Job ID = 1307008 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 10,244,227 reads read : 10,244,227 reads written : 10,244,227 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: 00:04:19 10244227 reads; of these: 10244227 (100.00%) were unpaired; of these: 289929 (2.83%) aligned 0 times 6788886 (66.27%) aligned exactly 1 time 3165412 (30.90%) aligned >1 times 97.17% overall alignment rate Time searching: 00:04:19 Overall time: 00:04:19 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_sort_core] merging from 8 files... [bam_rmdupse_core] 1431636 / 9954298 = 0.1438 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 22:14:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX511133/SRX511133.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX511133/SRX511133.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX511133/SRX511133.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX511133/SRX511133.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 22:14:25: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:14:25: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:14:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX511133/SRX511133.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX511133/SRX511133.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX511133/SRX511133.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX511133/SRX511133.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 22:14:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX511133/SRX511133.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX511133/SRX511133.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX511133/SRX511133.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX511133/SRX511133.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 22:14:25: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:14:25: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:14:25: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:14:25: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:14:36: 1000000 INFO @ Mon, 03 Jun 2019 22:14:36: 1000000 INFO @ Mon, 03 Jun 2019 22:14:36: 1000000 INFO @ Mon, 03 Jun 2019 22:14:46: 2000000 INFO @ Mon, 03 Jun 2019 22:14:46: 2000000 INFO @ Mon, 03 Jun 2019 22:14:47: 2000000 INFO @ Mon, 03 Jun 2019 22:14:57: 3000000 INFO @ Mon, 03 Jun 2019 22:14:57: 3000000 INFO @ Mon, 03 Jun 2019 22:14:57: 3000000 INFO @ Mon, 03 Jun 2019 22:15:07: 4000000 INFO @ Mon, 03 Jun 2019 22:15:07: 4000000 INFO @ Mon, 03 Jun 2019 22:15:07: 4000000 INFO @ Mon, 03 Jun 2019 22:15:17: 5000000 INFO @ Mon, 03 Jun 2019 22:15:18: 5000000 INFO @ Mon, 03 Jun 2019 22:15:18: 5000000 INFO @ Mon, 03 Jun 2019 22:15:27: 6000000 INFO @ Mon, 03 Jun 2019 22:15:28: 6000000 INFO @ Mon, 03 Jun 2019 22:15:28: 6000000 INFO @ Mon, 03 Jun 2019 22:15:38: 7000000 INFO @ Mon, 03 Jun 2019 22:15:38: 7000000 INFO @ Mon, 03 Jun 2019 22:15:39: 7000000 INFO @ Mon, 03 Jun 2019 22:15:48: 8000000 INFO @ Mon, 03 Jun 2019 22:15:49: 8000000 INFO @ Mon, 03 Jun 2019 22:15:49: 8000000 INFO @ Mon, 03 Jun 2019 22:15:54: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 22:15:54: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 22:15:54: #1 total tags in treatment: 8522662 INFO @ Mon, 03 Jun 2019 22:15:54: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:15:54: #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 22:15:54: #1 tags after filtering in treatment: 8522662 INFO @ Mon, 03 Jun 2019 22:15:54: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:15:54: #1 finished! INFO @ Mon, 03 Jun 2019 22:15:54: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:15:54: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:15:55: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 22:15:55: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 22:15:55: #1 total tags in treatment: 8522662 INFO @ Mon, 03 Jun 2019 22:15:55: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:15:55: #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 22:15:55: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 22:15:55: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 22:15:55: #1 total tags in treatment: 8522662 INFO @ Mon, 03 Jun 2019 22:15:55: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:15:55: #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 22:15:55: #1 tags after filtering in treatment: 8522662 INFO @ Mon, 03 Jun 2019 22:15:55: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:15:55: #1 finished! INFO @ Mon, 03 Jun 2019 22:15:55: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:15:55: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:15:55: #1 tags after filtering in treatment: 8522662 INFO @ Mon, 03 Jun 2019 22:15:55: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:15:55: #1 finished! INFO @ Mon, 03 Jun 2019 22:15:55: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:15:55: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:15:55: #2 number of paired peaks: 4050 INFO @ Mon, 03 Jun 2019 22:15:55: start model_add_line... INFO @ Mon, 03 Jun 2019 22:15:55: start X-correlation... INFO @ Mon, 03 Jun 2019 22:15:55: end of X-cor INFO @ Mon, 03 Jun 2019 22:15:55: #2 finished! INFO @ Mon, 03 Jun 2019 22:15:55: #2 predicted fragment length is 199 bps INFO @ Mon, 03 Jun 2019 22:15:55: #2 alternative fragment length(s) may be 199 bps INFO @ Mon, 03 Jun 2019 22:15:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX511133/SRX511133.05_model.r INFO @ Mon, 03 Jun 2019 22:15:55: #3 Call peaks... INFO @ Mon, 03 Jun 2019 22:15:55: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 22:15:56: #2 number of paired peaks: 4050 INFO @ Mon, 03 Jun 2019 22:15:56: start model_add_line... INFO @ Mon, 03 Jun 2019 22:15:56: #2 number of paired peaks: 4050 INFO @ Mon, 03 Jun 2019 22:15:56: start model_add_line... INFO @ Mon, 03 Jun 2019 22:15:56: start X-correlation... INFO @ Mon, 03 Jun 2019 22:15:56: end of X-cor INFO @ Mon, 03 Jun 2019 22:15:56: #2 finished! INFO @ Mon, 03 Jun 2019 22:15:56: #2 predicted fragment length is 199 bps INFO @ Mon, 03 Jun 2019 22:15:56: #2 alternative fragment length(s) may be 199 bps INFO @ Mon, 03 Jun 2019 22:15:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX511133/SRX511133.10_model.r INFO @ Mon, 03 Jun 2019 22:15:56: #3 Call peaks... INFO @ Mon, 03 Jun 2019 22:15:56: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 22:15:56: start X-correlation... INFO @ Mon, 03 Jun 2019 22:15:56: end of X-cor INFO @ Mon, 03 Jun 2019 22:15:56: #2 finished! INFO @ Mon, 03 Jun 2019 22:15:56: #2 predicted fragment length is 199 bps INFO @ Mon, 03 Jun 2019 22:15:56: #2 alternative fragment length(s) may be 199 bps INFO @ Mon, 03 Jun 2019 22:15:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX511133/SRX511133.20_model.r INFO @ Mon, 03 Jun 2019 22:15:56: #3 Call peaks... INFO @ Mon, 03 Jun 2019 22:15:56: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 22:16:24: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 22:16:24: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 22:16:25: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 22:16:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX511133/SRX511133.10_peaks.xls INFO @ Mon, 03 Jun 2019 22:16:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX511133/SRX511133.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 22:16:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX511133/SRX511133.10_summits.bed INFO @ Mon, 03 Jun 2019 22:16:38: Done! INFO @ Mon, 03 Jun 2019 22:16:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX511133/SRX511133.05_peaks.xls pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (5333 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 22:16:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX511133/SRX511133.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 22:16:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX511133/SRX511133.05_summits.bed INFO @ Mon, 03 Jun 2019 22:16:38: Done! pass1 - making usageList (14 chroms): 4 millis pass2 - checking and writing primary data (6761 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 22:16:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX511133/SRX511133.20_peaks.xls INFO @ Mon, 03 Jun 2019 22:16:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX511133/SRX511133.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 22:16:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX511133/SRX511133.20_summits.bed INFO @ Mon, 03 Jun 2019 22:16:39: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3993 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。