Job ID = 1294761 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 14,919,889 reads read : 14,919,889 reads written : 14,919,889 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: 00:04:37 14919889 reads; of these: 14919889 (100.00%) were unpaired; of these: 605358 (4.06%) aligned 0 times 12300558 (82.44%) aligned exactly 1 time 2013973 (13.50%) aligned >1 times 95.94% overall alignment rate Time searching: 00:04:37 Overall time: 00:04:37 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] 1827202 / 14314531 = 0.1276 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 10:09:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287864/SRX287864.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287864/SRX287864.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287864/SRX287864.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287864/SRX287864.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 10:09:37: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:09:37: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:09:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287864/SRX287864.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287864/SRX287864.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287864/SRX287864.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287864/SRX287864.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 10:09:37: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:09:37: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:09:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287864/SRX287864.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287864/SRX287864.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287864/SRX287864.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287864/SRX287864.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 10:09:37: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:09:37: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:09:47: 1000000 INFO @ Mon, 03 Jun 2019 10:09:47: 1000000 INFO @ Mon, 03 Jun 2019 10:09:47: 1000000 INFO @ Mon, 03 Jun 2019 10:09:57: 2000000 INFO @ Mon, 03 Jun 2019 10:09:57: 2000000 INFO @ Mon, 03 Jun 2019 10:09:57: 2000000 INFO @ Mon, 03 Jun 2019 10:10:07: 3000000 INFO @ Mon, 03 Jun 2019 10:10:07: 3000000 INFO @ Mon, 03 Jun 2019 10:10:07: 3000000 INFO @ Mon, 03 Jun 2019 10:10:16: 4000000 INFO @ Mon, 03 Jun 2019 10:10:16: 4000000 INFO @ Mon, 03 Jun 2019 10:10:17: 4000000 INFO @ Mon, 03 Jun 2019 10:10:25: 5000000 INFO @ Mon, 03 Jun 2019 10:10:26: 5000000 INFO @ Mon, 03 Jun 2019 10:10:26: 5000000 INFO @ Mon, 03 Jun 2019 10:10:34: 6000000 INFO @ Mon, 03 Jun 2019 10:10:35: 6000000 INFO @ Mon, 03 Jun 2019 10:10:36: 6000000 INFO @ Mon, 03 Jun 2019 10:10:43: 7000000 INFO @ Mon, 03 Jun 2019 10:10:45: 7000000 INFO @ Mon, 03 Jun 2019 10:10:45: 7000000 INFO @ Mon, 03 Jun 2019 10:10:54: 8000000 INFO @ Mon, 03 Jun 2019 10:10:54: 8000000 INFO @ Mon, 03 Jun 2019 10:10:55: 8000000 INFO @ Mon, 03 Jun 2019 10:11:03: 9000000 INFO @ Mon, 03 Jun 2019 10:11:03: 9000000 INFO @ Mon, 03 Jun 2019 10:11:04: 9000000 INFO @ Mon, 03 Jun 2019 10:11:12: 10000000 INFO @ Mon, 03 Jun 2019 10:11:13: 10000000 INFO @ Mon, 03 Jun 2019 10:11:13: 10000000 INFO @ Mon, 03 Jun 2019 10:11:23: 11000000 INFO @ Mon, 03 Jun 2019 10:11:23: 11000000 INFO @ Mon, 03 Jun 2019 10:11:24: 11000000 INFO @ Mon, 03 Jun 2019 10:11:32: 12000000 INFO @ Mon, 03 Jun 2019 10:11:32: 12000000 INFO @ Mon, 03 Jun 2019 10:11:32: 12000000 INFO @ Mon, 03 Jun 2019 10:11:36: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 10:11:36: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 10:11:36: #1 total tags in treatment: 12487329 INFO @ Mon, 03 Jun 2019 10:11:36: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:11:36: #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 10:11:36: #1 tags after filtering in treatment: 12487329 INFO @ Mon, 03 Jun 2019 10:11:36: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:11:36: #1 finished! INFO @ Mon, 03 Jun 2019 10:11:36: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:11:36: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:11:37: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 10:11:37: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 10:11:37: #1 total tags in treatment: 12487329 INFO @ Mon, 03 Jun 2019 10:11:37: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:11:37: #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 10:11:37: #1 tags after filtering in treatment: 12487329 INFO @ Mon, 03 Jun 2019 10:11:37: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:11:37: #1 finished! INFO @ Mon, 03 Jun 2019 10:11:37: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:11:37: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:11:37: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 10:11:37: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 10:11:37: #1 total tags in treatment: 12487329 INFO @ Mon, 03 Jun 2019 10:11:37: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:11:37: #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 10:11:38: #1 tags after filtering in treatment: 12487329 INFO @ Mon, 03 Jun 2019 10:11:38: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:11:38: #1 finished! INFO @ Mon, 03 Jun 2019 10:11:38: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:11:38: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:11:38: #2 number of paired peaks: 2840 INFO @ Mon, 03 Jun 2019 10:11:38: start model_add_line... INFO @ Mon, 03 Jun 2019 10:11:38: start X-correlation... INFO @ Mon, 03 Jun 2019 10:11:38: end of X-cor INFO @ Mon, 03 Jun 2019 10:11:38: #2 finished! INFO @ Mon, 03 Jun 2019 10:11:38: #2 predicted fragment length is 216 bps INFO @ Mon, 03 Jun 2019 10:11:38: #2 alternative fragment length(s) may be 3,216 bps INFO @ Mon, 03 Jun 2019 10:11:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287864/SRX287864.05_model.r INFO @ Mon, 03 Jun 2019 10:11:38: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:11:38: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:11:38: #2 number of paired peaks: 2840 INFO @ Mon, 03 Jun 2019 10:11:38: start model_add_line... INFO @ Mon, 03 Jun 2019 10:11:39: start X-correlation... INFO @ Mon, 03 Jun 2019 10:11:39: end of X-cor INFO @ Mon, 03 Jun 2019 10:11:39: #2 finished! INFO @ Mon, 03 Jun 2019 10:11:39: #2 predicted fragment length is 216 bps INFO @ Mon, 03 Jun 2019 10:11:39: #2 alternative fragment length(s) may be 3,216 bps INFO @ Mon, 03 Jun 2019 10:11:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287864/SRX287864.10_model.r INFO @ Mon, 03 Jun 2019 10:11:39: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:11:39: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:11:39: #2 number of paired peaks: 2840 INFO @ Mon, 03 Jun 2019 10:11:39: start model_add_line... INFO @ Mon, 03 Jun 2019 10:11:39: start X-correlation... INFO @ Mon, 03 Jun 2019 10:11:39: end of X-cor INFO @ Mon, 03 Jun 2019 10:11:39: #2 finished! INFO @ Mon, 03 Jun 2019 10:11:39: #2 predicted fragment length is 216 bps INFO @ Mon, 03 Jun 2019 10:11:39: #2 alternative fragment length(s) may be 3,216 bps INFO @ Mon, 03 Jun 2019 10:11:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287864/SRX287864.20_model.r INFO @ Mon, 03 Jun 2019 10:11:39: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:11:39: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:12:18: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:12:19: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:12:19: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:12:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287864/SRX287864.05_peaks.xls INFO @ Mon, 03 Jun 2019 10:12:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287864/SRX287864.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:12:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287864/SRX287864.05_summits.bed INFO @ Mon, 03 Jun 2019 10:12:36: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (5732 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 10:12:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287864/SRX287864.10_peaks.xls INFO @ Mon, 03 Jun 2019 10:12:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287864/SRX287864.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:12:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287864/SRX287864.20_peaks.xls INFO @ Mon, 03 Jun 2019 10:12:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287864/SRX287864.10_summits.bed INFO @ Mon, 03 Jun 2019 10:12:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287864/SRX287864.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:12:37: Done! INFO @ Mon, 03 Jun 2019 10:12:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287864/SRX287864.20_summits.bed INFO @ Mon, 03 Jun 2019 10:12:37: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (1222 records, 4 fields): 6 millis pass1 - making usageList (14 chroms): 2 millis CompletedMACS2peakCalling pass2 - checking and writing primary data (3245 records, 4 fields): 10 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。