Job ID = 10320348 sra ファイルのダウンロード中... Completed: 573395K bytes transferred in 79 seconds (59132K 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 24159113 spots for /home/okishinya/chipatlas/results/dm3/SRX3270985/SRR6159396.sra Written 24159113 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: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:08:51 24159113 reads; of these: 24159113 (100.00%) were unpaired; of these: 2049491 (8.48%) aligned 0 times 15879563 (65.73%) aligned exactly 1 time 6230059 (25.79%) aligned >1 times 91.52% overall alignment rate Time searching: 00:08:52 Overall time: 00:08:52 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] 8944477 / 22109622 = 0.4046 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 @ Thu, 11 Jan 2018 02:20:46: # Command line: callpeak -t SRX3270985.bam -f BAM -g dm -n SRX3270985.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3270985.20 # format = BAM # ChIP-seq file = ['SRX3270985.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 @ Thu, 11 Jan 2018 02:20:46: # Command line: callpeak -t SRX3270985.bam -f BAM -g dm -n SRX3270985.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3270985.10 # format = BAM # ChIP-seq file = ['SRX3270985.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 @ Thu, 11 Jan 2018 02:20:46: # Command line: callpeak -t SRX3270985.bam -f BAM -g dm -n SRX3270985.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3270985.05 # format = BAM # ChIP-seq file = ['SRX3270985.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 @ Thu, 11 Jan 2018 02:20:46: #1 read tag files... INFO @ Thu, 11 Jan 2018 02:20:46: #1 read tag files... INFO @ Thu, 11 Jan 2018 02:20:46: #1 read tag files... INFO @ Thu, 11 Jan 2018 02:20:46: #1 read treatment tags... INFO @ Thu, 11 Jan 2018 02:20:46: #1 read treatment tags... INFO @ Thu, 11 Jan 2018 02:20:46: #1 read treatment tags... INFO @ Thu, 11 Jan 2018 02:20:53: 1000000 INFO @ Thu, 11 Jan 2018 02:20:53: 1000000 INFO @ Thu, 11 Jan 2018 02:20:53: 1000000 INFO @ Thu, 11 Jan 2018 02:21:00: 2000000 INFO @ Thu, 11 Jan 2018 02:21:01: 2000000 INFO @ Thu, 11 Jan 2018 02:21:01: 2000000 INFO @ Thu, 11 Jan 2018 02:21:06: 3000000 INFO @ Thu, 11 Jan 2018 02:21:07: 3000000 INFO @ Thu, 11 Jan 2018 02:21:07: 3000000 INFO @ Thu, 11 Jan 2018 02:21:13: 4000000 INFO @ Thu, 11 Jan 2018 02:21:14: 4000000 INFO @ Thu, 11 Jan 2018 02:21:14: 4000000 INFO @ Thu, 11 Jan 2018 02:21:19: 5000000 INFO @ Thu, 11 Jan 2018 02:21:21: 5000000 INFO @ Thu, 11 Jan 2018 02:21:21: 5000000 INFO @ Thu, 11 Jan 2018 02:21:25: 6000000 INFO @ Thu, 11 Jan 2018 02:21:28: 6000000 INFO @ Thu, 11 Jan 2018 02:21:28: 6000000 INFO @ Thu, 11 Jan 2018 02:21:32: 7000000 INFO @ Thu, 11 Jan 2018 02:21:35: 7000000 INFO @ Thu, 11 Jan 2018 02:21:35: 7000000 INFO @ Thu, 11 Jan 2018 02:21:38: 8000000 INFO @ Thu, 11 Jan 2018 02:21:42: 8000000 INFO @ Thu, 11 Jan 2018 02:21:42: 8000000 INFO @ Thu, 11 Jan 2018 02:21:45: 9000000 INFO @ Thu, 11 Jan 2018 02:21:49: 9000000 INFO @ Thu, 11 Jan 2018 02:21:49: 9000000 INFO @ Thu, 11 Jan 2018 02:21:51: 10000000 INFO @ Thu, 11 Jan 2018 02:21:56: 10000000 INFO @ Thu, 11 Jan 2018 02:21:56: 10000000 INFO @ Thu, 11 Jan 2018 02:21:57: 11000000 INFO @ Thu, 11 Jan 2018 02:22:02: 11000000 INFO @ Thu, 11 Jan 2018 02:22:03: 11000000 INFO @ Thu, 11 Jan 2018 02:22:05: 12000000 INFO @ Thu, 11 Jan 2018 02:22:09: 12000000 INFO @ Thu, 11 Jan 2018 02:22:11: 12000000 INFO @ Thu, 11 Jan 2018 02:22:12: 13000000 INFO @ Thu, 11 Jan 2018 02:22:13: #1 tag size is determined as 45 bps INFO @ Thu, 11 Jan 2018 02:22:13: #1 tag size = 45 INFO @ Thu, 11 Jan 2018 02:22:13: #1 total tags in treatment: 13165145 INFO @ Thu, 11 Jan 2018 02:22:13: #1 user defined the maximum tags... INFO @ Thu, 11 Jan 2018 02:22:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 11 Jan 2018 02:22:13: #1 tags after filtering in treatment: 13165145 INFO @ Thu, 11 Jan 2018 02:22:13: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 11 Jan 2018 02:22:13: #1 finished! INFO @ Thu, 11 Jan 2018 02:22:13: #2 Build Peak Model... INFO @ Thu, 11 Jan 2018 02:22:13: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 11 Jan 2018 02:22:14: #2 number of paired peaks: 428 WARNING @ Thu, 11 Jan 2018 02:22:14: Fewer paired peaks (428) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 428 pairs to build model! INFO @ Thu, 11 Jan 2018 02:22:14: start model_add_line... INFO @ Thu, 11 Jan 2018 02:22:14: start X-correlation... INFO @ Thu, 11 Jan 2018 02:22:15: end of X-cor INFO @ Thu, 11 Jan 2018 02:22:15: #2 finished! INFO @ Thu, 11 Jan 2018 02:22:15: #2 predicted fragment length is 41 bps INFO @ Thu, 11 Jan 2018 02:22:15: #2 alternative fragment length(s) may be 41 bps INFO @ Thu, 11 Jan 2018 02:22:15: #2.2 Generate R script for model : SRX3270985.05_model.r WARNING @ Thu, 11 Jan 2018 02:22:15: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 11 Jan 2018 02:22:15: #2 You may need to consider one of the other alternative d(s): 41 WARNING @ Thu, 11 Jan 2018 02:22:15: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 11 Jan 2018 02:22:15: #3 Call peaks... INFO @ Thu, 11 Jan 2018 02:22:15: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 11 Jan 2018 02:22:15: 13000000 INFO @ Thu, 11 Jan 2018 02:22:17: #1 tag size is determined as 45 bps INFO @ Thu, 11 Jan 2018 02:22:17: #1 tag size = 45 INFO @ Thu, 11 Jan 2018 02:22:17: #1 total tags in treatment: 13165145 INFO @ Thu, 11 Jan 2018 02:22:17: #1 user defined the maximum tags... INFO @ Thu, 11 Jan 2018 02:22:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 11 Jan 2018 02:22:17: #1 tags after filtering in treatment: 13165145 INFO @ Thu, 11 Jan 2018 02:22:17: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 11 Jan 2018 02:22:17: #1 finished! INFO @ Thu, 11 Jan 2018 02:22:17: #2 Build Peak Model... INFO @ Thu, 11 Jan 2018 02:22:17: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 11 Jan 2018 02:22:18: #2 number of paired peaks: 428 WARNING @ Thu, 11 Jan 2018 02:22:18: Fewer paired peaks (428) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 428 pairs to build model! INFO @ Thu, 11 Jan 2018 02:22:18: start model_add_line... INFO @ Thu, 11 Jan 2018 02:22:18: start X-correlation... INFO @ Thu, 11 Jan 2018 02:22:18: end of X-cor INFO @ Thu, 11 Jan 2018 02:22:18: #2 finished! INFO @ Thu, 11 Jan 2018 02:22:18: #2 predicted fragment length is 41 bps INFO @ Thu, 11 Jan 2018 02:22:18: #2 alternative fragment length(s) may be 41 bps INFO @ Thu, 11 Jan 2018 02:22:18: #2.2 Generate R script for model : SRX3270985.20_model.r WARNING @ Thu, 11 Jan 2018 02:22:18: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 11 Jan 2018 02:22:18: #2 You may need to consider one of the other alternative d(s): 41 WARNING @ Thu, 11 Jan 2018 02:22:18: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 11 Jan 2018 02:22:18: #3 Call peaks... INFO @ Thu, 11 Jan 2018 02:22:18: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 11 Jan 2018 02:22:18: 13000000 INFO @ Thu, 11 Jan 2018 02:22:19: #1 tag size is determined as 45 bps INFO @ Thu, 11 Jan 2018 02:22:19: #1 tag size = 45 INFO @ Thu, 11 Jan 2018 02:22:19: #1 total tags in treatment: 13165145 INFO @ Thu, 11 Jan 2018 02:22:19: #1 user defined the maximum tags... INFO @ Thu, 11 Jan 2018 02:22:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 11 Jan 2018 02:22:19: #1 tags after filtering in treatment: 13165145 INFO @ Thu, 11 Jan 2018 02:22:19: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 11 Jan 2018 02:22:19: #1 finished! INFO @ Thu, 11 Jan 2018 02:22:19: #2 Build Peak Model... INFO @ Thu, 11 Jan 2018 02:22:19: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 11 Jan 2018 02:22:21: #2 number of paired peaks: 428 WARNING @ Thu, 11 Jan 2018 02:22:21: Fewer paired peaks (428) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 428 pairs to build model! INFO @ Thu, 11 Jan 2018 02:22:21: start model_add_line... INFO @ Thu, 11 Jan 2018 02:22:21: start X-correlation... INFO @ Thu, 11 Jan 2018 02:22:21: end of X-cor INFO @ Thu, 11 Jan 2018 02:22:21: #2 finished! INFO @ Thu, 11 Jan 2018 02:22:21: #2 predicted fragment length is 41 bps INFO @ Thu, 11 Jan 2018 02:22:21: #2 alternative fragment length(s) may be 41 bps INFO @ Thu, 11 Jan 2018 02:22:21: #2.2 Generate R script for model : SRX3270985.10_model.r WARNING @ Thu, 11 Jan 2018 02:22:21: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 11 Jan 2018 02:22:21: #2 You may need to consider one of the other alternative d(s): 41 WARNING @ Thu, 11 Jan 2018 02:22:21: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 11 Jan 2018 02:22:21: #3 Call peaks... INFO @ Thu, 11 Jan 2018 02:22:21: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 11 Jan 2018 02:22:44: #3 Call peaks for each chromosome... INFO @ Thu, 11 Jan 2018 02:22:47: #3 Call peaks for each chromosome... INFO @ Thu, 11 Jan 2018 02:22:47: #3 Call peaks for each chromosome... INFO @ Thu, 11 Jan 2018 02:22:59: #4 Write output xls file... SRX3270985.05_peaks.xls INFO @ Thu, 11 Jan 2018 02:22:59: #4 Write peak in narrowPeak format file... SRX3270985.05_peaks.narrowPeak INFO @ Thu, 11 Jan 2018 02:22:59: #4 Write summits bed file... SRX3270985.05_summits.bed INFO @ Thu, 11 Jan 2018 02:22:59: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2511 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Thu, 11 Jan 2018 02:23:02: #4 Write output xls file... SRX3270985.10_peaks.xls INFO @ Thu, 11 Jan 2018 02:23:02: #4 Write peak in narrowPeak format file... SRX3270985.10_peaks.narrowPeak INFO @ Thu, 11 Jan 2018 02:23:02: #4 Write summits bed file... SRX3270985.10_summits.bed INFO @ Thu, 11 Jan 2018 02:23:02: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1729 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Thu, 11 Jan 2018 02:23:03: #4 Write output xls file... SRX3270985.20_peaks.xls INFO @ Thu, 11 Jan 2018 02:23:03: #4 Write peak in narrowPeak format file... SRX3270985.20_peaks.narrowPeak INFO @ Thu, 11 Jan 2018 02:23:03: #4 Write summits bed file... SRX3270985.20_summits.bed INFO @ Thu, 11 Jan 2018 02:23:03: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (1013 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。