Job ID = 1294083 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 32,097,522 reads read : 32,097,522 reads written : 32,097,522 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: 00:07:14 32097522 reads; of these: 32097522 (100.00%) were unpaired; of these: 4883187 (15.21%) aligned 0 times 22973948 (71.58%) aligned exactly 1 time 4240387 (13.21%) aligned >1 times 84.79% overall alignment rate Time searching: 00:07:14 Overall time: 00:07:14 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] 18568469 / 27214335 = 0.6823 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 04:57:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX181440/SRX181440.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX181440/SRX181440.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX181440/SRX181440.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX181440/SRX181440.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 04:57:41: #1 read tag files... INFO @ Mon, 03 Jun 2019 04:57:41: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 04:57:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX181440/SRX181440.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX181440/SRX181440.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX181440/SRX181440.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX181440/SRX181440.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 04:57:41: #1 read tag files... INFO @ Mon, 03 Jun 2019 04:57:41: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 04:57:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX181440/SRX181440.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX181440/SRX181440.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX181440/SRX181440.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX181440/SRX181440.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 04:57:41: #1 read tag files... INFO @ Mon, 03 Jun 2019 04:57:41: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 04:57:48: 1000000 INFO @ Mon, 03 Jun 2019 04:57:48: 1000000 INFO @ Mon, 03 Jun 2019 04:57:48: 1000000 INFO @ Mon, 03 Jun 2019 04:57:54: 2000000 INFO @ Mon, 03 Jun 2019 04:57:55: 2000000 INFO @ Mon, 03 Jun 2019 04:57:55: 2000000 INFO @ Mon, 03 Jun 2019 04:58:00: 3000000 INFO @ Mon, 03 Jun 2019 04:58:02: 3000000 INFO @ Mon, 03 Jun 2019 04:58:02: 3000000 INFO @ Mon, 03 Jun 2019 04:58:06: 4000000 INFO @ Mon, 03 Jun 2019 04:58:09: 4000000 INFO @ Mon, 03 Jun 2019 04:58:09: 4000000 INFO @ Mon, 03 Jun 2019 04:58:13: 5000000 INFO @ Mon, 03 Jun 2019 04:58:15: 5000000 INFO @ Mon, 03 Jun 2019 04:58:16: 5000000 INFO @ Mon, 03 Jun 2019 04:58:19: 6000000 INFO @ Mon, 03 Jun 2019 04:58:22: 6000000 INFO @ Mon, 03 Jun 2019 04:58:22: 6000000 INFO @ Mon, 03 Jun 2019 04:58:25: 7000000 INFO @ Mon, 03 Jun 2019 04:58:29: 7000000 INFO @ Mon, 03 Jun 2019 04:58:29: 7000000 INFO @ Mon, 03 Jun 2019 04:58:32: 8000000 INFO @ Mon, 03 Jun 2019 04:58:36: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 04:58:36: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 04:58:36: #1 total tags in treatment: 8645866 INFO @ Mon, 03 Jun 2019 04:58:36: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 04:58:36: #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 04:58:36: 8000000 INFO @ Mon, 03 Jun 2019 04:58:36: #1 tags after filtering in treatment: 8645866 INFO @ Mon, 03 Jun 2019 04:58:36: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 04:58:36: #1 finished! INFO @ Mon, 03 Jun 2019 04:58:36: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 04:58:36: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 04:58:36: 8000000 INFO @ Mon, 03 Jun 2019 04:58:37: #2 number of paired peaks: 2404 INFO @ Mon, 03 Jun 2019 04:58:37: start model_add_line... INFO @ Mon, 03 Jun 2019 04:58:37: start X-correlation... INFO @ Mon, 03 Jun 2019 04:58:37: end of X-cor INFO @ Mon, 03 Jun 2019 04:58:37: #2 finished! INFO @ Mon, 03 Jun 2019 04:58:37: #2 predicted fragment length is 103 bps INFO @ Mon, 03 Jun 2019 04:58:37: #2 alternative fragment length(s) may be 103 bps INFO @ Mon, 03 Jun 2019 04:58:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX181440/SRX181440.10_model.r INFO @ Mon, 03 Jun 2019 04:58:37: #3 Call peaks... INFO @ Mon, 03 Jun 2019 04:58:37: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 04:58:40: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 04:58:40: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 04:58:40: #1 total tags in treatment: 8645866 INFO @ Mon, 03 Jun 2019 04:58:40: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 04:58:40: #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 04:58:40: #1 tags after filtering in treatment: 8645866 INFO @ Mon, 03 Jun 2019 04:58:40: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 04:58:40: #1 finished! INFO @ Mon, 03 Jun 2019 04:58:40: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 04:58:40: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 04:58:40: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 04:58:40: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 04:58:40: #1 total tags in treatment: 8645866 INFO @ Mon, 03 Jun 2019 04:58:40: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 04:58:40: #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 04:58:41: #1 tags after filtering in treatment: 8645866 INFO @ Mon, 03 Jun 2019 04:58:41: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 04:58:41: #1 finished! INFO @ Mon, 03 Jun 2019 04:58:41: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 04:58:41: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 04:58:41: #2 number of paired peaks: 2404 INFO @ Mon, 03 Jun 2019 04:58:41: start model_add_line... INFO @ Mon, 03 Jun 2019 04:58:42: start X-correlation... INFO @ Mon, 03 Jun 2019 04:58:42: end of X-cor INFO @ Mon, 03 Jun 2019 04:58:42: #2 finished! INFO @ Mon, 03 Jun 2019 04:58:42: #2 predicted fragment length is 103 bps INFO @ Mon, 03 Jun 2019 04:58:42: #2 alternative fragment length(s) may be 103 bps INFO @ Mon, 03 Jun 2019 04:58:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX181440/SRX181440.05_model.r INFO @ Mon, 03 Jun 2019 04:58:42: #3 Call peaks... INFO @ Mon, 03 Jun 2019 04:58:42: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 04:58:42: #2 number of paired peaks: 2404 INFO @ Mon, 03 Jun 2019 04:58:42: start model_add_line... INFO @ Mon, 03 Jun 2019 04:58:42: start X-correlation... INFO @ Mon, 03 Jun 2019 04:58:42: end of X-cor INFO @ Mon, 03 Jun 2019 04:58:42: #2 finished! INFO @ Mon, 03 Jun 2019 04:58:42: #2 predicted fragment length is 103 bps INFO @ Mon, 03 Jun 2019 04:58:42: #2 alternative fragment length(s) may be 103 bps INFO @ Mon, 03 Jun 2019 04:58:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX181440/SRX181440.20_model.r INFO @ Mon, 03 Jun 2019 04:58:42: #3 Call peaks... INFO @ Mon, 03 Jun 2019 04:58:42: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 04:59:03: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 04:59:08: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 04:59:08: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 04:59:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX181440/SRX181440.10_peaks.xls INFO @ Mon, 03 Jun 2019 04:59:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX181440/SRX181440.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 04:59:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX181440/SRX181440.10_summits.bed INFO @ Mon, 03 Jun 2019 04:59:16: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (5673 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 04:59:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX181440/SRX181440.05_peaks.xls INFO @ Mon, 03 Jun 2019 04:59:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX181440/SRX181440.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 04:59:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX181440/SRX181440.05_summits.bed INFO @ Mon, 03 Jun 2019 04:59:21: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (9360 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 04:59:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX181440/SRX181440.20_peaks.xls INFO @ Mon, 03 Jun 2019 04:59:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX181440/SRX181440.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 04:59:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX181440/SRX181440.20_summits.bed INFO @ Mon, 03 Jun 2019 04:59:21: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (2354 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。