Job ID = 1294545 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T23:43:59 fasterq-dump.2.9.6 fatal: SIGNAL - Segmentation fault spots read : 16,585,779 reads read : 16,585,779 reads written : 16,585,779 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: 00:03:56 16585779 reads; of these: 16585779 (100.00%) were unpaired; of these: 991390 (5.98%) aligned 0 times 14593889 (87.99%) aligned exactly 1 time 1000500 (6.03%) aligned >1 times 94.02% overall alignment rate Time searching: 00:03:56 Overall time: 00:03:56 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] 3147333 / 15594389 = 0.2018 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 09:02:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287732/SRX287732.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287732/SRX287732.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287732/SRX287732.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287732/SRX287732.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 09:02:08: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:02:08: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:02:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287732/SRX287732.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287732/SRX287732.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287732/SRX287732.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287732/SRX287732.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 09:02:08: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:02:08: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:02:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287732/SRX287732.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287732/SRX287732.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287732/SRX287732.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287732/SRX287732.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 09:02:08: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:02:08: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:02:15: 1000000 INFO @ Mon, 03 Jun 2019 09:02:16: 1000000 INFO @ Mon, 03 Jun 2019 09:02:17: 1000000 INFO @ Mon, 03 Jun 2019 09:02:22: 2000000 INFO @ Mon, 03 Jun 2019 09:02:24: 2000000 INFO @ Mon, 03 Jun 2019 09:02:25: 2000000 INFO @ Mon, 03 Jun 2019 09:02:29: 3000000 INFO @ Mon, 03 Jun 2019 09:02:32: 3000000 INFO @ Mon, 03 Jun 2019 09:02:34: 3000000 INFO @ Mon, 03 Jun 2019 09:02:36: 4000000 INFO @ Mon, 03 Jun 2019 09:02:40: 4000000 INFO @ Mon, 03 Jun 2019 09:02:42: 4000000 INFO @ Mon, 03 Jun 2019 09:02:42: 5000000 INFO @ Mon, 03 Jun 2019 09:02:48: 5000000 INFO @ Mon, 03 Jun 2019 09:02:49: 6000000 INFO @ Mon, 03 Jun 2019 09:02:50: 5000000 INFO @ Mon, 03 Jun 2019 09:02:56: 7000000 INFO @ Mon, 03 Jun 2019 09:02:56: 6000000 INFO @ Mon, 03 Jun 2019 09:02:59: 6000000 INFO @ Mon, 03 Jun 2019 09:03:03: 8000000 INFO @ Mon, 03 Jun 2019 09:03:04: 7000000 INFO @ Mon, 03 Jun 2019 09:03:07: 7000000 INFO @ Mon, 03 Jun 2019 09:03:10: 9000000 INFO @ Mon, 03 Jun 2019 09:03:12: 8000000 INFO @ Mon, 03 Jun 2019 09:03:16: 8000000 INFO @ Mon, 03 Jun 2019 09:03:17: 10000000 INFO @ Mon, 03 Jun 2019 09:03:20: 9000000 INFO @ Mon, 03 Jun 2019 09:03:24: 11000000 INFO @ Mon, 03 Jun 2019 09:03:25: 9000000 INFO @ Mon, 03 Jun 2019 09:03:28: 10000000 INFO @ Mon, 03 Jun 2019 09:03:31: 12000000 INFO @ Mon, 03 Jun 2019 09:03:34: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 09:03:34: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 09:03:34: #1 total tags in treatment: 12447056 INFO @ Mon, 03 Jun 2019 09:03:34: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:03:34: #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 09:03:34: 10000000 INFO @ Mon, 03 Jun 2019 09:03:34: #1 tags after filtering in treatment: 12447056 INFO @ Mon, 03 Jun 2019 09:03:34: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 09:03:34: #1 finished! INFO @ Mon, 03 Jun 2019 09:03:34: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:03:34: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:03:36: 11000000 INFO @ Mon, 03 Jun 2019 09:03:37: #2 number of paired peaks: 11145 INFO @ Mon, 03 Jun 2019 09:03:37: start model_add_line... INFO @ Mon, 03 Jun 2019 09:03:37: start X-correlation... INFO @ Mon, 03 Jun 2019 09:03:37: end of X-cor INFO @ Mon, 03 Jun 2019 09:03:37: #2 finished! INFO @ Mon, 03 Jun 2019 09:03:37: #2 predicted fragment length is 238 bps INFO @ Mon, 03 Jun 2019 09:03:37: #2 alternative fragment length(s) may be 238 bps INFO @ Mon, 03 Jun 2019 09:03:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287732/SRX287732.10_model.r INFO @ Mon, 03 Jun 2019 09:03:37: #3 Call peaks... INFO @ Mon, 03 Jun 2019 09:03:37: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 09:03:43: 11000000 INFO @ Mon, 03 Jun 2019 09:03:43: 12000000 INFO @ Mon, 03 Jun 2019 09:03:47: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 09:03:47: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 09:03:47: #1 total tags in treatment: 12447056 INFO @ Mon, 03 Jun 2019 09:03:47: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:03:47: #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 09:03:47: #1 tags after filtering in treatment: 12447056 INFO @ Mon, 03 Jun 2019 09:03:47: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 09:03:47: #1 finished! INFO @ Mon, 03 Jun 2019 09:03:47: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:03:47: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:03:49: #2 number of paired peaks: 11145 INFO @ Mon, 03 Jun 2019 09:03:49: start model_add_line... INFO @ Mon, 03 Jun 2019 09:03:50: start X-correlation... INFO @ Mon, 03 Jun 2019 09:03:50: end of X-cor INFO @ Mon, 03 Jun 2019 09:03:50: #2 finished! INFO @ Mon, 03 Jun 2019 09:03:50: #2 predicted fragment length is 238 bps INFO @ Mon, 03 Jun 2019 09:03:50: #2 alternative fragment length(s) may be 238 bps INFO @ Mon, 03 Jun 2019 09:03:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287732/SRX287732.20_model.r INFO @ Mon, 03 Jun 2019 09:03:50: #3 Call peaks... INFO @ Mon, 03 Jun 2019 09:03:50: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 09:03:51: 12000000 INFO @ Mon, 03 Jun 2019 09:03:55: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 09:03:55: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 09:03:55: #1 total tags in treatment: 12447056 INFO @ Mon, 03 Jun 2019 09:03:55: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:03:55: #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 09:03:55: #1 tags after filtering in treatment: 12447056 INFO @ Mon, 03 Jun 2019 09:03:55: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 09:03:55: #1 finished! INFO @ Mon, 03 Jun 2019 09:03:55: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:03:55: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:03:57: #2 number of paired peaks: 11145 INFO @ Mon, 03 Jun 2019 09:03:57: start model_add_line... INFO @ Mon, 03 Jun 2019 09:03:57: start X-correlation... INFO @ Mon, 03 Jun 2019 09:03:57: end of X-cor INFO @ Mon, 03 Jun 2019 09:03:57: #2 finished! INFO @ Mon, 03 Jun 2019 09:03:57: #2 predicted fragment length is 238 bps INFO @ Mon, 03 Jun 2019 09:03:57: #2 alternative fragment length(s) may be 238 bps INFO @ Mon, 03 Jun 2019 09:03:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287732/SRX287732.05_model.r INFO @ Mon, 03 Jun 2019 09:03:57: #3 Call peaks... INFO @ Mon, 03 Jun 2019 09:03:57: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 09:04:22: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 09:04:34: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 09:04:41: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 09:04:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287732/SRX287732.10_peaks.xls INFO @ Mon, 03 Jun 2019 09:04:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287732/SRX287732.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 09:04:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287732/SRX287732.10_summits.bed INFO @ Mon, 03 Jun 2019 09:04:43: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (7789 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 09:04:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287732/SRX287732.20_peaks.xls INFO @ Mon, 03 Jun 2019 09:04:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287732/SRX287732.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 09:04:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287732/SRX287732.20_summits.bed INFO @ Mon, 03 Jun 2019 09:04:52: Done! pass1 - making usageList (13 chroms): 4 millis pass2 - checking and writing primary data (6674 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 09:04:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287732/SRX287732.05_peaks.xls INFO @ Mon, 03 Jun 2019 09:04:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287732/SRX287732.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 09:04:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287732/SRX287732.05_summits.bed INFO @ Mon, 03 Jun 2019 09:04:59: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (8519 records, 4 fields): 12 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。