Job ID = 2589546 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 6,721,950 reads read : 6,721,950 reads written : 6,721,950 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR702399.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: 00:00:50 6721950 reads; of these: 6721950 (100.00%) were unpaired; of these: 2924520 (43.51%) aligned 0 times 3285230 (48.87%) aligned exactly 1 time 512200 (7.62%) aligned >1 times 56.49% overall alignment rate Time searching: 00:00:50 Overall time: 00:00:50 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] 452234 / 3797430 = 0.1191 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 17:56:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX233696/SRX233696.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX233696/SRX233696.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX233696/SRX233696.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX233696/SRX233696.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 17:56:48: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:56:48: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:56:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX233696/SRX233696.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX233696/SRX233696.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX233696/SRX233696.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX233696/SRX233696.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 17:56:49: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:56:49: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:56:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX233696/SRX233696.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX233696/SRX233696.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX233696/SRX233696.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX233696/SRX233696.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 17:56:50: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:56:50: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:56:55: 1000000 INFO @ Mon, 12 Aug 2019 17:56:56: 1000000 INFO @ Mon, 12 Aug 2019 17:56:59: 1000000 INFO @ Mon, 12 Aug 2019 17:57:02: 2000000 INFO @ Mon, 12 Aug 2019 17:57:03: 2000000 INFO @ Mon, 12 Aug 2019 17:57:08: 2000000 INFO @ Mon, 12 Aug 2019 17:57:09: 3000000 INFO @ Mon, 12 Aug 2019 17:57:10: 3000000 INFO @ Mon, 12 Aug 2019 17:57:11: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 17:57:11: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 17:57:11: #1 total tags in treatment: 3345196 INFO @ Mon, 12 Aug 2019 17:57:11: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:57:11: #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 17:57:11: #1 tags after filtering in treatment: 3345196 INFO @ Mon, 12 Aug 2019 17:57:11: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:57:11: #1 finished! INFO @ Mon, 12 Aug 2019 17:57:11: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:57:11: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:57:12: #2 number of paired peaks: 1058 INFO @ Mon, 12 Aug 2019 17:57:12: start model_add_line... INFO @ Mon, 12 Aug 2019 17:57:12: start X-correlation... INFO @ Mon, 12 Aug 2019 17:57:12: end of X-cor INFO @ Mon, 12 Aug 2019 17:57:12: #2 finished! INFO @ Mon, 12 Aug 2019 17:57:12: #2 predicted fragment length is 169 bps INFO @ Mon, 12 Aug 2019 17:57:12: #2 alternative fragment length(s) may be 169 bps INFO @ Mon, 12 Aug 2019 17:57:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX233696/SRX233696.05_model.r INFO @ Mon, 12 Aug 2019 17:57:12: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:57:12: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:57:12: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 17:57:12: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 17:57:12: #1 total tags in treatment: 3345196 INFO @ Mon, 12 Aug 2019 17:57:12: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:57:12: #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 17:57:12: #1 tags after filtering in treatment: 3345196 INFO @ Mon, 12 Aug 2019 17:57:12: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:57:12: #1 finished! INFO @ Mon, 12 Aug 2019 17:57:12: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:57:12: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:57:13: #2 number of paired peaks: 1058 INFO @ Mon, 12 Aug 2019 17:57:13: start model_add_line... INFO @ Mon, 12 Aug 2019 17:57:13: start X-correlation... INFO @ Mon, 12 Aug 2019 17:57:13: end of X-cor INFO @ Mon, 12 Aug 2019 17:57:13: #2 finished! INFO @ Mon, 12 Aug 2019 17:57:13: #2 predicted fragment length is 169 bps INFO @ Mon, 12 Aug 2019 17:57:13: #2 alternative fragment length(s) may be 169 bps INFO @ Mon, 12 Aug 2019 17:57:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX233696/SRX233696.10_model.r INFO @ Mon, 12 Aug 2019 17:57:13: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:57:13: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:57:16: 3000000 INFO @ Mon, 12 Aug 2019 17:57:19: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 17:57:19: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 17:57:19: #1 total tags in treatment: 3345196 INFO @ Mon, 12 Aug 2019 17:57:19: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:57:19: #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 17:57:19: #1 tags after filtering in treatment: 3345196 INFO @ Mon, 12 Aug 2019 17:57:19: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:57:19: #1 finished! INFO @ Mon, 12 Aug 2019 17:57:19: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:57:19: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:57:19: #2 number of paired peaks: 1058 INFO @ Mon, 12 Aug 2019 17:57:19: start model_add_line... INFO @ Mon, 12 Aug 2019 17:57:19: start X-correlation... INFO @ Mon, 12 Aug 2019 17:57:19: end of X-cor INFO @ Mon, 12 Aug 2019 17:57:19: #2 finished! INFO @ Mon, 12 Aug 2019 17:57:19: #2 predicted fragment length is 169 bps INFO @ Mon, 12 Aug 2019 17:57:19: #2 alternative fragment length(s) may be 169 bps INFO @ Mon, 12 Aug 2019 17:57:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX233696/SRX233696.20_model.r INFO @ Mon, 12 Aug 2019 17:57:19: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:57:19: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:57:22: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:57:23: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:57:28: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX233696/SRX233696.05_peaks.xls INFO @ Mon, 12 Aug 2019 17:57:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX233696/SRX233696.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:57:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX233696/SRX233696.05_summits.bed INFO @ Mon, 12 Aug 2019 17:57:28: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (3094 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 17:57:28: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX233696/SRX233696.10_peaks.xls INFO @ Mon, 12 Aug 2019 17:57:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX233696/SRX233696.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:57:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX233696/SRX233696.10_summits.bed INFO @ Mon, 12 Aug 2019 17:57:29: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (1584 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 17:57:30: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:57:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX233696/SRX233696.20_peaks.xls INFO @ Mon, 12 Aug 2019 17:57:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX233696/SRX233696.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:57:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX233696/SRX233696.20_summits.bed INFO @ Mon, 12 Aug 2019 17:57:35: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (666 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。