Job ID = 2589890 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 6,520,157 reads read : 6,520,157 reads written : 6,520,157 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR947531.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: 00:00:55 6520157 reads; of these: 6520157 (100.00%) were unpaired; of these: 1635319 (25.08%) aligned 0 times 4156120 (63.74%) aligned exactly 1 time 728718 (11.18%) aligned >1 times 74.92% overall alignment rate Time searching: 00:00:55 Overall time: 00:00:55 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] 767569 / 4884838 = 0.1571 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 18:43:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331294/SRX331294.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331294/SRX331294.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331294/SRX331294.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331294/SRX331294.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 18:43:27: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:43:27: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:43:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331294/SRX331294.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331294/SRX331294.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331294/SRX331294.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331294/SRX331294.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 18:43:28: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:43:28: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:43:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331294/SRX331294.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331294/SRX331294.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331294/SRX331294.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331294/SRX331294.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 18:43:29: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:43:29: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:43:36: 1000000 INFO @ Mon, 12 Aug 2019 18:43:37: 1000000 INFO @ Mon, 12 Aug 2019 18:43:38: 1000000 INFO @ Mon, 12 Aug 2019 18:43:42: 2000000 INFO @ Mon, 12 Aug 2019 18:43:46: 2000000 INFO @ Mon, 12 Aug 2019 18:43:47: 2000000 INFO @ Mon, 12 Aug 2019 18:43:49: 3000000 INFO @ Mon, 12 Aug 2019 18:43:55: 3000000 INFO @ Mon, 12 Aug 2019 18:43:55: 4000000 INFO @ Mon, 12 Aug 2019 18:43:56: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:43:56: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:43:56: #1 total tags in treatment: 4117269 INFO @ Mon, 12 Aug 2019 18:43:56: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:43:56: #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 18:43:56: #1 tags after filtering in treatment: 4117269 INFO @ Mon, 12 Aug 2019 18:43:56: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:43:56: #1 finished! INFO @ Mon, 12 Aug 2019 18:43:56: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:43:56: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:43:56: 3000000 INFO @ Mon, 12 Aug 2019 18:43:56: #2 number of paired peaks: 491 WARNING @ Mon, 12 Aug 2019 18:43:56: Fewer paired peaks (491) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 491 pairs to build model! INFO @ Mon, 12 Aug 2019 18:43:56: start model_add_line... INFO @ Mon, 12 Aug 2019 18:43:57: start X-correlation... INFO @ Mon, 12 Aug 2019 18:43:57: end of X-cor INFO @ Mon, 12 Aug 2019 18:43:57: #2 finished! INFO @ Mon, 12 Aug 2019 18:43:57: #2 predicted fragment length is 103 bps INFO @ Mon, 12 Aug 2019 18:43:57: #2 alternative fragment length(s) may be 4,103,598 bps INFO @ Mon, 12 Aug 2019 18:43:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331294/SRX331294.20_model.r INFO @ Mon, 12 Aug 2019 18:43:57: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:43:57: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:44:04: 4000000 INFO @ Mon, 12 Aug 2019 18:44:05: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:44:05: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:44:05: #1 total tags in treatment: 4117269 INFO @ Mon, 12 Aug 2019 18:44:05: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:44:05: #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 18:44:05: 4000000 INFO @ Mon, 12 Aug 2019 18:44:05: #1 tags after filtering in treatment: 4117269 INFO @ Mon, 12 Aug 2019 18:44:05: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:44:05: #1 finished! INFO @ Mon, 12 Aug 2019 18:44:05: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:44:05: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:44:05: #2 number of paired peaks: 491 WARNING @ Mon, 12 Aug 2019 18:44:05: Fewer paired peaks (491) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 491 pairs to build model! INFO @ Mon, 12 Aug 2019 18:44:05: start model_add_line... INFO @ Mon, 12 Aug 2019 18:44:05: start X-correlation... INFO @ Mon, 12 Aug 2019 18:44:05: end of X-cor INFO @ Mon, 12 Aug 2019 18:44:05: #2 finished! INFO @ Mon, 12 Aug 2019 18:44:05: #2 predicted fragment length is 103 bps INFO @ Mon, 12 Aug 2019 18:44:05: #2 alternative fragment length(s) may be 4,103,598 bps INFO @ Mon, 12 Aug 2019 18:44:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331294/SRX331294.05_model.r INFO @ Mon, 12 Aug 2019 18:44:05: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:44:05: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:44:06: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:44:06: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:44:06: #1 total tags in treatment: 4117269 INFO @ Mon, 12 Aug 2019 18:44:06: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:44:06: #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 18:44:06: #1 tags after filtering in treatment: 4117269 INFO @ Mon, 12 Aug 2019 18:44:06: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:44:06: #1 finished! INFO @ Mon, 12 Aug 2019 18:44:06: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:44:06: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:44:06: #2 number of paired peaks: 491 WARNING @ Mon, 12 Aug 2019 18:44:06: Fewer paired peaks (491) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 491 pairs to build model! INFO @ Mon, 12 Aug 2019 18:44:06: start model_add_line... INFO @ Mon, 12 Aug 2019 18:44:06: start X-correlation... INFO @ Mon, 12 Aug 2019 18:44:06: end of X-cor INFO @ Mon, 12 Aug 2019 18:44:06: #2 finished! INFO @ Mon, 12 Aug 2019 18:44:06: #2 predicted fragment length is 103 bps INFO @ Mon, 12 Aug 2019 18:44:06: #2 alternative fragment length(s) may be 4,103,598 bps INFO @ Mon, 12 Aug 2019 18:44:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331294/SRX331294.10_model.r INFO @ Mon, 12 Aug 2019 18:44:06: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:44:06: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:44:09: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:44:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331294/SRX331294.20_peaks.xls INFO @ Mon, 12 Aug 2019 18:44:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331294/SRX331294.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:44:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331294/SRX331294.20_summits.bed INFO @ Mon, 12 Aug 2019 18:44:15: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (160 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 18:44:18: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:44:19: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:44:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331294/SRX331294.05_peaks.xls INFO @ Mon, 12 Aug 2019 18:44:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331294/SRX331294.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:44:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331294/SRX331294.05_summits.bed INFO @ Mon, 12 Aug 2019 18:44:24: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (871 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 18:44:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331294/SRX331294.10_peaks.xls INFO @ Mon, 12 Aug 2019 18:44:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331294/SRX331294.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:44:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331294/SRX331294.10_summits.bed INFO @ Mon, 12 Aug 2019 18:44:25: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (408 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。