Job ID = 2590818 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 20,422,023 reads read : 40,844,046 reads written : 20,422,023 reads 0-length : 20,422,023 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: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:06:07 20422023 reads; of these: 20422023 (100.00%) were unpaired; of these: 3509320 (17.18%) aligned 0 times 13521349 (66.21%) aligned exactly 1 time 3391354 (16.61%) aligned >1 times 82.82% overall alignment rate Time searching: 00:06:07 Overall time: 00:06:07 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] 7863026 / 16912703 = 0.4649 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 23:33:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011057/SRX5011057.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011057/SRX5011057.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011057/SRX5011057.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011057/SRX5011057.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, 12 Aug 2019 23:33:17: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:33:17: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:33:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011057/SRX5011057.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011057/SRX5011057.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011057/SRX5011057.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011057/SRX5011057.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, 12 Aug 2019 23:33:18: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:33:18: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:33:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011057/SRX5011057.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011057/SRX5011057.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011057/SRX5011057.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011057/SRX5011057.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, 12 Aug 2019 23:33:18: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:33:18: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:33:23: 1000000 INFO @ Mon, 12 Aug 2019 23:33:25: 1000000 INFO @ Mon, 12 Aug 2019 23:33:28: 1000000 INFO @ Mon, 12 Aug 2019 23:33:30: 2000000 INFO @ Mon, 12 Aug 2019 23:33:33: 2000000 INFO @ Mon, 12 Aug 2019 23:33:36: 2000000 INFO @ Mon, 12 Aug 2019 23:33:37: 3000000 INFO @ Mon, 12 Aug 2019 23:33:40: 3000000 INFO @ Mon, 12 Aug 2019 23:33:44: 4000000 INFO @ Mon, 12 Aug 2019 23:33:45: 3000000 INFO @ Mon, 12 Aug 2019 23:33:47: 4000000 INFO @ Mon, 12 Aug 2019 23:33:51: 5000000 INFO @ Mon, 12 Aug 2019 23:33:54: 4000000 INFO @ Mon, 12 Aug 2019 23:33:55: 5000000 INFO @ Mon, 12 Aug 2019 23:33:57: 6000000 INFO @ Mon, 12 Aug 2019 23:34:02: 6000000 INFO @ Mon, 12 Aug 2019 23:34:02: 5000000 INFO @ Mon, 12 Aug 2019 23:34:04: 7000000 INFO @ Mon, 12 Aug 2019 23:34:09: 7000000 INFO @ Mon, 12 Aug 2019 23:34:11: 6000000 INFO @ Mon, 12 Aug 2019 23:34:11: 8000000 INFO @ Mon, 12 Aug 2019 23:34:17: 8000000 INFO @ Mon, 12 Aug 2019 23:34:18: 9000000 INFO @ Mon, 12 Aug 2019 23:34:18: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:34:18: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:34:18: #1 total tags in treatment: 9049677 INFO @ Mon, 12 Aug 2019 23:34:18: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:34:18: #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 23:34:18: #1 tags after filtering in treatment: 9049677 INFO @ Mon, 12 Aug 2019 23:34:18: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:34:18: #1 finished! INFO @ Mon, 12 Aug 2019 23:34:18: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:34:18: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:34:19: 7000000 INFO @ Mon, 12 Aug 2019 23:34:19: #2 number of paired peaks: 3039 INFO @ Mon, 12 Aug 2019 23:34:19: start model_add_line... INFO @ Mon, 12 Aug 2019 23:34:19: start X-correlation... INFO @ Mon, 12 Aug 2019 23:34:19: end of X-cor INFO @ Mon, 12 Aug 2019 23:34:19: #2 finished! INFO @ Mon, 12 Aug 2019 23:34:19: #2 predicted fragment length is 233 bps INFO @ Mon, 12 Aug 2019 23:34:19: #2 alternative fragment length(s) may be 233 bps INFO @ Mon, 12 Aug 2019 23:34:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011057/SRX5011057.05_model.r INFO @ Mon, 12 Aug 2019 23:34:19: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:34:19: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:34:24: 9000000 INFO @ Mon, 12 Aug 2019 23:34:24: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:34:24: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:34:24: #1 total tags in treatment: 9049677 INFO @ Mon, 12 Aug 2019 23:34:24: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:34:24: #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 23:34:25: #1 tags after filtering in treatment: 9049677 INFO @ Mon, 12 Aug 2019 23:34:25: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:34:25: #1 finished! INFO @ Mon, 12 Aug 2019 23:34:25: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:34:25: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:34:26: #2 number of paired peaks: 3039 INFO @ Mon, 12 Aug 2019 23:34:26: start model_add_line... INFO @ Mon, 12 Aug 2019 23:34:26: start X-correlation... INFO @ Mon, 12 Aug 2019 23:34:26: end of X-cor INFO @ Mon, 12 Aug 2019 23:34:26: #2 finished! INFO @ Mon, 12 Aug 2019 23:34:26: #2 predicted fragment length is 233 bps INFO @ Mon, 12 Aug 2019 23:34:26: #2 alternative fragment length(s) may be 233 bps INFO @ Mon, 12 Aug 2019 23:34:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011057/SRX5011057.10_model.r INFO @ Mon, 12 Aug 2019 23:34:26: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:34:26: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:34:28: 8000000 INFO @ Mon, 12 Aug 2019 23:34:36: 9000000 INFO @ Mon, 12 Aug 2019 23:34:36: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:34:36: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:34:36: #1 total tags in treatment: 9049677 INFO @ Mon, 12 Aug 2019 23:34:36: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:34:36: #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 23:34:36: #1 tags after filtering in treatment: 9049677 INFO @ Mon, 12 Aug 2019 23:34:36: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:34:36: #1 finished! INFO @ Mon, 12 Aug 2019 23:34:36: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:34:36: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:34:38: #2 number of paired peaks: 3039 INFO @ Mon, 12 Aug 2019 23:34:38: start model_add_line... INFO @ Mon, 12 Aug 2019 23:34:38: start X-correlation... INFO @ Mon, 12 Aug 2019 23:34:38: end of X-cor INFO @ Mon, 12 Aug 2019 23:34:38: #2 finished! INFO @ Mon, 12 Aug 2019 23:34:38: #2 predicted fragment length is 233 bps INFO @ Mon, 12 Aug 2019 23:34:38: #2 alternative fragment length(s) may be 233 bps INFO @ Mon, 12 Aug 2019 23:34:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011057/SRX5011057.20_model.r INFO @ Mon, 12 Aug 2019 23:34:38: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:34:38: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:34:50: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:34:57: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:35:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011057/SRX5011057.05_peaks.xls INFO @ Mon, 12 Aug 2019 23:35:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011057/SRX5011057.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:35:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011057/SRX5011057.05_summits.bed INFO @ Mon, 12 Aug 2019 23:35:04: Done! pass1 - making usageList (14 chroms): 5 millis pass2 - checking and writing primary data (9332 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:35:08: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:35:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011057/SRX5011057.10_peaks.xls INFO @ Mon, 12 Aug 2019 23:35:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011057/SRX5011057.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:35:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011057/SRX5011057.10_summits.bed INFO @ Mon, 12 Aug 2019 23:35:10: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (6520 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:35:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011057/SRX5011057.20_peaks.xls INFO @ Mon, 12 Aug 2019 23:35:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011057/SRX5011057.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:35:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011057/SRX5011057.20_summits.bed INFO @ Mon, 12 Aug 2019 23:35:23: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (3940 records, 4 fields): 11 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。