Job ID = 2590863 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 23,369,536 reads read : 46,739,072 reads written : 23,369,536 reads 0-length : 23,369,536 rm: cannot remove ‘[DSE]RR*’: No such file or directory 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: 00:08:39 23369536 reads; of these: 23369536 (100.00%) were unpaired; of these: 1723680 (7.38%) aligned 0 times 16805227 (71.91%) aligned exactly 1 time 4840629 (20.71%) aligned >1 times 92.62% overall alignment rate Time searching: 00:08:39 Overall time: 00:08:39 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 12 files... [bam_rmdupse_core] 10707447 / 21645856 = 0.4947 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, 12 Aug 2019 23:58:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011097/SRX5011097.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011097/SRX5011097.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011097/SRX5011097.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011097/SRX5011097.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, 12 Aug 2019 23:58:15: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:58:15: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:58:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011097/SRX5011097.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011097/SRX5011097.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011097/SRX5011097.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011097/SRX5011097.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, 12 Aug 2019 23:58:16: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:58:16: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:58:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011097/SRX5011097.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011097/SRX5011097.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011097/SRX5011097.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011097/SRX5011097.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, 12 Aug 2019 23:58:17: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:58:17: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:58:22: 1000000 INFO @ Mon, 12 Aug 2019 23:58:25: 1000000 INFO @ Mon, 12 Aug 2019 23:58:26: 1000000 INFO @ Mon, 12 Aug 2019 23:58:29: 2000000 INFO @ Mon, 12 Aug 2019 23:58:34: 2000000 INFO @ Mon, 12 Aug 2019 23:58:36: 2000000 INFO @ Mon, 12 Aug 2019 23:58:36: 3000000 INFO @ Mon, 12 Aug 2019 23:58:43: 4000000 INFO @ Mon, 12 Aug 2019 23:58:44: 3000000 INFO @ Mon, 12 Aug 2019 23:58:46: 3000000 INFO @ Mon, 12 Aug 2019 23:58:50: 5000000 INFO @ Mon, 12 Aug 2019 23:58:54: 4000000 INFO @ Mon, 12 Aug 2019 23:58:55: 4000000 INFO @ Mon, 12 Aug 2019 23:58:57: 6000000 INFO @ Mon, 12 Aug 2019 23:59:04: 5000000 INFO @ Mon, 12 Aug 2019 23:59:04: 7000000 INFO @ Mon, 12 Aug 2019 23:59:05: 5000000 INFO @ Mon, 12 Aug 2019 23:59:12: 8000000 INFO @ Mon, 12 Aug 2019 23:59:13: 6000000 INFO @ Mon, 12 Aug 2019 23:59:14: 6000000 INFO @ Mon, 12 Aug 2019 23:59:20: 9000000 INFO @ Mon, 12 Aug 2019 23:59:21: 7000000 INFO @ Mon, 12 Aug 2019 23:59:23: 7000000 INFO @ Mon, 12 Aug 2019 23:59:27: 10000000 INFO @ Mon, 12 Aug 2019 23:59:31: 8000000 INFO @ Mon, 12 Aug 2019 23:59:33: 8000000 INFO @ Mon, 12 Aug 2019 23:59:35: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:59:35: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:59:35: #1 total tags in treatment: 10938409 INFO @ Mon, 12 Aug 2019 23:59:35: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:59:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 23:59:35: #1 tags after filtering in treatment: 10938409 INFO @ Mon, 12 Aug 2019 23:59:35: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:59:35: #1 finished! INFO @ Mon, 12 Aug 2019 23:59:35: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:59:35: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:59:37: #2 number of paired peaks: 7304 INFO @ Mon, 12 Aug 2019 23:59:37: start model_add_line... INFO @ Mon, 12 Aug 2019 23:59:37: start X-correlation... INFO @ Mon, 12 Aug 2019 23:59:37: end of X-cor INFO @ Mon, 12 Aug 2019 23:59:37: #2 finished! INFO @ Mon, 12 Aug 2019 23:59:37: #2 predicted fragment length is 220 bps INFO @ Mon, 12 Aug 2019 23:59:37: #2 alternative fragment length(s) may be 220 bps INFO @ Mon, 12 Aug 2019 23:59:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011097/SRX5011097.05_model.r INFO @ Mon, 12 Aug 2019 23:59:37: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:59:37: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:59:41: 9000000 INFO @ Mon, 12 Aug 2019 23:59:43: 9000000 INFO @ Mon, 12 Aug 2019 23:59:49: 10000000 INFO @ Mon, 12 Aug 2019 23:59:51: 10000000 INFO @ Mon, 12 Aug 2019 23:59:58: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:59:58: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:59:58: #1 total tags in treatment: 10938409 INFO @ Mon, 12 Aug 2019 23:59:58: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:59:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 23:59:58: #1 tags after filtering in treatment: 10938409 INFO @ Mon, 12 Aug 2019 23:59:58: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:59:58: #1 finished! INFO @ Mon, 12 Aug 2019 23:59:58: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:59:58: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:59:59: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:59:59: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:59:59: #1 total tags in treatment: 10938409 INFO @ Mon, 12 Aug 2019 23:59:59: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:59:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 13 Aug 2019 00:00:00: #1 tags after filtering in treatment: 10938409 INFO @ Tue, 13 Aug 2019 00:00:00: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 13 Aug 2019 00:00:00: #1 finished! INFO @ Tue, 13 Aug 2019 00:00:00: #2 Build Peak Model... INFO @ Tue, 13 Aug 2019 00:00:00: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 13 Aug 2019 00:00:00: #2 number of paired peaks: 7304 INFO @ Tue, 13 Aug 2019 00:00:00: start model_add_line... INFO @ Tue, 13 Aug 2019 00:00:00: start X-correlation... INFO @ Tue, 13 Aug 2019 00:00:00: end of X-cor INFO @ Tue, 13 Aug 2019 00:00:00: #2 finished! INFO @ Tue, 13 Aug 2019 00:00:00: #2 predicted fragment length is 220 bps INFO @ Tue, 13 Aug 2019 00:00:00: #2 alternative fragment length(s) may be 220 bps INFO @ Tue, 13 Aug 2019 00:00:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011097/SRX5011097.10_model.r INFO @ Tue, 13 Aug 2019 00:00:00: #3 Call peaks... INFO @ Tue, 13 Aug 2019 00:00:00: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 13 Aug 2019 00:00:01: #2 number of paired peaks: 7304 INFO @ Tue, 13 Aug 2019 00:00:01: start model_add_line... INFO @ Tue, 13 Aug 2019 00:00:02: start X-correlation... INFO @ Tue, 13 Aug 2019 00:00:02: end of X-cor INFO @ Tue, 13 Aug 2019 00:00:02: #2 finished! INFO @ Tue, 13 Aug 2019 00:00:02: #2 predicted fragment length is 220 bps INFO @ Tue, 13 Aug 2019 00:00:02: #2 alternative fragment length(s) may be 220 bps INFO @ Tue, 13 Aug 2019 00:00:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011097/SRX5011097.20_model.r INFO @ Tue, 13 Aug 2019 00:00:02: #3 Call peaks... INFO @ Tue, 13 Aug 2019 00:00:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 13 Aug 2019 00:00:23: #3 Call peaks for each chromosome... INFO @ Tue, 13 Aug 2019 00:00:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011097/SRX5011097.05_peaks.xls INFO @ Tue, 13 Aug 2019 00:00:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011097/SRX5011097.05_peaks.narrowPeak INFO @ Tue, 13 Aug 2019 00:00:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011097/SRX5011097.05_summits.bed INFO @ Tue, 13 Aug 2019 00:00:39: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (11964 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Tue, 13 Aug 2019 00:00:45: #3 Call peaks for each chromosome... INFO @ Tue, 13 Aug 2019 00:00:47: #3 Call peaks for each chromosome... INFO @ Tue, 13 Aug 2019 00:01:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011097/SRX5011097.10_peaks.xls INFO @ Tue, 13 Aug 2019 00:01:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011097/SRX5011097.10_peaks.narrowPeak INFO @ Tue, 13 Aug 2019 00:01:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011097/SRX5011097.10_summits.bed INFO @ Tue, 13 Aug 2019 00:01:02: Done! pass1 - making usageList (15 chroms): 5 millis pass2 - checking and writing primary data (9777 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Tue, 13 Aug 2019 00:01:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011097/SRX5011097.20_peaks.xls INFO @ Tue, 13 Aug 2019 00:01:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011097/SRX5011097.20_peaks.narrowPeak INFO @ Tue, 13 Aug 2019 00:01:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011097/SRX5011097.20_summits.bed INFO @ Tue, 13 Aug 2019 00:01:03: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (7356 records, 4 fields): 12 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。