Job ID = 2589364 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 11,390,104 reads read : 11,390,104 reads written : 11,390,104 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: 00:03:05 11390104 reads; of these: 11390104 (100.00%) were unpaired; of these: 889047 (7.81%) aligned 0 times 8747430 (76.80%) aligned exactly 1 time 1753627 (15.40%) aligned >1 times 92.19% overall alignment rate Time searching: 00:03:05 Overall time: 00:03:05 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] 4739718 / 10501057 = 0.4514 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 17:42:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX1078717/SRX1078717.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX1078717/SRX1078717.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX1078717/SRX1078717.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX1078717/SRX1078717.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 17:42:13: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:42:13: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:42:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX1078717/SRX1078717.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX1078717/SRX1078717.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX1078717/SRX1078717.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX1078717/SRX1078717.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 17:42:13: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:42:13: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:42:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX1078717/SRX1078717.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX1078717/SRX1078717.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX1078717/SRX1078717.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX1078717/SRX1078717.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 17:42:14: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:42:14: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:42:21: 1000000 INFO @ Mon, 12 Aug 2019 17:42:23: 1000000 INFO @ Mon, 12 Aug 2019 17:42:24: 1000000 INFO @ Mon, 12 Aug 2019 17:42:29: 2000000 INFO @ Mon, 12 Aug 2019 17:42:32: 2000000 INFO @ Mon, 12 Aug 2019 17:42:33: 2000000 INFO @ Mon, 12 Aug 2019 17:42:38: 3000000 INFO @ Mon, 12 Aug 2019 17:42:40: 3000000 INFO @ Mon, 12 Aug 2019 17:42:43: 3000000 INFO @ Mon, 12 Aug 2019 17:42:46: 4000000 INFO @ Mon, 12 Aug 2019 17:42:48: 4000000 INFO @ Mon, 12 Aug 2019 17:42:52: 4000000 INFO @ Mon, 12 Aug 2019 17:42:54: 5000000 INFO @ Mon, 12 Aug 2019 17:42:56: 5000000 INFO @ Mon, 12 Aug 2019 17:43:00: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 17:43:00: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 17:43:00: #1 total tags in treatment: 5761339 INFO @ Mon, 12 Aug 2019 17:43:00: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:43:00: #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 17:43:00: #1 tags after filtering in treatment: 5761339 INFO @ Mon, 12 Aug 2019 17:43:00: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:43:00: #1 finished! INFO @ Mon, 12 Aug 2019 17:43:00: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:43:00: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:43:01: #2 number of paired peaks: 1272 INFO @ Mon, 12 Aug 2019 17:43:01: start model_add_line... INFO @ Mon, 12 Aug 2019 17:43:01: start X-correlation... INFO @ Mon, 12 Aug 2019 17:43:01: end of X-cor INFO @ Mon, 12 Aug 2019 17:43:01: #2 finished! INFO @ Mon, 12 Aug 2019 17:43:01: #2 predicted fragment length is 222 bps INFO @ Mon, 12 Aug 2019 17:43:01: #2 alternative fragment length(s) may be 222 bps INFO @ Mon, 12 Aug 2019 17:43:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX1078717/SRX1078717.05_model.r INFO @ Mon, 12 Aug 2019 17:43:01: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:43:01: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:43:02: 5000000 INFO @ Mon, 12 Aug 2019 17:43:02: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 17:43:02: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 17:43:02: #1 total tags in treatment: 5761339 INFO @ Mon, 12 Aug 2019 17:43:02: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:43:02: #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 17:43:03: #1 tags after filtering in treatment: 5761339 INFO @ Mon, 12 Aug 2019 17:43:03: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:43:03: #1 finished! INFO @ Mon, 12 Aug 2019 17:43:03: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:43:03: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:43:03: #2 number of paired peaks: 1272 INFO @ Mon, 12 Aug 2019 17:43:03: start model_add_line... INFO @ Mon, 12 Aug 2019 17:43:03: start X-correlation... INFO @ Mon, 12 Aug 2019 17:43:03: end of X-cor INFO @ Mon, 12 Aug 2019 17:43:03: #2 finished! INFO @ Mon, 12 Aug 2019 17:43:03: #2 predicted fragment length is 222 bps INFO @ Mon, 12 Aug 2019 17:43:03: #2 alternative fragment length(s) may be 222 bps INFO @ Mon, 12 Aug 2019 17:43:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX1078717/SRX1078717.20_model.r INFO @ Mon, 12 Aug 2019 17:43:03: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:43:03: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:43:09: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 17:43:09: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 17:43:09: #1 total tags in treatment: 5761339 INFO @ Mon, 12 Aug 2019 17:43:09: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:43:09: #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 17:43:09: #1 tags after filtering in treatment: 5761339 INFO @ Mon, 12 Aug 2019 17:43:09: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:43:09: #1 finished! INFO @ Mon, 12 Aug 2019 17:43:09: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:43:09: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:43:10: #2 number of paired peaks: 1272 INFO @ Mon, 12 Aug 2019 17:43:10: start model_add_line... INFO @ Mon, 12 Aug 2019 17:43:10: start X-correlation... INFO @ Mon, 12 Aug 2019 17:43:10: end of X-cor INFO @ Mon, 12 Aug 2019 17:43:10: #2 finished! INFO @ Mon, 12 Aug 2019 17:43:10: #2 predicted fragment length is 222 bps INFO @ Mon, 12 Aug 2019 17:43:10: #2 alternative fragment length(s) may be 222 bps INFO @ Mon, 12 Aug 2019 17:43:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX1078717/SRX1078717.10_model.r INFO @ Mon, 12 Aug 2019 17:43:10: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:43:10: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:43:20: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:43:23: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:43:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX1078717/SRX1078717.05_peaks.xls INFO @ Mon, 12 Aug 2019 17:43:29: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:43:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX1078717/SRX1078717.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:43:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX1078717/SRX1078717.05_summits.bed INFO @ Mon, 12 Aug 2019 17:43:29: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (4172 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 17:43:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX1078717/SRX1078717.20_peaks.xls INFO @ Mon, 12 Aug 2019 17:43:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX1078717/SRX1078717.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:43:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX1078717/SRX1078717.20_summits.bed INFO @ Mon, 12 Aug 2019 17:43:31: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1035 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 17:43:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX1078717/SRX1078717.10_peaks.xls INFO @ Mon, 12 Aug 2019 17:43:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX1078717/SRX1078717.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:43:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX1078717/SRX1078717.10_summits.bed INFO @ Mon, 12 Aug 2019 17:43:38: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (2347 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。