Job ID = 2589517 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 9,081,688 reads read : 9,081,688 reads written : 9,081,688 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR701493.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: 00:00:48 9081688 reads; of these: 9081688 (100.00%) were unpaired; of these: 7283083 (80.20%) aligned 0 times 1530235 (16.85%) aligned exactly 1 time 268370 (2.96%) aligned >1 times 19.80% overall alignment rate Time searching: 00:00:48 Overall time: 00:00:48 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] 241404 / 1798605 = 0.1342 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 17:52:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX233418/SRX233418.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX233418/SRX233418.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX233418/SRX233418.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX233418/SRX233418.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 17:52:52: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:52:52: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:52:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX233418/SRX233418.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX233418/SRX233418.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX233418/SRX233418.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX233418/SRX233418.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 17:52:53: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:52:53: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:52:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX233418/SRX233418.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX233418/SRX233418.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX233418/SRX233418.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX233418/SRX233418.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 17:52:54: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:52:54: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:52:58: 1000000 INFO @ Mon, 12 Aug 2019 17:53:00: 1000000 INFO @ Mon, 12 Aug 2019 17:53:01: 1000000 INFO @ Mon, 12 Aug 2019 17:53:02: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 17:53:02: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 17:53:02: #1 total tags in treatment: 1557201 INFO @ Mon, 12 Aug 2019 17:53:02: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:53:02: #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 17:53:02: #1 tags after filtering in treatment: 1557201 INFO @ Mon, 12 Aug 2019 17:53:02: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:53:02: #1 finished! INFO @ Mon, 12 Aug 2019 17:53:02: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:53:02: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:53:02: #2 number of paired peaks: 1625 INFO @ Mon, 12 Aug 2019 17:53:02: start model_add_line... INFO @ Mon, 12 Aug 2019 17:53:02: start X-correlation... INFO @ Mon, 12 Aug 2019 17:53:02: end of X-cor INFO @ Mon, 12 Aug 2019 17:53:02: #2 finished! INFO @ Mon, 12 Aug 2019 17:53:02: #2 predicted fragment length is 127 bps INFO @ Mon, 12 Aug 2019 17:53:02: #2 alternative fragment length(s) may be 127 bps INFO @ Mon, 12 Aug 2019 17:53:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX233418/SRX233418.05_model.r INFO @ Mon, 12 Aug 2019 17:53:02: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:53:02: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:53:03: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 17:53:03: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 17:53:03: #1 total tags in treatment: 1557201 INFO @ Mon, 12 Aug 2019 17:53:03: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:53:03: #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 17:53:03: #1 tags after filtering in treatment: 1557201 INFO @ Mon, 12 Aug 2019 17:53:03: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:53:03: #1 finished! INFO @ Mon, 12 Aug 2019 17:53:03: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:53:03: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:53:04: #2 number of paired peaks: 1625 INFO @ Mon, 12 Aug 2019 17:53:04: start model_add_line... INFO @ Mon, 12 Aug 2019 17:53:04: start X-correlation... INFO @ Mon, 12 Aug 2019 17:53:04: end of X-cor INFO @ Mon, 12 Aug 2019 17:53:04: #2 finished! INFO @ Mon, 12 Aug 2019 17:53:04: #2 predicted fragment length is 127 bps INFO @ Mon, 12 Aug 2019 17:53:04: #2 alternative fragment length(s) may be 127 bps INFO @ Mon, 12 Aug 2019 17:53:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX233418/SRX233418.10_model.r INFO @ Mon, 12 Aug 2019 17:53:04: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:53:04: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:53:04: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 17:53:04: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 17:53:04: #1 total tags in treatment: 1557201 INFO @ Mon, 12 Aug 2019 17:53:04: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:53:04: #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 17:53:04: #1 tags after filtering in treatment: 1557201 INFO @ Mon, 12 Aug 2019 17:53:04: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:53:04: #1 finished! INFO @ Mon, 12 Aug 2019 17:53:04: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:53:04: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:53:05: #2 number of paired peaks: 1625 INFO @ Mon, 12 Aug 2019 17:53:05: start model_add_line... INFO @ Mon, 12 Aug 2019 17:53:05: start X-correlation... INFO @ Mon, 12 Aug 2019 17:53:05: end of X-cor INFO @ Mon, 12 Aug 2019 17:53:05: #2 finished! INFO @ Mon, 12 Aug 2019 17:53:05: #2 predicted fragment length is 127 bps INFO @ Mon, 12 Aug 2019 17:53:05: #2 alternative fragment length(s) may be 127 bps INFO @ Mon, 12 Aug 2019 17:53:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX233418/SRX233418.20_model.r INFO @ Mon, 12 Aug 2019 17:53:05: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:53:05: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:53:07: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:53:09: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:53:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX233418/SRX233418.05_peaks.xls INFO @ Mon, 12 Aug 2019 17:53:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX233418/SRX233418.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:53:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX233418/SRX233418.05_summits.bed INFO @ Mon, 12 Aug 2019 17:53:09: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (2320 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 17:53:10: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:53:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX233418/SRX233418.10_peaks.xls INFO @ Mon, 12 Aug 2019 17:53:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX233418/SRX233418.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:53:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX233418/SRX233418.10_summits.bed INFO @ Mon, 12 Aug 2019 17:53:11: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (1458 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 17:53:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX233418/SRX233418.20_peaks.xls INFO @ Mon, 12 Aug 2019 17:53:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX233418/SRX233418.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:53:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX233418/SRX233418.20_summits.bed INFO @ Mon, 12 Aug 2019 17:53:12: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (801 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。