Job ID = 4178223 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-12-05T03:21:07 fasterq-dump.2.9.6 fatal: SIGNAL - Segmentation fault spots read : 13,293,366 reads read : 13,293,366 reads written : 13,293,366 rm: cannot remove ‘[DSE]RR*’: 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: 00:02:26 13293366 reads; of these: 13293366 (100.00%) were unpaired; of these: 2024866 (15.23%) aligned 0 times 10066715 (75.73%) aligned exactly 1 time 1201785 (9.04%) aligned >1 times 84.77% overall alignment rate Time searching: 00:02:26 Overall time: 00:02:26 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 4068043 / 11268500 = 0.3610 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 05 Dec 2019 12:32:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4107863/SRX4107863.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4107863/SRX4107863.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4107863/SRX4107863.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4107863/SRX4107863.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Thu, 05 Dec 2019 12:32:17: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:32:17: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:32:24: 1000000 INFO @ Thu, 05 Dec 2019 12:32:32: 2000000 INFO @ Thu, 05 Dec 2019 12:32:39: 3000000 INFO @ Thu, 05 Dec 2019 12:32:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4107863/SRX4107863.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4107863/SRX4107863.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4107863/SRX4107863.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4107863/SRX4107863.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Thu, 05 Dec 2019 12:32:45: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:32:45: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:32:46: 4000000 INFO @ Thu, 05 Dec 2019 12:32:53: 1000000 INFO @ Thu, 05 Dec 2019 12:32:53: 5000000 INFO @ Thu, 05 Dec 2019 12:33:01: 2000000 INFO @ Thu, 05 Dec 2019 12:33:01: 6000000 INFO @ Thu, 05 Dec 2019 12:33:08: 3000000 INFO @ Thu, 05 Dec 2019 12:33:09: 7000000 INFO @ Thu, 05 Dec 2019 12:33:10: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 12:33:10: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 12:33:10: #1 total tags in treatment: 7200457 INFO @ Thu, 05 Dec 2019 12:33:10: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:33:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 12:33:10: #1 tags after filtering in treatment: 7200457 INFO @ Thu, 05 Dec 2019 12:33:10: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 12:33:10: #1 finished! INFO @ Thu, 05 Dec 2019 12:33:10: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:33:10: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:33:12: #2 number of paired peaks: 6195 INFO @ Thu, 05 Dec 2019 12:33:12: start model_add_line... INFO @ Thu, 05 Dec 2019 12:33:12: start X-correlation... INFO @ Thu, 05 Dec 2019 12:33:12: end of X-cor INFO @ Thu, 05 Dec 2019 12:33:12: #2 finished! INFO @ Thu, 05 Dec 2019 12:33:12: #2 predicted fragment length is 128 bps INFO @ Thu, 05 Dec 2019 12:33:12: #2 alternative fragment length(s) may be 128 bps INFO @ Thu, 05 Dec 2019 12:33:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4107863/SRX4107863.05_model.r INFO @ Thu, 05 Dec 2019 12:33:12: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:33:12: #3 Pre-compute pvalue-qvalue table... BedGraph に変換中... INFO @ Thu, 05 Dec 2019 12:33:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4107863/SRX4107863.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4107863/SRX4107863.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4107863/SRX4107863.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4107863/SRX4107863.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Thu, 05 Dec 2019 12:33:15: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:33:15: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:33:15: 4000000 INFO @ Thu, 05 Dec 2019 12:33:23: 5000000 INFO @ Thu, 05 Dec 2019 12:33:23: 1000000 INFO @ Thu, 05 Dec 2019 12:33:31: 2000000 INFO @ Thu, 05 Dec 2019 12:33:31: 6000000 INFO @ Thu, 05 Dec 2019 12:33:34: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:33:38: 3000000 INFO @ Thu, 05 Dec 2019 12:33:39: 7000000 INFO @ Thu, 05 Dec 2019 12:33:41: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 12:33:41: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 12:33:41: #1 total tags in treatment: 7200457 INFO @ Thu, 05 Dec 2019 12:33:41: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:33:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 12:33:41: #1 tags after filtering in treatment: 7200457 INFO @ Thu, 05 Dec 2019 12:33:41: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 12:33:41: #1 finished! INFO @ Thu, 05 Dec 2019 12:33:41: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:33:41: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:33:42: #2 number of paired peaks: 6195 INFO @ Thu, 05 Dec 2019 12:33:42: start model_add_line... INFO @ Thu, 05 Dec 2019 12:33:42: start X-correlation... INFO @ Thu, 05 Dec 2019 12:33:42: end of X-cor INFO @ Thu, 05 Dec 2019 12:33:42: #2 finished! INFO @ Thu, 05 Dec 2019 12:33:42: #2 predicted fragment length is 128 bps INFO @ Thu, 05 Dec 2019 12:33:42: #2 alternative fragment length(s) may be 128 bps INFO @ Thu, 05 Dec 2019 12:33:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4107863/SRX4107863.10_model.r INFO @ Thu, 05 Dec 2019 12:33:42: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:33:42: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:33:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4107863/SRX4107863.05_peaks.xls INFO @ Thu, 05 Dec 2019 12:33:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4107863/SRX4107863.05_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:33:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4107863/SRX4107863.05_summits.bed INFO @ Thu, 05 Dec 2019 12:33:45: Done! pass1 - making usageList (6 chroms): 4 millis pass2 - checking and writing primary data (6865 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 12:33:46: 4000000 INFO @ Thu, 05 Dec 2019 12:33:53: 5000000 INFO @ Thu, 05 Dec 2019 12:34:01: 6000000 INFO @ Thu, 05 Dec 2019 12:34:05: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:34:09: 7000000 INFO @ Thu, 05 Dec 2019 12:34:11: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 12:34:11: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 12:34:11: #1 total tags in treatment: 7200457 INFO @ Thu, 05 Dec 2019 12:34:11: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:34:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 12:34:11: #1 tags after filtering in treatment: 7200457 INFO @ Thu, 05 Dec 2019 12:34:11: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 12:34:11: #1 finished! INFO @ Thu, 05 Dec 2019 12:34:11: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:34:11: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:34:12: #2 number of paired peaks: 6195 INFO @ Thu, 05 Dec 2019 12:34:12: start model_add_line... INFO @ Thu, 05 Dec 2019 12:34:12: start X-correlation... INFO @ Thu, 05 Dec 2019 12:34:12: end of X-cor INFO @ Thu, 05 Dec 2019 12:34:12: #2 finished! INFO @ Thu, 05 Dec 2019 12:34:12: #2 predicted fragment length is 128 bps INFO @ Thu, 05 Dec 2019 12:34:12: #2 alternative fragment length(s) may be 128 bps INFO @ Thu, 05 Dec 2019 12:34:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4107863/SRX4107863.20_model.r INFO @ Thu, 05 Dec 2019 12:34:12: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:34:12: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:34:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4107863/SRX4107863.10_peaks.xls INFO @ Thu, 05 Dec 2019 12:34:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4107863/SRX4107863.10_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:34:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4107863/SRX4107863.10_summits.bed INFO @ Thu, 05 Dec 2019 12:34:21: Done! pass1 - making usageList (6 chroms): 3 millis pass2 - checking and writing primary data (5606 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 12:34:35: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:34:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4107863/SRX4107863.20_peaks.xls INFO @ Thu, 05 Dec 2019 12:34:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4107863/SRX4107863.20_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:34:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4107863/SRX4107863.20_summits.bed INFO @ Thu, 05 Dec 2019 12:34:45: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (4502 records, 4 fields): 14 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。