Job ID = 2590608 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 29,586,313 reads read : 59,172,626 reads written : 29,586,313 reads 0-length : 29,586,313 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: 00:08:34 29586313 reads; of these: 29586313 (100.00%) were unpaired; of these: 785016 (2.65%) aligned 0 times 23618622 (79.83%) aligned exactly 1 time 5182675 (17.52%) aligned >1 times 97.35% overall alignment rate Time searching: 00:08:34 Overall time: 00:08:34 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] 15775156 / 28801297 = 0.5477 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 22:57:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4923192/SRX4923192.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4923192/SRX4923192.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4923192/SRX4923192.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4923192/SRX4923192.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 22:57:08: #1 read tag files... INFO @ Mon, 12 Aug 2019 22:57:08: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 22:57:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4923192/SRX4923192.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4923192/SRX4923192.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4923192/SRX4923192.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4923192/SRX4923192.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 22:57:09: #1 read tag files... INFO @ Mon, 12 Aug 2019 22:57:09: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 22:57:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4923192/SRX4923192.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4923192/SRX4923192.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4923192/SRX4923192.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4923192/SRX4923192.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 22:57:10: #1 read tag files... INFO @ Mon, 12 Aug 2019 22:57:10: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 22:57:15: 1000000 INFO @ Mon, 12 Aug 2019 22:57:16: 1000000 INFO @ Mon, 12 Aug 2019 22:57:17: 1000000 INFO @ Mon, 12 Aug 2019 22:57:21: 2000000 INFO @ Mon, 12 Aug 2019 22:57:23: 2000000 INFO @ Mon, 12 Aug 2019 22:57:23: 2000000 INFO @ Mon, 12 Aug 2019 22:57:28: 3000000 INFO @ Mon, 12 Aug 2019 22:57:29: 3000000 INFO @ Mon, 12 Aug 2019 22:57:30: 3000000 INFO @ Mon, 12 Aug 2019 22:57:34: 4000000 INFO @ Mon, 12 Aug 2019 22:57:36: 4000000 INFO @ Mon, 12 Aug 2019 22:57:36: 4000000 INFO @ Mon, 12 Aug 2019 22:57:41: 5000000 INFO @ Mon, 12 Aug 2019 22:57:42: 5000000 INFO @ Mon, 12 Aug 2019 22:57:43: 5000000 INFO @ Mon, 12 Aug 2019 22:57:47: 6000000 INFO @ Mon, 12 Aug 2019 22:57:49: 6000000 INFO @ Mon, 12 Aug 2019 22:57:49: 6000000 INFO @ Mon, 12 Aug 2019 22:57:54: 7000000 INFO @ Mon, 12 Aug 2019 22:57:55: 7000000 INFO @ Mon, 12 Aug 2019 22:57:56: 7000000 INFO @ Mon, 12 Aug 2019 22:58:01: 8000000 INFO @ Mon, 12 Aug 2019 22:58:02: 8000000 INFO @ Mon, 12 Aug 2019 22:58:03: 8000000 INFO @ Mon, 12 Aug 2019 22:58:07: 9000000 INFO @ Mon, 12 Aug 2019 22:58:08: 9000000 INFO @ Mon, 12 Aug 2019 22:58:09: 9000000 INFO @ Mon, 12 Aug 2019 22:58:14: 10000000 INFO @ Mon, 12 Aug 2019 22:58:15: 10000000 INFO @ Mon, 12 Aug 2019 22:58:15: 10000000 INFO @ Mon, 12 Aug 2019 22:58:20: 11000000 INFO @ Mon, 12 Aug 2019 22:58:21: 11000000 INFO @ Mon, 12 Aug 2019 22:58:22: 11000000 INFO @ Mon, 12 Aug 2019 22:58:27: 12000000 INFO @ Mon, 12 Aug 2019 22:58:28: 12000000 INFO @ Mon, 12 Aug 2019 22:58:28: 12000000 INFO @ Mon, 12 Aug 2019 22:58:33: 13000000 INFO @ Mon, 12 Aug 2019 22:58:33: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 22:58:33: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 22:58:33: #1 total tags in treatment: 13026141 INFO @ Mon, 12 Aug 2019 22:58:33: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 22:58:33: #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 22:58:34: #1 tags after filtering in treatment: 13026141 INFO @ Mon, 12 Aug 2019 22:58:34: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 22:58:34: #1 finished! INFO @ Mon, 12 Aug 2019 22:58:34: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 22:58:34: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 22:58:34: 13000000 INFO @ Mon, 12 Aug 2019 22:58:35: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 22:58:35: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 22:58:35: #1 total tags in treatment: 13026141 INFO @ Mon, 12 Aug 2019 22:58:35: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 22:58:35: #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 22:58:35: 13000000 INFO @ Mon, 12 Aug 2019 22:58:35: #1 tags after filtering in treatment: 13026141 INFO @ Mon, 12 Aug 2019 22:58:35: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 22:58:35: #1 finished! INFO @ Mon, 12 Aug 2019 22:58:35: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 22:58:35: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 22:58:35: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 22:58:35: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 22:58:35: #1 total tags in treatment: 13026141 INFO @ Mon, 12 Aug 2019 22:58:35: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 22:58:35: #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 22:58:35: #1 tags after filtering in treatment: 13026141 INFO @ Mon, 12 Aug 2019 22:58:35: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 22:58:35: #1 finished! INFO @ Mon, 12 Aug 2019 22:58:35: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 22:58:35: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 22:58:36: #2 number of paired peaks: 13971 INFO @ Mon, 12 Aug 2019 22:58:36: start model_add_line... INFO @ Mon, 12 Aug 2019 22:58:37: start X-correlation... INFO @ Mon, 12 Aug 2019 22:58:37: end of X-cor INFO @ Mon, 12 Aug 2019 22:58:37: #2 finished! INFO @ Mon, 12 Aug 2019 22:58:37: #2 predicted fragment length is 116 bps INFO @ Mon, 12 Aug 2019 22:58:37: #2 alternative fragment length(s) may be 116 bps INFO @ Mon, 12 Aug 2019 22:58:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4923192/SRX4923192.05_model.r INFO @ Mon, 12 Aug 2019 22:58:37: #3 Call peaks... INFO @ Mon, 12 Aug 2019 22:58:37: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 22:58:38: #2 number of paired peaks: 13971 INFO @ Mon, 12 Aug 2019 22:58:38: start model_add_line... INFO @ Mon, 12 Aug 2019 22:58:38: #2 number of paired peaks: 13971 INFO @ Mon, 12 Aug 2019 22:58:38: start model_add_line... INFO @ Mon, 12 Aug 2019 22:58:38: start X-correlation... INFO @ Mon, 12 Aug 2019 22:58:38: end of X-cor INFO @ Mon, 12 Aug 2019 22:58:38: #2 finished! INFO @ Mon, 12 Aug 2019 22:58:38: #2 predicted fragment length is 116 bps INFO @ Mon, 12 Aug 2019 22:58:38: #2 alternative fragment length(s) may be 116 bps INFO @ Mon, 12 Aug 2019 22:58:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4923192/SRX4923192.10_model.r INFO @ Mon, 12 Aug 2019 22:58:38: #3 Call peaks... INFO @ Mon, 12 Aug 2019 22:58:38: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 22:58:38: start X-correlation... INFO @ Mon, 12 Aug 2019 22:58:38: end of X-cor INFO @ Mon, 12 Aug 2019 22:58:38: #2 finished! INFO @ Mon, 12 Aug 2019 22:58:38: #2 predicted fragment length is 116 bps INFO @ Mon, 12 Aug 2019 22:58:38: #2 alternative fragment length(s) may be 116 bps INFO @ Mon, 12 Aug 2019 22:58:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4923192/SRX4923192.20_model.r INFO @ Mon, 12 Aug 2019 22:58:38: #3 Call peaks... INFO @ Mon, 12 Aug 2019 22:58:38: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 22:59:16: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 22:59:16: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 22:59:18: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 22:59:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4923192/SRX4923192.20_peaks.xls INFO @ Mon, 12 Aug 2019 22:59:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4923192/SRX4923192.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 22:59:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4923192/SRX4923192.20_summits.bed INFO @ Mon, 12 Aug 2019 22:59:32: Done! pass1 - making usageList (13 chroms): 5 millis pass2 - checking and writing primary data (7981 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 22:59:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4923192/SRX4923192.10_peaks.xls INFO @ Mon, 12 Aug 2019 22:59:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4923192/SRX4923192.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 22:59:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4923192/SRX4923192.10_summits.bed INFO @ Mon, 12 Aug 2019 22:59:32: Done! pass1 - making usageList (14 chroms): 5 millis pass2 - checking and writing primary data (9869 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 22:59:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4923192/SRX4923192.05_peaks.xls INFO @ Mon, 12 Aug 2019 22:59:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4923192/SRX4923192.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 22:59:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4923192/SRX4923192.05_summits.bed INFO @ Mon, 12 Aug 2019 22:59:41: Done! pass1 - making usageList (15 chroms): 5 millis pass2 - checking and writing primary data (11346 records, 4 fields): 16 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。