Job ID = 9156879 sra ファイルのダウンロード中... Completed: 656085K bytes transferred in 6 seconds (773544K 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 23585231 spots for /home/okishinya/chipatlas/results/ce10/SRX2228848/SRR4380304.sra Written 23585231 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: 00:04:57 23585231 reads; of these: 23585231 (100.00%) were unpaired; of these: 2090619 (8.86%) aligned 0 times 18032873 (76.46%) aligned exactly 1 time 3461739 (14.68%) aligned >1 times 91.14% overall alignment rate Time searching: 00:04:57 Overall time: 00:04:57 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] 11682048 / 21494612 = 0.5435 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 10:29:38: # Command line: callpeak -t SRX2228848.bam -f BAM -g ce -n SRX2228848.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2228848.20 # format = BAM # ChIP-seq file = ['SRX2228848.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 10:29:38: #1 read tag files... INFO @ Tue, 27 Jun 2017 10:29:38: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 10:29:38: # Command line: callpeak -t SRX2228848.bam -f BAM -g ce -n SRX2228848.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2228848.10 # format = BAM # ChIP-seq file = ['SRX2228848.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 10:29:38: #1 read tag files... INFO @ Tue, 27 Jun 2017 10:29:38: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 10:29:38: # Command line: callpeak -t SRX2228848.bam -f BAM -g ce -n SRX2228848.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2228848.05 # format = BAM # ChIP-seq file = ['SRX2228848.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 10:29:38: #1 read tag files... INFO @ Tue, 27 Jun 2017 10:29:38: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 10:29:45: 1000000 INFO @ Tue, 27 Jun 2017 10:29:45: 1000000 INFO @ Tue, 27 Jun 2017 10:29:45: 1000000 INFO @ Tue, 27 Jun 2017 10:29:52: 2000000 INFO @ Tue, 27 Jun 2017 10:29:53: 2000000 INFO @ Tue, 27 Jun 2017 10:29:53: 2000000 INFO @ Tue, 27 Jun 2017 10:29:59: 3000000 INFO @ Tue, 27 Jun 2017 10:30:00: 3000000 INFO @ Tue, 27 Jun 2017 10:30:00: 3000000 INFO @ Tue, 27 Jun 2017 10:30:06: 4000000 INFO @ Tue, 27 Jun 2017 10:30:08: 4000000 INFO @ Tue, 27 Jun 2017 10:30:08: 4000000 INFO @ Tue, 27 Jun 2017 10:30:13: 5000000 INFO @ Tue, 27 Jun 2017 10:30:16: 5000000 INFO @ Tue, 27 Jun 2017 10:30:16: 5000000 INFO @ Tue, 27 Jun 2017 10:30:20: 6000000 INFO @ Tue, 27 Jun 2017 10:30:24: 6000000 INFO @ Tue, 27 Jun 2017 10:30:24: 6000000 INFO @ Tue, 27 Jun 2017 10:30:27: 7000000 INFO @ Tue, 27 Jun 2017 10:30:32: 7000000 INFO @ Tue, 27 Jun 2017 10:30:32: 7000000 INFO @ Tue, 27 Jun 2017 10:30:34: 8000000 INFO @ Tue, 27 Jun 2017 10:30:40: 8000000 INFO @ Tue, 27 Jun 2017 10:30:40: 8000000 INFO @ Tue, 27 Jun 2017 10:30:41: 9000000 INFO @ Tue, 27 Jun 2017 10:30:46: #1 tag size is determined as 42 bps INFO @ Tue, 27 Jun 2017 10:30:46: #1 tag size = 42 INFO @ Tue, 27 Jun 2017 10:30:46: #1 total tags in treatment: 9812564 INFO @ Tue, 27 Jun 2017 10:30:46: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 10:30:46: #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 10:30:46: #1 tags after filtering in treatment: 9812564 INFO @ Tue, 27 Jun 2017 10:30:46: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 10:30:46: #1 finished! INFO @ Tue, 27 Jun 2017 10:30:46: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 10:30:46: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 10:30:47: #2 number of paired peaks: 684 WARNING @ Tue, 27 Jun 2017 10:30:47: Fewer paired peaks (684) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 684 pairs to build model! INFO @ Tue, 27 Jun 2017 10:30:47: start model_add_line... INFO @ Tue, 27 Jun 2017 10:30:47: start X-correlation... INFO @ Tue, 27 Jun 2017 10:30:47: end of X-cor INFO @ Tue, 27 Jun 2017 10:30:47: #2 finished! INFO @ Tue, 27 Jun 2017 10:30:47: #2 predicted fragment length is 129 bps INFO @ Tue, 27 Jun 2017 10:30:47: #2 alternative fragment length(s) may be 4,129 bps INFO @ Tue, 27 Jun 2017 10:30:47: #2.2 Generate R script for model : SRX2228848.10_model.r INFO @ Tue, 27 Jun 2017 10:30:47: #3 Call peaks... INFO @ Tue, 27 Jun 2017 10:30:47: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 10:30:48: 9000000 INFO @ Tue, 27 Jun 2017 10:30:48: 9000000 INFO @ Tue, 27 Jun 2017 10:30:54: #1 tag size is determined as 42 bps INFO @ Tue, 27 Jun 2017 10:30:54: #1 tag size is determined as 42 bps INFO @ Tue, 27 Jun 2017 10:30:54: #1 tag size = 42 INFO @ Tue, 27 Jun 2017 10:30:54: #1 tag size = 42 INFO @ Tue, 27 Jun 2017 10:30:54: #1 total tags in treatment: 9812564 INFO @ Tue, 27 Jun 2017 10:30:54: #1 total tags in treatment: 9812564 INFO @ Tue, 27 Jun 2017 10:30:54: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 10:30:54: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 10:30:54: #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 10:30:54: #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 10:30:54: #1 tags after filtering in treatment: 9812564 INFO @ Tue, 27 Jun 2017 10:30:54: #1 tags after filtering in treatment: 9812564 INFO @ Tue, 27 Jun 2017 10:30:54: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 10:30:54: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 10:30:54: #1 finished! INFO @ Tue, 27 Jun 2017 10:30:54: #1 finished! INFO @ Tue, 27 Jun 2017 10:30:54: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 10:30:54: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 10:30:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 10:30:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 10:30:55: #2 number of paired peaks: 684 WARNING @ Tue, 27 Jun 2017 10:30:55: Fewer paired peaks (684) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 684 pairs to build model! INFO @ Tue, 27 Jun 2017 10:30:55: start model_add_line... INFO @ Tue, 27 Jun 2017 10:30:55: #2 number of paired peaks: 684 WARNING @ Tue, 27 Jun 2017 10:30:55: Fewer paired peaks (684) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 684 pairs to build model! INFO @ Tue, 27 Jun 2017 10:30:55: start model_add_line... INFO @ Tue, 27 Jun 2017 10:30:55: start X-correlation... INFO @ Tue, 27 Jun 2017 10:30:55: start X-correlation... INFO @ Tue, 27 Jun 2017 10:30:55: end of X-cor INFO @ Tue, 27 Jun 2017 10:30:55: #2 finished! INFO @ Tue, 27 Jun 2017 10:30:55: #2 predicted fragment length is 129 bps INFO @ Tue, 27 Jun 2017 10:30:55: #2 alternative fragment length(s) may be 4,129 bps INFO @ Tue, 27 Jun 2017 10:30:55: #2.2 Generate R script for model : SRX2228848.20_model.r INFO @ Tue, 27 Jun 2017 10:30:55: end of X-cor INFO @ Tue, 27 Jun 2017 10:30:55: #2 finished! INFO @ Tue, 27 Jun 2017 10:30:55: #2 predicted fragment length is 129 bps INFO @ Tue, 27 Jun 2017 10:30:55: #2 alternative fragment length(s) may be 4,129 bps INFO @ Tue, 27 Jun 2017 10:30:55: #2.2 Generate R script for model : SRX2228848.05_model.r INFO @ Tue, 27 Jun 2017 10:30:55: #3 Call peaks... INFO @ Tue, 27 Jun 2017 10:30:55: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 10:30:55: #3 Call peaks... INFO @ Tue, 27 Jun 2017 10:30:55: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 10:31:12: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 10:31:18: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 10:31:19: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 10:31:24: #4 Write output xls file... SRX2228848.10_peaks.xls INFO @ Tue, 27 Jun 2017 10:31:24: #4 Write peak in narrowPeak format file... SRX2228848.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 10:31:24: #4 Write summits bed file... SRX2228848.10_summits.bed INFO @ Tue, 27 Jun 2017 10:31:24: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1431 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 10:31:30: #4 Write output xls file... SRX2228848.05_peaks.xls INFO @ Tue, 27 Jun 2017 10:31:30: #4 Write peak in narrowPeak format file... SRX2228848.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 10:31:30: #4 Write summits bed file... SRX2228848.05_summits.bed INFO @ Tue, 27 Jun 2017 10:31:30: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2886 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 10:31:31: #4 Write output xls file... SRX2228848.20_peaks.xls INFO @ Tue, 27 Jun 2017 10:31:31: #4 Write peak in narrowPeak format file... SRX2228848.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 10:31:31: #4 Write summits bed file... SRX2228848.20_summits.bed INFO @ Tue, 27 Jun 2017 10:31:31: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (626 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。