Job ID = 1294920 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 14,962,039 reads read : 14,962,039 reads written : 14,962,039 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: 00:04:16 14962039 reads; of these: 14962039 (100.00%) were unpaired; of these: 1143635 (7.64%) aligned 0 times 12632342 (84.43%) aligned exactly 1 time 1186062 (7.93%) aligned >1 times 92.36% overall alignment rate Time searching: 00:04:16 Overall time: 00:04:16 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] 1256067 / 13818404 = 0.0909 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 10:57:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287990/SRX287990.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287990/SRX287990.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287990/SRX287990.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287990/SRX287990.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 10:57:18: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:57:18: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:57:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287990/SRX287990.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287990/SRX287990.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287990/SRX287990.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287990/SRX287990.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 10:57:18: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:57:18: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:57:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287990/SRX287990.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287990/SRX287990.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287990/SRX287990.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287990/SRX287990.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 10:57:18: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:57:18: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:57:27: 1000000 INFO @ Mon, 03 Jun 2019 10:57:27: 1000000 INFO @ Mon, 03 Jun 2019 10:57:28: 1000000 INFO @ Mon, 03 Jun 2019 10:57:35: 2000000 INFO @ Mon, 03 Jun 2019 10:57:35: 2000000 INFO @ Mon, 03 Jun 2019 10:57:38: 2000000 INFO @ Mon, 03 Jun 2019 10:57:43: 3000000 INFO @ Mon, 03 Jun 2019 10:57:44: 3000000 INFO @ Mon, 03 Jun 2019 10:57:47: 3000000 INFO @ Mon, 03 Jun 2019 10:57:51: 4000000 INFO @ Mon, 03 Jun 2019 10:57:52: 4000000 INFO @ Mon, 03 Jun 2019 10:57:57: 4000000 INFO @ Mon, 03 Jun 2019 10:57:59: 5000000 INFO @ Mon, 03 Jun 2019 10:58:00: 5000000 INFO @ Mon, 03 Jun 2019 10:58:07: 5000000 INFO @ Mon, 03 Jun 2019 10:58:07: 6000000 INFO @ Mon, 03 Jun 2019 10:58:09: 6000000 INFO @ Mon, 03 Jun 2019 10:58:15: 7000000 INFO @ Mon, 03 Jun 2019 10:58:16: 6000000 INFO @ Mon, 03 Jun 2019 10:58:17: 7000000 INFO @ Mon, 03 Jun 2019 10:58:23: 8000000 INFO @ Mon, 03 Jun 2019 10:58:25: 8000000 INFO @ Mon, 03 Jun 2019 10:58:26: 7000000 INFO @ Mon, 03 Jun 2019 10:58:32: 9000000 INFO @ Mon, 03 Jun 2019 10:58:34: 9000000 INFO @ Mon, 03 Jun 2019 10:58:36: 8000000 INFO @ Mon, 03 Jun 2019 10:58:40: 10000000 INFO @ Mon, 03 Jun 2019 10:58:42: 10000000 INFO @ Mon, 03 Jun 2019 10:58:45: 9000000 INFO @ Mon, 03 Jun 2019 10:58:48: 11000000 INFO @ Mon, 03 Jun 2019 10:58:50: 11000000 INFO @ Mon, 03 Jun 2019 10:58:55: 10000000 INFO @ Mon, 03 Jun 2019 10:58:55: 12000000 INFO @ Mon, 03 Jun 2019 10:58:59: 12000000 INFO @ Mon, 03 Jun 2019 10:59:00: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 10:59:00: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 10:59:00: #1 total tags in treatment: 12562337 INFO @ Mon, 03 Jun 2019 10:59:00: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:59:00: #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 10:59:00: #1 tags after filtering in treatment: 12562337 INFO @ Mon, 03 Jun 2019 10:59:00: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:59:00: #1 finished! INFO @ Mon, 03 Jun 2019 10:59:00: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:59:00: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:59:01: #2 number of paired peaks: 397 WARNING @ Mon, 03 Jun 2019 10:59:01: Fewer paired peaks (397) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 397 pairs to build model! INFO @ Mon, 03 Jun 2019 10:59:01: start model_add_line... INFO @ Mon, 03 Jun 2019 10:59:01: start X-correlation... INFO @ Mon, 03 Jun 2019 10:59:01: end of X-cor INFO @ Mon, 03 Jun 2019 10:59:01: #2 finished! INFO @ Mon, 03 Jun 2019 10:59:01: #2 predicted fragment length is 181 bps INFO @ Mon, 03 Jun 2019 10:59:01: #2 alternative fragment length(s) may be 162,181 bps INFO @ Mon, 03 Jun 2019 10:59:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287990/SRX287990.20_model.r INFO @ Mon, 03 Jun 2019 10:59:01: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:59:01: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:59:03: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 10:59:03: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 10:59:03: #1 total tags in treatment: 12562337 INFO @ Mon, 03 Jun 2019 10:59:03: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:59:03: #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 10:59:04: #1 tags after filtering in treatment: 12562337 INFO @ Mon, 03 Jun 2019 10:59:04: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:59:04: #1 finished! INFO @ Mon, 03 Jun 2019 10:59:04: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:59:04: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:59:04: 11000000 INFO @ Mon, 03 Jun 2019 10:59:05: #2 number of paired peaks: 397 WARNING @ Mon, 03 Jun 2019 10:59:05: Fewer paired peaks (397) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 397 pairs to build model! INFO @ Mon, 03 Jun 2019 10:59:05: start model_add_line... INFO @ Mon, 03 Jun 2019 10:59:05: start X-correlation... INFO @ Mon, 03 Jun 2019 10:59:05: end of X-cor INFO @ Mon, 03 Jun 2019 10:59:05: #2 finished! INFO @ Mon, 03 Jun 2019 10:59:05: #2 predicted fragment length is 181 bps INFO @ Mon, 03 Jun 2019 10:59:05: #2 alternative fragment length(s) may be 162,181 bps INFO @ Mon, 03 Jun 2019 10:59:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287990/SRX287990.05_model.r INFO @ Mon, 03 Jun 2019 10:59:05: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:59:05: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:59:13: 12000000 INFO @ Mon, 03 Jun 2019 10:59:18: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 10:59:18: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 10:59:18: #1 total tags in treatment: 12562337 INFO @ Mon, 03 Jun 2019 10:59:18: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:59:18: #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 10:59:19: #1 tags after filtering in treatment: 12562337 INFO @ Mon, 03 Jun 2019 10:59:19: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:59:19: #1 finished! INFO @ Mon, 03 Jun 2019 10:59:19: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:59:19: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:59:20: #2 number of paired peaks: 397 WARNING @ Mon, 03 Jun 2019 10:59:20: Fewer paired peaks (397) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 397 pairs to build model! INFO @ Mon, 03 Jun 2019 10:59:20: start model_add_line... INFO @ Mon, 03 Jun 2019 10:59:20: start X-correlation... INFO @ Mon, 03 Jun 2019 10:59:20: end of X-cor INFO @ Mon, 03 Jun 2019 10:59:20: #2 finished! INFO @ Mon, 03 Jun 2019 10:59:20: #2 predicted fragment length is 181 bps INFO @ Mon, 03 Jun 2019 10:59:20: #2 alternative fragment length(s) may be 162,181 bps INFO @ Mon, 03 Jun 2019 10:59:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287990/SRX287990.10_model.r INFO @ Mon, 03 Jun 2019 10:59:20: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:59:20: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:59:37: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:59:41: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:59:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287990/SRX287990.20_peaks.xls INFO @ Mon, 03 Jun 2019 10:59:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287990/SRX287990.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:59:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287990/SRX287990.20_summits.bed INFO @ Mon, 03 Jun 2019 10:59:54: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (592 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 10:59:55: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:59:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287990/SRX287990.05_peaks.xls INFO @ Mon, 03 Jun 2019 10:59:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287990/SRX287990.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:59:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287990/SRX287990.05_summits.bed INFO @ Mon, 03 Jun 2019 10:59:59: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (4681 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 11:00:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287990/SRX287990.10_peaks.xls INFO @ Mon, 03 Jun 2019 11:00:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287990/SRX287990.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:00:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287990/SRX287990.10_summits.bed INFO @ Mon, 03 Jun 2019 11:00:13: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (2282 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。