Job ID = 1295721 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 26,949,113 reads read : 26,949,113 reads written : 26,949,113 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: 00:09:13 26949113 reads; of these: 26949113 (100.00%) were unpaired; of these: 2199840 (8.16%) aligned 0 times 19527263 (72.46%) aligned exactly 1 time 5222010 (19.38%) aligned >1 times 91.84% overall alignment rate Time searching: 00:09:13 Overall time: 00:09:13 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] 16721020 / 24749273 = 0.6756 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 15:27:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4375821/SRX4375821.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4375821/SRX4375821.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4375821/SRX4375821.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4375821/SRX4375821.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 15:27:38: #1 read tag files... INFO @ Mon, 03 Jun 2019 15:27:38: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 15:27:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4375821/SRX4375821.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4375821/SRX4375821.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4375821/SRX4375821.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4375821/SRX4375821.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 15:27:38: #1 read tag files... INFO @ Mon, 03 Jun 2019 15:27:38: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 15:27:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4375821/SRX4375821.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4375821/SRX4375821.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4375821/SRX4375821.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4375821/SRX4375821.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 15:27:38: #1 read tag files... INFO @ Mon, 03 Jun 2019 15:27:38: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 15:27:46: 1000000 INFO @ Mon, 03 Jun 2019 15:27:46: 1000000 INFO @ Mon, 03 Jun 2019 15:27:46: 1000000 INFO @ Mon, 03 Jun 2019 15:27:53: 2000000 INFO @ Mon, 03 Jun 2019 15:27:53: 2000000 INFO @ Mon, 03 Jun 2019 15:27:53: 2000000 INFO @ Mon, 03 Jun 2019 15:28:00: 3000000 INFO @ Mon, 03 Jun 2019 15:28:00: 3000000 INFO @ Mon, 03 Jun 2019 15:28:01: 3000000 INFO @ Mon, 03 Jun 2019 15:28:07: 4000000 INFO @ Mon, 03 Jun 2019 15:28:07: 4000000 INFO @ Mon, 03 Jun 2019 15:28:09: 4000000 INFO @ Mon, 03 Jun 2019 15:28:14: 5000000 INFO @ Mon, 03 Jun 2019 15:28:15: 5000000 INFO @ Mon, 03 Jun 2019 15:28:16: 5000000 INFO @ Mon, 03 Jun 2019 15:28:22: 6000000 INFO @ Mon, 03 Jun 2019 15:28:22: 6000000 INFO @ Mon, 03 Jun 2019 15:28:23: 6000000 INFO @ Mon, 03 Jun 2019 15:28:29: 7000000 INFO @ Mon, 03 Jun 2019 15:28:29: 7000000 INFO @ Mon, 03 Jun 2019 15:28:30: 7000000 INFO @ Mon, 03 Jun 2019 15:28:36: 8000000 INFO @ Mon, 03 Jun 2019 15:28:36: 8000000 INFO @ Mon, 03 Jun 2019 15:28:37: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 15:28:37: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 15:28:37: #1 total tags in treatment: 8028253 INFO @ Mon, 03 Jun 2019 15:28:37: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 15:28:37: #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 15:28:37: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 15:28:37: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 15:28:37: #1 total tags in treatment: 8028253 INFO @ Mon, 03 Jun 2019 15:28:37: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 15:28:37: #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 15:28:37: #1 tags after filtering in treatment: 8028253 INFO @ Mon, 03 Jun 2019 15:28:37: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 15:28:37: #1 finished! INFO @ Mon, 03 Jun 2019 15:28:37: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 15:28:37: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 15:28:37: #1 tags after filtering in treatment: 8028253 INFO @ Mon, 03 Jun 2019 15:28:37: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 15:28:37: #1 finished! INFO @ Mon, 03 Jun 2019 15:28:37: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 15:28:37: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 15:28:38: #2 number of paired peaks: 1737 INFO @ Mon, 03 Jun 2019 15:28:38: start model_add_line... INFO @ Mon, 03 Jun 2019 15:28:38: 8000000 INFO @ Mon, 03 Jun 2019 15:28:38: start X-correlation... INFO @ Mon, 03 Jun 2019 15:28:38: end of X-cor INFO @ Mon, 03 Jun 2019 15:28:38: #2 finished! INFO @ Mon, 03 Jun 2019 15:28:38: #2 predicted fragment length is 106 bps INFO @ Mon, 03 Jun 2019 15:28:38: #2 alternative fragment length(s) may be 106 bps INFO @ Mon, 03 Jun 2019 15:28:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4375821/SRX4375821.05_model.r INFO @ Mon, 03 Jun 2019 15:28:38: #3 Call peaks... INFO @ Mon, 03 Jun 2019 15:28:38: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 15:28:38: #2 number of paired peaks: 1737 INFO @ Mon, 03 Jun 2019 15:28:38: start model_add_line... INFO @ Mon, 03 Jun 2019 15:28:38: start X-correlation... INFO @ Mon, 03 Jun 2019 15:28:38: end of X-cor INFO @ Mon, 03 Jun 2019 15:28:38: #2 finished! INFO @ Mon, 03 Jun 2019 15:28:38: #2 predicted fragment length is 106 bps INFO @ Mon, 03 Jun 2019 15:28:38: #2 alternative fragment length(s) may be 106 bps INFO @ Mon, 03 Jun 2019 15:28:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4375821/SRX4375821.10_model.r INFO @ Mon, 03 Jun 2019 15:28:38: #3 Call peaks... INFO @ Mon, 03 Jun 2019 15:28:38: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 15:28:38: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 15:28:38: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 15:28:38: #1 total tags in treatment: 8028253 INFO @ Mon, 03 Jun 2019 15:28:38: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 15:28:38: #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 15:28:38: #1 tags after filtering in treatment: 8028253 INFO @ Mon, 03 Jun 2019 15:28:38: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 15:28:38: #1 finished! INFO @ Mon, 03 Jun 2019 15:28:38: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 15:28:38: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 15:28:39: #2 number of paired peaks: 1737 INFO @ Mon, 03 Jun 2019 15:28:39: start model_add_line... INFO @ Mon, 03 Jun 2019 15:28:39: start X-correlation... INFO @ Mon, 03 Jun 2019 15:28:39: end of X-cor INFO @ Mon, 03 Jun 2019 15:28:39: #2 finished! INFO @ Mon, 03 Jun 2019 15:28:39: #2 predicted fragment length is 106 bps INFO @ Mon, 03 Jun 2019 15:28:39: #2 alternative fragment length(s) may be 106 bps INFO @ Mon, 03 Jun 2019 15:28:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4375821/SRX4375821.20_model.r INFO @ Mon, 03 Jun 2019 15:28:39: #3 Call peaks... INFO @ Mon, 03 Jun 2019 15:28:39: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 15:29:02: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 15:29:02: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 15:29:03: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 15:29:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4375821/SRX4375821.05_peaks.xls INFO @ Mon, 03 Jun 2019 15:29:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4375821/SRX4375821.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 15:29:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4375821/SRX4375821.05_summits.bed INFO @ Mon, 03 Jun 2019 15:29:13: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (3670 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 15:29:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4375821/SRX4375821.10_peaks.xls INFO @ Mon, 03 Jun 2019 15:29:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4375821/SRX4375821.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 15:29:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4375821/SRX4375821.10_summits.bed INFO @ Mon, 03 Jun 2019 15:29:14: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2201 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 15:29:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4375821/SRX4375821.20_peaks.xls INFO @ Mon, 03 Jun 2019 15:29:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4375821/SRX4375821.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 15:29:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4375821/SRX4375821.20_summits.bed INFO @ Mon, 03 Jun 2019 15:29:16: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (1063 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。