Job ID = 1293361 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 15,213,485 reads read : 30,426,970 reads written : 30,426,970 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: 00:38:01 15213485 reads; of these: 15213485 (100.00%) were paired; of these: 1055599 (6.94%) aligned concordantly 0 times 10356730 (68.08%) aligned concordantly exactly 1 time 3801156 (24.99%) aligned concordantly >1 times ---- 1055599 pairs aligned concordantly 0 times; of these: 277623 (26.30%) aligned discordantly 1 time ---- 777976 pairs aligned 0 times concordantly or discordantly; of these: 1555952 mates make up the pairs; of these: 703341 (45.20%) aligned 0 times 485311 (31.19%) aligned exactly 1 time 367300 (23.61%) aligned >1 times 97.69% overall alignment rate Time searching: 00:38:01 Overall time: 00:38:01 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_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] 498712 / 14223444 = 0.0351 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 00:04:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX1818281/ERX1818281.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX1818281/ERX1818281.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX1818281/ERX1818281.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX1818281/ERX1818281.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 00:04:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX1818281/ERX1818281.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX1818281/ERX1818281.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX1818281/ERX1818281.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX1818281/ERX1818281.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 00:04:14: #1 read tag files... INFO @ Mon, 03 Jun 2019 00:04:14: #1 read tag files... INFO @ Mon, 03 Jun 2019 00:04:14: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 00:04:14: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 00:04:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX1818281/ERX1818281.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX1818281/ERX1818281.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX1818281/ERX1818281.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX1818281/ERX1818281.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 00:04:14: #1 read tag files... INFO @ Mon, 03 Jun 2019 00:04:14: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 00:04:24: 1000000 INFO @ Mon, 03 Jun 2019 00:04:25: 1000000 INFO @ Mon, 03 Jun 2019 00:04:25: 1000000 INFO @ Mon, 03 Jun 2019 00:04:33: 2000000 INFO @ Mon, 03 Jun 2019 00:04:36: 2000000 INFO @ Mon, 03 Jun 2019 00:04:36: 2000000 INFO @ Mon, 03 Jun 2019 00:04:42: 3000000 INFO @ Mon, 03 Jun 2019 00:04:47: 3000000 INFO @ Mon, 03 Jun 2019 00:04:47: 3000000 INFO @ Mon, 03 Jun 2019 00:04:52: 4000000 INFO @ Mon, 03 Jun 2019 00:04:58: 4000000 INFO @ Mon, 03 Jun 2019 00:04:58: 4000000 INFO @ Mon, 03 Jun 2019 00:05:01: 5000000 INFO @ Mon, 03 Jun 2019 00:05:10: 5000000 INFO @ Mon, 03 Jun 2019 00:05:10: 5000000 INFO @ Mon, 03 Jun 2019 00:05:11: 6000000 INFO @ Mon, 03 Jun 2019 00:05:21: 7000000 INFO @ Mon, 03 Jun 2019 00:05:21: 6000000 INFO @ Mon, 03 Jun 2019 00:05:21: 6000000 INFO @ Mon, 03 Jun 2019 00:05:31: 8000000 INFO @ Mon, 03 Jun 2019 00:05:33: 7000000 INFO @ Mon, 03 Jun 2019 00:05:33: 7000000 INFO @ Mon, 03 Jun 2019 00:05:40: 9000000 INFO @ Mon, 03 Jun 2019 00:05:44: 8000000 INFO @ Mon, 03 Jun 2019 00:05:44: 8000000 INFO @ Mon, 03 Jun 2019 00:05:50: 10000000 INFO @ Mon, 03 Jun 2019 00:05:55: 9000000 INFO @ Mon, 03 Jun 2019 00:05:55: 9000000 INFO @ Mon, 03 Jun 2019 00:06:00: 11000000 INFO @ Mon, 03 Jun 2019 00:06:07: 10000000 INFO @ Mon, 03 Jun 2019 00:06:07: 10000000 INFO @ Mon, 03 Jun 2019 00:06:10: 12000000 INFO @ Mon, 03 Jun 2019 00:06:18: 11000000 INFO @ Mon, 03 Jun 2019 00:06:18: 11000000 INFO @ Mon, 03 Jun 2019 00:06:20: 13000000 INFO @ Mon, 03 Jun 2019 00:06:29: 14000000 INFO @ Mon, 03 Jun 2019 00:06:29: 12000000 INFO @ Mon, 03 Jun 2019 00:06:30: 12000000 INFO @ Mon, 03 Jun 2019 00:06:39: 15000000 INFO @ Mon, 03 Jun 2019 00:06:41: 13000000 INFO @ Mon, 03 Jun 2019 00:06:41: 13000000 INFO @ Mon, 03 Jun 2019 00:06:49: 16000000 INFO @ Mon, 03 Jun 2019 00:06:52: 14000000 INFO @ Mon, 03 Jun 2019 00:06:52: 14000000 INFO @ Mon, 03 Jun 2019 00:06:59: 17000000 INFO @ Mon, 03 Jun 2019 00:07:04: 15000000 INFO @ Mon, 03 Jun 2019 00:07:04: 15000000 INFO @ Mon, 03 Jun 2019 00:07:09: 18000000 INFO @ Mon, 03 Jun 2019 00:07:15: 16000000 INFO @ Mon, 03 Jun 2019 00:07:15: 16000000 INFO @ Mon, 03 Jun 2019 00:07:19: 19000000 INFO @ Mon, 03 Jun 2019 00:07:27: 17000000 INFO @ Mon, 03 Jun 2019 00:07:27: 17000000 INFO @ Mon, 03 Jun 2019 00:07:28: 20000000 INFO @ Mon, 03 Jun 2019 00:07:38: 21000000 INFO @ Mon, 03 Jun 2019 00:07:38: 18000000 INFO @ Mon, 03 Jun 2019 00:07:39: 18000000 INFO @ Mon, 03 Jun 2019 00:07:48: 22000000 INFO @ Mon, 03 Jun 2019 00:07:50: 19000000 INFO @ Mon, 03 Jun 2019 00:07:50: 19000000 INFO @ Mon, 03 Jun 2019 00:07:58: 23000000 INFO @ Mon, 03 Jun 2019 00:08:02: 20000000 INFO @ Mon, 03 Jun 2019 00:08:02: 20000000 INFO @ Mon, 03 Jun 2019 00:08:08: 24000000 INFO @ Mon, 03 Jun 2019 00:08:13: 21000000 INFO @ Mon, 03 Jun 2019 00:08:14: 21000000 INFO @ Mon, 03 Jun 2019 00:08:18: 25000000 INFO @ Mon, 03 Jun 2019 00:08:25: 22000000 INFO @ Mon, 03 Jun 2019 00:08:25: 22000000 INFO @ Mon, 03 Jun 2019 00:08:28: 26000000 INFO @ Mon, 03 Jun 2019 00:08:37: 23000000 INFO @ Mon, 03 Jun 2019 00:08:37: 23000000 INFO @ Mon, 03 Jun 2019 00:08:38: 27000000 INFO @ Mon, 03 Jun 2019 00:08:47: 28000000 INFO @ Mon, 03 Jun 2019 00:08:48: 24000000 INFO @ Mon, 03 Jun 2019 00:08:49: 24000000 INFO @ Mon, 03 Jun 2019 00:08:54: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 00:08:54: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 00:08:54: #1 total tags in treatment: 13660954 INFO @ Mon, 03 Jun 2019 00:08:54: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 00:08:54: #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 00:08:54: #1 tags after filtering in treatment: 12962669 INFO @ Mon, 03 Jun 2019 00:08:54: #1 Redundant rate of treatment: 0.05 INFO @ Mon, 03 Jun 2019 00:08:54: #1 finished! INFO @ Mon, 03 Jun 2019 00:08:54: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 00:08:54: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 00:08:56: #2 number of paired peaks: 103 WARNING @ Mon, 03 Jun 2019 00:08:56: Fewer paired peaks (103) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 103 pairs to build model! INFO @ Mon, 03 Jun 2019 00:08:56: start model_add_line... INFO @ Mon, 03 Jun 2019 00:08:56: start X-correlation... INFO @ Mon, 03 Jun 2019 00:08:56: end of X-cor INFO @ Mon, 03 Jun 2019 00:08:56: #2 finished! INFO @ Mon, 03 Jun 2019 00:08:56: #2 predicted fragment length is 149 bps INFO @ Mon, 03 Jun 2019 00:08:56: #2 alternative fragment length(s) may be 139,149 bps INFO @ Mon, 03 Jun 2019 00:08:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX1818281/ERX1818281.20_model.r INFO @ Mon, 03 Jun 2019 00:08:56: #3 Call peaks... INFO @ Mon, 03 Jun 2019 00:08:56: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 00:09:00: 25000000 INFO @ Mon, 03 Jun 2019 00:09:00: 25000000 INFO @ Mon, 03 Jun 2019 00:09:11: 26000000 INFO @ Mon, 03 Jun 2019 00:09:11: 26000000 INFO @ Mon, 03 Jun 2019 00:09:22: 27000000 INFO @ Mon, 03 Jun 2019 00:09:23: 27000000 INFO @ Mon, 03 Jun 2019 00:09:31: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 00:09:33: 28000000 INFO @ Mon, 03 Jun 2019 00:09:34: 28000000 INFO @ Mon, 03 Jun 2019 00:09:41: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 00:09:41: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 00:09:41: #1 total tags in treatment: 13660954 INFO @ Mon, 03 Jun 2019 00:09:41: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 00:09:41: #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 00:09:42: #1 tags after filtering in treatment: 12962669 INFO @ Mon, 03 Jun 2019 00:09:42: #1 Redundant rate of treatment: 0.05 INFO @ Mon, 03 Jun 2019 00:09:42: #1 finished! INFO @ Mon, 03 Jun 2019 00:09:42: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 00:09:42: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 00:09:42: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 00:09:42: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 00:09:42: #1 total tags in treatment: 13660954 INFO @ Mon, 03 Jun 2019 00:09:42: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 00:09:42: #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 00:09:42: #1 tags after filtering in treatment: 12962669 INFO @ Mon, 03 Jun 2019 00:09:42: #1 Redundant rate of treatment: 0.05 INFO @ Mon, 03 Jun 2019 00:09:42: #1 finished! INFO @ Mon, 03 Jun 2019 00:09:42: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 00:09:42: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 00:09:43: #2 number of paired peaks: 103 WARNING @ Mon, 03 Jun 2019 00:09:43: Fewer paired peaks (103) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 103 pairs to build model! INFO @ Mon, 03 Jun 2019 00:09:43: start model_add_line... INFO @ Mon, 03 Jun 2019 00:09:43: start X-correlation... INFO @ Mon, 03 Jun 2019 00:09:43: end of X-cor INFO @ Mon, 03 Jun 2019 00:09:43: #2 finished! INFO @ Mon, 03 Jun 2019 00:09:43: #2 predicted fragment length is 149 bps INFO @ Mon, 03 Jun 2019 00:09:43: #2 alternative fragment length(s) may be 139,149 bps INFO @ Mon, 03 Jun 2019 00:09:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX1818281/ERX1818281.10_model.r INFO @ Mon, 03 Jun 2019 00:09:43: #3 Call peaks... INFO @ Mon, 03 Jun 2019 00:09:43: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 00:09:43: #2 number of paired peaks: 103 WARNING @ Mon, 03 Jun 2019 00:09:43: Fewer paired peaks (103) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 103 pairs to build model! INFO @ Mon, 03 Jun 2019 00:09:43: start model_add_line... INFO @ Mon, 03 Jun 2019 00:09:43: start X-correlation... INFO @ Mon, 03 Jun 2019 00:09:43: end of X-cor INFO @ Mon, 03 Jun 2019 00:09:43: #2 finished! INFO @ Mon, 03 Jun 2019 00:09:43: #2 predicted fragment length is 149 bps INFO @ Mon, 03 Jun 2019 00:09:43: #2 alternative fragment length(s) may be 139,149 bps INFO @ Mon, 03 Jun 2019 00:09:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX1818281/ERX1818281.05_model.r INFO @ Mon, 03 Jun 2019 00:09:43: #3 Call peaks... INFO @ Mon, 03 Jun 2019 00:09:43: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 00:09:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX1818281/ERX1818281.20_peaks.xls INFO @ Mon, 03 Jun 2019 00:09:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX1818281/ERX1818281.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 00:09:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX1818281/ERX1818281.20_summits.bed INFO @ Mon, 03 Jun 2019 00:09:48: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (424 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 00:10:18: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 00:10:19: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 00:10:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX1818281/ERX1818281.10_peaks.xls INFO @ Mon, 03 Jun 2019 00:10:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX1818281/ERX1818281.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 00:10:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX1818281/ERX1818281.10_summits.bed INFO @ Mon, 03 Jun 2019 00:10:35: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (812 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 00:10:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX1818281/ERX1818281.05_peaks.xls INFO @ Mon, 03 Jun 2019 00:10:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX1818281/ERX1818281.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 00:10:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX1818281/ERX1818281.05_summits.bed INFO @ Mon, 03 Jun 2019 00:10:36: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (1382 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。