Job ID = 10175269 sra ファイルのダウンロード中... Completed: 334301K bytes transferred in 5 seconds (529780K 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 18572951 spots for /home/okishinya/chipatlas/results/dm3/SRX3159471/SRR6004201.sra Written 18572951 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: 00:05:18 18572951 reads; of these: 18572951 (100.00%) were unpaired; of these: 1539806 (8.29%) aligned 0 times 14910534 (80.28%) aligned exactly 1 time 2122611 (11.43%) aligned >1 times 91.71% overall alignment rate Time searching: 00:05:18 Overall time: 00:05:18 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 4770420 / 17033145 = 0.2801 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, 06 Nov 2017 12:26:42: # Command line: callpeak -t SRX3159471.bam -f BAM -g dm -n SRX3159471.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3159471.10 # format = BAM # ChIP-seq file = ['SRX3159471.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 06 Nov 2017 12:26:42: #1 read tag files... INFO @ Mon, 06 Nov 2017 12:26:42: #1 read treatment tags... INFO @ Mon, 06 Nov 2017 12:26:42: # Command line: callpeak -t SRX3159471.bam -f BAM -g dm -n SRX3159471.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3159471.20 # format = BAM # ChIP-seq file = ['SRX3159471.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 06 Nov 2017 12:26:42: #1 read tag files... INFO @ Mon, 06 Nov 2017 12:26:42: #1 read treatment tags... INFO @ Mon, 06 Nov 2017 12:26:42: # Command line: callpeak -t SRX3159471.bam -f BAM -g dm -n SRX3159471.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3159471.05 # format = BAM # ChIP-seq file = ['SRX3159471.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 06 Nov 2017 12:26:42: #1 read tag files... INFO @ Mon, 06 Nov 2017 12:26:42: #1 read treatment tags... INFO @ Mon, 06 Nov 2017 12:26:48: 1000000 INFO @ Mon, 06 Nov 2017 12:26:49: 1000000 INFO @ Mon, 06 Nov 2017 12:26:49: 1000000 INFO @ Mon, 06 Nov 2017 12:26:55: 2000000 INFO @ Mon, 06 Nov 2017 12:26:56: 2000000 INFO @ Mon, 06 Nov 2017 12:26:56: 2000000 INFO @ Mon, 06 Nov 2017 12:27:02: 3000000 INFO @ Mon, 06 Nov 2017 12:27:03: 3000000 INFO @ Mon, 06 Nov 2017 12:27:03: 3000000 INFO @ Mon, 06 Nov 2017 12:27:09: 4000000 INFO @ Mon, 06 Nov 2017 12:27:09: 4000000 INFO @ Mon, 06 Nov 2017 12:27:11: 4000000 INFO @ Mon, 06 Nov 2017 12:27:16: 5000000 INFO @ Mon, 06 Nov 2017 12:27:16: 5000000 INFO @ Mon, 06 Nov 2017 12:27:19: 5000000 INFO @ Mon, 06 Nov 2017 12:27:23: 6000000 INFO @ Mon, 06 Nov 2017 12:27:24: 6000000 INFO @ Mon, 06 Nov 2017 12:27:29: 6000000 INFO @ Mon, 06 Nov 2017 12:27:31: 7000000 INFO @ Mon, 06 Nov 2017 12:27:32: 7000000 INFO @ Mon, 06 Nov 2017 12:27:38: 8000000 INFO @ Mon, 06 Nov 2017 12:27:38: 7000000 INFO @ Mon, 06 Nov 2017 12:27:41: 8000000 INFO @ Mon, 06 Nov 2017 12:27:46: 9000000 INFO @ Mon, 06 Nov 2017 12:27:48: 8000000 INFO @ Mon, 06 Nov 2017 12:27:49: 9000000 INFO @ Mon, 06 Nov 2017 12:27:53: 10000000 INFO @ Mon, 06 Nov 2017 12:27:58: 9000000 INFO @ Mon, 06 Nov 2017 12:27:58: 10000000 INFO @ Mon, 06 Nov 2017 12:28:01: 11000000 INFO @ Mon, 06 Nov 2017 12:28:06: 11000000 INFO @ Mon, 06 Nov 2017 12:28:08: 10000000 INFO @ Mon, 06 Nov 2017 12:28:08: 12000000 INFO @ Mon, 06 Nov 2017 12:28:10: #1 tag size is determined as 51 bps INFO @ Mon, 06 Nov 2017 12:28:10: #1 tag size = 51 INFO @ Mon, 06 Nov 2017 12:28:10: #1 total tags in treatment: 12262725 INFO @ Mon, 06 Nov 2017 12:28:10: #1 user defined the maximum tags... INFO @ Mon, 06 Nov 2017 12:28:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 06 Nov 2017 12:28:11: #1 tags after filtering in treatment: 12262725 INFO @ Mon, 06 Nov 2017 12:28:11: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 06 Nov 2017 12:28:11: #1 finished! INFO @ Mon, 06 Nov 2017 12:28:11: #2 Build Peak Model... INFO @ Mon, 06 Nov 2017 12:28:11: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 06 Nov 2017 12:28:12: #2 number of paired peaks: 4540 INFO @ Mon, 06 Nov 2017 12:28:12: start model_add_line... INFO @ Mon, 06 Nov 2017 12:28:12: start X-correlation... INFO @ Mon, 06 Nov 2017 12:28:12: end of X-cor INFO @ Mon, 06 Nov 2017 12:28:12: #2 finished! INFO @ Mon, 06 Nov 2017 12:28:12: #2 predicted fragment length is 149 bps INFO @ Mon, 06 Nov 2017 12:28:12: #2 alternative fragment length(s) may be 149 bps INFO @ Mon, 06 Nov 2017 12:28:12: #2.2 Generate R script for model : SRX3159471.05_model.r INFO @ Mon, 06 Nov 2017 12:28:12: #3 Call peaks... INFO @ Mon, 06 Nov 2017 12:28:12: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 06 Nov 2017 12:28:15: 12000000 INFO @ Mon, 06 Nov 2017 12:28:17: #1 tag size is determined as 51 bps INFO @ Mon, 06 Nov 2017 12:28:17: #1 tag size = 51 INFO @ Mon, 06 Nov 2017 12:28:17: #1 total tags in treatment: 12262725 INFO @ Mon, 06 Nov 2017 12:28:17: #1 user defined the maximum tags... INFO @ Mon, 06 Nov 2017 12:28:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 06 Nov 2017 12:28:17: 11000000 INFO @ Mon, 06 Nov 2017 12:28:17: #1 tags after filtering in treatment: 12262725 INFO @ Mon, 06 Nov 2017 12:28:17: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 06 Nov 2017 12:28:17: #1 finished! INFO @ Mon, 06 Nov 2017 12:28:17: #2 Build Peak Model... INFO @ Mon, 06 Nov 2017 12:28:17: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 06 Nov 2017 12:28:19: #2 number of paired peaks: 4540 INFO @ Mon, 06 Nov 2017 12:28:19: start model_add_line... INFO @ Mon, 06 Nov 2017 12:28:19: start X-correlation... INFO @ Mon, 06 Nov 2017 12:28:19: end of X-cor INFO @ Mon, 06 Nov 2017 12:28:19: #2 finished! INFO @ Mon, 06 Nov 2017 12:28:19: #2 predicted fragment length is 149 bps INFO @ Mon, 06 Nov 2017 12:28:19: #2 alternative fragment length(s) may be 149 bps INFO @ Mon, 06 Nov 2017 12:28:19: #2.2 Generate R script for model : SRX3159471.20_model.r INFO @ Mon, 06 Nov 2017 12:28:19: #3 Call peaks... INFO @ Mon, 06 Nov 2017 12:28:19: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 06 Nov 2017 12:28:27: 12000000 INFO @ Mon, 06 Nov 2017 12:28:29: #1 tag size is determined as 51 bps INFO @ Mon, 06 Nov 2017 12:28:29: #1 tag size = 51 INFO @ Mon, 06 Nov 2017 12:28:29: #1 total tags in treatment: 12262725 INFO @ Mon, 06 Nov 2017 12:28:29: #1 user defined the maximum tags... INFO @ Mon, 06 Nov 2017 12:28:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 06 Nov 2017 12:28:29: #1 tags after filtering in treatment: 12262725 INFO @ Mon, 06 Nov 2017 12:28:29: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 06 Nov 2017 12:28:29: #1 finished! INFO @ Mon, 06 Nov 2017 12:28:29: #2 Build Peak Model... INFO @ Mon, 06 Nov 2017 12:28:29: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 06 Nov 2017 12:28:30: #2 number of paired peaks: 4540 INFO @ Mon, 06 Nov 2017 12:28:30: start model_add_line... INFO @ Mon, 06 Nov 2017 12:28:31: start X-correlation... INFO @ Mon, 06 Nov 2017 12:28:31: end of X-cor INFO @ Mon, 06 Nov 2017 12:28:31: #2 finished! INFO @ Mon, 06 Nov 2017 12:28:31: #2 predicted fragment length is 149 bps INFO @ Mon, 06 Nov 2017 12:28:31: #2 alternative fragment length(s) may be 149 bps INFO @ Mon, 06 Nov 2017 12:28:31: #2.2 Generate R script for model : SRX3159471.10_model.r INFO @ Mon, 06 Nov 2017 12:28:31: #3 Call peaks... INFO @ Mon, 06 Nov 2017 12:28:31: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 06 Nov 2017 12:28:45: #3 Call peaks for each chromosome... INFO @ Mon, 06 Nov 2017 12:28:52: #3 Call peaks for each chromosome... INFO @ Mon, 06 Nov 2017 12:29:03: #4 Write output xls file... SRX3159471.05_peaks.xls INFO @ Mon, 06 Nov 2017 12:29:03: #4 Write peak in narrowPeak format file... SRX3159471.05_peaks.narrowPeak INFO @ Mon, 06 Nov 2017 12:29:03: #4 Write summits bed file... SRX3159471.05_summits.bed INFO @ Mon, 06 Nov 2017 12:29:03: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (7480 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Mon, 06 Nov 2017 12:29:04: #3 Call peaks for each chromosome... INFO @ Mon, 06 Nov 2017 12:29:09: #4 Write output xls file... SRX3159471.20_peaks.xls INFO @ Mon, 06 Nov 2017 12:29:09: #4 Write peak in narrowPeak format file... SRX3159471.20_peaks.narrowPeak INFO @ Mon, 06 Nov 2017 12:29:09: #4 Write summits bed file... SRX3159471.20_summits.bed INFO @ Mon, 06 Nov 2017 12:29:09: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (5105 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 06 Nov 2017 12:29:22: #4 Write output xls file... SRX3159471.10_peaks.xls INFO @ Mon, 06 Nov 2017 12:29:22: #4 Write peak in narrowPeak format file... SRX3159471.10_peaks.narrowPeak INFO @ Mon, 06 Nov 2017 12:29:22: #4 Write summits bed file... SRX3159471.10_summits.bed INFO @ Mon, 06 Nov 2017 12:29:22: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6305 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。