Job ID = 10201951 sra ファイルのダウンロード中... Completed: 379467K bytes transferred in 11 seconds (282343K 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 15742148 spots for /home/okishinya/chipatlas/results/ce10/SRX2576620/SRR5272577.sra Written 15742148 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: 00:07:41 15742148 reads; of these: 15742148 (100.00%) were unpaired; of these: 804604 (5.11%) aligned 0 times 12308362 (78.19%) aligned exactly 1 time 2629182 (16.70%) aligned >1 times 94.89% overall alignment rate Time searching: 00:07:41 Overall time: 00:07:41 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] 2246413 / 14937544 = 0.1504 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 13:21:44: # Command line: callpeak -t SRX2576620.bam -f BAM -g ce -n SRX2576620.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2576620.05 # format = BAM # ChIP-seq file = ['SRX2576620.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 13:21:44: #1 read tag files... INFO @ Mon, 13 Nov 2017 13:21:44: #1 read treatment tags... INFO @ Mon, 13 Nov 2017 13:21:44: # Command line: callpeak -t SRX2576620.bam -f BAM -g ce -n SRX2576620.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2576620.10 # format = BAM # ChIP-seq file = ['SRX2576620.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 13:21:44: #1 read tag files... INFO @ Mon, 13 Nov 2017 13:21:44: #1 read treatment tags... INFO @ Mon, 13 Nov 2017 13:21:44: # Command line: callpeak -t SRX2576620.bam -f BAM -g ce -n SRX2576620.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2576620.20 # format = BAM # ChIP-seq file = ['SRX2576620.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 13:21:44: #1 read tag files... INFO @ Mon, 13 Nov 2017 13:21:44: #1 read treatment tags... INFO @ Mon, 13 Nov 2017 13:21:56: 1000000 INFO @ Mon, 13 Nov 2017 13:21:56: 1000000 INFO @ Mon, 13 Nov 2017 13:21:58: 1000000 INFO @ Mon, 13 Nov 2017 13:22:07: 2000000 INFO @ Mon, 13 Nov 2017 13:22:10: 2000000 INFO @ Mon, 13 Nov 2017 13:22:12: 2000000 INFO @ Mon, 13 Nov 2017 13:22:21: 3000000 INFO @ Mon, 13 Nov 2017 13:22:25: 3000000 INFO @ Mon, 13 Nov 2017 13:22:26: 3000000 INFO @ Mon, 13 Nov 2017 13:22:34: 4000000 INFO @ Mon, 13 Nov 2017 13:22:40: 4000000 INFO @ Mon, 13 Nov 2017 13:22:41: 4000000 INFO @ Mon, 13 Nov 2017 13:22:46: 5000000 INFO @ Mon, 13 Nov 2017 13:22:55: 5000000 INFO @ Mon, 13 Nov 2017 13:22:57: 5000000 INFO @ Mon, 13 Nov 2017 13:23:00: 6000000 INFO @ Mon, 13 Nov 2017 13:23:08: 6000000 INFO @ Mon, 13 Nov 2017 13:23:12: 6000000 INFO @ Mon, 13 Nov 2017 13:23:13: 7000000 INFO @ Mon, 13 Nov 2017 13:23:22: 7000000 INFO @ Mon, 13 Nov 2017 13:23:25: 8000000 INFO @ Mon, 13 Nov 2017 13:23:28: 7000000 INFO @ Mon, 13 Nov 2017 13:23:36: 8000000 INFO @ Mon, 13 Nov 2017 13:23:38: 9000000 INFO @ Mon, 13 Nov 2017 13:23:42: 8000000 INFO @ Mon, 13 Nov 2017 13:23:47: 9000000 INFO @ Mon, 13 Nov 2017 13:23:51: 10000000 INFO @ Mon, 13 Nov 2017 13:23:56: 9000000 INFO @ Mon, 13 Nov 2017 13:23:59: 10000000 INFO @ Mon, 13 Nov 2017 13:24:03: 11000000 INFO @ Mon, 13 Nov 2017 13:24:11: 10000000 INFO @ Mon, 13 Nov 2017 13:24:14: 11000000 INFO @ Mon, 13 Nov 2017 13:24:17: 12000000 INFO @ Mon, 13 Nov 2017 13:24:26: 11000000 INFO @ Mon, 13 Nov 2017 13:24:27: #1 tag size is determined as 35 bps INFO @ Mon, 13 Nov 2017 13:24:27: #1 tag size = 35 INFO @ Mon, 13 Nov 2017 13:24:27: #1 total tags in treatment: 12691131 INFO @ Mon, 13 Nov 2017 13:24:27: #1 user defined the maximum tags... INFO @ Mon, 13 Nov 2017 13:24:27: #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 13:24:28: #1 tags after filtering in treatment: 12691131 INFO @ Mon, 13 Nov 2017 13:24:28: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 13 Nov 2017 13:24:28: #1 finished! INFO @ Mon, 13 Nov 2017 13:24:28: #2 Build Peak Model... INFO @ Mon, 13 Nov 2017 13:24:28: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 13 Nov 2017 13:24:28: 12000000 INFO @ Mon, 13 Nov 2017 13:24:29: #2 number of paired peaks: 491 WARNING @ Mon, 13 Nov 2017 13:24:29: Fewer paired peaks (491) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 491 pairs to build model! INFO @ Mon, 13 Nov 2017 13:24:29: start model_add_line... INFO @ Mon, 13 Nov 2017 13:24:29: start X-correlation... INFO @ Mon, 13 Nov 2017 13:24:29: end of X-cor INFO @ Mon, 13 Nov 2017 13:24:29: #2 finished! INFO @ Mon, 13 Nov 2017 13:24:29: #2 predicted fragment length is 132 bps INFO @ Mon, 13 Nov 2017 13:24:29: #2 alternative fragment length(s) may be 132 bps INFO @ Mon, 13 Nov 2017 13:24:29: #2.2 Generate R script for model : SRX2576620.20_model.r INFO @ Mon, 13 Nov 2017 13:24:29: #3 Call peaks... INFO @ Mon, 13 Nov 2017 13:24:29: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 13 Nov 2017 13:24:39: #1 tag size is determined as 35 bps INFO @ Mon, 13 Nov 2017 13:24:39: #1 tag size = 35 INFO @ Mon, 13 Nov 2017 13:24:39: #1 total tags in treatment: 12691131 INFO @ Mon, 13 Nov 2017 13:24:39: #1 user defined the maximum tags... INFO @ Mon, 13 Nov 2017 13:24:39: #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 13:24:39: #1 tags after filtering in treatment: 12691131 INFO @ Mon, 13 Nov 2017 13:24:39: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 13 Nov 2017 13:24:39: #1 finished! INFO @ Mon, 13 Nov 2017 13:24:39: #2 Build Peak Model... INFO @ Mon, 13 Nov 2017 13:24:39: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 13 Nov 2017 13:24:41: #2 number of paired peaks: 491 WARNING @ Mon, 13 Nov 2017 13:24:41: Fewer paired peaks (491) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 491 pairs to build model! INFO @ Mon, 13 Nov 2017 13:24:41: start model_add_line... INFO @ Mon, 13 Nov 2017 13:24:41: start X-correlation... INFO @ Mon, 13 Nov 2017 13:24:41: end of X-cor INFO @ Mon, 13 Nov 2017 13:24:41: #2 finished! INFO @ Mon, 13 Nov 2017 13:24:41: #2 predicted fragment length is 132 bps INFO @ Mon, 13 Nov 2017 13:24:41: #2 alternative fragment length(s) may be 132 bps INFO @ Mon, 13 Nov 2017 13:24:41: #2.2 Generate R script for model : SRX2576620.10_model.r INFO @ Mon, 13 Nov 2017 13:24:41: #3 Call peaks... INFO @ Mon, 13 Nov 2017 13:24:41: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 13 Nov 2017 13:24:41: 12000000 INFO @ Mon, 13 Nov 2017 13:24:52: #1 tag size is determined as 35 bps INFO @ Mon, 13 Nov 2017 13:24:52: #1 tag size = 35 INFO @ Mon, 13 Nov 2017 13:24:52: #1 total tags in treatment: 12691131 INFO @ Mon, 13 Nov 2017 13:24:52: #1 user defined the maximum tags... INFO @ Mon, 13 Nov 2017 13:24:52: #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 13:24:52: #1 tags after filtering in treatment: 12691131 INFO @ Mon, 13 Nov 2017 13:24:52: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 13 Nov 2017 13:24:52: #1 finished! INFO @ Mon, 13 Nov 2017 13:24:52: #2 Build Peak Model... INFO @ Mon, 13 Nov 2017 13:24:52: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 13 Nov 2017 13:24:53: #2 number of paired peaks: 491 WARNING @ Mon, 13 Nov 2017 13:24:53: Fewer paired peaks (491) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 491 pairs to build model! INFO @ Mon, 13 Nov 2017 13:24:53: start model_add_line... INFO @ Mon, 13 Nov 2017 13:24:54: start X-correlation... INFO @ Mon, 13 Nov 2017 13:24:54: end of X-cor INFO @ Mon, 13 Nov 2017 13:24:54: #2 finished! INFO @ Mon, 13 Nov 2017 13:24:54: #2 predicted fragment length is 132 bps INFO @ Mon, 13 Nov 2017 13:24:54: #2 alternative fragment length(s) may be 132 bps INFO @ Mon, 13 Nov 2017 13:24:54: #2.2 Generate R script for model : SRX2576620.05_model.r INFO @ Mon, 13 Nov 2017 13:24:54: #3 Call peaks... INFO @ Mon, 13 Nov 2017 13:24:54: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 13 Nov 2017 13:25:07: #3 Call peaks for each chromosome... INFO @ Mon, 13 Nov 2017 13:25:27: #3 Call peaks for each chromosome... INFO @ Mon, 13 Nov 2017 13:25:29: #4 Write output xls file... SRX2576620.20_peaks.xls INFO @ Mon, 13 Nov 2017 13:25:29: #4 Write peak in narrowPeak format file... SRX2576620.20_peaks.narrowPeak INFO @ Mon, 13 Nov 2017 13:25:29: #4 Write summits bed file... SRX2576620.20_summits.bed INFO @ Mon, 13 Nov 2017 13:25:29: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (1151 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 13 Nov 2017 13:25:32: #3 Call peaks for each chromosome... INFO @ Mon, 13 Nov 2017 13:25:53: #4 Write output xls file... SRX2576620.05_peaks.xls INFO @ Mon, 13 Nov 2017 13:25:53: #4 Write peak in narrowPeak format file... SRX2576620.05_peaks.narrowPeak INFO @ Mon, 13 Nov 2017 13:25:53: #4 Write summits bed file... SRX2576620.05_summits.bed INFO @ Mon, 13 Nov 2017 13:25:53: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (2436 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 13 Nov 2017 13:25:55: #4 Write output xls file... SRX2576620.10_peaks.xls INFO @ Mon, 13 Nov 2017 13:25:55: #4 Write peak in narrowPeak format file... SRX2576620.10_peaks.narrowPeak INFO @ Mon, 13 Nov 2017 13:25:55: #4 Write summits bed file... SRX2576620.10_summits.bed INFO @ Mon, 13 Nov 2017 13:25:55: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1726 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。