Job ID = 10201984 sra ファイルのダウンロード中... Completed: 425342K bytes transferred in 13 seconds (249524K bits/sec), in 1 file. 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 16703865 spots for /home/okishinya/chipatlas/results/ce10/SRX2576653/SRR5272610.sra Written 16703865 spots total rm: cannot remove `[DSE]RX*': そのようなファイルやディレクトリはありません 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: 00:08:00 16703865 reads; of these: 16703865 (100.00%) were unpaired; of these: 2312555 (13.84%) aligned 0 times 12117817 (72.54%) aligned exactly 1 time 2273493 (13.61%) aligned >1 times 86.16% overall alignment rate Time searching: 00:08:00 Overall time: 00:08:00 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] 4130086 / 14391310 = 0.2870 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 @ Mon, 13 Nov 2017 13:22:38: # Command line: callpeak -t SRX2576653.bam -f BAM -g ce -n SRX2576653.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2576653.10 # format = BAM # ChIP-seq file = ['SRX2576653.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 @ Mon, 13 Nov 2017 13:22:38: #1 read tag files... INFO @ Mon, 13 Nov 2017 13:22:38: #1 read treatment tags... INFO @ Mon, 13 Nov 2017 13:22:38: # Command line: callpeak -t SRX2576653.bam -f BAM -g ce -n SRX2576653.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2576653.20 # format = BAM # ChIP-seq file = ['SRX2576653.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 @ Mon, 13 Nov 2017 13:22:38: #1 read tag files... INFO @ Mon, 13 Nov 2017 13:22:38: #1 read treatment tags... INFO @ Mon, 13 Nov 2017 13:22:38: # Command line: callpeak -t SRX2576653.bam -f BAM -g ce -n SRX2576653.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2576653.05 # format = BAM # ChIP-seq file = ['SRX2576653.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 @ Mon, 13 Nov 2017 13:22:38: #1 read tag files... INFO @ Mon, 13 Nov 2017 13:22:38: #1 read treatment tags... INFO @ Mon, 13 Nov 2017 13:22:56: 1000000 INFO @ Mon, 13 Nov 2017 13:22:56: 1000000 INFO @ Mon, 13 Nov 2017 13:22:58: 1000000 INFO @ Mon, 13 Nov 2017 13:23:14: 2000000 INFO @ Mon, 13 Nov 2017 13:23:15: 2000000 INFO @ Mon, 13 Nov 2017 13:23:17: 2000000 INFO @ Mon, 13 Nov 2017 13:23:32: 3000000 INFO @ Mon, 13 Nov 2017 13:23:36: 3000000 INFO @ Mon, 13 Nov 2017 13:23:36: 3000000 INFO @ Mon, 13 Nov 2017 13:23:48: 4000000 INFO @ Mon, 13 Nov 2017 13:23:54: 4000000 INFO @ Mon, 13 Nov 2017 13:23:55: 4000000 INFO @ Mon, 13 Nov 2017 13:24:06: 5000000 INFO @ Mon, 13 Nov 2017 13:24:13: 5000000 INFO @ Mon, 13 Nov 2017 13:24:14: 5000000 INFO @ Mon, 13 Nov 2017 13:24:23: 6000000 INFO @ Mon, 13 Nov 2017 13:24:33: 6000000 INFO @ Mon, 13 Nov 2017 13:24:33: 6000000 INFO @ Mon, 13 Nov 2017 13:24:40: 7000000 INFO @ Mon, 13 Nov 2017 13:24:51: 7000000 INFO @ Mon, 13 Nov 2017 13:24:52: 7000000 INFO @ Mon, 13 Nov 2017 13:24:57: 8000000 INFO @ Mon, 13 Nov 2017 13:25:10: 9000000 INFO @ Mon, 13 Nov 2017 13:25:10: 8000000 INFO @ Mon, 13 Nov 2017 13:25:13: 8000000 INFO @ Mon, 13 Nov 2017 13:25:24: 10000000 INFO @ Mon, 13 Nov 2017 13:25:27: #1 tag size is determined as 36 bps INFO @ Mon, 13 Nov 2017 13:25:27: #1 tag size = 36 INFO @ Mon, 13 Nov 2017 13:25:27: #1 total tags in treatment: 10261224 INFO @ Mon, 13 Nov 2017 13:25:27: #1 user defined the maximum tags... INFO @ Mon, 13 Nov 2017 13:25:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 13 Nov 2017 13:25:27: #1 tags after filtering in treatment: 10261224 INFO @ Mon, 13 Nov 2017 13:25:27: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 13 Nov 2017 13:25:27: #1 finished! INFO @ Mon, 13 Nov 2017 13:25:27: #2 Build Peak Model... INFO @ Mon, 13 Nov 2017 13:25:27: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 13 Nov 2017 13:25:28: #2 number of paired peaks: 1028 INFO @ Mon, 13 Nov 2017 13:25:28: start model_add_line... INFO @ Mon, 13 Nov 2017 13:25:28: start X-correlation... INFO @ Mon, 13 Nov 2017 13:25:28: end of X-cor INFO @ Mon, 13 Nov 2017 13:25:28: #2 finished! INFO @ Mon, 13 Nov 2017 13:25:28: #2 predicted fragment length is 116 bps INFO @ Mon, 13 Nov 2017 13:25:28: #2 alternative fragment length(s) may be 116 bps INFO @ Mon, 13 Nov 2017 13:25:28: #2.2 Generate R script for model : SRX2576653.20_model.r INFO @ Mon, 13 Nov 2017 13:25:28: #3 Call peaks... INFO @ Mon, 13 Nov 2017 13:25:28: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 13 Nov 2017 13:25:30: 9000000 INFO @ Mon, 13 Nov 2017 13:25:36: 9000000 INFO @ Mon, 13 Nov 2017 13:25:47: 10000000 INFO @ Mon, 13 Nov 2017 13:25:51: #1 tag size is determined as 36 bps INFO @ Mon, 13 Nov 2017 13:25:51: #1 tag size = 36 INFO @ Mon, 13 Nov 2017 13:25:51: #1 total tags in treatment: 10261224 INFO @ Mon, 13 Nov 2017 13:25:51: #1 user defined the maximum tags... INFO @ Mon, 13 Nov 2017 13:25:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 13 Nov 2017 13:25:52: #1 tags after filtering in treatment: 10261224 INFO @ Mon, 13 Nov 2017 13:25:52: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 13 Nov 2017 13:25:52: #1 finished! INFO @ Mon, 13 Nov 2017 13:25:52: #2 Build Peak Model... INFO @ Mon, 13 Nov 2017 13:25:52: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 13 Nov 2017 13:25:53: #2 number of paired peaks: 1028 INFO @ Mon, 13 Nov 2017 13:25:53: start model_add_line... INFO @ Mon, 13 Nov 2017 13:25:53: start X-correlation... INFO @ Mon, 13 Nov 2017 13:25:53: end of X-cor INFO @ Mon, 13 Nov 2017 13:25:53: #2 finished! INFO @ Mon, 13 Nov 2017 13:25:53: #2 predicted fragment length is 116 bps INFO @ Mon, 13 Nov 2017 13:25:53: #2 alternative fragment length(s) may be 116 bps INFO @ Mon, 13 Nov 2017 13:25:53: #2.2 Generate R script for model : SRX2576653.05_model.r INFO @ Mon, 13 Nov 2017 13:25:53: #3 Call peaks... INFO @ Mon, 13 Nov 2017 13:25:53: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 13 Nov 2017 13:25:56: 10000000 INFO @ Mon, 13 Nov 2017 13:26:01: #3 Call peaks for each chromosome... INFO @ Mon, 13 Nov 2017 13:26:02: #1 tag size is determined as 36 bps INFO @ Mon, 13 Nov 2017 13:26:02: #1 tag size = 36 INFO @ Mon, 13 Nov 2017 13:26:02: #1 total tags in treatment: 10261224 INFO @ Mon, 13 Nov 2017 13:26:02: #1 user defined the maximum tags... INFO @ Mon, 13 Nov 2017 13:26:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 13 Nov 2017 13:26:02: #1 tags after filtering in treatment: 10261224 INFO @ Mon, 13 Nov 2017 13:26:02: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 13 Nov 2017 13:26:02: #1 finished! INFO @ Mon, 13 Nov 2017 13:26:02: #2 Build Peak Model... INFO @ Mon, 13 Nov 2017 13:26:02: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 13 Nov 2017 13:26:03: #2 number of paired peaks: 1028 INFO @ Mon, 13 Nov 2017 13:26:03: start model_add_line... INFO @ Mon, 13 Nov 2017 13:26:03: start X-correlation... INFO @ Mon, 13 Nov 2017 13:26:03: end of X-cor INFO @ Mon, 13 Nov 2017 13:26:03: #2 finished! INFO @ Mon, 13 Nov 2017 13:26:03: #2 predicted fragment length is 116 bps INFO @ Mon, 13 Nov 2017 13:26:03: #2 alternative fragment length(s) may be 116 bps INFO @ Mon, 13 Nov 2017 13:26:03: #2.2 Generate R script for model : SRX2576653.10_model.r INFO @ Mon, 13 Nov 2017 13:26:03: #3 Call peaks... INFO @ Mon, 13 Nov 2017 13:26:03: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 13 Nov 2017 13:26:19: #4 Write output xls file... SRX2576653.20_peaks.xls INFO @ Mon, 13 Nov 2017 13:26:19: #4 Write peak in narrowPeak format file... SRX2576653.20_peaks.narrowPeak INFO @ Mon, 13 Nov 2017 13:26:19: #4 Write summits bed file... SRX2576653.20_summits.bed INFO @ Mon, 13 Nov 2017 13:26:19: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2168 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 13 Nov 2017 13:26:26: #3 Call peaks for each chromosome... INFO @ Mon, 13 Nov 2017 13:26:37: #3 Call peaks for each chromosome... INFO @ Mon, 13 Nov 2017 13:26:45: #4 Write output xls file... SRX2576653.05_peaks.xls INFO @ Mon, 13 Nov 2017 13:26:45: #4 Write peak in narrowPeak format file... SRX2576653.05_peaks.narrowPeak INFO @ Mon, 13 Nov 2017 13:26:45: #4 Write summits bed file... SRX2576653.05_summits.bed INFO @ Mon, 13 Nov 2017 13:26:45: Done! pass1 - making usageList (6 chroms): 3 millis pass2 - checking and writing primary data (4966 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Mon, 13 Nov 2017 13:26:56: #4 Write output xls file... SRX2576653.10_peaks.xls INFO @ Mon, 13 Nov 2017 13:26:56: #4 Write peak in narrowPeak format file... SRX2576653.10_peaks.narrowPeak INFO @ Mon, 13 Nov 2017 13:26:56: #4 Write summits bed file... SRX2576653.10_summits.bed INFO @ Mon, 13 Nov 2017 13:26:56: Done! pass1 - making usageList (6 chroms): 3 millis pass2 - checking and writing primary data (3361 records, 4 fields): 10 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。