Job ID = 9157409 sra ファイルのダウンロード中... Completed: 536891K bytes transferred in 7 seconds (556139K 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 15778723 spots for /home/okishinya/chipatlas/results/ce10/SRX208775/SRR628909.sra Written 15778723 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: 00:05:38 15778723 reads; of these: 15778723 (100.00%) were unpaired; of these: 2775003 (17.59%) aligned 0 times 11026620 (69.88%) aligned exactly 1 time 1977100 (12.53%) aligned >1 times 82.41% overall alignment rate Time searching: 00:05:38 Overall time: 00:05:38 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] 7098092 / 13003720 = 0.5459 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 11:55:24: # Command line: callpeak -t SRX208775.bam -f BAM -g ce -n SRX208775.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX208775.10 # format = BAM # ChIP-seq file = ['SRX208775.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 11:55:24: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:55:24: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:55:24: # Command line: callpeak -t SRX208775.bam -f BAM -g ce -n SRX208775.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX208775.05 # format = BAM # ChIP-seq file = ['SRX208775.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 11:55:24: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:55:24: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:55:24: # Command line: callpeak -t SRX208775.bam -f BAM -g ce -n SRX208775.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX208775.20 # format = BAM # ChIP-seq file = ['SRX208775.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 11:55:24: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:55:24: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:55:31: 1000000 INFO @ Tue, 27 Jun 2017 11:55:31: 1000000 INFO @ Tue, 27 Jun 2017 11:55:31: 1000000 INFO @ Tue, 27 Jun 2017 11:55:38: 2000000 INFO @ Tue, 27 Jun 2017 11:55:38: 2000000 INFO @ Tue, 27 Jun 2017 11:55:38: 2000000 INFO @ Tue, 27 Jun 2017 11:55:44: 3000000 INFO @ Tue, 27 Jun 2017 11:55:45: 3000000 INFO @ Tue, 27 Jun 2017 11:55:46: 3000000 INFO @ Tue, 27 Jun 2017 11:55:51: 4000000 INFO @ Tue, 27 Jun 2017 11:55:52: 4000000 INFO @ Tue, 27 Jun 2017 11:55:53: 4000000 INFO @ Tue, 27 Jun 2017 11:55:58: 5000000 INFO @ Tue, 27 Jun 2017 11:55:59: 5000000 INFO @ Tue, 27 Jun 2017 11:56:00: 5000000 INFO @ Tue, 27 Jun 2017 11:56:04: #1 tag size is determined as 50 bps INFO @ Tue, 27 Jun 2017 11:56:04: #1 tag size = 50 INFO @ Tue, 27 Jun 2017 11:56:04: #1 total tags in treatment: 5905628 INFO @ Tue, 27 Jun 2017 11:56:04: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:56:04: #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 11:56:04: #1 tags after filtering in treatment: 5905628 INFO @ Tue, 27 Jun 2017 11:56:04: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:56:04: #1 finished! INFO @ Tue, 27 Jun 2017 11:56:04: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:56:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:56:04: #2 number of paired peaks: 435 WARNING @ Tue, 27 Jun 2017 11:56:04: Fewer paired peaks (435) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 435 pairs to build model! INFO @ Tue, 27 Jun 2017 11:56:04: start model_add_line... INFO @ Tue, 27 Jun 2017 11:56:04: start X-correlation... INFO @ Tue, 27 Jun 2017 11:56:04: end of X-cor INFO @ Tue, 27 Jun 2017 11:56:04: #2 finished! INFO @ Tue, 27 Jun 2017 11:56:04: #2 predicted fragment length is 232 bps INFO @ Tue, 27 Jun 2017 11:56:04: #2 alternative fragment length(s) may be 232 bps INFO @ Tue, 27 Jun 2017 11:56:04: #2.2 Generate R script for model : SRX208775.20_model.r INFO @ Tue, 27 Jun 2017 11:56:04: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:56:04: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:56:05: #1 tag size is determined as 50 bps INFO @ Tue, 27 Jun 2017 11:56:05: #1 tag size = 50 INFO @ Tue, 27 Jun 2017 11:56:05: #1 total tags in treatment: 5905628 INFO @ Tue, 27 Jun 2017 11:56:05: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:56:05: #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 11:56:05: #1 tags after filtering in treatment: 5905628 INFO @ Tue, 27 Jun 2017 11:56:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:56:05: #1 finished! INFO @ Tue, 27 Jun 2017 11:56:05: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:56:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:56:06: #2 number of paired peaks: 435 WARNING @ Tue, 27 Jun 2017 11:56:06: Fewer paired peaks (435) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 435 pairs to build model! INFO @ Tue, 27 Jun 2017 11:56:06: start model_add_line... INFO @ Tue, 27 Jun 2017 11:56:06: start X-correlation... INFO @ Tue, 27 Jun 2017 11:56:06: end of X-cor INFO @ Tue, 27 Jun 2017 11:56:06: #2 finished! INFO @ Tue, 27 Jun 2017 11:56:06: #2 predicted fragment length is 232 bps INFO @ Tue, 27 Jun 2017 11:56:06: #2 alternative fragment length(s) may be 232 bps INFO @ Tue, 27 Jun 2017 11:56:06: #2.2 Generate R script for model : SRX208775.10_model.r INFO @ Tue, 27 Jun 2017 11:56:06: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:56:06: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:56:06: #1 tag size is determined as 50 bps INFO @ Tue, 27 Jun 2017 11:56:06: #1 tag size = 50 INFO @ Tue, 27 Jun 2017 11:56:06: #1 total tags in treatment: 5905628 INFO @ Tue, 27 Jun 2017 11:56:06: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:56:06: #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 11:56:07: #1 tags after filtering in treatment: 5905628 INFO @ Tue, 27 Jun 2017 11:56:07: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:56:07: #1 finished! INFO @ Tue, 27 Jun 2017 11:56:07: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:56:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:56:07: #2 number of paired peaks: 435 WARNING @ Tue, 27 Jun 2017 11:56:07: Fewer paired peaks (435) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 435 pairs to build model! INFO @ Tue, 27 Jun 2017 11:56:07: start model_add_line... INFO @ Tue, 27 Jun 2017 11:56:07: start X-correlation... INFO @ Tue, 27 Jun 2017 11:56:07: end of X-cor INFO @ Tue, 27 Jun 2017 11:56:07: #2 finished! INFO @ Tue, 27 Jun 2017 11:56:07: #2 predicted fragment length is 232 bps INFO @ Tue, 27 Jun 2017 11:56:07: #2 alternative fragment length(s) may be 232 bps INFO @ Tue, 27 Jun 2017 11:56:07: #2.2 Generate R script for model : SRX208775.05_model.r INFO @ Tue, 27 Jun 2017 11:56:07: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:56:07: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:56:19: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:56:21: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:56:21: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:56:27: #4 Write output xls file... SRX208775.20_peaks.xls INFO @ Tue, 27 Jun 2017 11:56:27: #4 Write peak in narrowPeak format file... SRX208775.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:56:27: #4 Write summits bed file... SRX208775.20_summits.bed INFO @ Tue, 27 Jun 2017 11:56:27: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (471 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 11:56:29: #4 Write output xls file... SRX208775.05_peaks.xls INFO @ Tue, 27 Jun 2017 11:56:29: #4 Write peak in narrowPeak format file... SRX208775.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:56:29: #4 Write summits bed file... SRX208775.05_summits.bed INFO @ Tue, 27 Jun 2017 11:56:29: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1321 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 11:56:30: #4 Write output xls file... SRX208775.10_peaks.xls INFO @ Tue, 27 Jun 2017 11:56:30: #4 Write peak in narrowPeak format file... SRX208775.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:56:30: #4 Write summits bed file... SRX208775.10_summits.bed INFO @ Tue, 27 Jun 2017 11:56:30: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (814 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。