Job ID = 2589781 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 5,062,929 reads read : 5,062,929 reads written : 5,062,929 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR947398.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: 00:00:47 5062929 reads; of these: 5062929 (100.00%) were unpaired; of these: 1686618 (33.31%) aligned 0 times 2938355 (58.04%) aligned exactly 1 time 437956 (8.65%) aligned >1 times 66.69% overall alignment rate Time searching: 00:00:47 Overall time: 00:00:47 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] 854186 / 3376311 = 0.2530 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 18:27:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331166/SRX331166.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331166/SRX331166.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331166/SRX331166.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331166/SRX331166.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 18:27:56: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:27:56: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:27:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331166/SRX331166.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331166/SRX331166.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331166/SRX331166.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331166/SRX331166.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 18:27:57: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:27:57: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:27:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331166/SRX331166.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331166/SRX331166.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331166/SRX331166.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331166/SRX331166.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 18:27:58: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:27:58: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:28:03: 1000000 INFO @ Mon, 12 Aug 2019 18:28:05: 1000000 INFO @ Mon, 12 Aug 2019 18:28:06: 1000000 INFO @ Mon, 12 Aug 2019 18:28:10: 2000000 INFO @ Mon, 12 Aug 2019 18:28:12: 2000000 INFO @ Mon, 12 Aug 2019 18:28:13: 2000000 INFO @ Mon, 12 Aug 2019 18:28:13: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:28:13: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:28:13: #1 total tags in treatment: 2522125 INFO @ Mon, 12 Aug 2019 18:28:13: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:28:13: #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 18:28:13: #1 tags after filtering in treatment: 2522125 INFO @ Mon, 12 Aug 2019 18:28:13: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:28:13: #1 finished! INFO @ Mon, 12 Aug 2019 18:28:13: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:28:13: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:28:13: #2 number of paired peaks: 2168 INFO @ Mon, 12 Aug 2019 18:28:13: start model_add_line... INFO @ Mon, 12 Aug 2019 18:28:13: start X-correlation... INFO @ Mon, 12 Aug 2019 18:28:13: end of X-cor INFO @ Mon, 12 Aug 2019 18:28:13: #2 finished! INFO @ Mon, 12 Aug 2019 18:28:13: #2 predicted fragment length is 158 bps INFO @ Mon, 12 Aug 2019 18:28:13: #2 alternative fragment length(s) may be 158 bps INFO @ Mon, 12 Aug 2019 18:28:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331166/SRX331166.05_model.r INFO @ Mon, 12 Aug 2019 18:28:13: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:28:13: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:28:16: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:28:16: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:28:16: #1 total tags in treatment: 2522125 INFO @ Mon, 12 Aug 2019 18:28:16: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:28:16: #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 18:28:16: #1 tags after filtering in treatment: 2522125 INFO @ Mon, 12 Aug 2019 18:28:16: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:28:16: #1 finished! INFO @ Mon, 12 Aug 2019 18:28:16: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:28:16: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:28:16: #2 number of paired peaks: 2168 INFO @ Mon, 12 Aug 2019 18:28:16: start model_add_line... INFO @ Mon, 12 Aug 2019 18:28:16: start X-correlation... INFO @ Mon, 12 Aug 2019 18:28:16: end of X-cor INFO @ Mon, 12 Aug 2019 18:28:16: #2 finished! INFO @ Mon, 12 Aug 2019 18:28:16: #2 predicted fragment length is 158 bps INFO @ Mon, 12 Aug 2019 18:28:16: #2 alternative fragment length(s) may be 158 bps INFO @ Mon, 12 Aug 2019 18:28:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331166/SRX331166.10_model.r INFO @ Mon, 12 Aug 2019 18:28:16: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:28:16: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:28:16: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:28:16: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:28:16: #1 total tags in treatment: 2522125 INFO @ Mon, 12 Aug 2019 18:28:16: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:28:16: #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 18:28:17: #1 tags after filtering in treatment: 2522125 INFO @ Mon, 12 Aug 2019 18:28:17: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:28:17: #1 finished! INFO @ Mon, 12 Aug 2019 18:28:17: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:28:17: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:28:17: #2 number of paired peaks: 2168 INFO @ Mon, 12 Aug 2019 18:28:17: start model_add_line... INFO @ Mon, 12 Aug 2019 18:28:17: start X-correlation... INFO @ Mon, 12 Aug 2019 18:28:17: end of X-cor INFO @ Mon, 12 Aug 2019 18:28:17: #2 finished! INFO @ Mon, 12 Aug 2019 18:28:17: #2 predicted fragment length is 158 bps INFO @ Mon, 12 Aug 2019 18:28:17: #2 alternative fragment length(s) may be 158 bps INFO @ Mon, 12 Aug 2019 18:28:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331166/SRX331166.20_model.r INFO @ Mon, 12 Aug 2019 18:28:17: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:28:17: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:28:22: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:28:25: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:28:26: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:28:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331166/SRX331166.05_peaks.xls INFO @ Mon, 12 Aug 2019 18:28:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331166/SRX331166.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:28:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331166/SRX331166.05_summits.bed INFO @ Mon, 12 Aug 2019 18:28:26: Done! pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (3992 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 18:28:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331166/SRX331166.10_peaks.xls INFO @ Mon, 12 Aug 2019 18:28:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331166/SRX331166.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:28:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331166/SRX331166.10_summits.bed INFO @ Mon, 12 Aug 2019 18:28:29: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (2545 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 18:28:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331166/SRX331166.20_peaks.xls INFO @ Mon, 12 Aug 2019 18:28:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331166/SRX331166.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:28:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331166/SRX331166.20_summits.bed INFO @ Mon, 12 Aug 2019 18:28:30: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (1424 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。