Job ID = 2590183 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 12,966,659 reads read : 12,966,659 reads written : 12,966,659 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: 00:02:28 12966659 reads; of these: 12966659 (100.00%) were unpaired; of these: 1924117 (14.84%) aligned 0 times 9219607 (71.10%) aligned exactly 1 time 1822935 (14.06%) aligned >1 times 85.16% overall alignment rate Time searching: 00:02:28 Overall time: 00:02:28 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] 4838300 / 11042542 = 0.4382 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 20:08:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495071/SRX495071.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495071/SRX495071.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495071/SRX495071.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495071/SRX495071.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 20:08:21: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:08:21: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:08:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495071/SRX495071.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495071/SRX495071.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495071/SRX495071.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495071/SRX495071.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 20:08:22: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:08:22: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:08:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495071/SRX495071.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495071/SRX495071.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495071/SRX495071.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495071/SRX495071.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 20:08:23: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:08:23: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:08:29: 1000000 INFO @ Mon, 12 Aug 2019 20:08:29: 1000000 INFO @ Mon, 12 Aug 2019 20:08:30: 1000000 INFO @ Mon, 12 Aug 2019 20:08:36: 2000000 INFO @ Mon, 12 Aug 2019 20:08:37: 2000000 INFO @ Mon, 12 Aug 2019 20:08:37: 2000000 INFO @ Mon, 12 Aug 2019 20:08:43: 3000000 INFO @ Mon, 12 Aug 2019 20:08:44: 3000000 INFO @ Mon, 12 Aug 2019 20:08:45: 3000000 INFO @ Mon, 12 Aug 2019 20:08:50: 4000000 INFO @ Mon, 12 Aug 2019 20:08:51: 4000000 INFO @ Mon, 12 Aug 2019 20:08:52: 4000000 INFO @ Mon, 12 Aug 2019 20:08:58: 5000000 INFO @ Mon, 12 Aug 2019 20:08:58: 5000000 INFO @ Mon, 12 Aug 2019 20:08:59: 5000000 INFO @ Mon, 12 Aug 2019 20:09:05: 6000000 INFO @ Mon, 12 Aug 2019 20:09:06: 6000000 INFO @ Mon, 12 Aug 2019 20:09:06: 6000000 INFO @ Mon, 12 Aug 2019 20:09:07: #1 tag size is determined as 42 bps INFO @ Mon, 12 Aug 2019 20:09:07: #1 tag size = 42 INFO @ Mon, 12 Aug 2019 20:09:07: #1 total tags in treatment: 6204242 INFO @ Mon, 12 Aug 2019 20:09:07: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:09:07: #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 20:09:07: #1 tags after filtering in treatment: 6204242 INFO @ Mon, 12 Aug 2019 20:09:07: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:09:07: #1 finished! INFO @ Mon, 12 Aug 2019 20:09:07: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:09:07: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:09:07: #1 tag size is determined as 42 bps INFO @ Mon, 12 Aug 2019 20:09:07: #1 tag size = 42 INFO @ Mon, 12 Aug 2019 20:09:07: #1 total tags in treatment: 6204242 INFO @ Mon, 12 Aug 2019 20:09:07: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:09:07: #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 20:09:07: #1 tags after filtering in treatment: 6204242 INFO @ Mon, 12 Aug 2019 20:09:07: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:09:07: #1 finished! INFO @ Mon, 12 Aug 2019 20:09:07: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:09:07: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:09:07: #2 number of paired peaks: 768 WARNING @ Mon, 12 Aug 2019 20:09:07: Fewer paired peaks (768) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 768 pairs to build model! INFO @ Mon, 12 Aug 2019 20:09:07: start model_add_line... INFO @ Mon, 12 Aug 2019 20:09:08: start X-correlation... INFO @ Mon, 12 Aug 2019 20:09:08: end of X-cor INFO @ Mon, 12 Aug 2019 20:09:08: #2 finished! INFO @ Mon, 12 Aug 2019 20:09:08: #2 predicted fragment length is 103 bps INFO @ Mon, 12 Aug 2019 20:09:08: #2 alternative fragment length(s) may be 90,103,597 bps INFO @ Mon, 12 Aug 2019 20:09:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495071/SRX495071.05_model.r INFO @ Mon, 12 Aug 2019 20:09:08: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:09:08: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:09:08: #1 tag size is determined as 42 bps INFO @ Mon, 12 Aug 2019 20:09:08: #1 tag size = 42 INFO @ Mon, 12 Aug 2019 20:09:08: #1 total tags in treatment: 6204242 INFO @ Mon, 12 Aug 2019 20:09:08: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:09:08: #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 20:09:08: #1 tags after filtering in treatment: 6204242 INFO @ Mon, 12 Aug 2019 20:09:08: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:09:08: #1 finished! INFO @ Mon, 12 Aug 2019 20:09:08: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:09:08: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:09:08: #2 number of paired peaks: 768 WARNING @ Mon, 12 Aug 2019 20:09:08: Fewer paired peaks (768) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 768 pairs to build model! INFO @ Mon, 12 Aug 2019 20:09:08: start model_add_line... INFO @ Mon, 12 Aug 2019 20:09:08: start X-correlation... INFO @ Mon, 12 Aug 2019 20:09:08: end of X-cor INFO @ Mon, 12 Aug 2019 20:09:08: #2 finished! INFO @ Mon, 12 Aug 2019 20:09:08: #2 predicted fragment length is 103 bps INFO @ Mon, 12 Aug 2019 20:09:08: #2 alternative fragment length(s) may be 90,103,597 bps INFO @ Mon, 12 Aug 2019 20:09:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495071/SRX495071.10_model.r INFO @ Mon, 12 Aug 2019 20:09:08: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:09:08: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:09:08: #2 number of paired peaks: 768 WARNING @ Mon, 12 Aug 2019 20:09:08: Fewer paired peaks (768) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 768 pairs to build model! INFO @ Mon, 12 Aug 2019 20:09:08: start model_add_line... INFO @ Mon, 12 Aug 2019 20:09:09: start X-correlation... INFO @ Mon, 12 Aug 2019 20:09:09: end of X-cor INFO @ Mon, 12 Aug 2019 20:09:09: #2 finished! INFO @ Mon, 12 Aug 2019 20:09:09: #2 predicted fragment length is 103 bps INFO @ Mon, 12 Aug 2019 20:09:09: #2 alternative fragment length(s) may be 90,103,597 bps INFO @ Mon, 12 Aug 2019 20:09:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495071/SRX495071.20_model.r INFO @ Mon, 12 Aug 2019 20:09:09: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:09:09: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:09:27: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:09:27: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:09:27: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:09:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495071/SRX495071.10_peaks.xls INFO @ Mon, 12 Aug 2019 20:09:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495071/SRX495071.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:09:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495071/SRX495071.10_summits.bed INFO @ Mon, 12 Aug 2019 20:09:36: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (914 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 20:09:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495071/SRX495071.20_peaks.xls INFO @ Mon, 12 Aug 2019 20:09:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495071/SRX495071.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:09:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495071/SRX495071.20_summits.bed INFO @ Mon, 12 Aug 2019 20:09:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495071/SRX495071.05_peaks.xls INFO @ Mon, 12 Aug 2019 20:09:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495071/SRX495071.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:09:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495071/SRX495071.05_summits.bed INFO @ Mon, 12 Aug 2019 20:09:36: Done! INFO @ Mon, 12 Aug 2019 20:09:36: Done! pass1 - making usageList (7 chroms): 1 millis pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (458 records, 4 fields): 3 millis pass2 - checking and writing primary data (1436 records, 4 fields): 6 millis CompletedMACS2peakCalling CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。