Job ID = 2589789 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 8,980,981 reads read : 8,980,981 reads written : 8,980,981 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR947404.sra.cache’: 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: 00:01:26 8980981 reads; of these: 8980981 (100.00%) were unpaired; of these: 381244 (4.25%) aligned 0 times 7529589 (83.84%) aligned exactly 1 time 1070148 (11.92%) aligned >1 times 95.75% overall alignment rate Time searching: 00:01:26 Overall time: 00:01:26 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_rmdupse_core] 1768394 / 8599737 = 0.2056 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 18:30:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331172/SRX331172.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331172/SRX331172.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331172/SRX331172.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331172/SRX331172.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 18:30:56: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:30:56: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:30:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331172/SRX331172.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331172/SRX331172.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331172/SRX331172.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331172/SRX331172.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 18:30:57: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:30:57: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:30:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331172/SRX331172.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331172/SRX331172.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331172/SRX331172.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331172/SRX331172.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 18:30:58: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:30:58: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:31:03: 1000000 INFO @ Mon, 12 Aug 2019 18:31:07: 1000000 INFO @ Mon, 12 Aug 2019 18:31:09: 1000000 INFO @ Mon, 12 Aug 2019 18:31:12: 2000000 INFO @ Mon, 12 Aug 2019 18:31:18: 2000000 INFO @ Mon, 12 Aug 2019 18:31:19: 2000000 INFO @ Mon, 12 Aug 2019 18:31:20: 3000000 INFO @ Mon, 12 Aug 2019 18:31:28: 3000000 INFO @ Mon, 12 Aug 2019 18:31:28: 4000000 INFO @ Mon, 12 Aug 2019 18:31:29: 3000000 INFO @ Mon, 12 Aug 2019 18:31:36: 5000000 INFO @ Mon, 12 Aug 2019 18:31:38: 4000000 INFO @ Mon, 12 Aug 2019 18:31:38: 4000000 INFO @ Mon, 12 Aug 2019 18:31:44: 6000000 INFO @ Mon, 12 Aug 2019 18:31:48: 5000000 INFO @ Mon, 12 Aug 2019 18:31:48: 5000000 INFO @ Mon, 12 Aug 2019 18:31:51: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:31:51: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:31:51: #1 total tags in treatment: 6831343 INFO @ Mon, 12 Aug 2019 18:31:51: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:31:51: #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 18:31:51: #1 tags after filtering in treatment: 6831343 INFO @ Mon, 12 Aug 2019 18:31:51: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:31:51: #1 finished! INFO @ Mon, 12 Aug 2019 18:31:51: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:31:51: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:31:52: #2 number of paired peaks: 2168 INFO @ Mon, 12 Aug 2019 18:31:52: start model_add_line... INFO @ Mon, 12 Aug 2019 18:31:52: start X-correlation... INFO @ Mon, 12 Aug 2019 18:31:52: end of X-cor INFO @ Mon, 12 Aug 2019 18:31:52: #2 finished! INFO @ Mon, 12 Aug 2019 18:31:52: #2 predicted fragment length is 172 bps INFO @ Mon, 12 Aug 2019 18:31:52: #2 alternative fragment length(s) may be 172 bps INFO @ Mon, 12 Aug 2019 18:31:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331172/SRX331172.05_model.r INFO @ Mon, 12 Aug 2019 18:31:52: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:31:52: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:31:57: 6000000 INFO @ Mon, 12 Aug 2019 18:31:58: 6000000 INFO @ Mon, 12 Aug 2019 18:32:04: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:32:04: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:32:04: #1 total tags in treatment: 6831343 INFO @ Mon, 12 Aug 2019 18:32:04: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:32:04: #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 18:32:04: #1 tags after filtering in treatment: 6831343 INFO @ Mon, 12 Aug 2019 18:32:04: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:32:04: #1 finished! INFO @ Mon, 12 Aug 2019 18:32:04: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:32:04: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:32:05: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:32:05: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:32:05: #1 total tags in treatment: 6831343 INFO @ Mon, 12 Aug 2019 18:32:05: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:32:05: #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 18:32:05: #1 tags after filtering in treatment: 6831343 INFO @ Mon, 12 Aug 2019 18:32:05: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:32:05: #1 finished! INFO @ Mon, 12 Aug 2019 18:32:05: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:32:05: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:32:05: #2 number of paired peaks: 2168 INFO @ Mon, 12 Aug 2019 18:32:05: start model_add_line... INFO @ Mon, 12 Aug 2019 18:32:05: start X-correlation... INFO @ Mon, 12 Aug 2019 18:32:05: end of X-cor INFO @ Mon, 12 Aug 2019 18:32:05: #2 finished! INFO @ Mon, 12 Aug 2019 18:32:05: #2 predicted fragment length is 172 bps INFO @ Mon, 12 Aug 2019 18:32:05: #2 alternative fragment length(s) may be 172 bps INFO @ Mon, 12 Aug 2019 18:32:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331172/SRX331172.10_model.r INFO @ Mon, 12 Aug 2019 18:32:05: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:32:05: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:32:06: #2 number of paired peaks: 2168 INFO @ Mon, 12 Aug 2019 18:32:06: start model_add_line... INFO @ Mon, 12 Aug 2019 18:32:06: start X-correlation... INFO @ Mon, 12 Aug 2019 18:32:06: end of X-cor INFO @ Mon, 12 Aug 2019 18:32:06: #2 finished! INFO @ Mon, 12 Aug 2019 18:32:06: #2 predicted fragment length is 172 bps INFO @ Mon, 12 Aug 2019 18:32:06: #2 alternative fragment length(s) may be 172 bps INFO @ Mon, 12 Aug 2019 18:32:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331172/SRX331172.20_model.r INFO @ Mon, 12 Aug 2019 18:32:06: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:32:06: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:32:14: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:32:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331172/SRX331172.05_peaks.xls INFO @ Mon, 12 Aug 2019 18:32:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331172/SRX331172.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:32:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331172/SRX331172.05_summits.bed INFO @ Mon, 12 Aug 2019 18:32:25: Done! pass1 - making usageList (7 chroms): 4 millis pass2 - checking and writing primary data (7439 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 18:32:28: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:32:29: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:32:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331172/SRX331172.10_peaks.xls INFO @ Mon, 12 Aug 2019 18:32:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331172/SRX331172.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:32:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331172/SRX331172.10_summits.bed INFO @ Mon, 12 Aug 2019 18:32:38: Done! pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (5382 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 18:32:39: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331172/SRX331172.20_peaks.xls INFO @ Mon, 12 Aug 2019 18:32:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331172/SRX331172.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:32:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331172/SRX331172.20_summits.bed INFO @ Mon, 12 Aug 2019 18:32:39: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (3582 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。