Job ID = 1292543 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 10,739,261 reads read : 10,739,261 reads written : 10,739,261 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: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:02:11 10739261 reads; of these: 10739261 (100.00%) were unpaired; of these: 564270 (5.25%) aligned 0 times 9035539 (84.14%) aligned exactly 1 time 1139452 (10.61%) aligned >1 times 94.75% overall alignment rate Time searching: 00:02:11 Overall time: 00:02:11 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] 2117298 / 10174991 = 0.2081 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 19:30:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466557/SRX466557.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466557/SRX466557.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466557/SRX466557.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466557/SRX466557.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 19:30:32: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:30:32: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:30:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466557/SRX466557.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466557/SRX466557.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466557/SRX466557.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466557/SRX466557.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 19:30:32: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:30:32: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:30:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466557/SRX466557.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466557/SRX466557.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466557/SRX466557.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466557/SRX466557.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 19:30:32: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:30:32: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:30:40: 1000000 INFO @ Sun, 02 Jun 2019 19:30:40: 1000000 INFO @ Sun, 02 Jun 2019 19:30:41: 1000000 INFO @ Sun, 02 Jun 2019 19:30:48: 2000000 INFO @ Sun, 02 Jun 2019 19:30:48: 2000000 INFO @ Sun, 02 Jun 2019 19:30:48: 2000000 INFO @ Sun, 02 Jun 2019 19:30:56: 3000000 INFO @ Sun, 02 Jun 2019 19:30:56: 3000000 INFO @ Sun, 02 Jun 2019 19:30:56: 3000000 INFO @ Sun, 02 Jun 2019 19:31:03: 4000000 INFO @ Sun, 02 Jun 2019 19:31:03: 4000000 INFO @ Sun, 02 Jun 2019 19:31:04: 4000000 INFO @ Sun, 02 Jun 2019 19:31:11: 5000000 INFO @ Sun, 02 Jun 2019 19:31:11: 5000000 INFO @ Sun, 02 Jun 2019 19:31:13: 5000000 INFO @ Sun, 02 Jun 2019 19:31:18: 6000000 INFO @ Sun, 02 Jun 2019 19:31:18: 6000000 INFO @ Sun, 02 Jun 2019 19:31:21: 6000000 INFO @ Sun, 02 Jun 2019 19:31:25: 7000000 INFO @ Sun, 02 Jun 2019 19:31:25: 7000000 INFO @ Sun, 02 Jun 2019 19:31:29: 7000000 INFO @ Sun, 02 Jun 2019 19:31:32: 8000000 INFO @ Sun, 02 Jun 2019 19:31:32: 8000000 INFO @ Sun, 02 Jun 2019 19:31:32: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 19:31:32: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 19:31:32: #1 total tags in treatment: 8057693 INFO @ Sun, 02 Jun 2019 19:31:32: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:31:32: #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 19:31:32: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 19:31:32: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 19:31:32: #1 total tags in treatment: 8057693 INFO @ Sun, 02 Jun 2019 19:31:32: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:31:32: #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 19:31:32: #1 tags after filtering in treatment: 8057693 INFO @ Sun, 02 Jun 2019 19:31:32: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 19:31:32: #1 finished! INFO @ Sun, 02 Jun 2019 19:31:32: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:31:32: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:31:33: #1 tags after filtering in treatment: 8057693 INFO @ Sun, 02 Jun 2019 19:31:33: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 19:31:33: #1 finished! INFO @ Sun, 02 Jun 2019 19:31:33: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:31:33: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:31:34: #2 number of paired peaks: 3507 INFO @ Sun, 02 Jun 2019 19:31:34: start model_add_line... INFO @ Sun, 02 Jun 2019 19:31:34: #2 number of paired peaks: 3507 INFO @ Sun, 02 Jun 2019 19:31:34: start model_add_line... INFO @ Sun, 02 Jun 2019 19:31:34: start X-correlation... INFO @ Sun, 02 Jun 2019 19:31:34: end of X-cor INFO @ Sun, 02 Jun 2019 19:31:34: #2 finished! INFO @ Sun, 02 Jun 2019 19:31:34: start X-correlation... INFO @ Sun, 02 Jun 2019 19:31:34: #2 predicted fragment length is 192 bps INFO @ Sun, 02 Jun 2019 19:31:34: #2 alternative fragment length(s) may be 4,192 bps INFO @ Sun, 02 Jun 2019 19:31:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466557/SRX466557.10_model.r INFO @ Sun, 02 Jun 2019 19:31:34: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:31:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:31:34: end of X-cor INFO @ Sun, 02 Jun 2019 19:31:34: #2 finished! INFO @ Sun, 02 Jun 2019 19:31:34: #2 predicted fragment length is 192 bps INFO @ Sun, 02 Jun 2019 19:31:34: #2 alternative fragment length(s) may be 4,192 bps INFO @ Sun, 02 Jun 2019 19:31:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466557/SRX466557.05_model.r INFO @ Sun, 02 Jun 2019 19:31:34: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:31:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:31:36: 8000000 INFO @ Sun, 02 Jun 2019 19:31:36: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 19:31:36: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 19:31:36: #1 total tags in treatment: 8057693 INFO @ Sun, 02 Jun 2019 19:31:36: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:31:36: #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 19:31:36: #1 tags after filtering in treatment: 8057693 INFO @ Sun, 02 Jun 2019 19:31:36: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 19:31:36: #1 finished! INFO @ Sun, 02 Jun 2019 19:31:36: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:31:36: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:31:38: #2 number of paired peaks: 3507 INFO @ Sun, 02 Jun 2019 19:31:38: start model_add_line... INFO @ Sun, 02 Jun 2019 19:31:38: start X-correlation... INFO @ Sun, 02 Jun 2019 19:31:38: end of X-cor INFO @ Sun, 02 Jun 2019 19:31:38: #2 finished! INFO @ Sun, 02 Jun 2019 19:31:38: #2 predicted fragment length is 192 bps INFO @ Sun, 02 Jun 2019 19:31:38: #2 alternative fragment length(s) may be 4,192 bps INFO @ Sun, 02 Jun 2019 19:31:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466557/SRX466557.20_model.r INFO @ Sun, 02 Jun 2019 19:31:38: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:31:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:32:02: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:32:03: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:32:07: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:32:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466557/SRX466557.10_peaks.xls INFO @ Sun, 02 Jun 2019 19:32:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466557/SRX466557.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:32:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466557/SRX466557.10_summits.bed INFO @ Sun, 02 Jun 2019 19:32:15: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (2581 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 19:32:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466557/SRX466557.05_peaks.xls INFO @ Sun, 02 Jun 2019 19:32:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466557/SRX466557.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:32:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466557/SRX466557.05_summits.bed INFO @ Sun, 02 Jun 2019 19:32:15: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (4256 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 19:32:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466557/SRX466557.20_peaks.xls INFO @ Sun, 02 Jun 2019 19:32:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466557/SRX466557.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:32:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466557/SRX466557.20_summits.bed INFO @ Sun, 02 Jun 2019 19:32:20: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (1193 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。