Job ID = 1299731 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 19,414,246 reads read : 38,828,492 reads written : 38,828,492 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: 00:58:33 19414246 reads; of these: 19414246 (100.00%) were paired; of these: 2533996 (13.05%) aligned concordantly 0 times 11058126 (56.96%) aligned concordantly exactly 1 time 5822124 (29.99%) aligned concordantly >1 times ---- 2533996 pairs aligned concordantly 0 times; of these: 114716 (4.53%) aligned discordantly 1 time ---- 2419280 pairs aligned 0 times concordantly or discordantly; of these: 4838560 mates make up the pairs; of these: 4231054 (87.44%) aligned 0 times 383127 (7.92%) aligned exactly 1 time 224379 (4.64%) aligned >1 times 89.10% overall alignment rate Time searching: 00:58:33 Overall time: 00:58:33 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] 2425697 / 16959845 = 0.1430 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 19:54:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX474603/SRX474603.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX474603/SRX474603.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX474603/SRX474603.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX474603/SRX474603.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 19:54:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX474603/SRX474603.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX474603/SRX474603.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX474603/SRX474603.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX474603/SRX474603.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 19:54:41: #1 read tag files... INFO @ Mon, 03 Jun 2019 19:54:41: #1 read tag files... INFO @ Mon, 03 Jun 2019 19:54:41: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 19:54:41: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 19:54:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX474603/SRX474603.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX474603/SRX474603.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX474603/SRX474603.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX474603/SRX474603.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 19:54:41: #1 read tag files... INFO @ Mon, 03 Jun 2019 19:54:41: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 19:54:49: 1000000 INFO @ Mon, 03 Jun 2019 19:54:50: 1000000 INFO @ Mon, 03 Jun 2019 19:54:52: 1000000 INFO @ Mon, 03 Jun 2019 19:54:56: 2000000 INFO @ Mon, 03 Jun 2019 19:54:58: 2000000 INFO @ Mon, 03 Jun 2019 19:55:02: 2000000 INFO @ Mon, 03 Jun 2019 19:55:04: 3000000 INFO @ Mon, 03 Jun 2019 19:55:07: 3000000 INFO @ Mon, 03 Jun 2019 19:55:11: 4000000 INFO @ Mon, 03 Jun 2019 19:55:13: 3000000 INFO @ Mon, 03 Jun 2019 19:55:16: 4000000 INFO @ Mon, 03 Jun 2019 19:55:19: 5000000 INFO @ Mon, 03 Jun 2019 19:55:23: 4000000 INFO @ Mon, 03 Jun 2019 19:55:24: 5000000 INFO @ Mon, 03 Jun 2019 19:55:26: 6000000 INFO @ Mon, 03 Jun 2019 19:55:33: 6000000 INFO @ Mon, 03 Jun 2019 19:55:34: 7000000 INFO @ Mon, 03 Jun 2019 19:55:34: 5000000 INFO @ Mon, 03 Jun 2019 19:55:41: 8000000 INFO @ Mon, 03 Jun 2019 19:55:43: 7000000 INFO @ Mon, 03 Jun 2019 19:55:44: 6000000 INFO @ Mon, 03 Jun 2019 19:55:49: 9000000 INFO @ Mon, 03 Jun 2019 19:55:52: 8000000 INFO @ Mon, 03 Jun 2019 19:55:55: 7000000 INFO @ Mon, 03 Jun 2019 19:55:56: 10000000 INFO @ Mon, 03 Jun 2019 19:56:00: 9000000 INFO @ Mon, 03 Jun 2019 19:56:03: 11000000 INFO @ Mon, 03 Jun 2019 19:56:05: 8000000 INFO @ Mon, 03 Jun 2019 19:56:08: 10000000 INFO @ Mon, 03 Jun 2019 19:56:11: 12000000 INFO @ Mon, 03 Jun 2019 19:56:16: 9000000 INFO @ Mon, 03 Jun 2019 19:56:17: 11000000 INFO @ Mon, 03 Jun 2019 19:56:18: 13000000 INFO @ Mon, 03 Jun 2019 19:56:25: 12000000 INFO @ Mon, 03 Jun 2019 19:56:26: 14000000 INFO @ Mon, 03 Jun 2019 19:56:26: 10000000 INFO @ Mon, 03 Jun 2019 19:56:33: 15000000 INFO @ Mon, 03 Jun 2019 19:56:34: 13000000 INFO @ Mon, 03 Jun 2019 19:56:37: 11000000 INFO @ Mon, 03 Jun 2019 19:56:41: 16000000 INFO @ Mon, 03 Jun 2019 19:56:44: 14000000 INFO @ Mon, 03 Jun 2019 19:56:48: 12000000 INFO @ Mon, 03 Jun 2019 19:56:50: 17000000 INFO @ Mon, 03 Jun 2019 19:56:54: 15000000 INFO @ Mon, 03 Jun 2019 19:56:58: 18000000 INFO @ Mon, 03 Jun 2019 19:56:58: 13000000 INFO @ Mon, 03 Jun 2019 19:57:02: 16000000 INFO @ Mon, 03 Jun 2019 19:57:05: 19000000 INFO @ Mon, 03 Jun 2019 19:57:08: 14000000 INFO @ Mon, 03 Jun 2019 19:57:11: 17000000 INFO @ Mon, 03 Jun 2019 19:57:12: 20000000 INFO @ Mon, 03 Jun 2019 19:57:19: 18000000 INFO @ Mon, 03 Jun 2019 19:57:19: 15000000 INFO @ Mon, 03 Jun 2019 19:57:20: 21000000 INFO @ Mon, 03 Jun 2019 19:57:29: 19000000 INFO @ Mon, 03 Jun 2019 19:57:29: 22000000 INFO @ Mon, 03 Jun 2019 19:57:31: 16000000 INFO @ Mon, 03 Jun 2019 19:57:36: 23000000 INFO @ Mon, 03 Jun 2019 19:57:37: 20000000 INFO @ Mon, 03 Jun 2019 19:57:42: 17000000 INFO @ Mon, 03 Jun 2019 19:57:43: 24000000 INFO @ Mon, 03 Jun 2019 19:57:46: 21000000 INFO @ Mon, 03 Jun 2019 19:57:51: 25000000 INFO @ Mon, 03 Jun 2019 19:57:53: 18000000 INFO @ Mon, 03 Jun 2019 19:57:55: 22000000 INFO @ Mon, 03 Jun 2019 19:57:59: 26000000 INFO @ Mon, 03 Jun 2019 19:58:03: 19000000 INFO @ Mon, 03 Jun 2019 19:58:04: 23000000 INFO @ Mon, 03 Jun 2019 19:58:08: 27000000 INFO @ Mon, 03 Jun 2019 19:58:13: 24000000 INFO @ Mon, 03 Jun 2019 19:58:14: 20000000 INFO @ Mon, 03 Jun 2019 19:58:15: 28000000 INFO @ Mon, 03 Jun 2019 19:58:22: 25000000 INFO @ Mon, 03 Jun 2019 19:58:22: 29000000 INFO @ Mon, 03 Jun 2019 19:58:24: 21000000 INFO @ Mon, 03 Jun 2019 19:58:28: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 19:58:28: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 19:58:28: #1 total tags in treatment: 14460407 INFO @ Mon, 03 Jun 2019 19:58:28: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 19:58:28: #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 19:58:28: #1 tags after filtering in treatment: 13345987 INFO @ Mon, 03 Jun 2019 19:58:28: #1 Redundant rate of treatment: 0.08 INFO @ Mon, 03 Jun 2019 19:58:28: #1 finished! INFO @ Mon, 03 Jun 2019 19:58:28: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 19:58:28: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 19:58:29: #2 number of paired peaks: 356 WARNING @ Mon, 03 Jun 2019 19:58:29: Fewer paired peaks (356) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 356 pairs to build model! INFO @ Mon, 03 Jun 2019 19:58:29: start model_add_line... INFO @ Mon, 03 Jun 2019 19:58:29: start X-correlation... INFO @ Mon, 03 Jun 2019 19:58:30: end of X-cor INFO @ Mon, 03 Jun 2019 19:58:30: #2 finished! INFO @ Mon, 03 Jun 2019 19:58:30: #2 predicted fragment length is 101 bps INFO @ Mon, 03 Jun 2019 19:58:30: #2 alternative fragment length(s) may be 101 bps INFO @ Mon, 03 Jun 2019 19:58:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX474603/SRX474603.20_model.r INFO @ Mon, 03 Jun 2019 19:58:30: #3 Call peaks... INFO @ Mon, 03 Jun 2019 19:58:30: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 19:58:30: 26000000 INFO @ Mon, 03 Jun 2019 19:58:35: 22000000 INFO @ Mon, 03 Jun 2019 19:58:39: 27000000 INFO @ Mon, 03 Jun 2019 19:58:45: 23000000 INFO @ Mon, 03 Jun 2019 19:58:47: 28000000 INFO @ Mon, 03 Jun 2019 19:58:55: 24000000 INFO @ Mon, 03 Jun 2019 19:58:55: 29000000 INFO @ Mon, 03 Jun 2019 19:59:01: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 19:59:01: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 19:59:01: #1 total tags in treatment: 14460407 INFO @ Mon, 03 Jun 2019 19:59:01: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 19:59:01: #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 19:59:02: #1 tags after filtering in treatment: 13345987 INFO @ Mon, 03 Jun 2019 19:59:02: #1 Redundant rate of treatment: 0.08 INFO @ Mon, 03 Jun 2019 19:59:02: #1 finished! INFO @ Mon, 03 Jun 2019 19:59:02: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 19:59:02: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 19:59:03: #2 number of paired peaks: 356 WARNING @ Mon, 03 Jun 2019 19:59:03: Fewer paired peaks (356) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 356 pairs to build model! INFO @ Mon, 03 Jun 2019 19:59:03: start model_add_line... INFO @ Mon, 03 Jun 2019 19:59:03: start X-correlation... INFO @ Mon, 03 Jun 2019 19:59:03: end of X-cor INFO @ Mon, 03 Jun 2019 19:59:03: #2 finished! INFO @ Mon, 03 Jun 2019 19:59:03: #2 predicted fragment length is 101 bps INFO @ Mon, 03 Jun 2019 19:59:03: #2 alternative fragment length(s) may be 101 bps INFO @ Mon, 03 Jun 2019 19:59:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX474603/SRX474603.10_model.r INFO @ Mon, 03 Jun 2019 19:59:03: #3 Call peaks... INFO @ Mon, 03 Jun 2019 19:59:03: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 19:59:05: 25000000 INFO @ Mon, 03 Jun 2019 19:59:06: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 19:59:15: 26000000 INFO @ Mon, 03 Jun 2019 19:59:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX474603/SRX474603.20_peaks.xls INFO @ Mon, 03 Jun 2019 19:59:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX474603/SRX474603.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 19:59:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX474603/SRX474603.20_summits.bed INFO @ Mon, 03 Jun 2019 19:59:25: Done! INFO @ Mon, 03 Jun 2019 19:59:25: 27000000 pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (831 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 19:59:35: 28000000 INFO @ Mon, 03 Jun 2019 19:59:40: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 19:59:44: 29000000 INFO @ Mon, 03 Jun 2019 19:59:51: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 19:59:51: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 19:59:51: #1 total tags in treatment: 14460407 INFO @ Mon, 03 Jun 2019 19:59:51: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 19:59:51: #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 19:59:51: #1 tags after filtering in treatment: 13345987 INFO @ Mon, 03 Jun 2019 19:59:51: #1 Redundant rate of treatment: 0.08 INFO @ Mon, 03 Jun 2019 19:59:51: #1 finished! INFO @ Mon, 03 Jun 2019 19:59:51: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 19:59:51: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 19:59:52: #2 number of paired peaks: 356 WARNING @ Mon, 03 Jun 2019 19:59:52: Fewer paired peaks (356) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 356 pairs to build model! INFO @ Mon, 03 Jun 2019 19:59:52: start model_add_line... INFO @ Mon, 03 Jun 2019 19:59:52: start X-correlation... INFO @ Mon, 03 Jun 2019 19:59:52: end of X-cor INFO @ Mon, 03 Jun 2019 19:59:52: #2 finished! INFO @ Mon, 03 Jun 2019 19:59:52: #2 predicted fragment length is 101 bps INFO @ Mon, 03 Jun 2019 19:59:52: #2 alternative fragment length(s) may be 101 bps INFO @ Mon, 03 Jun 2019 19:59:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX474603/SRX474603.05_model.r INFO @ Mon, 03 Jun 2019 19:59:52: #3 Call peaks... INFO @ Mon, 03 Jun 2019 19:59:52: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 19:59:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX474603/SRX474603.10_peaks.xls INFO @ Mon, 03 Jun 2019 19:59:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX474603/SRX474603.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 19:59:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX474603/SRX474603.10_summits.bed INFO @ Mon, 03 Jun 2019 19:59:59: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1172 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 20:00:29: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 20:00:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX474603/SRX474603.05_peaks.xls INFO @ Mon, 03 Jun 2019 20:00:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX474603/SRX474603.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 20:00:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX474603/SRX474603.05_summits.bed INFO @ Mon, 03 Jun 2019 20:00:48: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (1783 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。