Job ID = 1294135 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T19:58:05 fasterq-dump.2.9.6 fatal: SIGNAL - Segmentation fault spots read : 13,661,717 reads read : 13,661,717 reads written : 13,661,717 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: 00:04:53 13661717 reads; of these: 13661717 (100.00%) were unpaired; of these: 1558656 (11.41%) aligned 0 times 7720865 (56.51%) aligned exactly 1 time 4382196 (32.08%) aligned >1 times 88.59% overall alignment rate Time searching: 00:04:53 Overall time: 00:04:53 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] 2790435 / 12103061 = 0.2306 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 05:08:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX193314/SRX193314.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX193314/SRX193314.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX193314/SRX193314.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX193314/SRX193314.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 05:08:29: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:08:29: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:08:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX193314/SRX193314.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX193314/SRX193314.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX193314/SRX193314.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX193314/SRX193314.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 05:08:29: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:08:29: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:08:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX193314/SRX193314.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX193314/SRX193314.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX193314/SRX193314.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX193314/SRX193314.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 05:08:29: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:08:29: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:08:37: 1000000 INFO @ Mon, 03 Jun 2019 05:08:38: 1000000 INFO @ Mon, 03 Jun 2019 05:08:40: 1000000 INFO @ Mon, 03 Jun 2019 05:08:45: 2000000 INFO @ Mon, 03 Jun 2019 05:08:48: 2000000 INFO @ Mon, 03 Jun 2019 05:08:51: 2000000 INFO @ Mon, 03 Jun 2019 05:08:53: 3000000 INFO @ Mon, 03 Jun 2019 05:08:57: 3000000 INFO @ Mon, 03 Jun 2019 05:09:01: 4000000 INFO @ Mon, 03 Jun 2019 05:09:01: 3000000 INFO @ Mon, 03 Jun 2019 05:09:06: 4000000 INFO @ Mon, 03 Jun 2019 05:09:10: 5000000 INFO @ Mon, 03 Jun 2019 05:09:12: 4000000 INFO @ Mon, 03 Jun 2019 05:09:15: 5000000 INFO @ Mon, 03 Jun 2019 05:09:18: 6000000 INFO @ Mon, 03 Jun 2019 05:09:23: 5000000 INFO @ Mon, 03 Jun 2019 05:09:25: 7000000 INFO @ Mon, 03 Jun 2019 05:09:26: 6000000 INFO @ Mon, 03 Jun 2019 05:09:33: 6000000 INFO @ Mon, 03 Jun 2019 05:09:35: 8000000 INFO @ Mon, 03 Jun 2019 05:09:35: 7000000 INFO @ Mon, 03 Jun 2019 05:09:44: 9000000 INFO @ Mon, 03 Jun 2019 05:09:44: 7000000 INFO @ Mon, 03 Jun 2019 05:09:45: 8000000 INFO @ Mon, 03 Jun 2019 05:09:46: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 05:09:46: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 05:09:46: #1 total tags in treatment: 9312626 INFO @ Mon, 03 Jun 2019 05:09:46: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:09:46: #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 05:09:47: #1 tags after filtering in treatment: 9312626 INFO @ Mon, 03 Jun 2019 05:09:47: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:09:47: #1 finished! INFO @ Mon, 03 Jun 2019 05:09:47: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:09:47: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:09:48: #2 number of paired peaks: 1246 INFO @ Mon, 03 Jun 2019 05:09:48: start model_add_line... INFO @ Mon, 03 Jun 2019 05:09:48: start X-correlation... INFO @ Mon, 03 Jun 2019 05:09:48: end of X-cor INFO @ Mon, 03 Jun 2019 05:09:48: #2 finished! INFO @ Mon, 03 Jun 2019 05:09:48: #2 predicted fragment length is 130 bps INFO @ Mon, 03 Jun 2019 05:09:48: #2 alternative fragment length(s) may be 130 bps INFO @ Mon, 03 Jun 2019 05:09:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX193314/SRX193314.10_model.r INFO @ Mon, 03 Jun 2019 05:09:48: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:09:48: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:09:54: 9000000 INFO @ Mon, 03 Jun 2019 05:09:55: 8000000 INFO @ Mon, 03 Jun 2019 05:09:56: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 05:09:56: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 05:09:56: #1 total tags in treatment: 9312626 INFO @ Mon, 03 Jun 2019 05:09:56: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:09:56: #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 05:09:56: #1 tags after filtering in treatment: 9312626 INFO @ Mon, 03 Jun 2019 05:09:56: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:09:56: #1 finished! INFO @ Mon, 03 Jun 2019 05:09:56: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:09:56: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:09:57: #2 number of paired peaks: 1246 INFO @ Mon, 03 Jun 2019 05:09:57: start model_add_line... INFO @ Mon, 03 Jun 2019 05:09:58: start X-correlation... INFO @ Mon, 03 Jun 2019 05:09:58: end of X-cor INFO @ Mon, 03 Jun 2019 05:09:58: #2 finished! INFO @ Mon, 03 Jun 2019 05:09:58: #2 predicted fragment length is 130 bps INFO @ Mon, 03 Jun 2019 05:09:58: #2 alternative fragment length(s) may be 130 bps INFO @ Mon, 03 Jun 2019 05:09:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX193314/SRX193314.20_model.r INFO @ Mon, 03 Jun 2019 05:09:58: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:09:58: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:10:05: 9000000 INFO @ Mon, 03 Jun 2019 05:10:08: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 05:10:08: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 05:10:08: #1 total tags in treatment: 9312626 INFO @ Mon, 03 Jun 2019 05:10:08: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:10:08: #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 05:10:08: #1 tags after filtering in treatment: 9312626 INFO @ Mon, 03 Jun 2019 05:10:08: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:10:08: #1 finished! INFO @ Mon, 03 Jun 2019 05:10:08: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:10:08: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:10:09: #2 number of paired peaks: 1246 INFO @ Mon, 03 Jun 2019 05:10:09: start model_add_line... INFO @ Mon, 03 Jun 2019 05:10:09: start X-correlation... INFO @ Mon, 03 Jun 2019 05:10:09: end of X-cor INFO @ Mon, 03 Jun 2019 05:10:09: #2 finished! INFO @ Mon, 03 Jun 2019 05:10:09: #2 predicted fragment length is 130 bps INFO @ Mon, 03 Jun 2019 05:10:09: #2 alternative fragment length(s) may be 130 bps INFO @ Mon, 03 Jun 2019 05:10:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX193314/SRX193314.05_model.r INFO @ Mon, 03 Jun 2019 05:10:09: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:10:09: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:10:16: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:10:27: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:10:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX193314/SRX193314.10_peaks.xls INFO @ Mon, 03 Jun 2019 05:10:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX193314/SRX193314.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:10:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX193314/SRX193314.10_summits.bed INFO @ Mon, 03 Jun 2019 05:10:30: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (4192 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 05:10:37: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:10:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX193314/SRX193314.20_peaks.xls INFO @ Mon, 03 Jun 2019 05:10:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX193314/SRX193314.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:10:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX193314/SRX193314.20_summits.bed INFO @ Mon, 03 Jun 2019 05:10:41: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2277 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 05:10:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX193314/SRX193314.05_peaks.xls INFO @ Mon, 03 Jun 2019 05:10:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX193314/SRX193314.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:10:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX193314/SRX193314.05_summits.bed INFO @ Mon, 03 Jun 2019 05:10:51: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6623 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。