Job ID = 1294214 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 30,914,266 reads read : 30,914,266 reads written : 30,914,266 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: 00:11:13 30914266 reads; of these: 30914266 (100.00%) were unpaired; of these: 855580 (2.77%) aligned 0 times 23504674 (76.03%) aligned exactly 1 time 6554012 (21.20%) aligned >1 times 97.23% overall alignment rate Time searching: 00:11:13 Overall time: 00:11:13 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 16 files... [bam_rmdupse_core] 5635065 / 30058686 = 0.1875 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 05:53:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX201891/SRX201891.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX201891/SRX201891.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX201891/SRX201891.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX201891/SRX201891.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 05:53:10: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:53:10: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:53:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX201891/SRX201891.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX201891/SRX201891.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX201891/SRX201891.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX201891/SRX201891.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 05:53:10: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:53:10: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:53:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX201891/SRX201891.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX201891/SRX201891.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX201891/SRX201891.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX201891/SRX201891.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 05:53:10: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:53:10: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:53:19: 1000000 INFO @ Mon, 03 Jun 2019 05:53:20: 1000000 INFO @ Mon, 03 Jun 2019 05:53:20: 1000000 INFO @ Mon, 03 Jun 2019 05:53:28: 2000000 INFO @ Mon, 03 Jun 2019 05:53:28: 2000000 INFO @ Mon, 03 Jun 2019 05:53:30: 2000000 INFO @ Mon, 03 Jun 2019 05:53:37: 3000000 INFO @ Mon, 03 Jun 2019 05:53:37: 3000000 INFO @ Mon, 03 Jun 2019 05:53:41: 3000000 INFO @ Mon, 03 Jun 2019 05:53:46: 4000000 INFO @ Mon, 03 Jun 2019 05:53:46: 4000000 INFO @ Mon, 03 Jun 2019 05:53:51: 4000000 INFO @ Mon, 03 Jun 2019 05:53:54: 5000000 INFO @ Mon, 03 Jun 2019 05:53:55: 5000000 INFO @ Mon, 03 Jun 2019 05:54:01: 5000000 INFO @ Mon, 03 Jun 2019 05:54:03: 6000000 INFO @ Mon, 03 Jun 2019 05:54:03: 6000000 INFO @ Mon, 03 Jun 2019 05:54:10: 6000000 INFO @ Mon, 03 Jun 2019 05:54:11: 7000000 INFO @ Mon, 03 Jun 2019 05:54:12: 7000000 INFO @ Mon, 03 Jun 2019 05:54:20: 8000000 INFO @ Mon, 03 Jun 2019 05:54:20: 7000000 INFO @ Mon, 03 Jun 2019 05:54:21: 8000000 INFO @ Mon, 03 Jun 2019 05:54:28: 9000000 INFO @ Mon, 03 Jun 2019 05:54:29: 9000000 INFO @ Mon, 03 Jun 2019 05:54:30: 8000000 INFO @ Mon, 03 Jun 2019 05:54:36: 10000000 INFO @ Mon, 03 Jun 2019 05:54:38: 10000000 INFO @ Mon, 03 Jun 2019 05:54:40: 9000000 INFO @ Mon, 03 Jun 2019 05:54:44: 11000000 INFO @ Mon, 03 Jun 2019 05:54:46: 11000000 INFO @ Mon, 03 Jun 2019 05:54:50: 10000000 INFO @ Mon, 03 Jun 2019 05:54:53: 12000000 INFO @ Mon, 03 Jun 2019 05:54:54: 12000000 INFO @ Mon, 03 Jun 2019 05:55:00: 11000000 INFO @ Mon, 03 Jun 2019 05:55:01: 13000000 INFO @ Mon, 03 Jun 2019 05:55:03: 13000000 INFO @ Mon, 03 Jun 2019 05:55:09: 12000000 INFO @ Mon, 03 Jun 2019 05:55:09: 14000000 INFO @ Mon, 03 Jun 2019 05:55:11: 14000000 INFO @ Mon, 03 Jun 2019 05:55:18: 15000000 INFO @ Mon, 03 Jun 2019 05:55:19: 13000000 INFO @ Mon, 03 Jun 2019 05:55:20: 15000000 INFO @ Mon, 03 Jun 2019 05:55:26: 16000000 INFO @ Mon, 03 Jun 2019 05:55:28: 16000000 INFO @ Mon, 03 Jun 2019 05:55:29: 14000000 INFO @ Mon, 03 Jun 2019 05:55:35: 17000000 INFO @ Mon, 03 Jun 2019 05:55:37: 17000000 INFO @ Mon, 03 Jun 2019 05:55:38: 15000000 INFO @ Mon, 03 Jun 2019 05:55:43: 18000000 INFO @ Mon, 03 Jun 2019 05:55:45: 18000000 INFO @ Mon, 03 Jun 2019 05:55:48: 16000000 INFO @ Mon, 03 Jun 2019 05:55:52: 19000000 INFO @ Mon, 03 Jun 2019 05:55:54: 19000000 INFO @ Mon, 03 Jun 2019 05:55:58: 17000000 INFO @ Mon, 03 Jun 2019 05:56:00: 20000000 INFO @ Mon, 03 Jun 2019 05:56:02: 20000000 INFO @ Mon, 03 Jun 2019 05:56:08: 18000000 INFO @ Mon, 03 Jun 2019 05:56:08: 21000000 INFO @ Mon, 03 Jun 2019 05:56:11: 21000000 INFO @ Mon, 03 Jun 2019 05:56:17: 22000000 INFO @ Mon, 03 Jun 2019 05:56:18: 19000000 INFO @ Mon, 03 Jun 2019 05:56:19: 22000000 INFO @ Mon, 03 Jun 2019 05:56:25: 23000000 INFO @ Mon, 03 Jun 2019 05:56:27: 20000000 INFO @ Mon, 03 Jun 2019 05:56:28: 23000000 INFO @ Mon, 03 Jun 2019 05:56:33: 24000000 INFO @ Mon, 03 Jun 2019 05:56:36: 24000000 INFO @ Mon, 03 Jun 2019 05:56:37: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 05:56:37: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 05:56:37: #1 total tags in treatment: 24423621 INFO @ Mon, 03 Jun 2019 05:56:37: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:56:37: #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 05:56:37: 21000000 INFO @ Mon, 03 Jun 2019 05:56:38: #1 tags after filtering in treatment: 24423621 INFO @ Mon, 03 Jun 2019 05:56:38: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:56:38: #1 finished! INFO @ Mon, 03 Jun 2019 05:56:38: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:56:38: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:56:40: #2 number of paired peaks: 161 WARNING @ Mon, 03 Jun 2019 05:56:40: Fewer paired peaks (161) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 161 pairs to build model! INFO @ Mon, 03 Jun 2019 05:56:40: start model_add_line... INFO @ Mon, 03 Jun 2019 05:56:40: start X-correlation... INFO @ Mon, 03 Jun 2019 05:56:40: end of X-cor INFO @ Mon, 03 Jun 2019 05:56:40: #2 finished! INFO @ Mon, 03 Jun 2019 05:56:40: #2 predicted fragment length is 127 bps INFO @ Mon, 03 Jun 2019 05:56:40: #2 alternative fragment length(s) may be 3,127 bps INFO @ Mon, 03 Jun 2019 05:56:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX201891/SRX201891.05_model.r INFO @ Mon, 03 Jun 2019 05:56:40: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:56:40: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:56:40: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 05:56:40: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 05:56:40: #1 total tags in treatment: 24423621 INFO @ Mon, 03 Jun 2019 05:56:40: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:56:40: #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 05:56:40: #1 tags after filtering in treatment: 24423621 INFO @ Mon, 03 Jun 2019 05:56:40: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:56:40: #1 finished! INFO @ Mon, 03 Jun 2019 05:56:40: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:56:40: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:56:43: #2 number of paired peaks: 161 WARNING @ Mon, 03 Jun 2019 05:56:43: Fewer paired peaks (161) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 161 pairs to build model! INFO @ Mon, 03 Jun 2019 05:56:43: start model_add_line... INFO @ Mon, 03 Jun 2019 05:56:43: start X-correlation... INFO @ Mon, 03 Jun 2019 05:56:43: end of X-cor INFO @ Mon, 03 Jun 2019 05:56:43: #2 finished! INFO @ Mon, 03 Jun 2019 05:56:43: #2 predicted fragment length is 127 bps INFO @ Mon, 03 Jun 2019 05:56:43: #2 alternative fragment length(s) may be 3,127 bps INFO @ Mon, 03 Jun 2019 05:56:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX201891/SRX201891.10_model.r INFO @ Mon, 03 Jun 2019 05:56:43: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:56:43: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:56:47: 22000000 INFO @ Mon, 03 Jun 2019 05:56:56: 23000000 INFO @ Mon, 03 Jun 2019 05:57:05: 24000000 INFO @ Mon, 03 Jun 2019 05:57:10: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 05:57:10: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 05:57:10: #1 total tags in treatment: 24423621 INFO @ Mon, 03 Jun 2019 05:57:10: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:57:10: #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 05:57:10: #1 tags after filtering in treatment: 24423621 INFO @ Mon, 03 Jun 2019 05:57:10: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:57:10: #1 finished! INFO @ Mon, 03 Jun 2019 05:57:10: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:57:10: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:57:12: #2 number of paired peaks: 161 WARNING @ Mon, 03 Jun 2019 05:57:12: Fewer paired peaks (161) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 161 pairs to build model! INFO @ Mon, 03 Jun 2019 05:57:12: start model_add_line... INFO @ Mon, 03 Jun 2019 05:57:12: start X-correlation... INFO @ Mon, 03 Jun 2019 05:57:12: end of X-cor INFO @ Mon, 03 Jun 2019 05:57:12: #2 finished! INFO @ Mon, 03 Jun 2019 05:57:12: #2 predicted fragment length is 127 bps INFO @ Mon, 03 Jun 2019 05:57:12: #2 alternative fragment length(s) may be 3,127 bps INFO @ Mon, 03 Jun 2019 05:57:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX201891/SRX201891.20_model.r INFO @ Mon, 03 Jun 2019 05:57:12: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:57:12: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:57:40: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:57:43: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:58:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX201891/SRX201891.05_peaks.xls INFO @ Mon, 03 Jun 2019 05:58:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX201891/SRX201891.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:58:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX201891/SRX201891.05_summits.bed INFO @ Mon, 03 Jun 2019 05:58:08: Done! pass1 - making usageList (14 chroms): 4 millis pass2 - checking and writing primary data (7824 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 05:58:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX201891/SRX201891.10_peaks.xls INFO @ Mon, 03 Jun 2019 05:58:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX201891/SRX201891.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:58:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX201891/SRX201891.10_summits.bed INFO @ Mon, 03 Jun 2019 05:58:11: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (1578 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 05:58:12: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:58:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX201891/SRX201891.20_peaks.xls INFO @ Mon, 03 Jun 2019 05:58:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX201891/SRX201891.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:58:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX201891/SRX201891.20_summits.bed INFO @ Mon, 03 Jun 2019 05:58:40: Done! pass1 - making usageList (11 chroms): 2 millis pass2 - checking and writing primary data (546 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。