Job ID = 1294994 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 27,426,198 reads read : 54,852,396 reads written : 54,852,396 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: 00:46:07 27426198 reads; of these: 27426198 (100.00%) were paired; of these: 1810239 (6.60%) aligned concordantly 0 times 19223826 (70.09%) aligned concordantly exactly 1 time 6392133 (23.31%) aligned concordantly >1 times ---- 1810239 pairs aligned concordantly 0 times; of these: 99397 (5.49%) aligned discordantly 1 time ---- 1710842 pairs aligned 0 times concordantly or discordantly; of these: 3421684 mates make up the pairs; of these: 2579979 (75.40%) aligned 0 times 562123 (16.43%) aligned exactly 1 time 279582 (8.17%) aligned >1 times 95.30% overall alignment rate Time searching: 00:46:07 Overall time: 00:46:07 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] 10726249 / 25645185 = 0.4183 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 12:17:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX300929/SRX300929.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX300929/SRX300929.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX300929/SRX300929.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX300929/SRX300929.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 12:17:36: #1 read tag files... INFO @ Mon, 03 Jun 2019 12:17:36: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 12:17:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX300929/SRX300929.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX300929/SRX300929.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX300929/SRX300929.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX300929/SRX300929.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 12:17:36: #1 read tag files... INFO @ Mon, 03 Jun 2019 12:17:36: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 12:17:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX300929/SRX300929.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX300929/SRX300929.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX300929/SRX300929.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX300929/SRX300929.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 12:17:36: #1 read tag files... INFO @ Mon, 03 Jun 2019 12:17:36: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 12:17:43: 1000000 INFO @ Mon, 03 Jun 2019 12:17:46: 1000000 INFO @ Mon, 03 Jun 2019 12:17:46: 1000000 INFO @ Mon, 03 Jun 2019 12:17:50: 2000000 INFO @ Mon, 03 Jun 2019 12:17:55: 2000000 INFO @ Mon, 03 Jun 2019 12:17:55: 2000000 INFO @ Mon, 03 Jun 2019 12:17:57: 3000000 INFO @ Mon, 03 Jun 2019 12:18:04: 4000000 INFO @ Mon, 03 Jun 2019 12:18:05: 3000000 INFO @ Mon, 03 Jun 2019 12:18:05: 3000000 INFO @ Mon, 03 Jun 2019 12:18:11: 5000000 INFO @ Mon, 03 Jun 2019 12:18:14: 4000000 INFO @ Mon, 03 Jun 2019 12:18:14: 4000000 INFO @ Mon, 03 Jun 2019 12:18:18: 6000000 INFO @ Mon, 03 Jun 2019 12:18:23: 5000000 INFO @ Mon, 03 Jun 2019 12:18:23: 5000000 INFO @ Mon, 03 Jun 2019 12:18:24: 7000000 INFO @ Mon, 03 Jun 2019 12:18:31: 8000000 INFO @ Mon, 03 Jun 2019 12:18:32: 6000000 INFO @ Mon, 03 Jun 2019 12:18:32: 6000000 INFO @ Mon, 03 Jun 2019 12:18:38: 9000000 INFO @ Mon, 03 Jun 2019 12:18:41: 7000000 INFO @ Mon, 03 Jun 2019 12:18:41: 7000000 INFO @ Mon, 03 Jun 2019 12:18:45: 10000000 INFO @ Mon, 03 Jun 2019 12:18:50: 8000000 INFO @ Mon, 03 Jun 2019 12:18:50: 8000000 INFO @ Mon, 03 Jun 2019 12:18:51: 11000000 INFO @ Mon, 03 Jun 2019 12:18:58: 12000000 INFO @ Mon, 03 Jun 2019 12:18:59: 9000000 INFO @ Mon, 03 Jun 2019 12:18:59: 9000000 INFO @ Mon, 03 Jun 2019 12:19:05: 13000000 INFO @ Mon, 03 Jun 2019 12:19:08: 10000000 INFO @ Mon, 03 Jun 2019 12:19:08: 10000000 INFO @ Mon, 03 Jun 2019 12:19:11: 14000000 INFO @ Mon, 03 Jun 2019 12:19:16: 11000000 INFO @ Mon, 03 Jun 2019 12:19:16: 11000000 INFO @ Mon, 03 Jun 2019 12:19:18: 15000000 INFO @ Mon, 03 Jun 2019 12:19:24: 16000000 INFO @ Mon, 03 Jun 2019 12:19:25: 12000000 INFO @ Mon, 03 Jun 2019 12:19:25: 12000000 INFO @ Mon, 03 Jun 2019 12:19:31: 17000000 INFO @ Mon, 03 Jun 2019 12:19:33: 13000000 INFO @ Mon, 03 Jun 2019 12:19:34: 13000000 INFO @ Mon, 03 Jun 2019 12:19:38: 18000000 INFO @ Mon, 03 Jun 2019 12:19:42: 14000000 INFO @ Mon, 03 Jun 2019 12:19:42: 14000000 INFO @ Mon, 03 Jun 2019 12:19:44: 19000000 INFO @ Mon, 03 Jun 2019 12:19:50: 15000000 INFO @ Mon, 03 Jun 2019 12:19:51: 20000000 INFO @ Mon, 03 Jun 2019 12:19:51: 15000000 INFO @ Mon, 03 Jun 2019 12:19:57: 21000000 INFO @ Mon, 03 Jun 2019 12:19:59: 16000000 INFO @ Mon, 03 Jun 2019 12:19:59: 16000000 INFO @ Mon, 03 Jun 2019 12:20:04: 22000000 INFO @ Mon, 03 Jun 2019 12:20:07: 17000000 INFO @ Mon, 03 Jun 2019 12:20:08: 17000000 INFO @ Mon, 03 Jun 2019 12:20:11: 23000000 INFO @ Mon, 03 Jun 2019 12:20:16: 18000000 INFO @ Mon, 03 Jun 2019 12:20:17: 18000000 INFO @ Mon, 03 Jun 2019 12:20:18: 24000000 INFO @ Mon, 03 Jun 2019 12:20:24: 19000000 INFO @ Mon, 03 Jun 2019 12:20:24: 25000000 INFO @ Mon, 03 Jun 2019 12:20:25: 19000000 INFO @ Mon, 03 Jun 2019 12:20:31: 26000000 INFO @ Mon, 03 Jun 2019 12:20:33: 20000000 INFO @ Mon, 03 Jun 2019 12:20:34: 20000000 INFO @ Mon, 03 Jun 2019 12:20:38: 27000000 INFO @ Mon, 03 Jun 2019 12:20:41: 21000000 INFO @ Mon, 03 Jun 2019 12:20:42: 21000000 INFO @ Mon, 03 Jun 2019 12:20:45: 28000000 INFO @ Mon, 03 Jun 2019 12:20:50: 22000000 INFO @ Mon, 03 Jun 2019 12:20:51: 22000000 INFO @ Mon, 03 Jun 2019 12:20:51: 29000000 INFO @ Mon, 03 Jun 2019 12:20:58: 30000000 INFO @ Mon, 03 Jun 2019 12:20:58: 23000000 INFO @ Mon, 03 Jun 2019 12:20:59: 23000000 INFO @ Mon, 03 Jun 2019 12:21:03: #1 tag size is determined as 24 bps INFO @ Mon, 03 Jun 2019 12:21:03: #1 tag size = 24 INFO @ Mon, 03 Jun 2019 12:21:03: #1 total tags in treatment: 14900229 INFO @ Mon, 03 Jun 2019 12:21:03: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 12:21:03: #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 12:21:04: #1 tags after filtering in treatment: 11311344 INFO @ Mon, 03 Jun 2019 12:21:04: #1 Redundant rate of treatment: 0.24 INFO @ Mon, 03 Jun 2019 12:21:04: #1 finished! INFO @ Mon, 03 Jun 2019 12:21:04: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 12:21:04: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 12:21:05: #2 number of paired peaks: 579 WARNING @ Mon, 03 Jun 2019 12:21:05: Fewer paired peaks (579) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 579 pairs to build model! INFO @ Mon, 03 Jun 2019 12:21:05: start model_add_line... INFO @ Mon, 03 Jun 2019 12:21:05: start X-correlation... INFO @ Mon, 03 Jun 2019 12:21:05: end of X-cor INFO @ Mon, 03 Jun 2019 12:21:05: #2 finished! INFO @ Mon, 03 Jun 2019 12:21:05: #2 predicted fragment length is 82 bps INFO @ Mon, 03 Jun 2019 12:21:05: #2 alternative fragment length(s) may be 4,82 bps INFO @ Mon, 03 Jun 2019 12:21:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX300929/SRX300929.05_model.r INFO @ Mon, 03 Jun 2019 12:21:05: #3 Call peaks... INFO @ Mon, 03 Jun 2019 12:21:05: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 12:21:07: 24000000 INFO @ Mon, 03 Jun 2019 12:21:08: 24000000 INFO @ Mon, 03 Jun 2019 12:21:15: 25000000 INFO @ Mon, 03 Jun 2019 12:21:16: 25000000 INFO @ Mon, 03 Jun 2019 12:21:23: 26000000 INFO @ Mon, 03 Jun 2019 12:21:25: 26000000 INFO @ Mon, 03 Jun 2019 12:21:32: 27000000 INFO @ Mon, 03 Jun 2019 12:21:34: 27000000 INFO @ Mon, 03 Jun 2019 12:21:37: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 12:21:41: 28000000 INFO @ Mon, 03 Jun 2019 12:21:42: 28000000 INFO @ Mon, 03 Jun 2019 12:21:49: 29000000 INFO @ Mon, 03 Jun 2019 12:21:51: 29000000 INFO @ Mon, 03 Jun 2019 12:21:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX300929/SRX300929.05_peaks.xls INFO @ Mon, 03 Jun 2019 12:21:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX300929/SRX300929.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 12:21:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX300929/SRX300929.05_summits.bed INFO @ Mon, 03 Jun 2019 12:21:53: Done! pass1 - making usageList (14 chroms): 4 millis pass2 - checking and writing primary data (5201 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 12:21:57: 30000000 INFO @ Mon, 03 Jun 2019 12:21:59: 30000000 INFO @ Mon, 03 Jun 2019 12:22:04: #1 tag size is determined as 24 bps INFO @ Mon, 03 Jun 2019 12:22:04: #1 tag size = 24 INFO @ Mon, 03 Jun 2019 12:22:04: #1 total tags in treatment: 14900229 INFO @ Mon, 03 Jun 2019 12:22:04: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 12:22:04: #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 12:22:05: #1 tags after filtering in treatment: 11311344 INFO @ Mon, 03 Jun 2019 12:22:05: #1 Redundant rate of treatment: 0.24 INFO @ Mon, 03 Jun 2019 12:22:05: #1 finished! INFO @ Mon, 03 Jun 2019 12:22:05: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 12:22:05: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 12:22:06: #2 number of paired peaks: 579 WARNING @ Mon, 03 Jun 2019 12:22:06: Fewer paired peaks (579) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 579 pairs to build model! INFO @ Mon, 03 Jun 2019 12:22:06: start model_add_line... INFO @ Mon, 03 Jun 2019 12:22:06: start X-correlation... INFO @ Mon, 03 Jun 2019 12:22:06: end of X-cor INFO @ Mon, 03 Jun 2019 12:22:06: #2 finished! INFO @ Mon, 03 Jun 2019 12:22:06: #2 predicted fragment length is 82 bps INFO @ Mon, 03 Jun 2019 12:22:06: #2 alternative fragment length(s) may be 4,82 bps INFO @ Mon, 03 Jun 2019 12:22:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX300929/SRX300929.10_model.r INFO @ Mon, 03 Jun 2019 12:22:06: #3 Call peaks... INFO @ Mon, 03 Jun 2019 12:22:06: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 12:22:06: #1 tag size is determined as 24 bps INFO @ Mon, 03 Jun 2019 12:22:06: #1 tag size = 24 INFO @ Mon, 03 Jun 2019 12:22:06: #1 total tags in treatment: 14900229 INFO @ Mon, 03 Jun 2019 12:22:06: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 12:22:06: #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 12:22:07: #1 tags after filtering in treatment: 11311344 INFO @ Mon, 03 Jun 2019 12:22:07: #1 Redundant rate of treatment: 0.24 INFO @ Mon, 03 Jun 2019 12:22:07: #1 finished! INFO @ Mon, 03 Jun 2019 12:22:07: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 12:22:07: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 12:22:08: #2 number of paired peaks: 579 WARNING @ Mon, 03 Jun 2019 12:22:08: Fewer paired peaks (579) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 579 pairs to build model! INFO @ Mon, 03 Jun 2019 12:22:08: start model_add_line... INFO @ Mon, 03 Jun 2019 12:22:08: start X-correlation... INFO @ Mon, 03 Jun 2019 12:22:08: end of X-cor INFO @ Mon, 03 Jun 2019 12:22:08: #2 finished! INFO @ Mon, 03 Jun 2019 12:22:08: #2 predicted fragment length is 82 bps INFO @ Mon, 03 Jun 2019 12:22:08: #2 alternative fragment length(s) may be 4,82 bps INFO @ Mon, 03 Jun 2019 12:22:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX300929/SRX300929.20_model.r INFO @ Mon, 03 Jun 2019 12:22:08: #3 Call peaks... INFO @ Mon, 03 Jun 2019 12:22:08: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 12:22:39: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 12:22:40: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 12:22:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX300929/SRX300929.10_peaks.xls INFO @ Mon, 03 Jun 2019 12:22:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX300929/SRX300929.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 12:22:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX300929/SRX300929.10_summits.bed INFO @ Mon, 03 Jun 2019 12:22:57: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (2402 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 12:22:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX300929/SRX300929.20_peaks.xls INFO @ Mon, 03 Jun 2019 12:22:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX300929/SRX300929.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 12:22:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX300929/SRX300929.20_summits.bed INFO @ Mon, 03 Jun 2019 12:22:58: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (601 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。