Job ID = 1293977 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 4,000,000 reads read : 4,000,000 reads written : 4,000,000 spots read : 4,000,000 reads read : 4,000,000 reads written : 4,000,000 spots read : 4,000,000 reads read : 4,000,000 reads written : 4,000,000 spots read : 3,810,961 reads read : 3,810,961 reads written : 3,810,961 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: 00:01:48 15810961 reads; of these: 15810961 (100.00%) were unpaired; of these: 13606239 (86.06%) aligned 0 times 1789444 (11.32%) aligned exactly 1 time 415278 (2.63%) aligned >1 times 13.94% overall alignment rate Time searching: 00:01:48 Overall time: 00:01:48 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] 435316 / 2204722 = 0.1974 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 03:50:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1550611/SRX1550611.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1550611/SRX1550611.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1550611/SRX1550611.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1550611/SRX1550611.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 03:50:08: #1 read tag files... INFO @ Mon, 03 Jun 2019 03:50:08: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 03:50:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1550611/SRX1550611.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1550611/SRX1550611.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1550611/SRX1550611.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1550611/SRX1550611.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 03:50:08: #1 read tag files... INFO @ Mon, 03 Jun 2019 03:50:08: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 03:50:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1550611/SRX1550611.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1550611/SRX1550611.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1550611/SRX1550611.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1550611/SRX1550611.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 03:50:08: #1 read tag files... INFO @ Mon, 03 Jun 2019 03:50:08: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 03:50:15: 1000000 INFO @ Mon, 03 Jun 2019 03:50:16: 1000000 INFO @ Mon, 03 Jun 2019 03:50:18: 1000000 INFO @ Mon, 03 Jun 2019 03:50:21: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 03:50:21: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 03:50:21: #1 total tags in treatment: 1769406 INFO @ Mon, 03 Jun 2019 03:50:21: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 03:50:21: #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 03:50:21: #1 tags after filtering in treatment: 1769406 INFO @ Mon, 03 Jun 2019 03:50:21: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 03:50:21: #1 finished! INFO @ Mon, 03 Jun 2019 03:50:21: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 03:50:21: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 03:50:21: #2 number of paired peaks: 2072 INFO @ Mon, 03 Jun 2019 03:50:21: start model_add_line... INFO @ Mon, 03 Jun 2019 03:50:21: start X-correlation... INFO @ Mon, 03 Jun 2019 03:50:21: end of X-cor INFO @ Mon, 03 Jun 2019 03:50:21: #2 finished! INFO @ Mon, 03 Jun 2019 03:50:21: #2 predicted fragment length is 118 bps INFO @ Mon, 03 Jun 2019 03:50:21: #2 alternative fragment length(s) may be 118 bps INFO @ Mon, 03 Jun 2019 03:50:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1550611/SRX1550611.05_model.r INFO @ Mon, 03 Jun 2019 03:50:21: #3 Call peaks... INFO @ Mon, 03 Jun 2019 03:50:21: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 03:50:22: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 03:50:22: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 03:50:22: #1 total tags in treatment: 1769406 INFO @ Mon, 03 Jun 2019 03:50:22: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 03:50:22: #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 03:50:22: #1 tags after filtering in treatment: 1769406 INFO @ Mon, 03 Jun 2019 03:50:22: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 03:50:22: #1 finished! INFO @ Mon, 03 Jun 2019 03:50:22: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 03:50:22: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 03:50:23: #2 number of paired peaks: 2072 INFO @ Mon, 03 Jun 2019 03:50:23: start model_add_line... INFO @ Mon, 03 Jun 2019 03:50:23: start X-correlation... INFO @ Mon, 03 Jun 2019 03:50:23: end of X-cor INFO @ Mon, 03 Jun 2019 03:50:23: #2 finished! INFO @ Mon, 03 Jun 2019 03:50:23: #2 predicted fragment length is 118 bps INFO @ Mon, 03 Jun 2019 03:50:23: #2 alternative fragment length(s) may be 118 bps INFO @ Mon, 03 Jun 2019 03:50:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1550611/SRX1550611.10_model.r INFO @ Mon, 03 Jun 2019 03:50:23: #3 Call peaks... INFO @ Mon, 03 Jun 2019 03:50:23: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 03:50:26: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 03:50:26: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 03:50:26: #1 total tags in treatment: 1769406 INFO @ Mon, 03 Jun 2019 03:50:26: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 03:50:26: #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 03:50:26: #1 tags after filtering in treatment: 1769406 INFO @ Mon, 03 Jun 2019 03:50:26: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 03:50:26: #1 finished! INFO @ Mon, 03 Jun 2019 03:50:26: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 03:50:26: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 03:50:27: #2 number of paired peaks: 2072 INFO @ Mon, 03 Jun 2019 03:50:27: start model_add_line... INFO @ Mon, 03 Jun 2019 03:50:27: start X-correlation... INFO @ Mon, 03 Jun 2019 03:50:27: end of X-cor INFO @ Mon, 03 Jun 2019 03:50:27: #2 finished! INFO @ Mon, 03 Jun 2019 03:50:27: #2 predicted fragment length is 118 bps INFO @ Mon, 03 Jun 2019 03:50:27: #2 alternative fragment length(s) may be 118 bps INFO @ Mon, 03 Jun 2019 03:50:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1550611/SRX1550611.20_model.r INFO @ Mon, 03 Jun 2019 03:50:27: #3 Call peaks... INFO @ Mon, 03 Jun 2019 03:50:27: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 03:50:27: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 03:50:28: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 03:50:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1550611/SRX1550611.05_peaks.xls INFO @ Mon, 03 Jun 2019 03:50:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1550611/SRX1550611.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 03:50:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1550611/SRX1550611.05_summits.bed INFO @ Mon, 03 Jun 2019 03:50:30: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (2808 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 03:50:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1550611/SRX1550611.10_peaks.xls INFO @ Mon, 03 Jun 2019 03:50:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1550611/SRX1550611.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 03:50:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1550611/SRX1550611.10_summits.bed INFO @ Mon, 03 Jun 2019 03:50:31: Done! pass1 - making usageList (11 chroms): 2 millis pass2 - checking and writing primary data (1503 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 03:50:32: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 03 Jun 2019 03:50:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1550611/SRX1550611.20_peaks.xls INFO @ Mon, 03 Jun 2019 03:50:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1550611/SRX1550611.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 03:50:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1550611/SRX1550611.20_summits.bed INFO @ Mon, 03 Jun 2019 03:50:35: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (815 records, 4 fields): 4 millis CompletedMACS2peakCalling BigWig に変換しました。