Job ID = 1293542 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 25,432,118 reads read : 25,432,118 reads written : 25,432,118 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: 00:03:42 25432118 reads; of these: 25432118 (100.00%) were unpaired; of these: 19303533 (75.90%) aligned 0 times 5376289 (21.14%) aligned exactly 1 time 752296 (2.96%) aligned >1 times 24.10% overall alignment rate Time searching: 00:03:42 Overall time: 00:03:42 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_rmdupse_core] 3017145 / 6128585 = 0.4923 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, 03 Jun 2019 00:53:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX100248/SRX100248.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX100248/SRX100248.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX100248/SRX100248.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX100248/SRX100248.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 03 Jun 2019 00:53:10: #1 read tag files... INFO @ Mon, 03 Jun 2019 00:53:10: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 00:53:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX100248/SRX100248.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX100248/SRX100248.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX100248/SRX100248.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX100248/SRX100248.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 03 Jun 2019 00:53:10: #1 read tag files... INFO @ Mon, 03 Jun 2019 00:53:10: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 00:53:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX100248/SRX100248.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX100248/SRX100248.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX100248/SRX100248.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX100248/SRX100248.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 03 Jun 2019 00:53:10: #1 read tag files... INFO @ Mon, 03 Jun 2019 00:53:10: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 00:53:22: 1000000 INFO @ Mon, 03 Jun 2019 00:53:22: 1000000 INFO @ Mon, 03 Jun 2019 00:53:22: 1000000 INFO @ Mon, 03 Jun 2019 00:53:32: 2000000 INFO @ Mon, 03 Jun 2019 00:53:33: 2000000 INFO @ Mon, 03 Jun 2019 00:53:34: 2000000 INFO @ Mon, 03 Jun 2019 00:53:43: 3000000 INFO @ Mon, 03 Jun 2019 00:53:44: 3000000 INFO @ Mon, 03 Jun 2019 00:53:44: #1 tag size is determined as 54 bps INFO @ Mon, 03 Jun 2019 00:53:44: #1 tag size = 54 INFO @ Mon, 03 Jun 2019 00:53:44: #1 total tags in treatment: 3111440 INFO @ Mon, 03 Jun 2019 00:53:44: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 00:53:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 00:53:44: #1 tags after filtering in treatment: 3111440 INFO @ Mon, 03 Jun 2019 00:53:44: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 00:53:44: #1 finished! INFO @ Mon, 03 Jun 2019 00:53:44: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 00:53:44: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 00:53:45: #2 number of paired peaks: 6287 INFO @ Mon, 03 Jun 2019 00:53:45: start model_add_line... INFO @ Mon, 03 Jun 2019 00:53:45: start X-correlation... INFO @ Mon, 03 Jun 2019 00:53:45: #1 tag size is determined as 54 bps INFO @ Mon, 03 Jun 2019 00:53:45: #1 tag size = 54 INFO @ Mon, 03 Jun 2019 00:53:45: #1 total tags in treatment: 3111440 INFO @ Mon, 03 Jun 2019 00:53:45: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 00:53:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 00:53:45: end of X-cor INFO @ Mon, 03 Jun 2019 00:53:45: #2 finished! INFO @ Mon, 03 Jun 2019 00:53:45: #2 predicted fragment length is 122 bps INFO @ Mon, 03 Jun 2019 00:53:45: #2 alternative fragment length(s) may be 122 bps INFO @ Mon, 03 Jun 2019 00:53:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX100248/SRX100248.20_model.r INFO @ Mon, 03 Jun 2019 00:53:45: #3 Call peaks... INFO @ Mon, 03 Jun 2019 00:53:45: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 00:53:45: #1 tags after filtering in treatment: 3111440 INFO @ Mon, 03 Jun 2019 00:53:45: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 00:53:45: #1 finished! INFO @ Mon, 03 Jun 2019 00:53:45: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 00:53:45: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 00:53:46: #2 number of paired peaks: 6287 INFO @ Mon, 03 Jun 2019 00:53:46: start model_add_line... INFO @ Mon, 03 Jun 2019 00:53:46: start X-correlation... INFO @ Mon, 03 Jun 2019 00:53:46: end of X-cor INFO @ Mon, 03 Jun 2019 00:53:46: #2 finished! INFO @ Mon, 03 Jun 2019 00:53:46: #2 predicted fragment length is 122 bps INFO @ Mon, 03 Jun 2019 00:53:46: #2 alternative fragment length(s) may be 122 bps INFO @ Mon, 03 Jun 2019 00:53:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX100248/SRX100248.05_model.r INFO @ Mon, 03 Jun 2019 00:53:46: #3 Call peaks... INFO @ Mon, 03 Jun 2019 00:53:46: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 00:53:46: 3000000 INFO @ Mon, 03 Jun 2019 00:53:47: #1 tag size is determined as 54 bps INFO @ Mon, 03 Jun 2019 00:53:47: #1 tag size = 54 INFO @ Mon, 03 Jun 2019 00:53:47: #1 total tags in treatment: 3111440 INFO @ Mon, 03 Jun 2019 00:53:47: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 00:53:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 00:53:47: #1 tags after filtering in treatment: 3111440 INFO @ Mon, 03 Jun 2019 00:53:47: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 00:53:47: #1 finished! INFO @ Mon, 03 Jun 2019 00:53:47: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 00:53:47: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 00:53:48: #2 number of paired peaks: 6287 INFO @ Mon, 03 Jun 2019 00:53:48: start model_add_line... INFO @ Mon, 03 Jun 2019 00:53:48: start X-correlation... INFO @ Mon, 03 Jun 2019 00:53:48: end of X-cor INFO @ Mon, 03 Jun 2019 00:53:48: #2 finished! INFO @ Mon, 03 Jun 2019 00:53:48: #2 predicted fragment length is 122 bps INFO @ Mon, 03 Jun 2019 00:53:48: #2 alternative fragment length(s) may be 122 bps INFO @ Mon, 03 Jun 2019 00:53:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX100248/SRX100248.10_model.r INFO @ Mon, 03 Jun 2019 00:53:48: #3 Call peaks... INFO @ Mon, 03 Jun 2019 00:53:48: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 00:53:55: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 00:53:56: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 00:53:58: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 00:54:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX100248/SRX100248.20_peaks.xls INFO @ Mon, 03 Jun 2019 00:54:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX100248/SRX100248.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 00:54:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX100248/SRX100248.20_summits.bed INFO @ Mon, 03 Jun 2019 00:54:01: Done! pass1 - making usageList (14 chroms): 4 millis pass2 - checking and writing primary data (5433 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 00:54:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX100248/SRX100248.05_peaks.xls INFO @ Mon, 03 Jun 2019 00:54:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX100248/SRX100248.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 00:54:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX100248/SRX100248.05_summits.bed INFO @ Mon, 03 Jun 2019 00:54:02: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (10498 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 00:54:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX100248/SRX100248.10_peaks.xls INFO @ Mon, 03 Jun 2019 00:54:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX100248/SRX100248.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 00:54:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX100248/SRX100248.10_summits.bed INFO @ Mon, 03 Jun 2019 00:54:03: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (7922 records, 4 fields): 13 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。