 2017 14:57:32: 5000000 INFO @ Fri, 04 Aug 2017 14:57:38: 5000000 INFO @ Fri, 04 Aug 2017 14:57:46: 6000000 INFO @ Fri, 04 Aug 2017 14:57:48: 6000000 INFO @ Fri, 04 Aug 2017 14:57:53: 6000000 INFO @ Fri, 04 Aug 2017 14:58:00: 7000000 INFO @ Fri, 04 Aug 2017 14:58:03: 7000000 INFO @ Fri, 04 Aug 2017 14:58:08: 7000000 INFO @ Fri, 04 Aug 2017 14:58:17: 8000000 INFO @ Fri, 04 Aug 2017 14:58:19: 8000000 INFO @ Fri, 04 Aug 2017 14:58:19: 8000000 INFO @ Fri, 04 Aug 2017 14:58:30: 9000000 INFO @ Fri, 04 Aug 2017 14:58:31: 9000000 INFO @ Fri, 04 Aug 2017 14:58:32: 9000000 INFO @ Fri, 04 Aug 2017 14:58:40: 10000000 INFO @ Fri, 04 Aug 2017 14:58:43: 10000000 INFO @ Fri, 04 Aug 2017 14:58:44: 10000000 INFO @ Fri, 04 Aug 2017 14:58:51: 11000000 INFO @ Fri, 04 Aug 2017 14:58:57: 11000000 INFO @ Fri, 04 Aug 2017 14:58:57: 11000000 INFO @ Fri, 04 Aug 2017 14:59:03: #1 tag size is determined as 50 bps INFO @ Fri, 04 Aug 2017 14:59:03: #1 tag size = 50 INFO @ Fri, 04 Aug 2017 14:59:03: #1 total tags in treatment: 11747722 INFO @ Fri, 04 Aug 2017 14:59:03: #1 user defined the maximum tags... INFO @ Fri, 04 Aug 2017 14:59:03: #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 14:59:03: #1 tags after filtering in treatment: 11747722 INFO @ Fri, 04 Aug 2017 14:59:03: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 Aug 2017 14:59:03: #1 finished! INFO @ Fri, 04 Aug 2017 14:59:03: #2 Build Peak Model... INFO @ Fri, 04 Aug 2017 14:59:03: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 Aug 2017 14:59:04: #2 number of paired peaks: 194 WARNING @ Fri, 04 Aug 2017 14:59:04: Fewer paired peaks (194) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 194 pairs to build model! INFO @ Fri, 04 Aug 2017 14:59:04: start model_add_line... INFO @ Fri, 04 Aug 2017 14:59:05: start X-correlation... INFO @ Fri, 04 Aug 2017 14:59:05: end of X-cor INFO @ Fri, 04 Aug 2017 14:59:05: #2 finished! INFO @ Fri, 04 Aug 2017 14:59:05: #2 predicted fragment length is 52 bps INFO @ Fri, 04 Aug 2017 14:59:05: #2 alternative fragment length(s) may be 2,34,52,84,497,577 bps INFO @ Fri, 04 Aug 2017 14:59:05: #2.2 Generate R script for model : SRX2520644.05_model.r WARNING @ Fri, 04 Aug 2017 14:59:05: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 04 Aug 2017 14:59:05: #2 You may need to consider one of the other alternative d(s): 2,34,52,84,497,577 WARNING @ Fri, 04 Aug 2017 14:59:05: #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 14:59:05: #3 Call peaks... INFO @ Fri, 04 Aug 2017 14:59:05: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 Aug 2017 14:59:07: #1 tag size is determined as 50 bps INFO @ Fri, 04 Aug 2017 14:59:07: #1 tag size = 50 INFO @ Fri, 04 Aug 2017 14:59:07: #1 total tags in treatment: 11747722 INFO @ Fri, 04 Aug 2017 14:59:07: #1 user defined the maximum tags... INFO @ Fri, 04 Aug 2017 14:59:07: #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 14:59:08: #1 tag size is determined as 50 bps INFO @ Fri, 04 Aug 2017 14:59:08: #1 tag size = 50 INFO @ Fri, 04 Aug 2017 14:59:08: #1 total tags in treatment: 11747722 INFO @ Fri, 04 Aug 2017 14:59:08: #1 user defined the maximum tags... INFO @ Fri, 04 Aug 2017 14:59:08: #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 14:59:08: #1 tags after filtering in treatment: 11747722 INFO @ Fri, 04 Aug 2017 14:59:08: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 Aug 2017 14:59:08: #1 finished! INFO @ Fri, 04 Aug 2017 14:59:08: #2 Build Peak Model... INFO @ Fri, 04 Aug 2017 14:59:08: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 Aug 2017 14:59:08: #1 tags after filtering in treatment: 11747722 INFO @ Fri, 04 Aug 2017 14:59:08: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 Aug 2017 14:59:08: #1 finished! INFO @ Fri, 04 Aug 2017 14:59:08: #2 Build Peak Model... INFO @ Fri, 04 Aug 2017 14:59:08: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 Aug 2017 14:59:09: #2 number of paired peaks: 194 WARNING @ Fri, 04 Aug 2017 14:59:09: Fewer paired peaks (194) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 194 pairs to build model! INFO @ Fri, 04 Aug 2017 14:59:09: start model_add_line... INFO @ Fri, 04 Aug 2017 14:59:09: start X-correlation... INFO @ Fri, 04 Aug 2017 14:59:09: end of X-cor INFO @ Fri, 04 Aug 2017 14:59:09: #2 finished! INFO @ Fri, 04 Aug 2017 14:59:09: #2 predicted fragment length is 52 bps INFO @ Fri, 04 Aug 2017 14:59:09: #2 alternative fragment length(s) may be 2,34,52,84,497,577 bps INFO @ Fri, 04 Aug 2017 14:59:09: #2.2 Generate R script for model : SRX2520644.10_model.r WARNING @ Fri, 04 Aug 2017 14:59:09: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 04 Aug 2017 14:59:09: #2 You may need to consider one of the other alternative d(s): 2,34,52,84,497,577 WARNING @ Fri, 04 Aug 2017 14:59:09: #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 14:59:09: #3 Call peaks... INFO @ Fri, 04 Aug 2017 14:59:09: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 Aug 2017 14:59:09: #2 number of paired peaks: 194 WARNING @ Fri, 04 Aug 2017 14:59:09: Fewer paired peaks (194) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 194 pairs to build model! INFO @ Fri, 04 Aug 2017 14:59:09: start model_add_line... INFO @ Fri, 04 Aug 2017 14:59:09: start X-correlation... INFO @ Fri, 04 Aug 2017 14:59:09: end of X-cor INFO @ Fri, 04 Aug 2017 14:59:09: #2 finished! INFO @ Fri, 04 Aug 2017 14:59:09: #2 predicted fragment length is 52 bps INFO @ Fri, 04 Aug 2017 14:59:09: #2 alternative fragment length(s) may be 2,34,52,84,497,577 bps INFO @ Fri, 04 Aug 2017 14:59:09: #2.2 Generate R script for model : SRX2520644.20_model.r WARNING @ Fri, 04 Aug 2017 14:59:09: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 04 Aug 2017 14:59:09: #2 You may need to consider one of the other alternative d(s): 2,34,52,84,497,577 WARNING @ Fri, 04 Aug 2017 14:59:09: #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 14:59:09: #3 Call peaks... INFO @ Fri, 04 Aug 2017 14:59:09: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 Aug 2017 14:59:40: #3 Call peaks for each chromosome... INFO @ Fri, 04 Aug 2017 14:59:42: #3 Call peaks for each chromosome... INFO @ Fri, 04 Aug 2017 14:59:42: #3 Call peaks for each chromosome... INFO @ Fri, 04 Aug 2017 15:00:00: #4 Write output xls file... SRX2520644.05_peaks.xls INFO @ Fri, 04 Aug 2017 15:00:00: #4 Write peak in narrowPeak format file... SRX2520644.05_peaks.narrowPeak INFO @ Fri, 04 Aug 2017 15:00:00: #4 Write summits bed file... SRX2520644.05_summits.bed INFO @ Fri, 04 Aug 2017 15:00:00: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (2389 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Fri, 04 Aug 2017 15:00:01: #4 Write output xls file... SRX2520644.20_peaks.xls INFO @ Fri, 04 Aug 2017 15:00:01: #4 Write peak in narrowPeak format file... SRX2520644.20_peaks.narrowPeak INFO @ Fri, 04 Aug 2017 15:00:01: #4 Write summits bed file... SRX2520644.20_summits.bed INFO @ Fri, 04 Aug 2017 15:00:01: Done! pass1 - making usageList (5 chroms): 1 millis pass2 - checking and writing primary data (419 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 04 Aug 2017 15:00:02: #4 Write output xls file... SRX2520644.10_peaks.xls INFO @ Fri, 04 Aug 2017 15:00:02: #4 Write peak in narrowPeak format file... SRX2520644.10_peaks.narrowPeak INFO @ Fri, 04 Aug 2017 15:00:02: #4 Write summits bed file... SRX2520644.10_summits.bed INFO @ Fri, 04 Aug 2017 15:00:02: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (1198 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。