Job ID = 4303127 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 40,635,891 reads read : 40,635,891 reads written : 40,635,891 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR1552293.sra.cache’: 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: 00:10:29 40635891 reads; of these: 40635891 (100.00%) were unpaired; of these: 7961724 (19.59%) aligned 0 times 28634220 (70.47%) aligned exactly 1 time 4039947 (9.94%) aligned >1 times 80.41% overall alignment rate Time searching: 00:10:29 Overall time: 00:10:29 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] 12477111 / 32674167 = 0.3819 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 12 Dec 2019 01:08:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX681824/SRX681824.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX681824/SRX681824.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX681824/SRX681824.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX681824/SRX681824.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 @ Thu, 12 Dec 2019 01:08:46: #1 read tag files... INFO @ Thu, 12 Dec 2019 01:08:46: #1 read treatment tags... INFO @ Thu, 12 Dec 2019 01:08:57: 1000000 INFO @ Thu, 12 Dec 2019 01:09:09: 2000000 INFO @ Thu, 12 Dec 2019 01:09:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX681824/SRX681824.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX681824/SRX681824.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX681824/SRX681824.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX681824/SRX681824.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 @ Thu, 12 Dec 2019 01:09:15: #1 read tag files... INFO @ Thu, 12 Dec 2019 01:09:15: #1 read treatment tags... INFO @ Thu, 12 Dec 2019 01:09:20: 3000000 INFO @ Thu, 12 Dec 2019 01:09:24: 1000000 INFO @ Thu, 12 Dec 2019 01:09:32: 4000000 INFO @ Thu, 12 Dec 2019 01:09:33: 2000000 INFO @ Thu, 12 Dec 2019 01:09:41: 3000000 BedGraph に変換中... INFO @ Thu, 12 Dec 2019 01:09:44: 5000000 INFO @ Thu, 12 Dec 2019 01:09:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX681824/SRX681824.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX681824/SRX681824.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX681824/SRX681824.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX681824/SRX681824.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 @ Thu, 12 Dec 2019 01:09:45: #1 read tag files... INFO @ Thu, 12 Dec 2019 01:09:45: #1 read treatment tags... INFO @ Thu, 12 Dec 2019 01:09:50: 4000000 INFO @ Thu, 12 Dec 2019 01:09:53: 1000000 INFO @ Thu, 12 Dec 2019 01:09:55: 6000000 INFO @ Thu, 12 Dec 2019 01:09:59: 5000000 INFO @ Thu, 12 Dec 2019 01:10:01: 2000000 INFO @ Thu, 12 Dec 2019 01:10:07: 7000000 INFO @ Thu, 12 Dec 2019 01:10:07: 6000000 INFO @ Thu, 12 Dec 2019 01:10:09: 3000000 INFO @ Thu, 12 Dec 2019 01:10:16: 7000000 INFO @ Thu, 12 Dec 2019 01:10:17: 4000000 INFO @ Thu, 12 Dec 2019 01:10:19: 8000000 INFO @ Thu, 12 Dec 2019 01:10:24: 5000000 INFO @ Thu, 12 Dec 2019 01:10:25: 8000000 INFO @ Thu, 12 Dec 2019 01:10:30: 9000000 INFO @ Thu, 12 Dec 2019 01:10:32: 6000000 INFO @ Thu, 12 Dec 2019 01:10:33: 9000000 INFO @ Thu, 12 Dec 2019 01:10:40: 7000000 INFO @ Thu, 12 Dec 2019 01:10:40: 10000000 INFO @ Thu, 12 Dec 2019 01:10:42: 10000000 INFO @ Thu, 12 Dec 2019 01:10:48: 8000000 INFO @ Thu, 12 Dec 2019 01:10:50: 11000000 INFO @ Thu, 12 Dec 2019 01:10:51: 11000000 INFO @ Thu, 12 Dec 2019 01:10:55: 9000000 INFO @ Thu, 12 Dec 2019 01:10:58: 12000000 INFO @ Thu, 12 Dec 2019 01:11:02: 12000000 INFO @ Thu, 12 Dec 2019 01:11:03: 10000000 INFO @ Thu, 12 Dec 2019 01:11:07: 13000000 INFO @ Thu, 12 Dec 2019 01:11:10: 11000000 INFO @ Thu, 12 Dec 2019 01:11:13: 13000000 INFO @ Thu, 12 Dec 2019 01:11:16: 14000000 INFO @ Thu, 12 Dec 2019 01:11:18: 12000000 INFO @ Thu, 12 Dec 2019 01:11:24: 14000000 INFO @ Thu, 12 Dec 2019 01:11:25: 15000000 INFO @ Thu, 12 Dec 2019 01:11:25: 13000000 INFO @ Thu, 12 Dec 2019 01:11:33: 14000000 INFO @ Thu, 12 Dec 2019 01:11:34: 16000000 INFO @ Thu, 12 Dec 2019 01:11:34: 15000000 INFO @ Thu, 12 Dec 2019 01:11:41: 15000000 INFO @ Thu, 12 Dec 2019 01:11:42: 17000000 INFO @ Thu, 12 Dec 2019 01:11:44: 16000000 INFO @ Thu, 12 Dec 2019 01:11:48: 16000000 INFO @ Thu, 12 Dec 2019 01:11:51: 18000000 INFO @ Thu, 12 Dec 2019 01:11:54: 17000000 INFO @ Thu, 12 Dec 2019 01:11:56: 17000000 INFO @ Thu, 12 Dec 2019 01:12:00: 19000000 INFO @ Thu, 12 Dec 2019 01:12:04: 18000000 INFO @ Thu, 12 Dec 2019 01:12:05: 18000000 INFO @ Thu, 12 Dec 2019 01:12:09: 20000000 INFO @ Thu, 12 Dec 2019 01:12:10: #1 tag size is determined as 50 bps INFO @ Thu, 12 Dec 2019 01:12:10: #1 tag size = 50 INFO @ Thu, 12 Dec 2019 01:12:10: #1 total tags in treatment: 20197056 INFO @ Thu, 12 Dec 2019 01:12:10: #1 user defined the maximum tags... INFO @ Thu, 12 Dec 2019 01:12:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 12 Dec 2019 01:12:11: #1 tags after filtering in treatment: 20197056 INFO @ Thu, 12 Dec 2019 01:12:11: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 12 Dec 2019 01:12:11: #1 finished! INFO @ Thu, 12 Dec 2019 01:12:11: #2 Build Peak Model... INFO @ Thu, 12 Dec 2019 01:12:11: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 12 Dec 2019 01:12:12: 19000000 INFO @ Thu, 12 Dec 2019 01:12:13: #2 number of paired peaks: 241 WARNING @ Thu, 12 Dec 2019 01:12:13: Fewer paired peaks (241) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 241 pairs to build model! INFO @ Thu, 12 Dec 2019 01:12:13: start model_add_line... INFO @ Thu, 12 Dec 2019 01:12:13: start X-correlation... INFO @ Thu, 12 Dec 2019 01:12:13: end of X-cor INFO @ Thu, 12 Dec 2019 01:12:13: #2 finished! INFO @ Thu, 12 Dec 2019 01:12:13: #2 predicted fragment length is 137 bps INFO @ Thu, 12 Dec 2019 01:12:13: #2 alternative fragment length(s) may be 137 bps INFO @ Thu, 12 Dec 2019 01:12:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX681824/SRX681824.10_model.r INFO @ Thu, 12 Dec 2019 01:12:13: #3 Call peaks... INFO @ Thu, 12 Dec 2019 01:12:13: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 12 Dec 2019 01:12:15: 19000000 INFO @ Thu, 12 Dec 2019 01:12:19: 20000000 INFO @ Thu, 12 Dec 2019 01:12:21: #1 tag size is determined as 50 bps INFO @ Thu, 12 Dec 2019 01:12:21: #1 tag size = 50 INFO @ Thu, 12 Dec 2019 01:12:21: #1 total tags in treatment: 20197056 INFO @ Thu, 12 Dec 2019 01:12:21: #1 user defined the maximum tags... INFO @ Thu, 12 Dec 2019 01:12:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 12 Dec 2019 01:12:21: #1 tags after filtering in treatment: 20197056 INFO @ Thu, 12 Dec 2019 01:12:21: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 12 Dec 2019 01:12:21: #1 finished! INFO @ Thu, 12 Dec 2019 01:12:21: #2 Build Peak Model... INFO @ Thu, 12 Dec 2019 01:12:21: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 12 Dec 2019 01:12:23: #2 number of paired peaks: 241 WARNING @ Thu, 12 Dec 2019 01:12:23: Fewer paired peaks (241) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 241 pairs to build model! INFO @ Thu, 12 Dec 2019 01:12:23: start model_add_line... INFO @ Thu, 12 Dec 2019 01:12:23: start X-correlation... INFO @ Thu, 12 Dec 2019 01:12:23: end of X-cor INFO @ Thu, 12 Dec 2019 01:12:23: #2 finished! INFO @ Thu, 12 Dec 2019 01:12:23: #2 predicted fragment length is 137 bps INFO @ Thu, 12 Dec 2019 01:12:23: #2 alternative fragment length(s) may be 137 bps INFO @ Thu, 12 Dec 2019 01:12:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX681824/SRX681824.20_model.r INFO @ Thu, 12 Dec 2019 01:12:24: #3 Call peaks... INFO @ Thu, 12 Dec 2019 01:12:24: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 12 Dec 2019 01:12:25: 20000000 INFO @ Thu, 12 Dec 2019 01:12:27: #1 tag size is determined as 50 bps INFO @ Thu, 12 Dec 2019 01:12:27: #1 tag size = 50 INFO @ Thu, 12 Dec 2019 01:12:27: #1 total tags in treatment: 20197056 INFO @ Thu, 12 Dec 2019 01:12:27: #1 user defined the maximum tags... INFO @ Thu, 12 Dec 2019 01:12:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 12 Dec 2019 01:12:27: #1 tags after filtering in treatment: 20197056 INFO @ Thu, 12 Dec 2019 01:12:27: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 12 Dec 2019 01:12:27: #1 finished! INFO @ Thu, 12 Dec 2019 01:12:27: #2 Build Peak Model... INFO @ Thu, 12 Dec 2019 01:12:27: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 12 Dec 2019 01:12:29: #2 number of paired peaks: 241 WARNING @ Thu, 12 Dec 2019 01:12:29: Fewer paired peaks (241) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 241 pairs to build model! INFO @ Thu, 12 Dec 2019 01:12:29: start model_add_line... INFO @ Thu, 12 Dec 2019 01:12:29: start X-correlation... INFO @ Thu, 12 Dec 2019 01:12:29: end of X-cor INFO @ Thu, 12 Dec 2019 01:12:29: #2 finished! INFO @ Thu, 12 Dec 2019 01:12:29: #2 predicted fragment length is 137 bps INFO @ Thu, 12 Dec 2019 01:12:29: #2 alternative fragment length(s) may be 137 bps INFO @ Thu, 12 Dec 2019 01:12:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX681824/SRX681824.05_model.r INFO @ Thu, 12 Dec 2019 01:12:29: #3 Call peaks... INFO @ Thu, 12 Dec 2019 01:12:29: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 12 Dec 2019 01:13:07: #3 Call peaks for each chromosome... INFO @ Thu, 12 Dec 2019 01:13:16: #3 Call peaks for each chromosome... INFO @ Thu, 12 Dec 2019 01:13:22: #3 Call peaks for each chromosome... INFO @ Thu, 12 Dec 2019 01:13:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX681824/SRX681824.10_peaks.xls INFO @ Thu, 12 Dec 2019 01:13:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX681824/SRX681824.10_peaks.narrowPeak INFO @ Thu, 12 Dec 2019 01:13:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX681824/SRX681824.10_summits.bed INFO @ Thu, 12 Dec 2019 01:13:34: Done! pass1 - making usageList (15 chroms): 6 millis pass2 - checking and writing primary data (14324 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Thu, 12 Dec 2019 01:13:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX681824/SRX681824.20_peaks.xls INFO @ Thu, 12 Dec 2019 01:13:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX681824/SRX681824.20_peaks.narrowPeak INFO @ Thu, 12 Dec 2019 01:13:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX681824/SRX681824.20_summits.bed INFO @ Thu, 12 Dec 2019 01:13:42: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (4627 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Thu, 12 Dec 2019 01:13:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX681824/SRX681824.05_peaks.xls INFO @ Thu, 12 Dec 2019 01:13:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX681824/SRX681824.05_peaks.narrowPeak INFO @ Thu, 12 Dec 2019 01:13:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX681824/SRX681824.05_summits.bed INFO @ Thu, 12 Dec 2019 01:13:50: Done! pass1 - making usageList (15 chroms): 6 millis pass2 - checking and writing primary data (28769 records, 4 fields): 36 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。