Job ID = 10201981 sra ファイルのダウンロード中... Completed: 765172K bytes transferred in 20 seconds (307303K 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 22612410 spots for /home/okishinya/chipatlas/results/ce10/SRX2576650/SRR5272607.sra Written 22612410 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: 00:05:36 22612410 reads; of these: 22612410 (100.00%) were unpaired; of these: 2461730 (10.89%) aligned 0 times 16782396 (74.22%) aligned exactly 1 time 3368284 (14.90%) aligned >1 times 89.11% overall alignment rate Time searching: 00:05:36 Overall time: 00:05:36 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 12 files... [bam_rmdupse_core] 10338258 / 20150680 = 0.5130 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 13:19:42: # Command line: callpeak -t SRX2576650.bam -f BAM -g ce -n SRX2576650.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2576650.10 # format = BAM # ChIP-seq file = ['SRX2576650.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 13:19:42: # Command line: callpeak -t SRX2576650.bam -f BAM -g ce -n SRX2576650.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2576650.20 # format = BAM # ChIP-seq file = ['SRX2576650.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 13:19:42: # Command line: callpeak -t SRX2576650.bam -f BAM -g ce -n SRX2576650.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2576650.05 # format = BAM # ChIP-seq file = ['SRX2576650.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 13:19:42: #1 read tag files... INFO @ Mon, 13 Nov 2017 13:19:42: #1 read tag files... INFO @ Mon, 13 Nov 2017 13:19:42: #1 read tag files... INFO @ Mon, 13 Nov 2017 13:19:42: #1 read treatment tags... INFO @ Mon, 13 Nov 2017 13:19:42: #1 read treatment tags... INFO @ Mon, 13 Nov 2017 13:19:42: #1 read treatment tags... INFO @ Mon, 13 Nov 2017 13:19:49: 1000000 INFO @ Mon, 13 Nov 2017 13:19:50: 1000000 INFO @ Mon, 13 Nov 2017 13:19:50: 1000000 INFO @ Mon, 13 Nov 2017 13:19:57: 2000000 INFO @ Mon, 13 Nov 2017 13:19:57: 2000000 INFO @ Mon, 13 Nov 2017 13:19:57: 2000000 INFO @ Mon, 13 Nov 2017 13:20:04: 3000000 INFO @ Mon, 13 Nov 2017 13:20:04: 3000000 INFO @ Mon, 13 Nov 2017 13:20:04: 3000000 INFO @ Mon, 13 Nov 2017 13:20:11: 4000000 INFO @ Mon, 13 Nov 2017 13:20:12: 4000000 INFO @ Mon, 13 Nov 2017 13:20:12: 4000000 INFO @ Mon, 13 Nov 2017 13:20:18: 5000000 INFO @ Mon, 13 Nov 2017 13:20:19: 5000000 INFO @ Mon, 13 Nov 2017 13:20:19: 5000000 INFO @ Mon, 13 Nov 2017 13:20:25: 6000000 INFO @ Mon, 13 Nov 2017 13:20:26: 6000000 INFO @ Mon, 13 Nov 2017 13:20:26: 6000000 INFO @ Mon, 13 Nov 2017 13:20:32: 7000000 INFO @ Mon, 13 Nov 2017 13:20:34: 7000000 INFO @ Mon, 13 Nov 2017 13:20:34: 7000000 INFO @ Mon, 13 Nov 2017 13:20:39: 8000000 INFO @ Mon, 13 Nov 2017 13:20:41: 8000000 INFO @ Mon, 13 Nov 2017 13:20:41: 8000000 INFO @ Mon, 13 Nov 2017 13:20:46: 9000000 INFO @ Mon, 13 Nov 2017 13:20:48: 9000000 INFO @ Mon, 13 Nov 2017 13:20:49: 9000000 INFO @ Mon, 13 Nov 2017 13:20:52: #1 tag size is determined as 50 bps INFO @ Mon, 13 Nov 2017 13:20:52: #1 tag size = 50 INFO @ Mon, 13 Nov 2017 13:20:52: #1 total tags in treatment: 9812422 INFO @ Mon, 13 Nov 2017 13:20:52: #1 user defined the maximum tags... INFO @ Mon, 13 Nov 2017 13:20:52: #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 13:20:52: #1 tags after filtering in treatment: 9812422 INFO @ Mon, 13 Nov 2017 13:20:52: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 13 Nov 2017 13:20:52: #1 finished! INFO @ Mon, 13 Nov 2017 13:20:52: #2 Build Peak Model... INFO @ Mon, 13 Nov 2017 13:20:52: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 13 Nov 2017 13:20:53: #2 number of paired peaks: 1286 INFO @ Mon, 13 Nov 2017 13:20:53: start model_add_line... INFO @ Mon, 13 Nov 2017 13:20:53: start X-correlation... INFO @ Mon, 13 Nov 2017 13:20:53: end of X-cor INFO @ Mon, 13 Nov 2017 13:20:53: #2 finished! INFO @ Mon, 13 Nov 2017 13:20:53: #2 predicted fragment length is 174 bps INFO @ Mon, 13 Nov 2017 13:20:53: #2 alternative fragment length(s) may be 174 bps INFO @ Mon, 13 Nov 2017 13:20:53: #2.2 Generate R script for model : SRX2576650.10_model.r INFO @ Mon, 13 Nov 2017 13:20:53: #3 Call peaks... INFO @ Mon, 13 Nov 2017 13:20:53: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 13 Nov 2017 13:20:54: #1 tag size is determined as 50 bps INFO @ Mon, 13 Nov 2017 13:20:54: #1 tag size = 50 INFO @ Mon, 13 Nov 2017 13:20:54: #1 total tags in treatment: 9812422 INFO @ Mon, 13 Nov 2017 13:20:54: #1 user defined the maximum tags... INFO @ Mon, 13 Nov 2017 13:20:54: #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 13:20:54: #1 tags after filtering in treatment: 9812422 INFO @ Mon, 13 Nov 2017 13:20:54: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 13 Nov 2017 13:20:54: #1 finished! INFO @ Mon, 13 Nov 2017 13:20:54: #2 Build Peak Model... INFO @ Mon, 13 Nov 2017 13:20:54: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 13 Nov 2017 13:20:54: #1 tag size is determined as 50 bps INFO @ Mon, 13 Nov 2017 13:20:54: #1 tag size = 50 INFO @ Mon, 13 Nov 2017 13:20:54: #1 total tags in treatment: 9812422 INFO @ Mon, 13 Nov 2017 13:20:54: #1 user defined the maximum tags... INFO @ Mon, 13 Nov 2017 13:20:54: #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 13:20:55: #1 tags after filtering in treatment: 9812422 INFO @ Mon, 13 Nov 2017 13:20:55: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 13 Nov 2017 13:20:55: #1 finished! INFO @ Mon, 13 Nov 2017 13:20:55: #2 Build Peak Model... INFO @ Mon, 13 Nov 2017 13:20:55: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 13 Nov 2017 13:20:55: #2 number of paired peaks: 1286 INFO @ Mon, 13 Nov 2017 13:20:55: start model_add_line... INFO @ Mon, 13 Nov 2017 13:20:55: start X-correlation... INFO @ Mon, 13 Nov 2017 13:20:55: end of X-cor INFO @ Mon, 13 Nov 2017 13:20:55: #2 finished! INFO @ Mon, 13 Nov 2017 13:20:55: #2 predicted fragment length is 174 bps INFO @ Mon, 13 Nov 2017 13:20:55: #2 alternative fragment length(s) may be 174 bps INFO @ Mon, 13 Nov 2017 13:20:55: #2.2 Generate R script for model : SRX2576650.20_model.r INFO @ Mon, 13 Nov 2017 13:20:55: #3 Call peaks... INFO @ Mon, 13 Nov 2017 13:20:55: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 13 Nov 2017 13:20:55: #2 number of paired peaks: 1286 INFO @ Mon, 13 Nov 2017 13:20:55: start model_add_line... INFO @ Mon, 13 Nov 2017 13:20:56: start X-correlation... INFO @ Mon, 13 Nov 2017 13:20:56: end of X-cor INFO @ Mon, 13 Nov 2017 13:20:56: #2 finished! INFO @ Mon, 13 Nov 2017 13:20:56: #2 predicted fragment length is 174 bps INFO @ Mon, 13 Nov 2017 13:20:56: #2 alternative fragment length(s) may be 174 bps INFO @ Mon, 13 Nov 2017 13:20:56: #2.2 Generate R script for model : SRX2576650.05_model.r INFO @ Mon, 13 Nov 2017 13:20:56: #3 Call peaks... INFO @ Mon, 13 Nov 2017 13:20:56: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 13 Nov 2017 13:21:19: #3 Call peaks for each chromosome... INFO @ Mon, 13 Nov 2017 13:21:20: #3 Call peaks for each chromosome... INFO @ Mon, 13 Nov 2017 13:21:21: #3 Call peaks for each chromosome... INFO @ Mon, 13 Nov 2017 13:21:31: #4 Write output xls file... SRX2576650.10_peaks.xls INFO @ Mon, 13 Nov 2017 13:21:31: #4 Write peak in narrowPeak format file... SRX2576650.10_peaks.narrowPeak INFO @ Mon, 13 Nov 2017 13:21:31: #4 Write summits bed file... SRX2576650.10_summits.bed INFO @ Mon, 13 Nov 2017 13:21:31: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2816 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 13 Nov 2017 13:21:33: #4 Write output xls file... SRX2576650.20_peaks.xls INFO @ Mon, 13 Nov 2017 13:21:33: #4 Write peak in narrowPeak format file... SRX2576650.20_peaks.narrowPeak INFO @ Mon, 13 Nov 2017 13:21:33: #4 Write summits bed file... SRX2576650.20_summits.bed INFO @ Mon, 13 Nov 2017 13:21:33: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1993 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 13 Nov 2017 13:21:34: #4 Write output xls file... SRX2576650.05_peaks.xls INFO @ Mon, 13 Nov 2017 13:21:34: #4 Write peak in narrowPeak format file... SRX2576650.05_peaks.narrowPeak INFO @ Mon, 13 Nov 2017 13:21:34: #4 Write summits bed file... SRX2576650.05_summits.bed INFO @ Mon, 13 Nov 2017 13:21:34: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3617 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。