Job ID = 1308794 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 24,672,355 reads read : 24,672,355 reads written : 24,672,355 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘fastqDump_tmp*’: 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: 00:08:18 24672355 reads; of these: 24672355 (100.00%) were unpaired; of these: 4537466 (18.39%) aligned 0 times 10646261 (43.15%) aligned exactly 1 time 9488628 (38.46%) aligned >1 times 81.61% overall alignment rate Time searching: 00:08:18 Overall time: 00:08:18 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 12 files... [bam_rmdupse_core] 7382063 / 20134889 = 0.3666 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, 03 Jun 2019 23:17:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5379466/SRX5379466.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5379466/SRX5379466.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5379466/SRX5379466.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5379466/SRX5379466.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, 03 Jun 2019 23:17:10: #1 read tag files... INFO @ Mon, 03 Jun 2019 23:17:10: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 23:17:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5379466/SRX5379466.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5379466/SRX5379466.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5379466/SRX5379466.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5379466/SRX5379466.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, 03 Jun 2019 23:17:10: #1 read tag files... INFO @ Mon, 03 Jun 2019 23:17:10: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 23:17:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5379466/SRX5379466.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5379466/SRX5379466.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5379466/SRX5379466.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5379466/SRX5379466.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, 03 Jun 2019 23:17:10: #1 read tag files... INFO @ Mon, 03 Jun 2019 23:17:10: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 23:17:18: 1000000 INFO @ Mon, 03 Jun 2019 23:17:21: 1000000 INFO @ Mon, 03 Jun 2019 23:17:21: 1000000 INFO @ Mon, 03 Jun 2019 23:17:25: 2000000 INFO @ Mon, 03 Jun 2019 23:17:32: 2000000 INFO @ Mon, 03 Jun 2019 23:17:32: 2000000 INFO @ Mon, 03 Jun 2019 23:17:33: 3000000 INFO @ Mon, 03 Jun 2019 23:17:40: 4000000 INFO @ Mon, 03 Jun 2019 23:17:43: 3000000 INFO @ Mon, 03 Jun 2019 23:17:43: 3000000 INFO @ Mon, 03 Jun 2019 23:17:48: 5000000 INFO @ Mon, 03 Jun 2019 23:17:54: 4000000 INFO @ Mon, 03 Jun 2019 23:17:54: 4000000 INFO @ Mon, 03 Jun 2019 23:17:56: 6000000 INFO @ Mon, 03 Jun 2019 23:18:03: 5000000 INFO @ Mon, 03 Jun 2019 23:18:04: 7000000 INFO @ Mon, 03 Jun 2019 23:18:05: 5000000 INFO @ Mon, 03 Jun 2019 23:18:11: 6000000 INFO @ Mon, 03 Jun 2019 23:18:11: 8000000 INFO @ Mon, 03 Jun 2019 23:18:16: 6000000 INFO @ Mon, 03 Jun 2019 23:18:19: 9000000 INFO @ Mon, 03 Jun 2019 23:18:19: 7000000 INFO @ Mon, 03 Jun 2019 23:18:26: 7000000 INFO @ Mon, 03 Jun 2019 23:18:27: 10000000 INFO @ Mon, 03 Jun 2019 23:18:27: 8000000 INFO @ Mon, 03 Jun 2019 23:18:35: 9000000 INFO @ Mon, 03 Jun 2019 23:18:35: 11000000 INFO @ Mon, 03 Jun 2019 23:18:36: 8000000 INFO @ Mon, 03 Jun 2019 23:18:42: 10000000 INFO @ Mon, 03 Jun 2019 23:18:43: 12000000 INFO @ Mon, 03 Jun 2019 23:18:47: 9000000 INFO @ Mon, 03 Jun 2019 23:18:49: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 23:18:49: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 23:18:49: #1 total tags in treatment: 12752826 INFO @ Mon, 03 Jun 2019 23:18:49: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 23:18:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 23:18:49: #1 tags after filtering in treatment: 12752826 INFO @ Mon, 03 Jun 2019 23:18:49: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 23:18:49: #1 finished! INFO @ Mon, 03 Jun 2019 23:18:49: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 23:18:49: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 23:18:50: 11000000 INFO @ Mon, 03 Jun 2019 23:18:50: #2 number of paired peaks: 3489 INFO @ Mon, 03 Jun 2019 23:18:50: start model_add_line... INFO @ Mon, 03 Jun 2019 23:18:51: start X-correlation... INFO @ Mon, 03 Jun 2019 23:18:51: end of X-cor INFO @ Mon, 03 Jun 2019 23:18:51: #2 finished! INFO @ Mon, 03 Jun 2019 23:18:51: #2 predicted fragment length is 112 bps INFO @ Mon, 03 Jun 2019 23:18:51: #2 alternative fragment length(s) may be 4,112 bps INFO @ Mon, 03 Jun 2019 23:18:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5379466/SRX5379466.10_model.r INFO @ Mon, 03 Jun 2019 23:18:51: #3 Call peaks... INFO @ Mon, 03 Jun 2019 23:18:51: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 23:18:58: 12000000 INFO @ Mon, 03 Jun 2019 23:18:58: 10000000 INFO @ Mon, 03 Jun 2019 23:19:04: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 23:19:04: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 23:19:04: #1 total tags in treatment: 12752826 INFO @ Mon, 03 Jun 2019 23:19:04: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 23:19:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 23:19:04: #1 tags after filtering in treatment: 12752826 INFO @ Mon, 03 Jun 2019 23:19:04: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 23:19:04: #1 finished! INFO @ Mon, 03 Jun 2019 23:19:04: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 23:19:04: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 23:19:06: #2 number of paired peaks: 3489 INFO @ Mon, 03 Jun 2019 23:19:06: start model_add_line... INFO @ Mon, 03 Jun 2019 23:19:07: start X-correlation... INFO @ Mon, 03 Jun 2019 23:19:07: end of X-cor INFO @ Mon, 03 Jun 2019 23:19:07: #2 finished! INFO @ Mon, 03 Jun 2019 23:19:07: #2 predicted fragment length is 112 bps INFO @ Mon, 03 Jun 2019 23:19:07: #2 alternative fragment length(s) may be 4,112 bps INFO @ Mon, 03 Jun 2019 23:19:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5379466/SRX5379466.05_model.r INFO @ Mon, 03 Jun 2019 23:19:07: #3 Call peaks... INFO @ Mon, 03 Jun 2019 23:19:07: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 23:19:10: 11000000 INFO @ Mon, 03 Jun 2019 23:19:21: 12000000 INFO @ Mon, 03 Jun 2019 23:19:28: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 23:19:28: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 23:19:28: #1 total tags in treatment: 12752826 INFO @ Mon, 03 Jun 2019 23:19:28: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 23:19:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 23:19:28: #1 tags after filtering in treatment: 12752826 INFO @ Mon, 03 Jun 2019 23:19:28: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 23:19:28: #1 finished! INFO @ Mon, 03 Jun 2019 23:19:28: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 23:19:28: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 23:19:30: #2 number of paired peaks: 3489 INFO @ Mon, 03 Jun 2019 23:19:30: start model_add_line... INFO @ Mon, 03 Jun 2019 23:19:30: start X-correlation... INFO @ Mon, 03 Jun 2019 23:19:30: end of X-cor INFO @ Mon, 03 Jun 2019 23:19:30: #2 finished! INFO @ Mon, 03 Jun 2019 23:19:30: #2 predicted fragment length is 112 bps INFO @ Mon, 03 Jun 2019 23:19:30: #2 alternative fragment length(s) may be 4,112 bps INFO @ Mon, 03 Jun 2019 23:19:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5379466/SRX5379466.20_model.r INFO @ Mon, 03 Jun 2019 23:19:30: #3 Call peaks... INFO @ Mon, 03 Jun 2019 23:19:30: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 23:19:31: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 23:19:46: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 23:19:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5379466/SRX5379466.10_peaks.xls INFO @ Mon, 03 Jun 2019 23:19:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5379466/SRX5379466.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 23:19:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5379466/SRX5379466.10_summits.bed INFO @ Mon, 03 Jun 2019 23:19:49: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (4730 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 23:20:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5379466/SRX5379466.05_peaks.xls INFO @ Mon, 03 Jun 2019 23:20:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5379466/SRX5379466.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 23:20:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5379466/SRX5379466.05_summits.bed INFO @ Mon, 03 Jun 2019 23:20:05: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (8643 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 23:20:12: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 23:20:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5379466/SRX5379466.20_peaks.xls INFO @ Mon, 03 Jun 2019 23:20:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5379466/SRX5379466.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 23:20:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5379466/SRX5379466.20_summits.bed INFO @ Mon, 03 Jun 2019 23:20:30: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (2308 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。