Job ID = 1295140 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 20,011,622 reads read : 40,023,244 reads written : 20,011,622 reads 0-length : 20,011,622 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: 00:07:36 20011622 reads; of these: 20011622 (100.00%) were unpaired; of these: 214857 (1.07%) aligned 0 times 18564258 (92.77%) aligned exactly 1 time 1232507 (6.16%) aligned >1 times 98.93% overall alignment rate Time searching: 00:07:36 Overall time: 00:07:36 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 12 files... [bam_rmdupse_core] 5855498 / 19796765 = 0.2958 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 12:31:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3279757/SRX3279757.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3279757/SRX3279757.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3279757/SRX3279757.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3279757/SRX3279757.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 12:31:52: #1 read tag files... INFO @ Mon, 03 Jun 2019 12:31:52: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 12:31:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3279757/SRX3279757.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3279757/SRX3279757.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3279757/SRX3279757.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3279757/SRX3279757.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 12:31:52: #1 read tag files... INFO @ Mon, 03 Jun 2019 12:31:52: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 12:31:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3279757/SRX3279757.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3279757/SRX3279757.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3279757/SRX3279757.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3279757/SRX3279757.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 12:31:52: #1 read tag files... INFO @ Mon, 03 Jun 2019 12:31:52: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 12:32:02: 1000000 INFO @ Mon, 03 Jun 2019 12:32:03: 1000000 INFO @ Mon, 03 Jun 2019 12:32:05: 1000000 INFO @ Mon, 03 Jun 2019 12:32:12: 2000000 INFO @ Mon, 03 Jun 2019 12:32:16: 2000000 INFO @ Mon, 03 Jun 2019 12:32:20: 2000000 INFO @ Mon, 03 Jun 2019 12:32:22: 3000000 INFO @ Mon, 03 Jun 2019 12:32:27: 3000000 INFO @ Mon, 03 Jun 2019 12:32:32: 4000000 INFO @ Mon, 03 Jun 2019 12:32:33: 3000000 INFO @ Mon, 03 Jun 2019 12:32:39: 4000000 INFO @ Mon, 03 Jun 2019 12:32:41: 5000000 INFO @ Mon, 03 Jun 2019 12:32:46: 4000000 INFO @ Mon, 03 Jun 2019 12:32:50: 5000000 INFO @ Mon, 03 Jun 2019 12:32:51: 6000000 INFO @ Mon, 03 Jun 2019 12:33:00: 5000000 INFO @ Mon, 03 Jun 2019 12:33:01: 7000000 INFO @ Mon, 03 Jun 2019 12:33:01: 6000000 INFO @ Mon, 03 Jun 2019 12:33:11: 8000000 INFO @ Mon, 03 Jun 2019 12:33:12: 7000000 INFO @ Mon, 03 Jun 2019 12:33:13: 6000000 INFO @ Mon, 03 Jun 2019 12:33:20: 9000000 INFO @ Mon, 03 Jun 2019 12:33:23: 8000000 INFO @ Mon, 03 Jun 2019 12:33:25: 7000000 INFO @ Mon, 03 Jun 2019 12:33:30: 10000000 INFO @ Mon, 03 Jun 2019 12:33:34: 9000000 INFO @ Mon, 03 Jun 2019 12:33:38: 8000000 INFO @ Mon, 03 Jun 2019 12:33:40: 11000000 INFO @ Mon, 03 Jun 2019 12:33:45: 10000000 INFO @ Mon, 03 Jun 2019 12:33:50: 12000000 INFO @ Mon, 03 Jun 2019 12:33:51: 9000000 INFO @ Mon, 03 Jun 2019 12:33:56: 11000000 INFO @ Mon, 03 Jun 2019 12:33:59: 13000000 INFO @ Mon, 03 Jun 2019 12:34:05: 10000000 INFO @ Mon, 03 Jun 2019 12:34:08: 12000000 INFO @ Mon, 03 Jun 2019 12:34:09: #1 tag size is determined as 79 bps INFO @ Mon, 03 Jun 2019 12:34:09: #1 tag size = 79 INFO @ Mon, 03 Jun 2019 12:34:09: #1 total tags in treatment: 13941267 INFO @ Mon, 03 Jun 2019 12:34:09: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 12:34:09: #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 12:34:09: #1 tags after filtering in treatment: 13941267 INFO @ Mon, 03 Jun 2019 12:34:09: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 12:34:09: #1 finished! INFO @ Mon, 03 Jun 2019 12:34:09: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 12:34:09: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 12:34:12: #2 number of paired peaks: 14451 INFO @ Mon, 03 Jun 2019 12:34:12: start model_add_line... INFO @ Mon, 03 Jun 2019 12:34:12: start X-correlation... INFO @ Mon, 03 Jun 2019 12:34:12: end of X-cor INFO @ Mon, 03 Jun 2019 12:34:12: #2 finished! INFO @ Mon, 03 Jun 2019 12:34:12: #2 predicted fragment length is 181 bps INFO @ Mon, 03 Jun 2019 12:34:12: #2 alternative fragment length(s) may be 181 bps INFO @ Mon, 03 Jun 2019 12:34:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3279757/SRX3279757.20_model.r INFO @ Mon, 03 Jun 2019 12:34:12: #3 Call peaks... INFO @ Mon, 03 Jun 2019 12:34:12: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 12:34:18: 11000000 INFO @ Mon, 03 Jun 2019 12:34:19: 13000000 INFO @ Mon, 03 Jun 2019 12:34:29: #1 tag size is determined as 79 bps INFO @ Mon, 03 Jun 2019 12:34:29: #1 tag size = 79 INFO @ Mon, 03 Jun 2019 12:34:29: #1 total tags in treatment: 13941267 INFO @ Mon, 03 Jun 2019 12:34:29: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 12:34:29: #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 12:34:29: #1 tags after filtering in treatment: 13941267 INFO @ Mon, 03 Jun 2019 12:34:29: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 12:34:29: #1 finished! INFO @ Mon, 03 Jun 2019 12:34:29: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 12:34:29: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 12:34:31: 12000000 INFO @ Mon, 03 Jun 2019 12:34:32: #2 number of paired peaks: 14451 INFO @ Mon, 03 Jun 2019 12:34:32: start model_add_line... INFO @ Mon, 03 Jun 2019 12:34:32: start X-correlation... INFO @ Mon, 03 Jun 2019 12:34:32: end of X-cor INFO @ Mon, 03 Jun 2019 12:34:32: #2 finished! INFO @ Mon, 03 Jun 2019 12:34:32: #2 predicted fragment length is 181 bps INFO @ Mon, 03 Jun 2019 12:34:32: #2 alternative fragment length(s) may be 181 bps INFO @ Mon, 03 Jun 2019 12:34:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3279757/SRX3279757.05_model.r INFO @ Mon, 03 Jun 2019 12:34:32: #3 Call peaks... INFO @ Mon, 03 Jun 2019 12:34:32: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 12:34:43: 13000000 INFO @ Mon, 03 Jun 2019 12:34:55: #1 tag size is determined as 79 bps INFO @ Mon, 03 Jun 2019 12:34:55: #1 tag size = 79 INFO @ Mon, 03 Jun 2019 12:34:55: #1 total tags in treatment: 13941267 INFO @ Mon, 03 Jun 2019 12:34:55: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 12:34:55: #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 12:34:55: #1 tags after filtering in treatment: 13941267 INFO @ Mon, 03 Jun 2019 12:34:55: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 12:34:55: #1 finished! INFO @ Mon, 03 Jun 2019 12:34:55: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 12:34:55: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 12:34:58: #2 number of paired peaks: 14451 INFO @ Mon, 03 Jun 2019 12:34:58: start model_add_line... INFO @ Mon, 03 Jun 2019 12:34:58: start X-correlation... INFO @ Mon, 03 Jun 2019 12:34:58: end of X-cor INFO @ Mon, 03 Jun 2019 12:34:58: #2 finished! INFO @ Mon, 03 Jun 2019 12:34:58: #2 predicted fragment length is 181 bps INFO @ Mon, 03 Jun 2019 12:34:58: #2 alternative fragment length(s) may be 181 bps INFO @ Mon, 03 Jun 2019 12:34:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3279757/SRX3279757.10_model.r INFO @ Mon, 03 Jun 2019 12:34:58: #3 Call peaks... INFO @ Mon, 03 Jun 2019 12:34:58: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 12:35:01: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 03 Jun 2019 12:35:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3279757/SRX3279757.20_peaks.xls INFO @ Mon, 03 Jun 2019 12:35:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3279757/SRX3279757.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 12:35:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3279757/SRX3279757.20_summits.bed INFO @ Mon, 03 Jun 2019 12:35:19: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (7567 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 12:35:22: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 12:35:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3279757/SRX3279757.05_peaks.xls INFO @ Mon, 03 Jun 2019 12:35:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3279757/SRX3279757.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 12:35:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3279757/SRX3279757.05_summits.bed INFO @ Mon, 03 Jun 2019 12:35:41: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (8587 records, 4 fields): 16 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Mon, 03 Jun 2019 12:35:53: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 12:36:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3279757/SRX3279757.10_peaks.xls INFO @ Mon, 03 Jun 2019 12:36:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3279757/SRX3279757.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 12:36:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3279757/SRX3279757.10_summits.bed INFO @ Mon, 03 Jun 2019 12:36:13: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (8185 records, 4 fields): 1315 millis CompletedMACS2peakCalling