Job ID = 1293830 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 31,535,696 reads read : 31,535,696 reads written : 31,535,696 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: 00:07:58 31535696 reads; of these: 31535696 (100.00%) were unpaired; of these: 6898110 (21.87%) aligned 0 times 20491757 (64.98%) aligned exactly 1 time 4145829 (13.15%) aligned >1 times 78.13% overall alignment rate Time searching: 00:07:58 Overall time: 00:07:58 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] 7290263 / 24637586 = 0.2959 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 02:54:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX127437/SRX127437.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX127437/SRX127437.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX127437/SRX127437.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX127437/SRX127437.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 02:54:40: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:54:40: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:54:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX127437/SRX127437.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX127437/SRX127437.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX127437/SRX127437.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX127437/SRX127437.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 02:54:40: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:54:40: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:54:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX127437/SRX127437.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX127437/SRX127437.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX127437/SRX127437.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX127437/SRX127437.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 02:54:40: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:54:40: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:54:47: 1000000 INFO @ Mon, 03 Jun 2019 02:54:48: 1000000 INFO @ Mon, 03 Jun 2019 02:54:48: 1000000 INFO @ Mon, 03 Jun 2019 02:54:54: 2000000 INFO @ Mon, 03 Jun 2019 02:54:56: 2000000 INFO @ Mon, 03 Jun 2019 02:54:56: 2000000 INFO @ Mon, 03 Jun 2019 02:55:00: 3000000 INFO @ Mon, 03 Jun 2019 02:55:03: 3000000 INFO @ Mon, 03 Jun 2019 02:55:03: 3000000 INFO @ Mon, 03 Jun 2019 02:55:07: 4000000 INFO @ Mon, 03 Jun 2019 02:55:10: 4000000 INFO @ Mon, 03 Jun 2019 02:55:11: 4000000 INFO @ Mon, 03 Jun 2019 02:55:14: 5000000 INFO @ Mon, 03 Jun 2019 02:55:18: 5000000 INFO @ Mon, 03 Jun 2019 02:55:19: 5000000 INFO @ Mon, 03 Jun 2019 02:55:21: 6000000 INFO @ Mon, 03 Jun 2019 02:55:25: 6000000 INFO @ Mon, 03 Jun 2019 02:55:26: 6000000 INFO @ Mon, 03 Jun 2019 02:55:28: 7000000 INFO @ Mon, 03 Jun 2019 02:55:32: 7000000 INFO @ Mon, 03 Jun 2019 02:55:33: 7000000 INFO @ Mon, 03 Jun 2019 02:55:34: 8000000 INFO @ Mon, 03 Jun 2019 02:55:40: 8000000 INFO @ Mon, 03 Jun 2019 02:55:41: 8000000 INFO @ Mon, 03 Jun 2019 02:55:41: 9000000 INFO @ Mon, 03 Jun 2019 02:55:47: 9000000 INFO @ Mon, 03 Jun 2019 02:55:48: 10000000 INFO @ Mon, 03 Jun 2019 02:55:49: 9000000 INFO @ Mon, 03 Jun 2019 02:55:55: 11000000 INFO @ Mon, 03 Jun 2019 02:55:55: 10000000 INFO @ Mon, 03 Jun 2019 02:55:57: 10000000 INFO @ Mon, 03 Jun 2019 02:56:02: 12000000 INFO @ Mon, 03 Jun 2019 02:56:03: 11000000 INFO @ Mon, 03 Jun 2019 02:56:04: 11000000 INFO @ Mon, 03 Jun 2019 02:56:08: 13000000 INFO @ Mon, 03 Jun 2019 02:56:10: 12000000 INFO @ Mon, 03 Jun 2019 02:56:12: 12000000 INFO @ Mon, 03 Jun 2019 02:56:15: 14000000 INFO @ Mon, 03 Jun 2019 02:56:17: 13000000 INFO @ Mon, 03 Jun 2019 02:56:20: 13000000 INFO @ Mon, 03 Jun 2019 02:56:22: 15000000 INFO @ Mon, 03 Jun 2019 02:56:25: 14000000 INFO @ Mon, 03 Jun 2019 02:56:27: 14000000 INFO @ Mon, 03 Jun 2019 02:56:29: 16000000 INFO @ Mon, 03 Jun 2019 02:56:32: 15000000 INFO @ Mon, 03 Jun 2019 02:56:35: 15000000 INFO @ Mon, 03 Jun 2019 02:56:36: 17000000 INFO @ Mon, 03 Jun 2019 02:56:38: #1 tag size is determined as 45 bps INFO @ Mon, 03 Jun 2019 02:56:38: #1 tag size = 45 INFO @ Mon, 03 Jun 2019 02:56:38: #1 total tags in treatment: 17347323 INFO @ Mon, 03 Jun 2019 02:56:38: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:56:38: #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 02:56:39: #1 tags after filtering in treatment: 17347323 INFO @ Mon, 03 Jun 2019 02:56:39: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:56:39: #1 finished! INFO @ Mon, 03 Jun 2019 02:56:39: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:56:39: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:56:40: 16000000 INFO @ Mon, 03 Jun 2019 02:56:41: #2 number of paired peaks: 4341 INFO @ Mon, 03 Jun 2019 02:56:41: start model_add_line... INFO @ Mon, 03 Jun 2019 02:56:41: start X-correlation... INFO @ Mon, 03 Jun 2019 02:56:41: end of X-cor INFO @ Mon, 03 Jun 2019 02:56:41: #2 finished! INFO @ Mon, 03 Jun 2019 02:56:41: #2 predicted fragment length is 133 bps INFO @ Mon, 03 Jun 2019 02:56:41: #2 alternative fragment length(s) may be 133 bps INFO @ Mon, 03 Jun 2019 02:56:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX127437/SRX127437.10_model.r INFO @ Mon, 03 Jun 2019 02:56:41: #3 Call peaks... INFO @ Mon, 03 Jun 2019 02:56:41: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 02:56:43: 16000000 INFO @ Mon, 03 Jun 2019 02:56:47: 17000000 INFO @ Mon, 03 Jun 2019 02:56:50: #1 tag size is determined as 45 bps INFO @ Mon, 03 Jun 2019 02:56:50: #1 tag size = 45 INFO @ Mon, 03 Jun 2019 02:56:50: #1 total tags in treatment: 17347323 INFO @ Mon, 03 Jun 2019 02:56:50: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:56:50: #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 02:56:50: 17000000 INFO @ Mon, 03 Jun 2019 02:56:50: #1 tags after filtering in treatment: 17347323 INFO @ Mon, 03 Jun 2019 02:56:50: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:56:50: #1 finished! INFO @ Mon, 03 Jun 2019 02:56:50: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:56:50: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:56:52: #2 number of paired peaks: 4341 INFO @ Mon, 03 Jun 2019 02:56:52: start model_add_line... INFO @ Mon, 03 Jun 2019 02:56:53: start X-correlation... INFO @ Mon, 03 Jun 2019 02:56:53: end of X-cor INFO @ Mon, 03 Jun 2019 02:56:53: #2 finished! INFO @ Mon, 03 Jun 2019 02:56:53: #2 predicted fragment length is 133 bps INFO @ Mon, 03 Jun 2019 02:56:53: #2 alternative fragment length(s) may be 133 bps INFO @ Mon, 03 Jun 2019 02:56:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX127437/SRX127437.05_model.r INFO @ Mon, 03 Jun 2019 02:56:53: #3 Call peaks... INFO @ Mon, 03 Jun 2019 02:56:53: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 02:56:53: #1 tag size is determined as 45 bps INFO @ Mon, 03 Jun 2019 02:56:53: #1 tag size = 45 INFO @ Mon, 03 Jun 2019 02:56:53: #1 total tags in treatment: 17347323 INFO @ Mon, 03 Jun 2019 02:56:53: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:56:53: #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 02:56:53: #1 tags after filtering in treatment: 17347323 INFO @ Mon, 03 Jun 2019 02:56:53: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:56:53: #1 finished! INFO @ Mon, 03 Jun 2019 02:56:53: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:56:53: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:56:55: #2 number of paired peaks: 4341 INFO @ Mon, 03 Jun 2019 02:56:55: start model_add_line... INFO @ Mon, 03 Jun 2019 02:56:56: start X-correlation... INFO @ Mon, 03 Jun 2019 02:56:56: end of X-cor INFO @ Mon, 03 Jun 2019 02:56:56: #2 finished! INFO @ Mon, 03 Jun 2019 02:56:56: #2 predicted fragment length is 133 bps INFO @ Mon, 03 Jun 2019 02:56:56: #2 alternative fragment length(s) may be 133 bps INFO @ Mon, 03 Jun 2019 02:56:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX127437/SRX127437.20_model.r INFO @ Mon, 03 Jun 2019 02:56:56: #3 Call peaks... INFO @ Mon, 03 Jun 2019 02:56:56: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 02:57:35: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 02:57:46: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 02:57:50: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 02:57:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX127437/SRX127437.10_peaks.xls INFO @ Mon, 03 Jun 2019 02:57:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX127437/SRX127437.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 02:57:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX127437/SRX127437.10_summits.bed INFO @ Mon, 03 Jun 2019 02:57:58: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6498 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 02:58:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX127437/SRX127437.05_peaks.xls INFO @ Mon, 03 Jun 2019 02:58:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX127437/SRX127437.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 02:58:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX127437/SRX127437.05_summits.bed INFO @ Mon, 03 Jun 2019 02:58:09: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (9740 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 02:58:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX127437/SRX127437.20_peaks.xls INFO @ Mon, 03 Jun 2019 02:58:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX127437/SRX127437.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 02:58:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX127437/SRX127437.20_summits.bed INFO @ Mon, 03 Jun 2019 02:58:13: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (4094 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。