Job ID = 4303091 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 17,385,191 reads read : 34,770,382 reads written : 34,770,382 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR1151102.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: 00:35:59 17385191 reads; of these: 17385191 (100.00%) were paired; of these: 3063826 (17.62%) aligned concordantly 0 times 10878421 (62.57%) aligned concordantly exactly 1 time 3442944 (19.80%) aligned concordantly >1 times ---- 3063826 pairs aligned concordantly 0 times; of these: 8372 (0.27%) aligned discordantly 1 time ---- 3055454 pairs aligned 0 times concordantly or discordantly; of these: 6110908 mates make up the pairs; of these: 5801149 (94.93%) aligned 0 times 227138 (3.72%) aligned exactly 1 time 82621 (1.35%) aligned >1 times 83.32% overall alignment rate Time searching: 00:35:59 Overall time: 00:35:59 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_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 462814 / 14320462 = 0.0323 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 12 Dec 2019 01:29:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX456154/SRX456154.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX456154/SRX456154.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX456154/SRX456154.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX456154/SRX456154.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 01:29:07: #1 read tag files... INFO @ Thu, 12 Dec 2019 01:29:07: #1 read treatment tags... INFO @ Thu, 12 Dec 2019 01:29:16: 1000000 INFO @ Thu, 12 Dec 2019 01:29:26: 2000000 INFO @ Thu, 12 Dec 2019 01:29:35: 3000000 INFO @ Thu, 12 Dec 2019 01:29:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX456154/SRX456154.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX456154/SRX456154.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX456154/SRX456154.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX456154/SRX456154.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 01:29:37: #1 read tag files... INFO @ Thu, 12 Dec 2019 01:29:37: #1 read treatment tags... INFO @ Thu, 12 Dec 2019 01:29:45: 4000000 INFO @ Thu, 12 Dec 2019 01:29:46: 1000000 INFO @ Thu, 12 Dec 2019 01:29:55: 5000000 INFO @ Thu, 12 Dec 2019 01:29:56: 2000000 INFO @ Thu, 12 Dec 2019 01:30:04: 6000000 BedGraph に変換中... INFO @ Thu, 12 Dec 2019 01:30:05: 3000000 INFO @ Thu, 12 Dec 2019 01:30:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX456154/SRX456154.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX456154/SRX456154.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX456154/SRX456154.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX456154/SRX456154.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 01:30:07: #1 read tag files... INFO @ Thu, 12 Dec 2019 01:30:07: #1 read treatment tags... INFO @ Thu, 12 Dec 2019 01:30:14: 7000000 INFO @ Thu, 12 Dec 2019 01:30:15: 4000000 INFO @ Thu, 12 Dec 2019 01:30:17: 1000000 INFO @ Thu, 12 Dec 2019 01:30:24: 8000000 INFO @ Thu, 12 Dec 2019 01:30:25: 5000000 INFO @ Thu, 12 Dec 2019 01:30:28: 2000000 INFO @ Thu, 12 Dec 2019 01:30:34: 9000000 INFO @ Thu, 12 Dec 2019 01:30:36: 6000000 INFO @ Thu, 12 Dec 2019 01:30:38: 3000000 INFO @ Thu, 12 Dec 2019 01:30:44: 10000000 INFO @ Thu, 12 Dec 2019 01:30:46: 7000000 INFO @ Thu, 12 Dec 2019 01:30:48: 4000000 INFO @ Thu, 12 Dec 2019 01:30:54: 11000000 INFO @ Thu, 12 Dec 2019 01:30:56: 8000000 INFO @ Thu, 12 Dec 2019 01:30:59: 5000000 INFO @ Thu, 12 Dec 2019 01:31:04: 12000000 INFO @ Thu, 12 Dec 2019 01:31:07: 9000000 INFO @ Thu, 12 Dec 2019 01:31:09: 6000000 INFO @ Thu, 12 Dec 2019 01:31:14: 13000000 INFO @ Thu, 12 Dec 2019 01:31:17: 10000000 INFO @ Thu, 12 Dec 2019 01:31:20: 7000000 INFO @ Thu, 12 Dec 2019 01:31:24: 14000000 INFO @ Thu, 12 Dec 2019 01:31:27: 11000000 INFO @ Thu, 12 Dec 2019 01:31:30: 8000000 INFO @ Thu, 12 Dec 2019 01:31:34: 15000000 INFO @ Thu, 12 Dec 2019 01:31:37: 12000000 INFO @ Thu, 12 Dec 2019 01:31:40: 9000000 INFO @ Thu, 12 Dec 2019 01:31:44: 16000000 INFO @ Thu, 12 Dec 2019 01:31:47: 13000000 INFO @ Thu, 12 Dec 2019 01:31:50: 10000000 INFO @ Thu, 12 Dec 2019 01:31:54: 17000000 INFO @ Thu, 12 Dec 2019 01:31:57: 14000000 INFO @ Thu, 12 Dec 2019 01:32:01: 11000000 INFO @ Thu, 12 Dec 2019 01:32:04: 18000000 INFO @ Thu, 12 Dec 2019 01:32:08: 15000000 INFO @ Thu, 12 Dec 2019 01:32:11: 12000000 INFO @ Thu, 12 Dec 2019 01:32:14: 19000000 INFO @ Thu, 12 Dec 2019 01:32:18: 16000000 INFO @ Thu, 12 Dec 2019 01:32:21: 13000000 INFO @ Thu, 12 Dec 2019 01:32:24: 20000000 INFO @ Thu, 12 Dec 2019 01:32:28: 17000000 INFO @ Thu, 12 Dec 2019 01:32:32: 14000000 INFO @ Thu, 12 Dec 2019 01:32:34: 21000000 INFO @ Thu, 12 Dec 2019 01:32:39: 18000000 INFO @ Thu, 12 Dec 2019 01:32:42: 15000000 INFO @ Thu, 12 Dec 2019 01:32:44: 22000000 INFO @ Thu, 12 Dec 2019 01:32:48: 19000000 INFO @ Thu, 12 Dec 2019 01:32:52: 16000000 INFO @ Thu, 12 Dec 2019 01:32:54: 23000000 INFO @ Thu, 12 Dec 2019 01:32:58: 20000000 INFO @ Thu, 12 Dec 2019 01:33:02: 17000000 INFO @ Thu, 12 Dec 2019 01:33:04: 24000000 INFO @ Thu, 12 Dec 2019 01:33:07: 21000000 INFO @ Thu, 12 Dec 2019 01:33:12: 18000000 INFO @ Thu, 12 Dec 2019 01:33:14: 25000000 INFO @ Thu, 12 Dec 2019 01:33:17: 22000000 INFO @ Thu, 12 Dec 2019 01:33:22: 19000000 INFO @ Thu, 12 Dec 2019 01:33:24: 26000000 INFO @ Thu, 12 Dec 2019 01:33:27: 23000000 INFO @ Thu, 12 Dec 2019 01:33:32: 20000000 INFO @ Thu, 12 Dec 2019 01:33:34: 27000000 INFO @ Thu, 12 Dec 2019 01:33:37: 24000000 INFO @ Thu, 12 Dec 2019 01:33:42: 21000000 INFO @ Thu, 12 Dec 2019 01:33:43: 28000000 INFO @ Thu, 12 Dec 2019 01:33:44: #1 tag size is determined as 50 bps INFO @ Thu, 12 Dec 2019 01:33:44: #1 tag size = 50 INFO @ Thu, 12 Dec 2019 01:33:44: #1 total tags in treatment: 13858682 INFO @ Thu, 12 Dec 2019 01:33:44: #1 user defined the maximum tags... INFO @ Thu, 12 Dec 2019 01:33:44: #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 01:33:44: #1 tags after filtering in treatment: 12870404 INFO @ Thu, 12 Dec 2019 01:33:44: #1 Redundant rate of treatment: 0.07 INFO @ Thu, 12 Dec 2019 01:33:44: #1 finished! INFO @ Thu, 12 Dec 2019 01:33:44: #2 Build Peak Model... INFO @ Thu, 12 Dec 2019 01:33:44: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 12 Dec 2019 01:33:45: #2 number of paired peaks: 183 WARNING @ Thu, 12 Dec 2019 01:33:45: Fewer paired peaks (183) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 183 pairs to build model! INFO @ Thu, 12 Dec 2019 01:33:45: start model_add_line... INFO @ Thu, 12 Dec 2019 01:33:46: start X-correlation... INFO @ Thu, 12 Dec 2019 01:33:46: end of X-cor INFO @ Thu, 12 Dec 2019 01:33:46: #2 finished! INFO @ Thu, 12 Dec 2019 01:33:46: #2 predicted fragment length is 107 bps INFO @ Thu, 12 Dec 2019 01:33:46: #2 alternative fragment length(s) may be 107 bps INFO @ Thu, 12 Dec 2019 01:33:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX456154/SRX456154.05_model.r INFO @ Thu, 12 Dec 2019 01:33:46: #3 Call peaks... INFO @ Thu, 12 Dec 2019 01:33:46: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 12 Dec 2019 01:33:46: 25000000 INFO @ Thu, 12 Dec 2019 01:33:52: 22000000 INFO @ Thu, 12 Dec 2019 01:33:55: 26000000 INFO @ Thu, 12 Dec 2019 01:34:02: 23000000 INFO @ Thu, 12 Dec 2019 01:34:05: 27000000 INFO @ Thu, 12 Dec 2019 01:34:12: 24000000 INFO @ Thu, 12 Dec 2019 01:34:14: 28000000 INFO @ Thu, 12 Dec 2019 01:34:14: #1 tag size is determined as 50 bps INFO @ Thu, 12 Dec 2019 01:34:14: #1 tag size = 50 INFO @ Thu, 12 Dec 2019 01:34:14: #1 total tags in treatment: 13858682 INFO @ Thu, 12 Dec 2019 01:34:14: #1 user defined the maximum tags... INFO @ Thu, 12 Dec 2019 01:34:14: #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 01:34:15: #1 tags after filtering in treatment: 12870404 INFO @ Thu, 12 Dec 2019 01:34:15: #1 Redundant rate of treatment: 0.07 INFO @ Thu, 12 Dec 2019 01:34:15: #1 finished! INFO @ Thu, 12 Dec 2019 01:34:15: #2 Build Peak Model... INFO @ Thu, 12 Dec 2019 01:34:15: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 12 Dec 2019 01:34:16: #2 number of paired peaks: 183 WARNING @ Thu, 12 Dec 2019 01:34:16: Fewer paired peaks (183) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 183 pairs to build model! INFO @ Thu, 12 Dec 2019 01:34:16: start model_add_line... INFO @ Thu, 12 Dec 2019 01:34:16: start X-correlation... INFO @ Thu, 12 Dec 2019 01:34:16: end of X-cor INFO @ Thu, 12 Dec 2019 01:34:16: #2 finished! INFO @ Thu, 12 Dec 2019 01:34:16: #2 predicted fragment length is 107 bps INFO @ Thu, 12 Dec 2019 01:34:16: #2 alternative fragment length(s) may be 107 bps INFO @ Thu, 12 Dec 2019 01:34:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX456154/SRX456154.10_model.r INFO @ Thu, 12 Dec 2019 01:34:16: #3 Call peaks... INFO @ Thu, 12 Dec 2019 01:34:16: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 12 Dec 2019 01:34:21: 25000000 INFO @ Thu, 12 Dec 2019 01:34:24: #3 Call peaks for each chromosome... INFO @ Thu, 12 Dec 2019 01:34:31: 26000000 INFO @ Thu, 12 Dec 2019 01:34:40: 27000000 INFO @ Thu, 12 Dec 2019 01:34:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX456154/SRX456154.05_peaks.xls INFO @ Thu, 12 Dec 2019 01:34:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX456154/SRX456154.05_peaks.narrowPeak INFO @ Thu, 12 Dec 2019 01:34:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX456154/SRX456154.05_summits.bed INFO @ Thu, 12 Dec 2019 01:34:45: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (4312 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Thu, 12 Dec 2019 01:34:49: 28000000 INFO @ Thu, 12 Dec 2019 01:34:49: #1 tag size is determined as 50 bps INFO @ Thu, 12 Dec 2019 01:34:49: #1 tag size = 50 INFO @ Thu, 12 Dec 2019 01:34:49: #1 total tags in treatment: 13858682 INFO @ Thu, 12 Dec 2019 01:34:49: #1 user defined the maximum tags... INFO @ Thu, 12 Dec 2019 01:34:49: #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 01:34:50: #1 tags after filtering in treatment: 12870404 INFO @ Thu, 12 Dec 2019 01:34:50: #1 Redundant rate of treatment: 0.07 INFO @ Thu, 12 Dec 2019 01:34:50: #1 finished! INFO @ Thu, 12 Dec 2019 01:34:50: #2 Build Peak Model... INFO @ Thu, 12 Dec 2019 01:34:50: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 12 Dec 2019 01:34:51: #2 number of paired peaks: 183 WARNING @ Thu, 12 Dec 2019 01:34:51: Fewer paired peaks (183) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 183 pairs to build model! INFO @ Thu, 12 Dec 2019 01:34:51: start model_add_line... INFO @ Thu, 12 Dec 2019 01:34:51: start X-correlation... INFO @ Thu, 12 Dec 2019 01:34:51: end of X-cor INFO @ Thu, 12 Dec 2019 01:34:51: #2 finished! INFO @ Thu, 12 Dec 2019 01:34:51: #2 predicted fragment length is 107 bps INFO @ Thu, 12 Dec 2019 01:34:51: #2 alternative fragment length(s) may be 107 bps INFO @ Thu, 12 Dec 2019 01:34:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX456154/SRX456154.20_model.r INFO @ Thu, 12 Dec 2019 01:34:51: #3 Call peaks... INFO @ Thu, 12 Dec 2019 01:34:51: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 12 Dec 2019 01:34:54: #3 Call peaks for each chromosome... INFO @ Thu, 12 Dec 2019 01:35:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX456154/SRX456154.10_peaks.xls INFO @ Thu, 12 Dec 2019 01:35:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX456154/SRX456154.10_peaks.narrowPeak INFO @ Thu, 12 Dec 2019 01:35:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX456154/SRX456154.10_summits.bed INFO @ Thu, 12 Dec 2019 01:35:14: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (1832 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Thu, 12 Dec 2019 01:35:29: #3 Call peaks for each chromosome... INFO @ Thu, 12 Dec 2019 01:35:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX456154/SRX456154.20_peaks.xls INFO @ Thu, 12 Dec 2019 01:35:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX456154/SRX456154.20_peaks.narrowPeak INFO @ Thu, 12 Dec 2019 01:35:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX456154/SRX456154.20_summits.bed INFO @ Thu, 12 Dec 2019 01:35:48: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (750 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。