Job ID = 1293866 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 20,608,002 reads read : 20,608,002 reads written : 20,608,002 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: 00:06:47 20608002 reads; of these: 20608002 (100.00%) were unpaired; of these: 823045 (3.99%) aligned 0 times 16615178 (80.62%) aligned exactly 1 time 3169779 (15.38%) aligned >1 times 96.01% overall alignment rate Time searching: 00:06:47 Overall time: 00:06:47 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_rmdupse_core] 2053821 / 19784957 = 0.1038 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 03:05:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1299944/SRX1299944.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1299944/SRX1299944.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1299944/SRX1299944.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1299944/SRX1299944.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 03:05:24: #1 read tag files... INFO @ Mon, 03 Jun 2019 03:05:24: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 03:05:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1299944/SRX1299944.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1299944/SRX1299944.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1299944/SRX1299944.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1299944/SRX1299944.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 03:05:24: #1 read tag files... INFO @ Mon, 03 Jun 2019 03:05:24: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 03:05:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1299944/SRX1299944.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1299944/SRX1299944.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1299944/SRX1299944.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1299944/SRX1299944.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 03:05:24: #1 read tag files... INFO @ Mon, 03 Jun 2019 03:05:24: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 03:05:32: 1000000 INFO @ Mon, 03 Jun 2019 03:05:33: 1000000 INFO @ Mon, 03 Jun 2019 03:05:33: 1000000 INFO @ Mon, 03 Jun 2019 03:05:39: 2000000 INFO @ Mon, 03 Jun 2019 03:05:42: 2000000 INFO @ Mon, 03 Jun 2019 03:05:42: 2000000 INFO @ Mon, 03 Jun 2019 03:05:47: 3000000 INFO @ Mon, 03 Jun 2019 03:05:50: 3000000 INFO @ Mon, 03 Jun 2019 03:05:50: 3000000 INFO @ Mon, 03 Jun 2019 03:05:55: 4000000 INFO @ Mon, 03 Jun 2019 03:05:59: 4000000 INFO @ Mon, 03 Jun 2019 03:05:59: 4000000 INFO @ Mon, 03 Jun 2019 03:06:02: 5000000 INFO @ Mon, 03 Jun 2019 03:06:07: 5000000 INFO @ Mon, 03 Jun 2019 03:06:07: 5000000 INFO @ Mon, 03 Jun 2019 03:06:10: 6000000 INFO @ Mon, 03 Jun 2019 03:06:16: 6000000 INFO @ Mon, 03 Jun 2019 03:06:16: 6000000 INFO @ Mon, 03 Jun 2019 03:06:17: 7000000 INFO @ Mon, 03 Jun 2019 03:06:24: 7000000 INFO @ Mon, 03 Jun 2019 03:06:24: 7000000 INFO @ Mon, 03 Jun 2019 03:06:25: 8000000 INFO @ Mon, 03 Jun 2019 03:06:32: 9000000 INFO @ Mon, 03 Jun 2019 03:06:32: 8000000 INFO @ Mon, 03 Jun 2019 03:06:33: 8000000 INFO @ Mon, 03 Jun 2019 03:06:40: 10000000 INFO @ Mon, 03 Jun 2019 03:06:41: 9000000 INFO @ Mon, 03 Jun 2019 03:06:41: 9000000 INFO @ Mon, 03 Jun 2019 03:06:47: 11000000 INFO @ Mon, 03 Jun 2019 03:06:49: 10000000 INFO @ Mon, 03 Jun 2019 03:06:50: 10000000 INFO @ Mon, 03 Jun 2019 03:06:55: 12000000 INFO @ Mon, 03 Jun 2019 03:06:58: 11000000 INFO @ Mon, 03 Jun 2019 03:06:58: 11000000 INFO @ Mon, 03 Jun 2019 03:07:02: 13000000 INFO @ Mon, 03 Jun 2019 03:07:06: 12000000 INFO @ Mon, 03 Jun 2019 03:07:07: 12000000 INFO @ Mon, 03 Jun 2019 03:07:10: 14000000 INFO @ Mon, 03 Jun 2019 03:07:14: 13000000 INFO @ Mon, 03 Jun 2019 03:07:16: 13000000 INFO @ Mon, 03 Jun 2019 03:07:18: 15000000 INFO @ Mon, 03 Jun 2019 03:07:23: 14000000 INFO @ Mon, 03 Jun 2019 03:07:25: 14000000 INFO @ Mon, 03 Jun 2019 03:07:26: 16000000 INFO @ Mon, 03 Jun 2019 03:07:32: 15000000 INFO @ Mon, 03 Jun 2019 03:07:34: 17000000 INFO @ Mon, 03 Jun 2019 03:07:35: 15000000 INFO @ Mon, 03 Jun 2019 03:07:39: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 03:07:39: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 03:07:39: #1 total tags in treatment: 17731136 INFO @ Mon, 03 Jun 2019 03:07:39: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 03:07:39: #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 03:07:40: #1 tags after filtering in treatment: 17731136 INFO @ Mon, 03 Jun 2019 03:07:40: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 03:07:40: #1 finished! INFO @ Mon, 03 Jun 2019 03:07:40: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 03:07:40: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 03:07:41: 16000000 INFO @ Mon, 03 Jun 2019 03:07:41: #2 number of paired peaks: 167 WARNING @ Mon, 03 Jun 2019 03:07:41: Fewer paired peaks (167) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 167 pairs to build model! INFO @ Mon, 03 Jun 2019 03:07:41: start model_add_line... INFO @ Mon, 03 Jun 2019 03:07:41: start X-correlation... INFO @ Mon, 03 Jun 2019 03:07:42: end of X-cor INFO @ Mon, 03 Jun 2019 03:07:42: #2 finished! INFO @ Mon, 03 Jun 2019 03:07:42: #2 predicted fragment length is 107 bps INFO @ Mon, 03 Jun 2019 03:07:42: #2 alternative fragment length(s) may be 4,83,107,598 bps INFO @ Mon, 03 Jun 2019 03:07:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1299944/SRX1299944.20_model.r INFO @ Mon, 03 Jun 2019 03:07:42: #3 Call peaks... INFO @ Mon, 03 Jun 2019 03:07:42: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 03:07:44: 16000000 INFO @ Mon, 03 Jun 2019 03:07:50: 17000000 INFO @ Mon, 03 Jun 2019 03:07:53: 17000000 INFO @ Mon, 03 Jun 2019 03:07:56: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 03:07:56: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 03:07:56: #1 total tags in treatment: 17731136 INFO @ Mon, 03 Jun 2019 03:07:56: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 03:07:56: #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 03:07:56: #1 tags after filtering in treatment: 17731136 INFO @ Mon, 03 Jun 2019 03:07:56: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 03:07:56: #1 finished! INFO @ Mon, 03 Jun 2019 03:07:56: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 03:07:56: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 03:07:58: #2 number of paired peaks: 167 WARNING @ Mon, 03 Jun 2019 03:07:58: Fewer paired peaks (167) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 167 pairs to build model! INFO @ Mon, 03 Jun 2019 03:07:58: start model_add_line... INFO @ Mon, 03 Jun 2019 03:07:58: start X-correlation... INFO @ Mon, 03 Jun 2019 03:07:58: end of X-cor INFO @ Mon, 03 Jun 2019 03:07:58: #2 finished! INFO @ Mon, 03 Jun 2019 03:07:58: #2 predicted fragment length is 107 bps INFO @ Mon, 03 Jun 2019 03:07:58: #2 alternative fragment length(s) may be 4,83,107,598 bps INFO @ Mon, 03 Jun 2019 03:07:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1299944/SRX1299944.10_model.r INFO @ Mon, 03 Jun 2019 03:07:58: #3 Call peaks... INFO @ Mon, 03 Jun 2019 03:07:58: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 03:07:59: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 03:07:59: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 03:07:59: #1 total tags in treatment: 17731136 INFO @ Mon, 03 Jun 2019 03:07:59: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 03:07:59: #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 03:08:00: #1 tags after filtering in treatment: 17731136 INFO @ Mon, 03 Jun 2019 03:08:00: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 03:08:00: #1 finished! INFO @ Mon, 03 Jun 2019 03:08:00: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 03:08:00: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 03:08:01: #2 number of paired peaks: 167 WARNING @ Mon, 03 Jun 2019 03:08:01: Fewer paired peaks (167) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 167 pairs to build model! INFO @ Mon, 03 Jun 2019 03:08:01: start model_add_line... INFO @ Mon, 03 Jun 2019 03:08:01: start X-correlation... INFO @ Mon, 03 Jun 2019 03:08:02: end of X-cor INFO @ Mon, 03 Jun 2019 03:08:02: #2 finished! INFO @ Mon, 03 Jun 2019 03:08:02: #2 predicted fragment length is 107 bps INFO @ Mon, 03 Jun 2019 03:08:02: #2 alternative fragment length(s) may be 4,83,107,598 bps INFO @ Mon, 03 Jun 2019 03:08:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1299944/SRX1299944.05_model.r INFO @ Mon, 03 Jun 2019 03:08:02: #3 Call peaks... INFO @ Mon, 03 Jun 2019 03:08:02: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 03:08:30: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 03:08:46: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 03:08:50: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 03:08:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1299944/SRX1299944.20_peaks.xls INFO @ Mon, 03 Jun 2019 03:08:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1299944/SRX1299944.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 03:08:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1299944/SRX1299944.20_summits.bed INFO @ Mon, 03 Jun 2019 03:08:53: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (364 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 03:09:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1299944/SRX1299944.10_peaks.xls INFO @ Mon, 03 Jun 2019 03:09:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1299944/SRX1299944.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 03:09:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1299944/SRX1299944.10_summits.bed INFO @ Mon, 03 Jun 2019 03:09:10: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (1443 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 03:09:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1299944/SRX1299944.05_peaks.xls INFO @ Mon, 03 Jun 2019 03:09:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1299944/SRX1299944.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 03:09:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1299944/SRX1299944.05_summits.bed INFO @ Mon, 03 Jun 2019 03:09:14: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (4562 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。