Job ID = 9156952 sra ファイルのダウンロード中... Completed: 242718K bytes transferred in 5 seconds (347436K 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 8992104 spots for /home/okishinya/chipatlas/results/ce10/SRX2228852/SRR4380308.sra Written 8992104 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: 00:02:04 8992104 reads; of these: 8992104 (100.00%) were unpaired; of these: 573362 (6.38%) aligned 0 times 7117543 (79.15%) aligned exactly 1 time 1301199 (14.47%) aligned >1 times 93.62% overall alignment rate Time searching: 00:02:04 Overall time: 00:02:04 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] 948891 / 8418742 = 0.1127 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 10:31:18: # Command line: callpeak -t SRX2228852.bam -f BAM -g ce -n SRX2228852.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2228852.20 # format = BAM # ChIP-seq file = ['SRX2228852.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 10:31:18: #1 read tag files... INFO @ Tue, 27 Jun 2017 10:31:18: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 10:31:18: # Command line: callpeak -t SRX2228852.bam -f BAM -g ce -n SRX2228852.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2228852.05 # format = BAM # ChIP-seq file = ['SRX2228852.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 10:31:18: #1 read tag files... INFO @ Tue, 27 Jun 2017 10:31:18: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 10:31:18: # Command line: callpeak -t SRX2228852.bam -f BAM -g ce -n SRX2228852.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2228852.10 # format = BAM # ChIP-seq file = ['SRX2228852.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 10:31:18: #1 read tag files... INFO @ Tue, 27 Jun 2017 10:31:18: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 10:31:25: 1000000 INFO @ Tue, 27 Jun 2017 10:31:25: 1000000 INFO @ Tue, 27 Jun 2017 10:31:27: 1000000 INFO @ Tue, 27 Jun 2017 10:31:33: 2000000 INFO @ Tue, 27 Jun 2017 10:31:33: 2000000 INFO @ Tue, 27 Jun 2017 10:31:34: 2000000 INFO @ Tue, 27 Jun 2017 10:31:41: 3000000 INFO @ Tue, 27 Jun 2017 10:31:41: 3000000 INFO @ Tue, 27 Jun 2017 10:31:42: 3000000 INFO @ Tue, 27 Jun 2017 10:31:48: 4000000 INFO @ Tue, 27 Jun 2017 10:31:48: 4000000 INFO @ Tue, 27 Jun 2017 10:31:50: 4000000 INFO @ Tue, 27 Jun 2017 10:31:56: 5000000 INFO @ Tue, 27 Jun 2017 10:31:56: 5000000 INFO @ Tue, 27 Jun 2017 10:31:57: 5000000 INFO @ Tue, 27 Jun 2017 10:32:03: 6000000 INFO @ Tue, 27 Jun 2017 10:32:03: 6000000 INFO @ Tue, 27 Jun 2017 10:32:05: 6000000 INFO @ Tue, 27 Jun 2017 10:32:11: 7000000 INFO @ Tue, 27 Jun 2017 10:32:11: 7000000 INFO @ Tue, 27 Jun 2017 10:32:13: 7000000 INFO @ Tue, 27 Jun 2017 10:32:15: #1 tag size is determined as 35 bps INFO @ Tue, 27 Jun 2017 10:32:15: #1 tag size is determined as 35 bps INFO @ Tue, 27 Jun 2017 10:32:15: #1 tag size = 35 INFO @ Tue, 27 Jun 2017 10:32:15: #1 tag size = 35 INFO @ Tue, 27 Jun 2017 10:32:15: #1 total tags in treatment: 7469851 INFO @ Tue, 27 Jun 2017 10:32:15: #1 total tags in treatment: 7469851 INFO @ Tue, 27 Jun 2017 10:32:15: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 10:32:15: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 10:32:15: #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 10:32:15: #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 10:32:15: #1 tags after filtering in treatment: 7469851 INFO @ Tue, 27 Jun 2017 10:32:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 10:32:15: #1 tags after filtering in treatment: 7469851 INFO @ Tue, 27 Jun 2017 10:32:15: #1 finished! INFO @ Tue, 27 Jun 2017 10:32:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 10:32:15: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 10:32:15: #1 finished! INFO @ Tue, 27 Jun 2017 10:32:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 10:32:15: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 10:32:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 10:32:15: #2 number of paired peaks: 370 WARNING @ Tue, 27 Jun 2017 10:32:15: Fewer paired peaks (370) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 370 pairs to build model! INFO @ Tue, 27 Jun 2017 10:32:15: start model_add_line... INFO @ Tue, 27 Jun 2017 10:32:15: #2 number of paired peaks: 370 WARNING @ Tue, 27 Jun 2017 10:32:15: Fewer paired peaks (370) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 370 pairs to build model! INFO @ Tue, 27 Jun 2017 10:32:15: start model_add_line... INFO @ Tue, 27 Jun 2017 10:32:15: start X-correlation... INFO @ Tue, 27 Jun 2017 10:32:15: end of X-cor INFO @ Tue, 27 Jun 2017 10:32:15: #2 finished! INFO @ Tue, 27 Jun 2017 10:32:15: #2 predicted fragment length is 113 bps INFO @ Tue, 27 Jun 2017 10:32:15: #2 alternative fragment length(s) may be 113 bps INFO @ Tue, 27 Jun 2017 10:32:15: #2.2 Generate R script for model : SRX2228852.20_model.r INFO @ Tue, 27 Jun 2017 10:32:15: #3 Call peaks... INFO @ Tue, 27 Jun 2017 10:32:15: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 10:32:15: start X-correlation... INFO @ Tue, 27 Jun 2017 10:32:15: end of X-cor INFO @ Tue, 27 Jun 2017 10:32:15: #2 finished! INFO @ Tue, 27 Jun 2017 10:32:15: #2 predicted fragment length is 113 bps INFO @ Tue, 27 Jun 2017 10:32:15: #2 alternative fragment length(s) may be 113 bps INFO @ Tue, 27 Jun 2017 10:32:15: #2.2 Generate R script for model : SRX2228852.05_model.r INFO @ Tue, 27 Jun 2017 10:32:15: #3 Call peaks... INFO @ Tue, 27 Jun 2017 10:32:15: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 10:32:17: #1 tag size is determined as 35 bps INFO @ Tue, 27 Jun 2017 10:32:17: #1 tag size = 35 INFO @ Tue, 27 Jun 2017 10:32:17: #1 total tags in treatment: 7469851 INFO @ Tue, 27 Jun 2017 10:32:17: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 10:32:17: #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 10:32:17: #1 tags after filtering in treatment: 7469851 INFO @ Tue, 27 Jun 2017 10:32:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 10:32:17: #1 finished! INFO @ Tue, 27 Jun 2017 10:32:17: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 10:32:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 10:32:18: #2 number of paired peaks: 370 WARNING @ Tue, 27 Jun 2017 10:32:18: Fewer paired peaks (370) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 370 pairs to build model! INFO @ Tue, 27 Jun 2017 10:32:18: start model_add_line... INFO @ Tue, 27 Jun 2017 10:32:18: start X-correlation... INFO @ Tue, 27 Jun 2017 10:32:18: end of X-cor INFO @ Tue, 27 Jun 2017 10:32:18: #2 finished! INFO @ Tue, 27 Jun 2017 10:32:18: #2 predicted fragment length is 113 bps INFO @ Tue, 27 Jun 2017 10:32:18: #2 alternative fragment length(s) may be 113 bps INFO @ Tue, 27 Jun 2017 10:32:18: #2.2 Generate R script for model : SRX2228852.10_model.r INFO @ Tue, 27 Jun 2017 10:32:18: #3 Call peaks... INFO @ Tue, 27 Jun 2017 10:32:18: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 10:32:33: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 10:32:34: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 10:32:35: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 10:32:42: #4 Write output xls file... SRX2228852.05_peaks.xls INFO @ Tue, 27 Jun 2017 10:32:42: #4 Write peak in narrowPeak format file... SRX2228852.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 10:32:42: #4 Write summits bed file... SRX2228852.05_summits.bed INFO @ Tue, 27 Jun 2017 10:32:42: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (862 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 10:32:42: #4 Write output xls file... SRX2228852.20_peaks.xls INFO @ Tue, 27 Jun 2017 10:32:42: #4 Write peak in narrowPeak format file... SRX2228852.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 10:32:42: #4 Write summits bed file... SRX2228852.20_summits.bed INFO @ Tue, 27 Jun 2017 10:32:42: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (249 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 10:32:45: #4 Write output xls file... SRX2228852.10_peaks.xls INFO @ Tue, 27 Jun 2017 10:32:45: #4 Write peak in narrowPeak format file... SRX2228852.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 10:32:45: #4 Write summits bed file... SRX2228852.10_summits.bed INFO @ Tue, 27 Jun 2017 10:32:45: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (506 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。