Job ID = 2589787 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 9,164,852 reads read : 9,164,852 reads written : 9,164,852 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR947402.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: 00:01:33 9164852 reads; of these: 9164852 (100.00%) were unpaired; of these: 546711 (5.97%) aligned 0 times 7532237 (82.19%) aligned exactly 1 time 1085904 (11.85%) aligned >1 times 94.03% overall alignment rate Time searching: 00:01:33 Overall time: 00:01:33 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] 1858752 / 8618141 = 0.2157 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 18:30:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331170/SRX331170.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331170/SRX331170.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331170/SRX331170.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331170/SRX331170.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 18:30:44: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:30:44: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:30:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331170/SRX331170.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331170/SRX331170.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331170/SRX331170.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331170/SRX331170.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 18:30:45: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:30:45: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:30:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331170/SRX331170.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331170/SRX331170.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331170/SRX331170.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331170/SRX331170.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 18:30:46: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:30:46: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:30:51: 1000000 INFO @ Mon, 12 Aug 2019 18:30:52: 1000000 INFO @ Mon, 12 Aug 2019 18:30:53: 1000000 INFO @ Mon, 12 Aug 2019 18:30:58: 2000000 INFO @ Mon, 12 Aug 2019 18:30:59: 2000000 INFO @ Mon, 12 Aug 2019 18:31:02: 2000000 INFO @ Mon, 12 Aug 2019 18:31:04: 3000000 INFO @ Mon, 12 Aug 2019 18:31:05: 3000000 INFO @ Mon, 12 Aug 2019 18:31:10: 3000000 INFO @ Mon, 12 Aug 2019 18:31:11: 4000000 INFO @ Mon, 12 Aug 2019 18:31:12: 4000000 INFO @ Mon, 12 Aug 2019 18:31:17: 5000000 INFO @ Mon, 12 Aug 2019 18:31:18: 5000000 INFO @ Mon, 12 Aug 2019 18:31:18: 4000000 INFO @ Mon, 12 Aug 2019 18:31:23: 6000000 INFO @ Mon, 12 Aug 2019 18:31:24: 6000000 INFO @ Mon, 12 Aug 2019 18:31:26: 5000000 INFO @ Mon, 12 Aug 2019 18:31:28: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:31:28: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:31:28: #1 total tags in treatment: 6759389 INFO @ Mon, 12 Aug 2019 18:31:28: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:31:28: #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 18:31:28: #1 tags after filtering in treatment: 6759389 INFO @ Mon, 12 Aug 2019 18:31:28: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:31:28: #1 finished! INFO @ Mon, 12 Aug 2019 18:31:28: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:31:28: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:31:29: #2 number of paired peaks: 1929 INFO @ Mon, 12 Aug 2019 18:31:29: start model_add_line... INFO @ Mon, 12 Aug 2019 18:31:29: start X-correlation... INFO @ Mon, 12 Aug 2019 18:31:29: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:31:29: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:31:29: #1 total tags in treatment: 6759389 INFO @ Mon, 12 Aug 2019 18:31:29: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:31:29: #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 18:31:29: end of X-cor INFO @ Mon, 12 Aug 2019 18:31:29: #2 finished! INFO @ Mon, 12 Aug 2019 18:31:29: #2 predicted fragment length is 173 bps INFO @ Mon, 12 Aug 2019 18:31:29: #2 alternative fragment length(s) may be 173 bps INFO @ Mon, 12 Aug 2019 18:31:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331170/SRX331170.10_model.r INFO @ Mon, 12 Aug 2019 18:31:29: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:31:29: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:31:29: #1 tags after filtering in treatment: 6759389 INFO @ Mon, 12 Aug 2019 18:31:29: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:31:29: #1 finished! INFO @ Mon, 12 Aug 2019 18:31:29: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:31:29: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:31:30: #2 number of paired peaks: 1929 INFO @ Mon, 12 Aug 2019 18:31:30: start model_add_line... INFO @ Mon, 12 Aug 2019 18:31:30: start X-correlation... INFO @ Mon, 12 Aug 2019 18:31:30: end of X-cor INFO @ Mon, 12 Aug 2019 18:31:30: #2 finished! INFO @ Mon, 12 Aug 2019 18:31:30: #2 predicted fragment length is 173 bps INFO @ Mon, 12 Aug 2019 18:31:30: #2 alternative fragment length(s) may be 173 bps INFO @ Mon, 12 Aug 2019 18:31:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331170/SRX331170.20_model.r INFO @ Mon, 12 Aug 2019 18:31:30: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:31:30: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:31:33: 6000000 INFO @ Mon, 12 Aug 2019 18:31:39: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:31:39: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:31:39: #1 total tags in treatment: 6759389 INFO @ Mon, 12 Aug 2019 18:31:39: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:31:39: #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 18:31:39: #1 tags after filtering in treatment: 6759389 INFO @ Mon, 12 Aug 2019 18:31:39: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:31:39: #1 finished! INFO @ Mon, 12 Aug 2019 18:31:39: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:31:39: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:31:40: #2 number of paired peaks: 1929 INFO @ Mon, 12 Aug 2019 18:31:40: start model_add_line... INFO @ Mon, 12 Aug 2019 18:31:40: start X-correlation... INFO @ Mon, 12 Aug 2019 18:31:40: end of X-cor INFO @ Mon, 12 Aug 2019 18:31:40: #2 finished! INFO @ Mon, 12 Aug 2019 18:31:40: #2 predicted fragment length is 173 bps INFO @ Mon, 12 Aug 2019 18:31:40: #2 alternative fragment length(s) may be 173 bps INFO @ Mon, 12 Aug 2019 18:31:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331170/SRX331170.05_model.r INFO @ Mon, 12 Aug 2019 18:31:40: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:31:40: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:31:51: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:31:52: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:32:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331170/SRX331170.10_peaks.xls INFO @ Mon, 12 Aug 2019 18:32:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331170/SRX331170.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:32:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331170/SRX331170.10_summits.bed INFO @ Mon, 12 Aug 2019 18:32:01: Done! pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (4844 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 18:32:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331170/SRX331170.20_peaks.xls INFO @ Mon, 12 Aug 2019 18:32:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331170/SRX331170.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:32:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331170/SRX331170.20_summits.bed INFO @ Mon, 12 Aug 2019 18:32:02: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (3191 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 18:32:02: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:32:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331170/SRX331170.05_peaks.xls INFO @ Mon, 12 Aug 2019 18:32:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331170/SRX331170.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:32:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331170/SRX331170.05_summits.bed INFO @ Mon, 12 Aug 2019 18:32:13: Done! pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (6640 records, 4 fields): 15 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。