Job ID = 10201959 sra ファイルのダウンロード中... Completed: 334205K bytes transferred in 11 seconds (241751K 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 18751435 spots for /home/okishinya/chipatlas/results/ce10/SRX2576628/SRR5272585.sra Written 18751435 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: 00:11:40 18751435 reads; of these: 18751435 (100.00%) were unpaired; of these: 2652314 (14.14%) aligned 0 times 12988709 (69.27%) aligned exactly 1 time 3110412 (16.59%) aligned >1 times 85.86% overall alignment rate Time searching: 00:11:40 Overall time: 00:11:40 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] 5332850 / 16099121 = 0.3313 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 13:26:18: # Command line: callpeak -t SRX2576628.bam -f BAM -g ce -n SRX2576628.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2576628.05 # format = BAM # ChIP-seq file = ['SRX2576628.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 13:26:18: #1 read tag files... INFO @ Mon, 13 Nov 2017 13:26:18: #1 read treatment tags... INFO @ Mon, 13 Nov 2017 13:26:18: # Command line: callpeak -t SRX2576628.bam -f BAM -g ce -n SRX2576628.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2576628.10 # format = BAM # ChIP-seq file = ['SRX2576628.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 13:26:18: #1 read tag files... INFO @ Mon, 13 Nov 2017 13:26:18: #1 read treatment tags... INFO @ Mon, 13 Nov 2017 13:26:18: # Command line: callpeak -t SRX2576628.bam -f BAM -g ce -n SRX2576628.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2576628.20 # format = BAM # ChIP-seq file = ['SRX2576628.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 13:26:18: #1 read tag files... INFO @ Mon, 13 Nov 2017 13:26:18: #1 read treatment tags... INFO @ Mon, 13 Nov 2017 13:26:28: 1000000 INFO @ Mon, 13 Nov 2017 13:26:35: 1000000 INFO @ Mon, 13 Nov 2017 13:26:36: 1000000 INFO @ Mon, 13 Nov 2017 13:26:38: 2000000 INFO @ Mon, 13 Nov 2017 13:26:47: 3000000 INFO @ Mon, 13 Nov 2017 13:26:51: 2000000 INFO @ Mon, 13 Nov 2017 13:26:53: 2000000 INFO @ Mon, 13 Nov 2017 13:26:57: 4000000 INFO @ Mon, 13 Nov 2017 13:27:07: 5000000 INFO @ Mon, 13 Nov 2017 13:27:08: 3000000 INFO @ Mon, 13 Nov 2017 13:27:09: 3000000 INFO @ Mon, 13 Nov 2017 13:27:16: 6000000 INFO @ Mon, 13 Nov 2017 13:27:23: 4000000 INFO @ Mon, 13 Nov 2017 13:27:24: 4000000 INFO @ Mon, 13 Nov 2017 13:27:27: 7000000 INFO @ Mon, 13 Nov 2017 13:27:39: 5000000 INFO @ Mon, 13 Nov 2017 13:27:40: 8000000 INFO @ Mon, 13 Nov 2017 13:27:44: 5000000 INFO @ Mon, 13 Nov 2017 13:27:53: 9000000 INFO @ Mon, 13 Nov 2017 13:27:54: 6000000 INFO @ Mon, 13 Nov 2017 13:28:03: 6000000 INFO @ Mon, 13 Nov 2017 13:28:06: 10000000 INFO @ Mon, 13 Nov 2017 13:28:12: 7000000 INFO @ Mon, 13 Nov 2017 13:28:15: #1 tag size is determined as 51 bps INFO @ Mon, 13 Nov 2017 13:28:15: #1 tag size = 51 INFO @ Mon, 13 Nov 2017 13:28:15: #1 total tags in treatment: 10766271 INFO @ Mon, 13 Nov 2017 13:28:15: #1 user defined the maximum tags... INFO @ Mon, 13 Nov 2017 13:28:15: #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 13:28:16: #1 tags after filtering in treatment: 10766271 INFO @ Mon, 13 Nov 2017 13:28:16: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 13 Nov 2017 13:28:16: #1 finished! INFO @ Mon, 13 Nov 2017 13:28:16: #2 Build Peak Model... INFO @ Mon, 13 Nov 2017 13:28:16: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 13 Nov 2017 13:28:17: #2 number of paired peaks: 1287 INFO @ Mon, 13 Nov 2017 13:28:17: start model_add_line... INFO @ Mon, 13 Nov 2017 13:28:17: start X-correlation... INFO @ Mon, 13 Nov 2017 13:28:17: end of X-cor INFO @ Mon, 13 Nov 2017 13:28:17: #2 finished! INFO @ Mon, 13 Nov 2017 13:28:17: #2 predicted fragment length is 254 bps INFO @ Mon, 13 Nov 2017 13:28:17: #2 alternative fragment length(s) may be 254 bps INFO @ Mon, 13 Nov 2017 13:28:17: #2.2 Generate R script for model : SRX2576628.20_model.r INFO @ Mon, 13 Nov 2017 13:28:17: #3 Call peaks... INFO @ Mon, 13 Nov 2017 13:28:17: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 13 Nov 2017 13:28:23: 7000000 INFO @ Mon, 13 Nov 2017 13:28:30: 8000000 INFO @ Mon, 13 Nov 2017 13:28:43: 8000000 INFO @ Mon, 13 Nov 2017 13:28:48: 9000000 INFO @ Mon, 13 Nov 2017 13:28:59: #3 Call peaks for each chromosome... INFO @ Mon, 13 Nov 2017 13:29:03: 9000000 INFO @ Mon, 13 Nov 2017 13:29:07: 10000000 INFO @ Mon, 13 Nov 2017 13:29:18: #4 Write output xls file... SRX2576628.20_peaks.xls INFO @ Mon, 13 Nov 2017 13:29:18: #4 Write peak in narrowPeak format file... SRX2576628.20_peaks.narrowPeak INFO @ Mon, 13 Nov 2017 13:29:18: #4 Write summits bed file... SRX2576628.20_summits.bed INFO @ Mon, 13 Nov 2017 13:29:18: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (1737 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 13 Nov 2017 13:29:20: #1 tag size is determined as 51 bps INFO @ Mon, 13 Nov 2017 13:29:20: #1 tag size = 51 INFO @ Mon, 13 Nov 2017 13:29:20: #1 total tags in treatment: 10766271 INFO @ Mon, 13 Nov 2017 13:29:20: #1 user defined the maximum tags... INFO @ Mon, 13 Nov 2017 13:29:20: #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 13:29:21: #1 tags after filtering in treatment: 10766271 INFO @ Mon, 13 Nov 2017 13:29:21: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 13 Nov 2017 13:29:21: #1 finished! INFO @ Mon, 13 Nov 2017 13:29:21: #2 Build Peak Model... INFO @ Mon, 13 Nov 2017 13:29:21: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 13 Nov 2017 13:29:22: #2 number of paired peaks: 1287 INFO @ Mon, 13 Nov 2017 13:29:22: start model_add_line... INFO @ Mon, 13 Nov 2017 13:29:22: start X-correlation... INFO @ Mon, 13 Nov 2017 13:29:22: end of X-cor INFO @ Mon, 13 Nov 2017 13:29:22: #2 finished! INFO @ Mon, 13 Nov 2017 13:29:22: #2 predicted fragment length is 254 bps INFO @ Mon, 13 Nov 2017 13:29:22: #2 alternative fragment length(s) may be 254 bps INFO @ Mon, 13 Nov 2017 13:29:22: #2.2 Generate R script for model : SRX2576628.10_model.r INFO @ Mon, 13 Nov 2017 13:29:22: #3 Call peaks... INFO @ Mon, 13 Nov 2017 13:29:22: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 13 Nov 2017 13:29:22: 10000000 INFO @ Mon, 13 Nov 2017 13:29:37: #1 tag size is determined as 51 bps INFO @ Mon, 13 Nov 2017 13:29:37: #1 tag size = 51 INFO @ Mon, 13 Nov 2017 13:29:37: #1 total tags in treatment: 10766271 INFO @ Mon, 13 Nov 2017 13:29:37: #1 user defined the maximum tags... INFO @ Mon, 13 Nov 2017 13:29:37: #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 13:29:38: #1 tags after filtering in treatment: 10766271 INFO @ Mon, 13 Nov 2017 13:29:38: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 13 Nov 2017 13:29:38: #1 finished! INFO @ Mon, 13 Nov 2017 13:29:38: #2 Build Peak Model... INFO @ Mon, 13 Nov 2017 13:29:38: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 13 Nov 2017 13:29:39: #2 number of paired peaks: 1287 INFO @ Mon, 13 Nov 2017 13:29:39: start model_add_line... INFO @ Mon, 13 Nov 2017 13:29:39: start X-correlation... INFO @ Mon, 13 Nov 2017 13:29:39: end of X-cor INFO @ Mon, 13 Nov 2017 13:29:39: #2 finished! INFO @ Mon, 13 Nov 2017 13:29:39: #2 predicted fragment length is 254 bps INFO @ Mon, 13 Nov 2017 13:29:39: #2 alternative fragment length(s) may be 254 bps INFO @ Mon, 13 Nov 2017 13:29:39: #2.2 Generate R script for model : SRX2576628.05_model.r INFO @ Mon, 13 Nov 2017 13:29:39: #3 Call peaks... INFO @ Mon, 13 Nov 2017 13:29:39: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 13 Nov 2017 13:30:04: #3 Call peaks for each chromosome... INFO @ Mon, 13 Nov 2017 13:30:21: #3 Call peaks for each chromosome... INFO @ Mon, 13 Nov 2017 13:30:23: #4 Write output xls file... SRX2576628.10_peaks.xls INFO @ Mon, 13 Nov 2017 13:30:23: #4 Write peak in narrowPeak format file... SRX2576628.10_peaks.narrowPeak INFO @ Mon, 13 Nov 2017 13:30:23: #4 Write summits bed file... SRX2576628.10_summits.bed INFO @ Mon, 13 Nov 2017 13:30:23: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (2302 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 13 Nov 2017 13:30:40: #4 Write output xls file... SRX2576628.05_peaks.xls INFO @ Mon, 13 Nov 2017 13:30:40: #4 Write peak in narrowPeak format file... SRX2576628.05_peaks.narrowPeak INFO @ Mon, 13 Nov 2017 13:30:40: #4 Write summits bed file... SRX2576628.05_summits.bed INFO @ Mon, 13 Nov 2017 13:30:40: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (2990 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。