Job ID = 1294488 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 21,539,662 reads read : 21,539,662 reads written : 21,539,662 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:08:51 21539662 reads; of these: 21539662 (100.00%) were unpaired; of these: 1150057 (5.34%) aligned 0 times 13605787 (63.17%) aligned exactly 1 time 6783818 (31.49%) aligned >1 times 94.66% overall alignment rate Time searching: 00:08:52 Overall time: 00:08:52 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] 2197630 / 20389605 = 0.1078 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 08:46:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287688/SRX287688.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287688/SRX287688.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287688/SRX287688.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287688/SRX287688.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 08:46:20: #1 read tag files... INFO @ Mon, 03 Jun 2019 08:46:20: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 08:46:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287688/SRX287688.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287688/SRX287688.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287688/SRX287688.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287688/SRX287688.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 08:46:20: #1 read tag files... INFO @ Mon, 03 Jun 2019 08:46:20: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 08:46:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287688/SRX287688.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287688/SRX287688.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287688/SRX287688.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287688/SRX287688.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 08:46:20: #1 read tag files... INFO @ Mon, 03 Jun 2019 08:46:20: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 08:46:27: 1000000 INFO @ Mon, 03 Jun 2019 08:46:29: 1000000 INFO @ Mon, 03 Jun 2019 08:46:29: 1000000 INFO @ Mon, 03 Jun 2019 08:46:35: 2000000 INFO @ Mon, 03 Jun 2019 08:46:37: 2000000 INFO @ Mon, 03 Jun 2019 08:46:38: 2000000 INFO @ Mon, 03 Jun 2019 08:46:44: 3000000 INFO @ Mon, 03 Jun 2019 08:46:46: 3000000 INFO @ Mon, 03 Jun 2019 08:46:46: 3000000 INFO @ Mon, 03 Jun 2019 08:46:52: 4000000 INFO @ Mon, 03 Jun 2019 08:46:54: 4000000 INFO @ Mon, 03 Jun 2019 08:46:55: 4000000 INFO @ Mon, 03 Jun 2019 08:47:01: 5000000 INFO @ Mon, 03 Jun 2019 08:47:03: 5000000 INFO @ Mon, 03 Jun 2019 08:47:03: 5000000 INFO @ Mon, 03 Jun 2019 08:47:09: 6000000 INFO @ Mon, 03 Jun 2019 08:47:11: 6000000 INFO @ Mon, 03 Jun 2019 08:47:12: 6000000 INFO @ Mon, 03 Jun 2019 08:47:18: 7000000 INFO @ Mon, 03 Jun 2019 08:47:20: 7000000 INFO @ Mon, 03 Jun 2019 08:47:21: 7000000 INFO @ Mon, 03 Jun 2019 08:47:26: 8000000 INFO @ Mon, 03 Jun 2019 08:47:29: 8000000 INFO @ Mon, 03 Jun 2019 08:47:29: 8000000 INFO @ Mon, 03 Jun 2019 08:47:35: 9000000 INFO @ Mon, 03 Jun 2019 08:47:37: 9000000 INFO @ Mon, 03 Jun 2019 08:47:38: 9000000 INFO @ Mon, 03 Jun 2019 08:47:43: 10000000 INFO @ Mon, 03 Jun 2019 08:47:46: 10000000 INFO @ Mon, 03 Jun 2019 08:47:46: 10000000 INFO @ Mon, 03 Jun 2019 08:47:52: 11000000 INFO @ Mon, 03 Jun 2019 08:47:54: 11000000 INFO @ Mon, 03 Jun 2019 08:47:55: 11000000 INFO @ Mon, 03 Jun 2019 08:48:00: 12000000 INFO @ Mon, 03 Jun 2019 08:48:03: 12000000 INFO @ Mon, 03 Jun 2019 08:48:03: 12000000 INFO @ Mon, 03 Jun 2019 08:48:09: 13000000 INFO @ Mon, 03 Jun 2019 08:48:12: 13000000 INFO @ Mon, 03 Jun 2019 08:48:12: 13000000 INFO @ Mon, 03 Jun 2019 08:48:17: 14000000 INFO @ Mon, 03 Jun 2019 08:48:20: 14000000 INFO @ Mon, 03 Jun 2019 08:48:21: 14000000 INFO @ Mon, 03 Jun 2019 08:48:26: 15000000 INFO @ Mon, 03 Jun 2019 08:48:29: 15000000 INFO @ Mon, 03 Jun 2019 08:48:29: 15000000 INFO @ Mon, 03 Jun 2019 08:48:34: 16000000 INFO @ Mon, 03 Jun 2019 08:48:37: 16000000 INFO @ Mon, 03 Jun 2019 08:48:38: 16000000 INFO @ Mon, 03 Jun 2019 08:48:43: 17000000 INFO @ Mon, 03 Jun 2019 08:48:46: 17000000 INFO @ Mon, 03 Jun 2019 08:48:46: 17000000 INFO @ Mon, 03 Jun 2019 08:48:51: 18000000 INFO @ Mon, 03 Jun 2019 08:48:53: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 08:48:53: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 08:48:53: #1 total tags in treatment: 18191975 INFO @ Mon, 03 Jun 2019 08:48:53: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 08:48:53: #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 08:48:53: #1 tags after filtering in treatment: 18191975 INFO @ Mon, 03 Jun 2019 08:48:53: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 08:48:53: #1 finished! INFO @ Mon, 03 Jun 2019 08:48:53: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 08:48:53: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 08:48:55: 18000000 INFO @ Mon, 03 Jun 2019 08:48:55: 18000000 INFO @ Mon, 03 Jun 2019 08:48:55: #2 number of paired peaks: 198 WARNING @ Mon, 03 Jun 2019 08:48:55: Fewer paired peaks (198) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 198 pairs to build model! INFO @ Mon, 03 Jun 2019 08:48:55: start model_add_line... INFO @ Mon, 03 Jun 2019 08:48:55: start X-correlation... INFO @ Mon, 03 Jun 2019 08:48:55: end of X-cor INFO @ Mon, 03 Jun 2019 08:48:55: #2 finished! INFO @ Mon, 03 Jun 2019 08:48:55: #2 predicted fragment length is 118 bps INFO @ Mon, 03 Jun 2019 08:48:55: #2 alternative fragment length(s) may be 118 bps INFO @ Mon, 03 Jun 2019 08:48:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287688/SRX287688.20_model.r INFO @ Mon, 03 Jun 2019 08:48:55: #3 Call peaks... INFO @ Mon, 03 Jun 2019 08:48:55: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 08:48:56: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 08:48:56: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 08:48:56: #1 total tags in treatment: 18191975 INFO @ Mon, 03 Jun 2019 08:48:56: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 08:48:56: #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 08:48:57: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 08:48:57: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 08:48:57: #1 total tags in treatment: 18191975 INFO @ Mon, 03 Jun 2019 08:48:57: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 08:48:57: #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 08:48:57: #1 tags after filtering in treatment: 18191975 INFO @ Mon, 03 Jun 2019 08:48:57: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 08:48:57: #1 finished! INFO @ Mon, 03 Jun 2019 08:48:57: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 08:48:57: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 08:48:57: #1 tags after filtering in treatment: 18191975 INFO @ Mon, 03 Jun 2019 08:48:57: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 08:48:57: #1 finished! INFO @ Mon, 03 Jun 2019 08:48:57: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 08:48:57: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 08:48:58: #2 number of paired peaks: 198 WARNING @ Mon, 03 Jun 2019 08:48:58: Fewer paired peaks (198) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 198 pairs to build model! INFO @ Mon, 03 Jun 2019 08:48:58: start model_add_line... INFO @ Mon, 03 Jun 2019 08:48:58: #2 number of paired peaks: 198 WARNING @ Mon, 03 Jun 2019 08:48:58: Fewer paired peaks (198) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 198 pairs to build model! INFO @ Mon, 03 Jun 2019 08:48:58: start model_add_line... INFO @ Mon, 03 Jun 2019 08:48:59: start X-correlation... INFO @ Mon, 03 Jun 2019 08:48:59: end of X-cor INFO @ Mon, 03 Jun 2019 08:48:59: #2 finished! INFO @ Mon, 03 Jun 2019 08:48:59: #2 predicted fragment length is 118 bps INFO @ Mon, 03 Jun 2019 08:48:59: #2 alternative fragment length(s) may be 118 bps INFO @ Mon, 03 Jun 2019 08:48:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287688/SRX287688.10_model.r INFO @ Mon, 03 Jun 2019 08:48:59: #3 Call peaks... INFO @ Mon, 03 Jun 2019 08:48:59: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 08:48:59: start X-correlation... INFO @ Mon, 03 Jun 2019 08:48:59: end of X-cor INFO @ Mon, 03 Jun 2019 08:48:59: #2 finished! INFO @ Mon, 03 Jun 2019 08:48:59: #2 predicted fragment length is 118 bps INFO @ Mon, 03 Jun 2019 08:48:59: #2 alternative fragment length(s) may be 118 bps INFO @ Mon, 03 Jun 2019 08:48:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287688/SRX287688.05_model.r INFO @ Mon, 03 Jun 2019 08:48:59: #3 Call peaks... INFO @ Mon, 03 Jun 2019 08:48:59: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 08:49:44: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 08:49:47: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 08:49:47: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 08:50:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287688/SRX287688.20_peaks.xls INFO @ Mon, 03 Jun 2019 08:50:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287688/SRX287688.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 08:50:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287688/SRX287688.20_summits.bed INFO @ Mon, 03 Jun 2019 08:50:07: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1110 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 08:50:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287688/SRX287688.05_peaks.xls INFO @ Mon, 03 Jun 2019 08:50:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287688/SRX287688.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 08:50:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287688/SRX287688.05_summits.bed INFO @ Mon, 03 Jun 2019 08:50:11: Done! INFO @ Mon, 03 Jun 2019 08:50:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287688/SRX287688.10_peaks.xls INFO @ Mon, 03 Jun 2019 08:50:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287688/SRX287688.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 08:50:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287688/SRX287688.10_summits.bed INFO @ Mon, 03 Jun 2019 08:50:11: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (4698 records, 4 fields): 7 millis CompletedMACS2peakCalling pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2336 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。