Job ID = 9370021 sra ファイルのダウンロード中... Completed: 1180266K bytes transferred in 86 seconds (111639K 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 34013526 spots for /home/okishinya/chipatlas/results/ce10/SRX2710282/SRR5418736.sra Written 34013526 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: 00:12:45 34013526 reads; of these: 34013526 (100.00%) were unpaired; of these: 20496198 (60.26%) aligned 0 times 9372744 (27.56%) aligned exactly 1 time 4144584 (12.19%) aligned >1 times 39.74% overall alignment rate Time searching: 00:12:45 Overall time: 00:12:45 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] 9074637 / 13517328 = 0.6713 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 @ Fri, 04 Aug 2017 12:14:10: # Command line: callpeak -t SRX2710282.bam -f BAM -g ce -n SRX2710282.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2710282.10 # format = BAM # ChIP-seq file = ['SRX2710282.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 @ Fri, 04 Aug 2017 12:14:10: # Command line: callpeak -t SRX2710282.bam -f BAM -g ce -n SRX2710282.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2710282.05 # format = BAM # ChIP-seq file = ['SRX2710282.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 @ Fri, 04 Aug 2017 12:14:10: #1 read tag files... INFO @ Fri, 04 Aug 2017 12:14:10: #1 read tag files... INFO @ Fri, 04 Aug 2017 12:14:10: #1 read treatment tags... INFO @ Fri, 04 Aug 2017 12:14:10: #1 read treatment tags... INFO @ Fri, 04 Aug 2017 12:14:10: # Command line: callpeak -t SRX2710282.bam -f BAM -g ce -n SRX2710282.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2710282.20 # format = BAM # ChIP-seq file = ['SRX2710282.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 @ Fri, 04 Aug 2017 12:14:10: #1 read tag files... INFO @ Fri, 04 Aug 2017 12:14:10: #1 read treatment tags... INFO @ Fri, 04 Aug 2017 12:14:27: 1000000 INFO @ Fri, 04 Aug 2017 12:14:28: 1000000 INFO @ Fri, 04 Aug 2017 12:14:29: 1000000 INFO @ Fri, 04 Aug 2017 12:14:45: 2000000 INFO @ Fri, 04 Aug 2017 12:14:47: 2000000 INFO @ Fri, 04 Aug 2017 12:14:50: 2000000 INFO @ Fri, 04 Aug 2017 12:15:03: 3000000 INFO @ Fri, 04 Aug 2017 12:15:08: 3000000 INFO @ Fri, 04 Aug 2017 12:15:14: 3000000 INFO @ Fri, 04 Aug 2017 12:15:23: 4000000 INFO @ Fri, 04 Aug 2017 12:15:29: #1 tag size is determined as 50 bps INFO @ Fri, 04 Aug 2017 12:15:29: #1 tag size = 50 INFO @ Fri, 04 Aug 2017 12:15:29: #1 total tags in treatment: 4442691 INFO @ Fri, 04 Aug 2017 12:15:29: #1 user defined the maximum tags... INFO @ Fri, 04 Aug 2017 12:15:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 Aug 2017 12:15:29: #1 tags after filtering in treatment: 4442691 INFO @ Fri, 04 Aug 2017 12:15:29: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 Aug 2017 12:15:29: #1 finished! INFO @ Fri, 04 Aug 2017 12:15:29: #2 Build Peak Model... INFO @ Fri, 04 Aug 2017 12:15:29: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 Aug 2017 12:15:30: #2 number of paired peaks: 4017 INFO @ Fri, 04 Aug 2017 12:15:30: start model_add_line... INFO @ Fri, 04 Aug 2017 12:15:31: start X-correlation... INFO @ Fri, 04 Aug 2017 12:15:31: end of X-cor INFO @ Fri, 04 Aug 2017 12:15:31: #2 finished! INFO @ Fri, 04 Aug 2017 12:15:31: #2 predicted fragment length is 175 bps INFO @ Fri, 04 Aug 2017 12:15:31: #2 alternative fragment length(s) may be 175 bps INFO @ Fri, 04 Aug 2017 12:15:31: #2.2 Generate R script for model : SRX2710282.05_model.r INFO @ Fri, 04 Aug 2017 12:15:31: #3 Call peaks... INFO @ Fri, 04 Aug 2017 12:15:31: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 Aug 2017 12:15:31: 4000000 INFO @ Fri, 04 Aug 2017 12:15:35: 4000000 INFO @ Fri, 04 Aug 2017 12:15:39: #1 tag size is determined as 50 bps INFO @ Fri, 04 Aug 2017 12:15:39: #1 tag size = 50 INFO @ Fri, 04 Aug 2017 12:15:39: #1 total tags in treatment: 4442691 INFO @ Fri, 04 Aug 2017 12:15:39: #1 user defined the maximum tags... INFO @ Fri, 04 Aug 2017 12:15:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 Aug 2017 12:15:39: #1 tags after filtering in treatment: 4442691 INFO @ Fri, 04 Aug 2017 12:15:39: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 Aug 2017 12:15:39: #1 finished! INFO @ Fri, 04 Aug 2017 12:15:39: #2 Build Peak Model... INFO @ Fri, 04 Aug 2017 12:15:39: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 Aug 2017 12:15:40: #2 number of paired peaks: 4017 INFO @ Fri, 04 Aug 2017 12:15:40: start model_add_line... INFO @ Fri, 04 Aug 2017 12:15:40: start X-correlation... INFO @ Fri, 04 Aug 2017 12:15:40: end of X-cor INFO @ Fri, 04 Aug 2017 12:15:40: #2 finished! INFO @ Fri, 04 Aug 2017 12:15:40: #2 predicted fragment length is 175 bps INFO @ Fri, 04 Aug 2017 12:15:40: #2 alternative fragment length(s) may be 175 bps INFO @ Fri, 04 Aug 2017 12:15:40: #2.2 Generate R script for model : SRX2710282.10_model.r INFO @ Fri, 04 Aug 2017 12:15:40: #3 Call peaks... INFO @ Fri, 04 Aug 2017 12:15:40: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 Aug 2017 12:15:43: #1 tag size is determined as 50 bps INFO @ Fri, 04 Aug 2017 12:15:43: #1 tag size = 50 INFO @ Fri, 04 Aug 2017 12:15:43: #1 total tags in treatment: 4442691 INFO @ Fri, 04 Aug 2017 12:15:43: #1 user defined the maximum tags... INFO @ Fri, 04 Aug 2017 12:15:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 Aug 2017 12:15:43: #1 tags after filtering in treatment: 4442691 INFO @ Fri, 04 Aug 2017 12:15:43: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 Aug 2017 12:15:43: #1 finished! INFO @ Fri, 04 Aug 2017 12:15:43: #2 Build Peak Model... INFO @ Fri, 04 Aug 2017 12:15:43: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 Aug 2017 12:15:44: #2 number of paired peaks: 4017 INFO @ Fri, 04 Aug 2017 12:15:44: start model_add_line... INFO @ Fri, 04 Aug 2017 12:15:45: start X-correlation... INFO @ Fri, 04 Aug 2017 12:15:45: end of X-cor INFO @ Fri, 04 Aug 2017 12:15:45: #2 finished! INFO @ Fri, 04 Aug 2017 12:15:45: #2 predicted fragment length is 175 bps INFO @ Fri, 04 Aug 2017 12:15:45: #2 alternative fragment length(s) may be 175 bps INFO @ Fri, 04 Aug 2017 12:15:45: #2.2 Generate R script for model : SRX2710282.20_model.r INFO @ Fri, 04 Aug 2017 12:15:45: #3 Call peaks... INFO @ Fri, 04 Aug 2017 12:15:45: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 Aug 2017 12:15:58: #3 Call peaks for each chromosome... INFO @ Fri, 04 Aug 2017 12:16:07: #3 Call peaks for each chromosome... INFO @ Fri, 04 Aug 2017 12:16:14: #4 Write output xls file... SRX2710282.05_peaks.xls INFO @ Fri, 04 Aug 2017 12:16:14: #4 Write peak in narrowPeak format file... SRX2710282.05_peaks.narrowPeak INFO @ Fri, 04 Aug 2017 12:16:14: #4 Write summits bed file... SRX2710282.05_summits.bed INFO @ Fri, 04 Aug 2017 12:16:14: Done! pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (6208 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Fri, 04 Aug 2017 12:16:16: #3 Call peaks for each chromosome... INFO @ Fri, 04 Aug 2017 12:16:19: #4 Write output xls file... SRX2710282.10_peaks.xls INFO @ Fri, 04 Aug 2017 12:16:19: #4 Write peak in narrowPeak format file... SRX2710282.10_peaks.narrowPeak INFO @ Fri, 04 Aug 2017 12:16:19: #4 Write summits bed file... SRX2710282.10_summits.bed INFO @ Fri, 04 Aug 2017 12:16:19: Done! pass1 - making usageList (7 chroms): 4 millis pass2 - checking and writing primary data (5148 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Fri, 04 Aug 2017 12:16:33: #4 Write output xls file... SRX2710282.20_peaks.xls INFO @ Fri, 04 Aug 2017 12:16:33: #4 Write peak in narrowPeak format file... SRX2710282.20_peaks.narrowPeak INFO @ Fri, 04 Aug 2017 12:16:33: #4 Write summits bed file... SRX2710282.20_summits.bed INFO @ Fri, 04 Aug 2017 12:16:33: Done! pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (4257 records, 4 fields): 11 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。