Job ID = 2590242 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 19,194,338 reads read : 19,194,338 reads written : 19,194,338 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: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:07:00 19194338 reads; of these: 19194338 (100.00%) were unpaired; of these: 152906 (0.80%) aligned 0 times 17318915 (90.23%) aligned exactly 1 time 1722517 (8.97%) aligned >1 times 99.20% overall alignment rate Time searching: 00:07:01 Overall time: 00:07:01 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] 3065404 / 19041432 = 0.1610 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 20:41:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5985674/SRX5985674.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5985674/SRX5985674.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5985674/SRX5985674.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5985674/SRX5985674.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 20:41:31: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:41:31: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:41:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5985674/SRX5985674.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5985674/SRX5985674.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5985674/SRX5985674.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5985674/SRX5985674.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 20:41:31: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:41:31: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:41:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5985674/SRX5985674.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5985674/SRX5985674.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5985674/SRX5985674.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5985674/SRX5985674.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 20:41:32: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:41:32: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:41:41: 1000000 INFO @ Mon, 12 Aug 2019 20:41:42: 1000000 INFO @ Mon, 12 Aug 2019 20:41:43: 1000000 INFO @ Mon, 12 Aug 2019 20:41:50: 2000000 INFO @ Mon, 12 Aug 2019 20:41:51: 2000000 INFO @ Mon, 12 Aug 2019 20:41:53: 2000000 INFO @ Mon, 12 Aug 2019 20:41:59: 3000000 INFO @ Mon, 12 Aug 2019 20:42:00: 3000000 INFO @ Mon, 12 Aug 2019 20:42:03: 3000000 INFO @ Mon, 12 Aug 2019 20:42:08: 4000000 INFO @ Mon, 12 Aug 2019 20:42:09: 4000000 INFO @ Mon, 12 Aug 2019 20:42:12: 4000000 INFO @ Mon, 12 Aug 2019 20:42:16: 5000000 INFO @ Mon, 12 Aug 2019 20:42:19: 5000000 INFO @ Mon, 12 Aug 2019 20:42:22: 5000000 INFO @ Mon, 12 Aug 2019 20:42:25: 6000000 INFO @ Mon, 12 Aug 2019 20:42:28: 6000000 INFO @ Mon, 12 Aug 2019 20:42:32: 6000000 INFO @ Mon, 12 Aug 2019 20:42:33: 7000000 INFO @ Mon, 12 Aug 2019 20:42:37: 7000000 INFO @ Mon, 12 Aug 2019 20:42:42: 7000000 INFO @ Mon, 12 Aug 2019 20:42:42: 8000000 INFO @ Mon, 12 Aug 2019 20:42:46: 8000000 INFO @ Mon, 12 Aug 2019 20:42:51: 9000000 INFO @ Mon, 12 Aug 2019 20:42:51: 8000000 INFO @ Mon, 12 Aug 2019 20:42:56: 9000000 INFO @ Mon, 12 Aug 2019 20:43:01: 10000000 INFO @ Mon, 12 Aug 2019 20:43:01: 9000000 INFO @ Mon, 12 Aug 2019 20:43:06: 10000000 INFO @ Mon, 12 Aug 2019 20:43:10: 10000000 INFO @ Mon, 12 Aug 2019 20:43:11: 11000000 INFO @ Mon, 12 Aug 2019 20:43:17: 11000000 INFO @ Mon, 12 Aug 2019 20:43:18: 11000000 INFO @ Mon, 12 Aug 2019 20:43:22: 12000000 INFO @ Mon, 12 Aug 2019 20:43:26: 12000000 INFO @ Mon, 12 Aug 2019 20:43:28: 12000000 INFO @ Mon, 12 Aug 2019 20:43:32: 13000000 INFO @ Mon, 12 Aug 2019 20:43:34: 13000000 INFO @ Mon, 12 Aug 2019 20:43:38: 13000000 INFO @ Mon, 12 Aug 2019 20:43:42: 14000000 INFO @ Mon, 12 Aug 2019 20:43:42: 14000000 INFO @ Mon, 12 Aug 2019 20:43:48: 14000000 INFO @ Mon, 12 Aug 2019 20:43:50: 15000000 INFO @ Mon, 12 Aug 2019 20:43:52: 15000000 INFO @ Mon, 12 Aug 2019 20:43:58: #1 tag size is determined as 76 bps INFO @ Mon, 12 Aug 2019 20:43:58: #1 tag size = 76 INFO @ Mon, 12 Aug 2019 20:43:58: #1 total tags in treatment: 15976028 INFO @ Mon, 12 Aug 2019 20:43:58: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:43:58: #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 20:43:58: 15000000 INFO @ Mon, 12 Aug 2019 20:43:59: #1 tags after filtering in treatment: 15976028 INFO @ Mon, 12 Aug 2019 20:43:59: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:43:59: #1 finished! INFO @ Mon, 12 Aug 2019 20:43:59: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:43:59: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:44:00: #2 number of paired peaks: 1256 INFO @ Mon, 12 Aug 2019 20:44:00: start model_add_line... INFO @ Mon, 12 Aug 2019 20:44:00: start X-correlation... INFO @ Mon, 12 Aug 2019 20:44:00: end of X-cor INFO @ Mon, 12 Aug 2019 20:44:00: #2 finished! INFO @ Mon, 12 Aug 2019 20:44:00: #2 predicted fragment length is 181 bps INFO @ Mon, 12 Aug 2019 20:44:00: #2 alternative fragment length(s) may be 2,181,204,206,237 bps INFO @ Mon, 12 Aug 2019 20:44:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5985674/SRX5985674.05_model.r INFO @ Mon, 12 Aug 2019 20:44:00: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:44:00: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:44:02: #1 tag size is determined as 76 bps INFO @ Mon, 12 Aug 2019 20:44:02: #1 tag size = 76 INFO @ Mon, 12 Aug 2019 20:44:02: #1 total tags in treatment: 15976028 INFO @ Mon, 12 Aug 2019 20:44:02: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:44:02: #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 20:44:03: #1 tags after filtering in treatment: 15976028 INFO @ Mon, 12 Aug 2019 20:44:03: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:44:03: #1 finished! INFO @ Mon, 12 Aug 2019 20:44:03: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:44:03: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:44:04: #2 number of paired peaks: 1256 INFO @ Mon, 12 Aug 2019 20:44:04: start model_add_line... INFO @ Mon, 12 Aug 2019 20:44:04: start X-correlation... INFO @ Mon, 12 Aug 2019 20:44:04: end of X-cor INFO @ Mon, 12 Aug 2019 20:44:04: #2 finished! INFO @ Mon, 12 Aug 2019 20:44:04: #2 predicted fragment length is 181 bps INFO @ Mon, 12 Aug 2019 20:44:04: #2 alternative fragment length(s) may be 2,181,204,206,237 bps INFO @ Mon, 12 Aug 2019 20:44:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5985674/SRX5985674.20_model.r INFO @ Mon, 12 Aug 2019 20:44:04: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:44:04: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:44:09: #1 tag size is determined as 76 bps INFO @ Mon, 12 Aug 2019 20:44:09: #1 tag size = 76 INFO @ Mon, 12 Aug 2019 20:44:09: #1 total tags in treatment: 15976028 INFO @ Mon, 12 Aug 2019 20:44:09: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:44:09: #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 20:44:09: #1 tags after filtering in treatment: 15976028 INFO @ Mon, 12 Aug 2019 20:44:09: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:44:09: #1 finished! INFO @ Mon, 12 Aug 2019 20:44:09: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:44:09: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:44:10: #2 number of paired peaks: 1256 INFO @ Mon, 12 Aug 2019 20:44:10: start model_add_line... INFO @ Mon, 12 Aug 2019 20:44:11: start X-correlation... INFO @ Mon, 12 Aug 2019 20:44:11: end of X-cor INFO @ Mon, 12 Aug 2019 20:44:11: #2 finished! INFO @ Mon, 12 Aug 2019 20:44:11: #2 predicted fragment length is 181 bps INFO @ Mon, 12 Aug 2019 20:44:11: #2 alternative fragment length(s) may be 2,181,204,206,237 bps INFO @ Mon, 12 Aug 2019 20:44:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5985674/SRX5985674.10_model.r INFO @ Mon, 12 Aug 2019 20:44:11: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:44:11: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:44:44: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:44:50: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:44:53: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:45:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5985674/SRX5985674.05_peaks.xls INFO @ Mon, 12 Aug 2019 20:45:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5985674/SRX5985674.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:45:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5985674/SRX5985674.05_summits.bed INFO @ Mon, 12 Aug 2019 20:45:03: Done! pass1 - making usageList (6 chroms): 3 millis pass2 - checking and writing primary data (6496 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 20:45:10: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5985674/SRX5985674.20_peaks.xls INFO @ Mon, 12 Aug 2019 20:45:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5985674/SRX5985674.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:45:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5985674/SRX5985674.20_summits.bed INFO @ Mon, 12 Aug 2019 20:45:10: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (840 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 20:45:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5985674/SRX5985674.10_peaks.xls INFO @ Mon, 12 Aug 2019 20:45:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5985674/SRX5985674.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:45:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5985674/SRX5985674.10_summits.bed INFO @ Mon, 12 Aug 2019 20:45:12: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3102 records, 4 fields): 9 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。