Job ID = 2589529 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 5,725,492 reads read : 5,725,492 reads written : 5,725,492 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR701504.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: 00:00:49 5725492 reads; of these: 5725492 (100.00%) were unpaired; of these: 2491172 (43.51%) aligned 0 times 2719565 (47.50%) aligned exactly 1 time 514755 (8.99%) aligned >1 times 56.49% overall alignment rate Time searching: 00:00:49 Overall time: 00:00:49 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] 401903 / 3234320 = 0.1243 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 17:53:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX233449/SRX233449.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX233449/SRX233449.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX233449/SRX233449.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX233449/SRX233449.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 17:53:56: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:53:56: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:53:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX233449/SRX233449.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX233449/SRX233449.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX233449/SRX233449.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX233449/SRX233449.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 17:53:57: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:53:57: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:53:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX233449/SRX233449.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX233449/SRX233449.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX233449/SRX233449.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX233449/SRX233449.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 17:53:58: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:53:58: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:54:03: 1000000 INFO @ Mon, 12 Aug 2019 17:54:05: 1000000 INFO @ Mon, 12 Aug 2019 17:54:06: 1000000 INFO @ Mon, 12 Aug 2019 17:54:12: 2000000 INFO @ Mon, 12 Aug 2019 17:54:13: 2000000 INFO @ Mon, 12 Aug 2019 17:54:16: 2000000 INFO @ Mon, 12 Aug 2019 17:54:18: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 17:54:18: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 17:54:18: #1 total tags in treatment: 2832417 INFO @ Mon, 12 Aug 2019 17:54:18: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:54:18: #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 17:54:18: #1 tags after filtering in treatment: 2832417 INFO @ Mon, 12 Aug 2019 17:54:18: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:54:18: #1 finished! INFO @ Mon, 12 Aug 2019 17:54:18: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:54:18: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:54:18: #2 number of paired peaks: 972 WARNING @ Mon, 12 Aug 2019 17:54:18: Fewer paired peaks (972) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 972 pairs to build model! INFO @ Mon, 12 Aug 2019 17:54:18: start model_add_line... INFO @ Mon, 12 Aug 2019 17:54:18: start X-correlation... INFO @ Mon, 12 Aug 2019 17:54:18: end of X-cor INFO @ Mon, 12 Aug 2019 17:54:18: #2 finished! INFO @ Mon, 12 Aug 2019 17:54:18: #2 predicted fragment length is 166 bps INFO @ Mon, 12 Aug 2019 17:54:18: #2 alternative fragment length(s) may be 166 bps INFO @ Mon, 12 Aug 2019 17:54:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX233449/SRX233449.20_model.r INFO @ Mon, 12 Aug 2019 17:54:18: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:54:18: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:54:21: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 17:54:21: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 17:54:21: #1 total tags in treatment: 2832417 INFO @ Mon, 12 Aug 2019 17:54:21: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:54:21: #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 17:54:21: #1 tags after filtering in treatment: 2832417 INFO @ Mon, 12 Aug 2019 17:54:21: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:54:21: #1 finished! INFO @ Mon, 12 Aug 2019 17:54:21: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:54:21: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:54:21: #2 number of paired peaks: 972 WARNING @ Mon, 12 Aug 2019 17:54:21: Fewer paired peaks (972) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 972 pairs to build model! INFO @ Mon, 12 Aug 2019 17:54:21: start model_add_line... INFO @ Mon, 12 Aug 2019 17:54:21: start X-correlation... INFO @ Mon, 12 Aug 2019 17:54:21: end of X-cor INFO @ Mon, 12 Aug 2019 17:54:21: #2 finished! INFO @ Mon, 12 Aug 2019 17:54:21: #2 predicted fragment length is 166 bps INFO @ Mon, 12 Aug 2019 17:54:21: #2 alternative fragment length(s) may be 166 bps INFO @ Mon, 12 Aug 2019 17:54:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX233449/SRX233449.05_model.r INFO @ Mon, 12 Aug 2019 17:54:21: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:54:21: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:54:23: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 17:54:23: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 17:54:23: #1 total tags in treatment: 2832417 INFO @ Mon, 12 Aug 2019 17:54:23: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:54:23: #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 17:54:23: #1 tags after filtering in treatment: 2832417 INFO @ Mon, 12 Aug 2019 17:54:23: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:54:23: #1 finished! INFO @ Mon, 12 Aug 2019 17:54:23: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:54:23: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:54:24: #2 number of paired peaks: 972 WARNING @ Mon, 12 Aug 2019 17:54:24: Fewer paired peaks (972) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 972 pairs to build model! INFO @ Mon, 12 Aug 2019 17:54:24: start model_add_line... INFO @ Mon, 12 Aug 2019 17:54:24: start X-correlation... INFO @ Mon, 12 Aug 2019 17:54:24: end of X-cor INFO @ Mon, 12 Aug 2019 17:54:24: #2 finished! INFO @ Mon, 12 Aug 2019 17:54:24: #2 predicted fragment length is 166 bps INFO @ Mon, 12 Aug 2019 17:54:24: #2 alternative fragment length(s) may be 166 bps INFO @ Mon, 12 Aug 2019 17:54:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX233449/SRX233449.10_model.r INFO @ Mon, 12 Aug 2019 17:54:24: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:54:24: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:54:28: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:54:31: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:54:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX233449/SRX233449.20_peaks.xls INFO @ Mon, 12 Aug 2019 17:54:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX233449/SRX233449.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:54:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX233449/SRX233449.20_summits.bed INFO @ Mon, 12 Aug 2019 17:54:32: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (538 records, 4 fields): 36 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 17:54:33: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:54:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX233449/SRX233449.05_peaks.xls INFO @ Mon, 12 Aug 2019 17:54:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX233449/SRX233449.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:54:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX233449/SRX233449.05_summits.bed INFO @ Mon, 12 Aug 2019 17:54:36: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1630 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 17:54:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX233449/SRX233449.10_peaks.xls INFO @ Mon, 12 Aug 2019 17:54:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX233449/SRX233449.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:54:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX233449/SRX233449.10_summits.bed INFO @ Mon, 12 Aug 2019 17:54:38: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (958 records, 4 fields): 71 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。