Job ID = 2590210 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 13,002,342 reads read : 13,002,342 reads written : 13,002,342 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: 00:02:09 13002342 reads; of these: 13002342 (100.00%) were unpaired; of these: 3210889 (24.69%) aligned 0 times 6926255 (53.27%) aligned exactly 1 time 2865198 (22.04%) aligned >1 times 75.31% overall alignment rate Time searching: 00:02:09 Overall time: 00:02:09 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_rmdupse_core] 1427455 / 9791453 = 0.1458 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, 12 Aug 2019 20:11:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX529217/SRX529217.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX529217/SRX529217.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX529217/SRX529217.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX529217/SRX529217.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 @ Mon, 12 Aug 2019 20:11:27: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:11:27: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:11:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX529217/SRX529217.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX529217/SRX529217.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX529217/SRX529217.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX529217/SRX529217.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 @ Mon, 12 Aug 2019 20:11:28: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:11:28: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:11:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX529217/SRX529217.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX529217/SRX529217.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX529217/SRX529217.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX529217/SRX529217.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 @ Mon, 12 Aug 2019 20:11:29: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:11:29: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:11:34: 1000000 INFO @ Mon, 12 Aug 2019 20:11:36: 1000000 INFO @ Mon, 12 Aug 2019 20:11:36: 1000000 INFO @ Mon, 12 Aug 2019 20:11:41: 2000000 INFO @ Mon, 12 Aug 2019 20:11:43: 2000000 INFO @ Mon, 12 Aug 2019 20:11:44: 2000000 INFO @ Mon, 12 Aug 2019 20:11:48: 3000000 INFO @ Mon, 12 Aug 2019 20:11:51: 3000000 INFO @ Mon, 12 Aug 2019 20:11:53: 3000000 INFO @ Mon, 12 Aug 2019 20:11:55: 4000000 INFO @ Mon, 12 Aug 2019 20:11:58: 4000000 INFO @ Mon, 12 Aug 2019 20:12:01: 4000000 INFO @ Mon, 12 Aug 2019 20:12:02: 5000000 INFO @ Mon, 12 Aug 2019 20:12:05: 5000000 INFO @ Mon, 12 Aug 2019 20:12:09: 5000000 INFO @ Mon, 12 Aug 2019 20:12:09: 6000000 INFO @ Mon, 12 Aug 2019 20:12:12: 6000000 INFO @ Mon, 12 Aug 2019 20:12:16: 7000000 INFO @ Mon, 12 Aug 2019 20:12:17: 6000000 INFO @ Mon, 12 Aug 2019 20:12:19: 7000000 INFO @ Mon, 12 Aug 2019 20:12:23: 8000000 INFO @ Mon, 12 Aug 2019 20:12:25: 7000000 INFO @ Mon, 12 Aug 2019 20:12:26: #1 tag size is determined as 28 bps INFO @ Mon, 12 Aug 2019 20:12:26: #1 tag size = 28 INFO @ Mon, 12 Aug 2019 20:12:26: #1 total tags in treatment: 8363998 INFO @ Mon, 12 Aug 2019 20:12:26: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:12:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 20:12:26: #1 tags after filtering in treatment: 8363998 INFO @ Mon, 12 Aug 2019 20:12:26: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:12:26: #1 finished! INFO @ Mon, 12 Aug 2019 20:12:26: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:12:26: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:12:26: 8000000 INFO @ Mon, 12 Aug 2019 20:12:27: #2 number of paired peaks: 2086 INFO @ Mon, 12 Aug 2019 20:12:27: start model_add_line... INFO @ Mon, 12 Aug 2019 20:12:27: start X-correlation... INFO @ Mon, 12 Aug 2019 20:12:27: end of X-cor INFO @ Mon, 12 Aug 2019 20:12:27: #2 finished! INFO @ Mon, 12 Aug 2019 20:12:27: #2 predicted fragment length is 132 bps INFO @ Mon, 12 Aug 2019 20:12:27: #2 alternative fragment length(s) may be 2,132,150 bps INFO @ Mon, 12 Aug 2019 20:12:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX529217/SRX529217.05_model.r INFO @ Mon, 12 Aug 2019 20:12:27: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:12:27: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:12:29: #1 tag size is determined as 28 bps INFO @ Mon, 12 Aug 2019 20:12:29: #1 tag size = 28 INFO @ Mon, 12 Aug 2019 20:12:29: #1 total tags in treatment: 8363998 INFO @ Mon, 12 Aug 2019 20:12:29: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:12:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 20:12:29: #1 tags after filtering in treatment: 8363998 INFO @ Mon, 12 Aug 2019 20:12:29: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:12:29: #1 finished! INFO @ Mon, 12 Aug 2019 20:12:29: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:12:29: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:12:30: #2 number of paired peaks: 2086 INFO @ Mon, 12 Aug 2019 20:12:30: start model_add_line... INFO @ Mon, 12 Aug 2019 20:12:30: start X-correlation... INFO @ Mon, 12 Aug 2019 20:12:30: end of X-cor INFO @ Mon, 12 Aug 2019 20:12:30: #2 finished! INFO @ Mon, 12 Aug 2019 20:12:30: #2 predicted fragment length is 132 bps INFO @ Mon, 12 Aug 2019 20:12:30: #2 alternative fragment length(s) may be 2,132,150 bps INFO @ Mon, 12 Aug 2019 20:12:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX529217/SRX529217.20_model.r INFO @ Mon, 12 Aug 2019 20:12:30: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:12:30: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:12:33: 8000000 INFO @ Mon, 12 Aug 2019 20:12:36: #1 tag size is determined as 28 bps INFO @ Mon, 12 Aug 2019 20:12:36: #1 tag size = 28 INFO @ Mon, 12 Aug 2019 20:12:36: #1 total tags in treatment: 8363998 INFO @ Mon, 12 Aug 2019 20:12:36: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:12:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 20:12:36: #1 tags after filtering in treatment: 8363998 INFO @ Mon, 12 Aug 2019 20:12:36: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:12:36: #1 finished! INFO @ Mon, 12 Aug 2019 20:12:36: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:12:36: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:12:37: #2 number of paired peaks: 2086 INFO @ Mon, 12 Aug 2019 20:12:37: start model_add_line... INFO @ Mon, 12 Aug 2019 20:12:38: start X-correlation... INFO @ Mon, 12 Aug 2019 20:12:38: end of X-cor INFO @ Mon, 12 Aug 2019 20:12:38: #2 finished! INFO @ Mon, 12 Aug 2019 20:12:38: #2 predicted fragment length is 132 bps INFO @ Mon, 12 Aug 2019 20:12:38: #2 alternative fragment length(s) may be 2,132,150 bps INFO @ Mon, 12 Aug 2019 20:12:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX529217/SRX529217.10_model.r INFO @ Mon, 12 Aug 2019 20:12:38: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:12:38: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:12:53: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:12:56: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:13:04: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:13:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX529217/SRX529217.05_peaks.xls INFO @ Mon, 12 Aug 2019 20:13:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX529217/SRX529217.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:13:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX529217/SRX529217.05_summits.bed INFO @ Mon, 12 Aug 2019 20:13:05: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (3186 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 20:13:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX529217/SRX529217.20_peaks.xls INFO @ Mon, 12 Aug 2019 20:13:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX529217/SRX529217.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:13:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX529217/SRX529217.20_summits.bed INFO @ Mon, 12 Aug 2019 20:13:07: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (319 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 20:13:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX529217/SRX529217.10_peaks.xls INFO @ Mon, 12 Aug 2019 20:13:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX529217/SRX529217.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:13:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX529217/SRX529217.10_summits.bed INFO @ Mon, 12 Aug 2019 20:13:15: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1153 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。