Job ID = 1291493 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 12,547,783 reads read : 12,547,783 reads written : 12,547,783 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘fastqDump_tmp*’: 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:04:00 12547783 reads; of these: 12547783 (100.00%) were unpaired; of these: 210863 (1.68%) aligned 0 times 5638611 (44.94%) aligned exactly 1 time 6698309 (53.38%) aligned >1 times 98.32% overall alignment rate Time searching: 00:04:01 Overall time: 00:04:01 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_sort_core] merging from 8 files... [bam_rmdupse_core] 8013083 / 12336920 = 0.6495 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 @ Sun, 02 Jun 2019 16:01:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/ERX1999196/ERX1999196.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/ERX1999196/ERX1999196.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/ERX1999196/ERX1999196.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/ERX1999196/ERX1999196.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 @ Sun, 02 Jun 2019 16:01:28: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:01:28: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:01:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/ERX1999196/ERX1999196.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/ERX1999196/ERX1999196.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/ERX1999196/ERX1999196.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/ERX1999196/ERX1999196.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 @ Sun, 02 Jun 2019 16:01:28: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:01:28: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:01:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/ERX1999196/ERX1999196.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/ERX1999196/ERX1999196.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/ERX1999196/ERX1999196.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/ERX1999196/ERX1999196.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 @ Sun, 02 Jun 2019 16:01:28: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:01:28: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:01:36: 1000000 INFO @ Sun, 02 Jun 2019 16:01:36: 1000000 INFO @ Sun, 02 Jun 2019 16:01:36: 1000000 INFO @ Sun, 02 Jun 2019 16:01:44: 2000000 INFO @ Sun, 02 Jun 2019 16:01:44: 2000000 INFO @ Sun, 02 Jun 2019 16:01:44: 2000000 INFO @ Sun, 02 Jun 2019 16:01:52: 3000000 INFO @ Sun, 02 Jun 2019 16:01:52: 3000000 INFO @ Sun, 02 Jun 2019 16:01:52: 3000000 INFO @ Sun, 02 Jun 2019 16:02:00: 4000000 INFO @ Sun, 02 Jun 2019 16:02:00: 4000000 INFO @ Sun, 02 Jun 2019 16:02:00: 4000000 INFO @ Sun, 02 Jun 2019 16:02:02: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 16:02:02: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 16:02:02: #1 total tags in treatment: 4323837 INFO @ Sun, 02 Jun 2019 16:02:02: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:02:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 16:02:02: #1 tags after filtering in treatment: 4323837 INFO @ Sun, 02 Jun 2019 16:02:02: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:02:02: #1 finished! INFO @ Sun, 02 Jun 2019 16:02:02: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:02:02: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:02:02: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 16:02:02: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 16:02:02: #1 total tags in treatment: 4323837 INFO @ Sun, 02 Jun 2019 16:02:02: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:02:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 16:02:02: #1 tags after filtering in treatment: 4323837 INFO @ Sun, 02 Jun 2019 16:02:02: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:02:02: #1 finished! INFO @ Sun, 02 Jun 2019 16:02:02: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:02:02: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:02:03: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 16:02:03: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 16:02:03: #1 total tags in treatment: 4323837 INFO @ Sun, 02 Jun 2019 16:02:03: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:02:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 16:02:03: #1 tags after filtering in treatment: 4323837 INFO @ Sun, 02 Jun 2019 16:02:03: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:02:03: #1 finished! INFO @ Sun, 02 Jun 2019 16:02:03: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:02:03: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:02:03: #2 number of paired peaks: 8150 INFO @ Sun, 02 Jun 2019 16:02:03: start model_add_line... INFO @ Sun, 02 Jun 2019 16:02:04: #2 number of paired peaks: 8150 INFO @ Sun, 02 Jun 2019 16:02:04: start model_add_line... INFO @ Sun, 02 Jun 2019 16:02:04: start X-correlation... INFO @ Sun, 02 Jun 2019 16:02:04: end of X-cor INFO @ Sun, 02 Jun 2019 16:02:04: #2 finished! INFO @ Sun, 02 Jun 2019 16:02:04: #2 predicted fragment length is 152 bps INFO @ Sun, 02 Jun 2019 16:02:04: #2 alternative fragment length(s) may be 3,152 bps INFO @ Sun, 02 Jun 2019 16:02:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/ERX1999196/ERX1999196.05_model.r INFO @ Sun, 02 Jun 2019 16:02:04: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:02:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:02:04: start X-correlation... INFO @ Sun, 02 Jun 2019 16:02:04: end of X-cor INFO @ Sun, 02 Jun 2019 16:02:04: #2 finished! INFO @ Sun, 02 Jun 2019 16:02:04: #2 predicted fragment length is 152 bps INFO @ Sun, 02 Jun 2019 16:02:04: #2 alternative fragment length(s) may be 3,152 bps INFO @ Sun, 02 Jun 2019 16:02:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/ERX1999196/ERX1999196.10_model.r INFO @ Sun, 02 Jun 2019 16:02:04: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:02:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:02:04: #2 number of paired peaks: 8150 INFO @ Sun, 02 Jun 2019 16:02:04: start model_add_line... INFO @ Sun, 02 Jun 2019 16:02:04: start X-correlation... INFO @ Sun, 02 Jun 2019 16:02:04: end of X-cor INFO @ Sun, 02 Jun 2019 16:02:04: #2 finished! INFO @ Sun, 02 Jun 2019 16:02:04: #2 predicted fragment length is 152 bps INFO @ Sun, 02 Jun 2019 16:02:04: #2 alternative fragment length(s) may be 3,152 bps INFO @ Sun, 02 Jun 2019 16:02:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/ERX1999196/ERX1999196.20_model.r INFO @ Sun, 02 Jun 2019 16:02:04: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:02:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:02:20: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:02:21: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:02:21: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:02:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/ERX1999196/ERX1999196.05_peaks.xls INFO @ Sun, 02 Jun 2019 16:02:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/ERX1999196/ERX1999196.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:02:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/ERX1999196/ERX1999196.05_summits.bed INFO @ Sun, 02 Jun 2019 16:02:27: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (3560 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 16:02:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/ERX1999196/ERX1999196.20_peaks.xls INFO @ Sun, 02 Jun 2019 16:02:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/ERX1999196/ERX1999196.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:02:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/ERX1999196/ERX1999196.20_summits.bed INFO @ Sun, 02 Jun 2019 16:02:27: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (523 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 16:02:28: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/ERX1999196/ERX1999196.10_peaks.xls INFO @ Sun, 02 Jun 2019 16:02:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/ERX1999196/ERX1999196.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:02:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/ERX1999196/ERX1999196.10_summits.bed INFO @ Sun, 02 Jun 2019 16:02:28: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (1686 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。