Job ID = 9157207 sra ファイルのダウンロード中... Completed: 763434K bytes transferred in 9 seconds (685686K 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 17660826 spots for /home/okishinya/chipatlas/results/ce10/SRX2350718/SRR5024027.sra Written 17660826 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: 00:05:05 17660826 reads; of these: 17660826 (100.00%) were unpaired; of these: 306021 (1.73%) aligned 0 times 12743799 (72.16%) aligned exactly 1 time 4611006 (26.11%) aligned >1 times 98.27% overall alignment rate Time searching: 00:05:05 Overall time: 00:05:05 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 3927812 / 17354805 = 0.2263 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 @ Tue, 27 Jun 2017 11:12:26: # Command line: callpeak -t SRX2350718.bam -f BAM -g ce -n SRX2350718.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2350718.05 # format = BAM # ChIP-seq file = ['SRX2350718.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Tue, 27 Jun 2017 11:12:26: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:12:26: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:12:26: # Command line: callpeak -t SRX2350718.bam -f BAM -g ce -n SRX2350718.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2350718.10 # format = BAM # ChIP-seq file = ['SRX2350718.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Tue, 27 Jun 2017 11:12:26: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:12:26: # Command line: callpeak -t SRX2350718.bam -f BAM -g ce -n SRX2350718.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2350718.20 # format = BAM # ChIP-seq file = ['SRX2350718.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Tue, 27 Jun 2017 11:12:26: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:12:26: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:12:26: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:12:34: 1000000 INFO @ Tue, 27 Jun 2017 11:12:34: 1000000 INFO @ Tue, 27 Jun 2017 11:12:34: 1000000 INFO @ Tue, 27 Jun 2017 11:12:41: 2000000 INFO @ Tue, 27 Jun 2017 11:12:42: 2000000 INFO @ Tue, 27 Jun 2017 11:12:42: 2000000 INFO @ Tue, 27 Jun 2017 11:12:49: 3000000 INFO @ Tue, 27 Jun 2017 11:12:50: 3000000 INFO @ Tue, 27 Jun 2017 11:12:50: 3000000 INFO @ Tue, 27 Jun 2017 11:12:56: 4000000 INFO @ Tue, 27 Jun 2017 11:12:58: 4000000 INFO @ Tue, 27 Jun 2017 11:12:58: 4000000 INFO @ Tue, 27 Jun 2017 11:13:04: 5000000 INFO @ Tue, 27 Jun 2017 11:13:06: 5000000 INFO @ Tue, 27 Jun 2017 11:13:06: 5000000 INFO @ Tue, 27 Jun 2017 11:13:11: 6000000 INFO @ Tue, 27 Jun 2017 11:13:14: 6000000 INFO @ Tue, 27 Jun 2017 11:13:14: 6000000 INFO @ Tue, 27 Jun 2017 11:13:19: 7000000 INFO @ Tue, 27 Jun 2017 11:13:23: 7000000 INFO @ Tue, 27 Jun 2017 11:13:23: 7000000 INFO @ Tue, 27 Jun 2017 11:13:27: 8000000 INFO @ Tue, 27 Jun 2017 11:13:31: 8000000 INFO @ Tue, 27 Jun 2017 11:13:31: 8000000 INFO @ Tue, 27 Jun 2017 11:13:34: 9000000 INFO @ Tue, 27 Jun 2017 11:13:39: 9000000 INFO @ Tue, 27 Jun 2017 11:13:39: 9000000 INFO @ Tue, 27 Jun 2017 11:13:42: 10000000 INFO @ Tue, 27 Jun 2017 11:13:47: 10000000 INFO @ Tue, 27 Jun 2017 11:13:47: 10000000 INFO @ Tue, 27 Jun 2017 11:13:50: 11000000 INFO @ Tue, 27 Jun 2017 11:13:55: 11000000 INFO @ Tue, 27 Jun 2017 11:13:55: 11000000 INFO @ Tue, 27 Jun 2017 11:13:57: 12000000 INFO @ Tue, 27 Jun 2017 11:14:04: 12000000 INFO @ Tue, 27 Jun 2017 11:14:04: 12000000 INFO @ Tue, 27 Jun 2017 11:14:06: 13000000 INFO @ Tue, 27 Jun 2017 11:14:10: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 11:14:10: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 11:14:10: #1 total tags in treatment: 13426993 INFO @ Tue, 27 Jun 2017 11:14:10: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:14:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 11:14:10: #1 tags after filtering in treatment: 13426993 INFO @ Tue, 27 Jun 2017 11:14:10: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:14:10: #1 finished! INFO @ Tue, 27 Jun 2017 11:14:10: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:14:10: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:14:11: #2 number of paired peaks: 471 WARNING @ Tue, 27 Jun 2017 11:14:11: Fewer paired peaks (471) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 471 pairs to build model! INFO @ Tue, 27 Jun 2017 11:14:11: start model_add_line... INFO @ Tue, 27 Jun 2017 11:14:12: start X-correlation... INFO @ Tue, 27 Jun 2017 11:14:12: end of X-cor INFO @ Tue, 27 Jun 2017 11:14:12: #2 finished! INFO @ Tue, 27 Jun 2017 11:14:12: #2 predicted fragment length is 42 bps INFO @ Tue, 27 Jun 2017 11:14:12: #2 alternative fragment length(s) may be 2,42,480,537,595 bps INFO @ Tue, 27 Jun 2017 11:14:12: #2.2 Generate R script for model : SRX2350718.10_model.r WARNING @ Tue, 27 Jun 2017 11:14:12: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 11:14:12: #2 You may need to consider one of the other alternative d(s): 2,42,480,537,595 WARNING @ Tue, 27 Jun 2017 11:14:12: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 27 Jun 2017 11:14:12: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:14:12: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:14:14: 13000000 INFO @ Tue, 27 Jun 2017 11:14:14: 13000000 INFO @ Tue, 27 Jun 2017 11:14:18: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 11:14:18: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 11:14:18: #1 total tags in treatment: 13426993 INFO @ Tue, 27 Jun 2017 11:14:18: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:14:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 11:14:18: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 11:14:18: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 11:14:18: #1 total tags in treatment: 13426993 INFO @ Tue, 27 Jun 2017 11:14:18: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:14:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 11:14:18: #1 tags after filtering in treatment: 13426993 INFO @ Tue, 27 Jun 2017 11:14:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:14:18: #1 finished! INFO @ Tue, 27 Jun 2017 11:14:18: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:14:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:14:18: #1 tags after filtering in treatment: 13426993 INFO @ Tue, 27 Jun 2017 11:14:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:14:18: #1 finished! INFO @ Tue, 27 Jun 2017 11:14:18: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:14:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:14:19: #2 number of paired peaks: 471 WARNING @ Tue, 27 Jun 2017 11:14:19: Fewer paired peaks (471) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 471 pairs to build model! INFO @ Tue, 27 Jun 2017 11:14:19: start model_add_line... INFO @ Tue, 27 Jun 2017 11:14:19: #2 number of paired peaks: 471 WARNING @ Tue, 27 Jun 2017 11:14:19: Fewer paired peaks (471) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 471 pairs to build model! INFO @ Tue, 27 Jun 2017 11:14:19: start model_add_line... INFO @ Tue, 27 Jun 2017 11:14:19: start X-correlation... INFO @ Tue, 27 Jun 2017 11:14:19: end of X-cor INFO @ Tue, 27 Jun 2017 11:14:19: #2 finished! INFO @ Tue, 27 Jun 2017 11:14:19: #2 predicted fragment length is 42 bps INFO @ Tue, 27 Jun 2017 11:14:19: #2 alternative fragment length(s) may be 2,42,480,537,595 bps INFO @ Tue, 27 Jun 2017 11:14:19: #2.2 Generate R script for model : SRX2350718.20_model.r WARNING @ Tue, 27 Jun 2017 11:14:19: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 11:14:19: #2 You may need to consider one of the other alternative d(s): 2,42,480,537,595 WARNING @ Tue, 27 Jun 2017 11:14:19: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 27 Jun 2017 11:14:19: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:14:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:14:19: start X-correlation... INFO @ Tue, 27 Jun 2017 11:14:19: end of X-cor INFO @ Tue, 27 Jun 2017 11:14:19: #2 finished! INFO @ Tue, 27 Jun 2017 11:14:19: #2 predicted fragment length is 42 bps INFO @ Tue, 27 Jun 2017 11:14:19: #2 alternative fragment length(s) may be 2,42,480,537,595 bps INFO @ Tue, 27 Jun 2017 11:14:19: #2.2 Generate R script for model : SRX2350718.05_model.r WARNING @ Tue, 27 Jun 2017 11:14:19: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 11:14:19: #2 You may need to consider one of the other alternative d(s): 2,42,480,537,595 WARNING @ Tue, 27 Jun 2017 11:14:19: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 27 Jun 2017 11:14:19: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:14:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:14:43: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:14:48: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:14:49: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:14:59: #4 Write output xls file... SRX2350718.10_peaks.xls INFO @ Tue, 27 Jun 2017 11:14:59: #4 Write peak in narrowPeak format file... SRX2350718.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:14:59: #4 Write summits bed file... SRX2350718.10_summits.bed INFO @ Tue, 27 Jun 2017 11:14:59: Done! pass1 - making usageList (6 chroms): 8 millis pass2 - checking and writing primary data (439 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 11:15:05: #4 Write output xls file... SRX2350718.05_peaks.xls INFO @ Tue, 27 Jun 2017 11:15:05: #4 Write peak in narrowPeak format file... SRX2350718.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:15:05: #4 Write summits bed file... SRX2350718.05_summits.bed INFO @ Tue, 27 Jun 2017 11:15:05: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (731 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 11:15:05: #4 Write output xls file... SRX2350718.20_peaks.xls INFO @ Tue, 27 Jun 2017 11:15:05: #4 Write peak in narrowPeak format file... SRX2350718.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:15:05: #4 Write summits bed file... SRX2350718.20_summits.bed INFO @ Tue, 27 Jun 2017 11:15:05: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (129 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。