Job ID = 1295185 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 13,556,446 reads read : 13,556,446 reads written : 13,556,446 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: 00:03:34 13556446 reads; of these: 13556446 (100.00%) were unpaired; of these: 890926 (6.57%) aligned 0 times 11931154 (88.01%) aligned exactly 1 time 734366 (5.42%) aligned >1 times 93.43% overall alignment rate Time searching: 00:03:34 Overall time: 00:03:34 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 8 files... [bam_rmdupse_core] 1647656 / 12665520 = 0.1301 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 12:38:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX331372/SRX331372.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX331372/SRX331372.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX331372/SRX331372.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX331372/SRX331372.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 12:38:15: #1 read tag files... INFO @ Mon, 03 Jun 2019 12:38:15: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 12:38:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX331372/SRX331372.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX331372/SRX331372.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX331372/SRX331372.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX331372/SRX331372.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 12:38:15: #1 read tag files... INFO @ Mon, 03 Jun 2019 12:38:15: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 12:38:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX331372/SRX331372.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX331372/SRX331372.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX331372/SRX331372.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX331372/SRX331372.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 12:38:15: #1 read tag files... INFO @ Mon, 03 Jun 2019 12:38:15: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 12:38:25: 1000000 INFO @ Mon, 03 Jun 2019 12:38:25: 1000000 INFO @ Mon, 03 Jun 2019 12:38:26: 1000000 INFO @ Mon, 03 Jun 2019 12:38:34: 2000000 INFO @ Mon, 03 Jun 2019 12:38:34: 2000000 INFO @ Mon, 03 Jun 2019 12:38:37: 2000000 INFO @ Mon, 03 Jun 2019 12:38:44: 3000000 INFO @ Mon, 03 Jun 2019 12:38:44: 3000000 INFO @ Mon, 03 Jun 2019 12:38:47: 3000000 INFO @ Mon, 03 Jun 2019 12:38:53: 4000000 INFO @ Mon, 03 Jun 2019 12:38:53: 4000000 INFO @ Mon, 03 Jun 2019 12:38:58: 4000000 INFO @ Mon, 03 Jun 2019 12:39:02: 5000000 INFO @ Mon, 03 Jun 2019 12:39:03: 5000000 INFO @ Mon, 03 Jun 2019 12:39:10: 5000000 INFO @ Mon, 03 Jun 2019 12:39:12: 6000000 INFO @ Mon, 03 Jun 2019 12:39:12: 6000000 INFO @ Mon, 03 Jun 2019 12:39:21: 7000000 INFO @ Mon, 03 Jun 2019 12:39:21: 6000000 INFO @ Mon, 03 Jun 2019 12:39:21: 7000000 INFO @ Mon, 03 Jun 2019 12:39:30: 8000000 INFO @ Mon, 03 Jun 2019 12:39:30: 8000000 INFO @ Mon, 03 Jun 2019 12:39:32: 7000000 INFO @ Mon, 03 Jun 2019 12:39:39: 9000000 INFO @ Mon, 03 Jun 2019 12:39:39: 9000000 INFO @ Mon, 03 Jun 2019 12:39:42: 8000000 INFO @ Mon, 03 Jun 2019 12:39:48: 10000000 INFO @ Mon, 03 Jun 2019 12:39:49: 10000000 INFO @ Mon, 03 Jun 2019 12:39:53: 9000000 INFO @ Mon, 03 Jun 2019 12:39:58: 11000000 INFO @ Mon, 03 Jun 2019 12:39:59: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 12:39:59: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 12:39:59: #1 total tags in treatment: 11017864 INFO @ Mon, 03 Jun 2019 12:39:59: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 12:39:59: #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 12:39:59: #1 tags after filtering in treatment: 11017864 INFO @ Mon, 03 Jun 2019 12:39:59: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 12:39:59: #1 finished! INFO @ Mon, 03 Jun 2019 12:39:59: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 12:39:59: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 12:40:00: 11000000 INFO @ Mon, 03 Jun 2019 12:40:00: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 12:40:00: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 12:40:00: #1 total tags in treatment: 11017864 INFO @ Mon, 03 Jun 2019 12:40:00: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 12:40:00: #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 12:40:00: #1 tags after filtering in treatment: 11017864 INFO @ Mon, 03 Jun 2019 12:40:00: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 12:40:00: #1 finished! INFO @ Mon, 03 Jun 2019 12:40:00: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 12:40:00: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 12:40:01: #2 number of paired peaks: 4876 INFO @ Mon, 03 Jun 2019 12:40:01: start model_add_line... INFO @ Mon, 03 Jun 2019 12:40:01: start X-correlation... INFO @ Mon, 03 Jun 2019 12:40:01: end of X-cor INFO @ Mon, 03 Jun 2019 12:40:01: #2 finished! INFO @ Mon, 03 Jun 2019 12:40:01: #2 predicted fragment length is 226 bps INFO @ Mon, 03 Jun 2019 12:40:01: #2 alternative fragment length(s) may be 226 bps INFO @ Mon, 03 Jun 2019 12:40:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX331372/SRX331372.20_model.r INFO @ Mon, 03 Jun 2019 12:40:01: #3 Call peaks... INFO @ Mon, 03 Jun 2019 12:40:01: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 12:40:02: #2 number of paired peaks: 4876 INFO @ Mon, 03 Jun 2019 12:40:02: start model_add_line... INFO @ Mon, 03 Jun 2019 12:40:02: start X-correlation... INFO @ Mon, 03 Jun 2019 12:40:02: end of X-cor INFO @ Mon, 03 Jun 2019 12:40:02: #2 finished! INFO @ Mon, 03 Jun 2019 12:40:02: #2 predicted fragment length is 226 bps INFO @ Mon, 03 Jun 2019 12:40:02: #2 alternative fragment length(s) may be 226 bps INFO @ Mon, 03 Jun 2019 12:40:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX331372/SRX331372.05_model.r INFO @ Mon, 03 Jun 2019 12:40:02: #3 Call peaks... INFO @ Mon, 03 Jun 2019 12:40:02: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 12:40:04: 10000000 INFO @ Mon, 03 Jun 2019 12:40:13: 11000000 INFO @ Mon, 03 Jun 2019 12:40:14: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 12:40:14: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 12:40:14: #1 total tags in treatment: 11017864 INFO @ Mon, 03 Jun 2019 12:40:14: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 12:40:14: #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 12:40:14: #1 tags after filtering in treatment: 11017864 INFO @ Mon, 03 Jun 2019 12:40:14: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 12:40:14: #1 finished! INFO @ Mon, 03 Jun 2019 12:40:14: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 12:40:14: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 12:40:15: #2 number of paired peaks: 4876 INFO @ Mon, 03 Jun 2019 12:40:15: start model_add_line... INFO @ Mon, 03 Jun 2019 12:40:15: start X-correlation... INFO @ Mon, 03 Jun 2019 12:40:15: end of X-cor INFO @ Mon, 03 Jun 2019 12:40:15: #2 finished! INFO @ Mon, 03 Jun 2019 12:40:15: #2 predicted fragment length is 226 bps INFO @ Mon, 03 Jun 2019 12:40:15: #2 alternative fragment length(s) may be 226 bps INFO @ Mon, 03 Jun 2019 12:40:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX331372/SRX331372.10_model.r INFO @ Mon, 03 Jun 2019 12:40:15: #3 Call peaks... INFO @ Mon, 03 Jun 2019 12:40:15: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 12:40:39: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 12:40:40: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 12:40:53: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 12:40:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX331372/SRX331372.20_peaks.xls INFO @ Mon, 03 Jun 2019 12:40:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX331372/SRX331372.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 12:40:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX331372/SRX331372.20_summits.bed INFO @ Mon, 03 Jun 2019 12:40:58: Done! INFO @ Mon, 03 Jun 2019 12:40:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX331372/SRX331372.05_peaks.xls pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (2487 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 12:40:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX331372/SRX331372.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 12:40:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX331372/SRX331372.05_summits.bed INFO @ Mon, 03 Jun 2019 12:40:58: Done! pass1 - making usageList (13 chroms): 4 millis pass2 - checking and writing primary data (7719 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 12:41:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX331372/SRX331372.10_peaks.xls INFO @ Mon, 03 Jun 2019 12:41:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX331372/SRX331372.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 12:41:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX331372/SRX331372.10_summits.bed INFO @ Mon, 03 Jun 2019 12:41:11: Done! pass1 - making usageList (13 chroms): 3 millis pass2 - checking and writing primary data (4840 records, 4 fields): 13 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。