Job ID = 10201966 sra ファイルのダウンロード中... Completed: 748794K bytes transferred in 17 seconds (345271K 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 21938757 spots for /home/okishinya/chipatlas/results/ce10/SRX2576635/SRR5272592.sra Written 21938757 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:03:12 21938757 reads; of these: 21938757 (100.00%) were unpaired; of these: 15349040 (69.96%) aligned 0 times 5392547 (24.58%) aligned exactly 1 time 1197170 (5.46%) aligned >1 times 30.04% overall alignment rate Time searching: 00:03:13 Overall time: 00:03:13 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_rmdupse_core] 2856797 / 6589717 = 0.4335 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 @ Mon, 13 Nov 2017 13:13:51: # Command line: callpeak -t SRX2576635.bam -f BAM -g ce -n SRX2576635.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2576635.20 # format = BAM # ChIP-seq file = ['SRX2576635.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 @ Mon, 13 Nov 2017 13:13:51: # Command line: callpeak -t SRX2576635.bam -f BAM -g ce -n SRX2576635.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2576635.10 # format = BAM # ChIP-seq file = ['SRX2576635.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 @ Mon, 13 Nov 2017 13:13:51: # Command line: callpeak -t SRX2576635.bam -f BAM -g ce -n SRX2576635.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2576635.05 # format = BAM # ChIP-seq file = ['SRX2576635.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 @ Mon, 13 Nov 2017 13:13:51: #1 read tag files... INFO @ Mon, 13 Nov 2017 13:13:51: #1 read tag files... INFO @ Mon, 13 Nov 2017 13:13:51: #1 read tag files... INFO @ Mon, 13 Nov 2017 13:13:51: #1 read treatment tags... INFO @ Mon, 13 Nov 2017 13:13:51: #1 read treatment tags... INFO @ Mon, 13 Nov 2017 13:13:51: #1 read treatment tags... INFO @ Mon, 13 Nov 2017 13:13:57: 1000000 INFO @ Mon, 13 Nov 2017 13:13:57: 1000000 INFO @ Mon, 13 Nov 2017 13:13:57: 1000000 INFO @ Mon, 13 Nov 2017 13:14:03: 2000000 INFO @ Mon, 13 Nov 2017 13:14:04: 2000000 INFO @ Mon, 13 Nov 2017 13:14:04: 2000000 INFO @ Mon, 13 Nov 2017 13:14:09: 3000000 INFO @ Mon, 13 Nov 2017 13:14:11: 3000000 INFO @ Mon, 13 Nov 2017 13:14:12: 3000000 INFO @ Mon, 13 Nov 2017 13:14:14: #1 tag size is determined as 50 bps INFO @ Mon, 13 Nov 2017 13:14:14: #1 tag size = 50 INFO @ Mon, 13 Nov 2017 13:14:14: #1 total tags in treatment: 3732920 INFO @ Mon, 13 Nov 2017 13:14:14: #1 user defined the maximum tags... INFO @ Mon, 13 Nov 2017 13:14:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 13 Nov 2017 13:14:14: #1 tags after filtering in treatment: 3732920 INFO @ Mon, 13 Nov 2017 13:14:14: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 13 Nov 2017 13:14:14: #1 finished! INFO @ Mon, 13 Nov 2017 13:14:14: #2 Build Peak Model... INFO @ Mon, 13 Nov 2017 13:14:14: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 13 Nov 2017 13:14:14: #2 number of paired peaks: 498 WARNING @ Mon, 13 Nov 2017 13:14:14: Fewer paired peaks (498) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 498 pairs to build model! INFO @ Mon, 13 Nov 2017 13:14:14: start model_add_line... INFO @ Mon, 13 Nov 2017 13:14:14: start X-correlation... INFO @ Mon, 13 Nov 2017 13:14:15: end of X-cor INFO @ Mon, 13 Nov 2017 13:14:15: #2 finished! INFO @ Mon, 13 Nov 2017 13:14:15: #2 predicted fragment length is 48 bps INFO @ Mon, 13 Nov 2017 13:14:15: #2 alternative fragment length(s) may be 4,48 bps INFO @ Mon, 13 Nov 2017 13:14:15: #2.2 Generate R script for model : SRX2576635.10_model.r WARNING @ Mon, 13 Nov 2017 13:14:15: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 13 Nov 2017 13:14:15: #2 You may need to consider one of the other alternative d(s): 4,48 WARNING @ Mon, 13 Nov 2017 13:14:15: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 13 Nov 2017 13:14:15: #3 Call peaks... INFO @ Mon, 13 Nov 2017 13:14:15: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 13 Nov 2017 13:14:16: #1 tag size is determined as 50 bps INFO @ Mon, 13 Nov 2017 13:14:16: #1 tag size = 50 INFO @ Mon, 13 Nov 2017 13:14:16: #1 total tags in treatment: 3732920 INFO @ Mon, 13 Nov 2017 13:14:16: #1 user defined the maximum tags... INFO @ Mon, 13 Nov 2017 13:14:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 13 Nov 2017 13:14:16: #1 tags after filtering in treatment: 3732920 INFO @ Mon, 13 Nov 2017 13:14:16: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 13 Nov 2017 13:14:16: #1 finished! INFO @ Mon, 13 Nov 2017 13:14:16: #2 Build Peak Model... INFO @ Mon, 13 Nov 2017 13:14:16: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 13 Nov 2017 13:14:16: #2 number of paired peaks: 498 WARNING @ Mon, 13 Nov 2017 13:14:16: Fewer paired peaks (498) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 498 pairs to build model! INFO @ Mon, 13 Nov 2017 13:14:16: start model_add_line... INFO @ Mon, 13 Nov 2017 13:14:16: start X-correlation... INFO @ Mon, 13 Nov 2017 13:14:16: end of X-cor INFO @ Mon, 13 Nov 2017 13:14:16: #2 finished! INFO @ Mon, 13 Nov 2017 13:14:16: #2 predicted fragment length is 48 bps INFO @ Mon, 13 Nov 2017 13:14:16: #2 alternative fragment length(s) may be 4,48 bps INFO @ Mon, 13 Nov 2017 13:14:16: #2.2 Generate R script for model : SRX2576635.05_model.r WARNING @ Mon, 13 Nov 2017 13:14:16: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 13 Nov 2017 13:14:16: #2 You may need to consider one of the other alternative d(s): 4,48 WARNING @ Mon, 13 Nov 2017 13:14:16: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 13 Nov 2017 13:14:16: #3 Call peaks... INFO @ Mon, 13 Nov 2017 13:14:16: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 13 Nov 2017 13:14:17: #1 tag size is determined as 50 bps INFO @ Mon, 13 Nov 2017 13:14:17: #1 tag size = 50 INFO @ Mon, 13 Nov 2017 13:14:17: #1 total tags in treatment: 3732920 INFO @ Mon, 13 Nov 2017 13:14:17: #1 user defined the maximum tags... INFO @ Mon, 13 Nov 2017 13:14:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 13 Nov 2017 13:14:17: #1 tags after filtering in treatment: 3732920 INFO @ Mon, 13 Nov 2017 13:14:17: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 13 Nov 2017 13:14:17: #1 finished! INFO @ Mon, 13 Nov 2017 13:14:17: #2 Build Peak Model... INFO @ Mon, 13 Nov 2017 13:14:17: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 13 Nov 2017 13:14:17: #2 number of paired peaks: 498 WARNING @ Mon, 13 Nov 2017 13:14:17: Fewer paired peaks (498) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 498 pairs to build model! INFO @ Mon, 13 Nov 2017 13:14:17: start model_add_line... INFO @ Mon, 13 Nov 2017 13:14:17: start X-correlation... INFO @ Mon, 13 Nov 2017 13:14:17: end of X-cor INFO @ Mon, 13 Nov 2017 13:14:17: #2 finished! INFO @ Mon, 13 Nov 2017 13:14:17: #2 predicted fragment length is 48 bps INFO @ Mon, 13 Nov 2017 13:14:17: #2 alternative fragment length(s) may be 4,48 bps INFO @ Mon, 13 Nov 2017 13:14:17: #2.2 Generate R script for model : SRX2576635.20_model.r WARNING @ Mon, 13 Nov 2017 13:14:17: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 13 Nov 2017 13:14:17: #2 You may need to consider one of the other alternative d(s): 4,48 WARNING @ Mon, 13 Nov 2017 13:14:17: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 13 Nov 2017 13:14:17: #3 Call peaks... INFO @ Mon, 13 Nov 2017 13:14:17: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 13 Nov 2017 13:14:24: #3 Call peaks for each chromosome... INFO @ Mon, 13 Nov 2017 13:14:25: #3 Call peaks for each chromosome... INFO @ Mon, 13 Nov 2017 13:14:26: #3 Call peaks for each chromosome... INFO @ Mon, 13 Nov 2017 13:14:28: #4 Write output xls file... SRX2576635.10_peaks.xls INFO @ Mon, 13 Nov 2017 13:14:28: #4 Write peak in narrowPeak format file... SRX2576635.10_peaks.narrowPeak INFO @ Mon, 13 Nov 2017 13:14:28: #4 Write summits bed file... SRX2576635.10_summits.bed INFO @ Mon, 13 Nov 2017 13:14:28: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (364 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 13 Nov 2017 13:14:29: #4 Write output xls file... SRX2576635.05_peaks.xls INFO @ Mon, 13 Nov 2017 13:14:29: #4 Write peak in narrowPeak format file... SRX2576635.05_peaks.narrowPeak INFO @ Mon, 13 Nov 2017 13:14:29: #4 Write summits bed file... SRX2576635.05_summits.bed INFO @ Mon, 13 Nov 2017 13:14:29: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (690 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 13 Nov 2017 13:14:31: #4 Write output xls file... SRX2576635.20_peaks.xls INFO @ Mon, 13 Nov 2017 13:14:31: #4 Write peak in narrowPeak format file... SRX2576635.20_peaks.narrowPeak INFO @ Mon, 13 Nov 2017 13:14:31: #4 Write summits bed file... SRX2576635.20_summits.bed INFO @ Mon, 13 Nov 2017 13:14:31: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (153 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。