Job ID = 9157128 sra ファイルのダウンロード中... Completed: 262494K bytes transferred in 5 seconds (408173K 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 14827846 spots for /home/okishinya/chipatlas/results/ce10/SRX2228867/SRR4380323.sra Written 14827846 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:01:25 14827846 reads; of these: 14827846 (100.00%) were unpaired; of these: 9474630 (63.90%) aligned 0 times 4668017 (31.48%) aligned exactly 1 time 685199 (4.62%) aligned >1 times 36.10% overall alignment rate Time searching: 00:01:26 Overall time: 00:01:26 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] 620729 / 5353216 = 0.1160 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 10:39:19: # Command line: callpeak -t SRX2228867.bam -f BAM -g ce -n SRX2228867.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2228867.10 # format = BAM # ChIP-seq file = ['SRX2228867.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 10:39:19: #1 read tag files... INFO @ Tue, 27 Jun 2017 10:39:19: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 10:39:19: # Command line: callpeak -t SRX2228867.bam -f BAM -g ce -n SRX2228867.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2228867.05 # format = BAM # ChIP-seq file = ['SRX2228867.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 10:39:19: #1 read tag files... INFO @ Tue, 27 Jun 2017 10:39:19: # Command line: callpeak -t SRX2228867.bam -f BAM -g ce -n SRX2228867.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2228867.20 # format = BAM # ChIP-seq file = ['SRX2228867.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 10:39:19: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 10:39:19: #1 read tag files... INFO @ Tue, 27 Jun 2017 10:39:19: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 10:39:25: 1000000 INFO @ Tue, 27 Jun 2017 10:39:26: 1000000 INFO @ Tue, 27 Jun 2017 10:39:26: 1000000 INFO @ Tue, 27 Jun 2017 10:39:31: 2000000 INFO @ Tue, 27 Jun 2017 10:39:34: 2000000 INFO @ Tue, 27 Jun 2017 10:39:34: 2000000 INFO @ Tue, 27 Jun 2017 10:39:37: 3000000 INFO @ Tue, 27 Jun 2017 10:39:41: 3000000 INFO @ Tue, 27 Jun 2017 10:39:41: 3000000 INFO @ Tue, 27 Jun 2017 10:39:43: 4000000 INFO @ Tue, 27 Jun 2017 10:39:47: #1 tag size is determined as 35 bps INFO @ Tue, 27 Jun 2017 10:39:47: #1 tag size = 35 INFO @ Tue, 27 Jun 2017 10:39:47: #1 total tags in treatment: 4732487 INFO @ Tue, 27 Jun 2017 10:39:47: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 10:39:47: #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 10:39:47: #1 tags after filtering in treatment: 4732487 INFO @ Tue, 27 Jun 2017 10:39:47: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 10:39:47: #1 finished! INFO @ Tue, 27 Jun 2017 10:39:47: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 10:39:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 10:39:48: #2 number of paired peaks: 2919 INFO @ Tue, 27 Jun 2017 10:39:48: start model_add_line... INFO @ Tue, 27 Jun 2017 10:39:48: start X-correlation... INFO @ Tue, 27 Jun 2017 10:39:48: end of X-cor INFO @ Tue, 27 Jun 2017 10:39:48: #2 finished! INFO @ Tue, 27 Jun 2017 10:39:48: #2 predicted fragment length is 242 bps INFO @ Tue, 27 Jun 2017 10:39:48: #2 alternative fragment length(s) may be 242 bps INFO @ Tue, 27 Jun 2017 10:39:48: #2.2 Generate R script for model : SRX2228867.10_model.r INFO @ Tue, 27 Jun 2017 10:39:48: #3 Call peaks... INFO @ Tue, 27 Jun 2017 10:39:48: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 10:39:49: 4000000 INFO @ Tue, 27 Jun 2017 10:39:49: 4000000 INFO @ Tue, 27 Jun 2017 10:39:54: #1 tag size is determined as 35 bps INFO @ Tue, 27 Jun 2017 10:39:54: #1 tag size is determined as 35 bps INFO @ Tue, 27 Jun 2017 10:39:54: #1 tag size = 35 INFO @ Tue, 27 Jun 2017 10:39:54: #1 tag size = 35 INFO @ Tue, 27 Jun 2017 10:39:54: #1 total tags in treatment: 4732487 INFO @ Tue, 27 Jun 2017 10:39:54: #1 total tags in treatment: 4732487 INFO @ Tue, 27 Jun 2017 10:39:54: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 10:39:54: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 10:39:54: #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 10:39:54: #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 10:39:54: #1 tags after filtering in treatment: 4732487 INFO @ Tue, 27 Jun 2017 10:39:54: #1 tags after filtering in treatment: 4732487 INFO @ Tue, 27 Jun 2017 10:39:54: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 10:39:54: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 10:39:54: #1 finished! INFO @ Tue, 27 Jun 2017 10:39:54: #1 finished! INFO @ Tue, 27 Jun 2017 10:39:54: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 10:39:54: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 10:39:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 10:39:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 10:39:55: #2 number of paired peaks: 2919 INFO @ Tue, 27 Jun 2017 10:39:55: start model_add_line... INFO @ Tue, 27 Jun 2017 10:39:55: #2 number of paired peaks: 2919 INFO @ Tue, 27 Jun 2017 10:39:55: start model_add_line... INFO @ Tue, 27 Jun 2017 10:39:55: start X-correlation... INFO @ Tue, 27 Jun 2017 10:39:55: end of X-cor INFO @ Tue, 27 Jun 2017 10:39:55: #2 finished! INFO @ Tue, 27 Jun 2017 10:39:55: start X-correlation... INFO @ Tue, 27 Jun 2017 10:39:55: #2 predicted fragment length is 242 bps INFO @ Tue, 27 Jun 2017 10:39:55: #2 alternative fragment length(s) may be 242 bps INFO @ Tue, 27 Jun 2017 10:39:55: #2.2 Generate R script for model : SRX2228867.20_model.r INFO @ Tue, 27 Jun 2017 10:39:55: end of X-cor INFO @ Tue, 27 Jun 2017 10:39:55: #2 finished! INFO @ Tue, 27 Jun 2017 10:39:55: #2 predicted fragment length is 242 bps INFO @ Tue, 27 Jun 2017 10:39:55: #2 alternative fragment length(s) may be 242 bps INFO @ Tue, 27 Jun 2017 10:39:55: #2.2 Generate R script for model : SRX2228867.05_model.r INFO @ Tue, 27 Jun 2017 10:39:55: #3 Call peaks... INFO @ Tue, 27 Jun 2017 10:39:55: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 10:39:55: #3 Call peaks... INFO @ Tue, 27 Jun 2017 10:39:55: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 10:40:02: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 10:40:09: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 10:40:09: #4 Write output xls file... SRX2228867.10_peaks.xls INFO @ Tue, 27 Jun 2017 10:40:09: #4 Write peak in narrowPeak format file... SRX2228867.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 10:40:09: #4 Write summits bed file... SRX2228867.10_summits.bed INFO @ Tue, 27 Jun 2017 10:40:09: Done! INFO @ Tue, 27 Jun 2017 10:40:09: #3 Call peaks for each chromosome... pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3086 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 10:40:16: #4 Write output xls file... SRX2228867.05_peaks.xls INFO @ Tue, 27 Jun 2017 10:40:16: #4 Write peak in narrowPeak format file... SRX2228867.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 10:40:16: #4 Write output xls file... SRX2228867.20_peaks.xls INFO @ Tue, 27 Jun 2017 10:40:16: #4 Write peak in narrowPeak format file... SRX2228867.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 10:40:16: #4 Write summits bed file... SRX2228867.05_summits.bed INFO @ Tue, 27 Jun 2017 10:40:16: #4 Write summits bed file... SRX2228867.20_summits.bed INFO @ Tue, 27 Jun 2017 10:40:16: Done! INFO @ Tue, 27 Jun 2017 10:40:16: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2120 records, 4 fields): 4 millis pass1 - making usageList (7 chroms): 1 millis CompletedMACS2peakCalling pass2 - checking and writing primary data (3890 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。