Job ID = 2590849 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 21,996,208 reads read : 21,996,208 reads written : 21,996,208 rm: cannot remove ‘[DSE]RR*’: 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: 00:00:01 Multiseed full-index search: 00:09:31 21996208 reads; of these: 21996208 (100.00%) were unpaired; of these: 1737512 (7.90%) aligned 0 times 14473428 (65.80%) aligned exactly 1 time 5785268 (26.30%) aligned >1 times 92.10% overall alignment rate Time searching: 00:09:32 Overall time: 00:09:32 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] 5665702 / 20258696 = 0.2797 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, 12 Aug 2019 23:56:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011083/SRX5011083.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011083/SRX5011083.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011083/SRX5011083.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011083/SRX5011083.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, 12 Aug 2019 23:56:59: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:56:59: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:56:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011083/SRX5011083.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011083/SRX5011083.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011083/SRX5011083.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011083/SRX5011083.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, 12 Aug 2019 23:56:59: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:56:59: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:57:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011083/SRX5011083.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011083/SRX5011083.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011083/SRX5011083.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011083/SRX5011083.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, 12 Aug 2019 23:57:00: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:57:00: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:57:07: 1000000 INFO @ Mon, 12 Aug 2019 23:57:07: 1000000 INFO @ Mon, 12 Aug 2019 23:57:08: 1000000 INFO @ Mon, 12 Aug 2019 23:57:14: 2000000 INFO @ Mon, 12 Aug 2019 23:57:15: 2000000 INFO @ Mon, 12 Aug 2019 23:57:17: 2000000 INFO @ Mon, 12 Aug 2019 23:57:21: 3000000 INFO @ Mon, 12 Aug 2019 23:57:22: 3000000 INFO @ Mon, 12 Aug 2019 23:57:25: 3000000 INFO @ Mon, 12 Aug 2019 23:57:27: 4000000 INFO @ Mon, 12 Aug 2019 23:57:29: 4000000 INFO @ Mon, 12 Aug 2019 23:57:34: 4000000 INFO @ Mon, 12 Aug 2019 23:57:34: 5000000 INFO @ Mon, 12 Aug 2019 23:57:35: 5000000 INFO @ Mon, 12 Aug 2019 23:57:40: 6000000 INFO @ Mon, 12 Aug 2019 23:57:42: 5000000 INFO @ Mon, 12 Aug 2019 23:57:42: 6000000 INFO @ Mon, 12 Aug 2019 23:57:47: 7000000 INFO @ Mon, 12 Aug 2019 23:57:49: 7000000 INFO @ Mon, 12 Aug 2019 23:57:50: 6000000 INFO @ Mon, 12 Aug 2019 23:57:53: 8000000 INFO @ Mon, 12 Aug 2019 23:57:57: 8000000 INFO @ Mon, 12 Aug 2019 23:57:59: 7000000 INFO @ Mon, 12 Aug 2019 23:58:00: 9000000 INFO @ Mon, 12 Aug 2019 23:58:04: 9000000 INFO @ Mon, 12 Aug 2019 23:58:06: 10000000 INFO @ Mon, 12 Aug 2019 23:58:07: 8000000 INFO @ Mon, 12 Aug 2019 23:58:11: 10000000 INFO @ Mon, 12 Aug 2019 23:58:13: 11000000 INFO @ Mon, 12 Aug 2019 23:58:16: 9000000 INFO @ Mon, 12 Aug 2019 23:58:18: 11000000 INFO @ Mon, 12 Aug 2019 23:58:19: 12000000 INFO @ Mon, 12 Aug 2019 23:58:24: 10000000 INFO @ Mon, 12 Aug 2019 23:58:25: 12000000 INFO @ Mon, 12 Aug 2019 23:58:26: 13000000 INFO @ Mon, 12 Aug 2019 23:58:31: 13000000 INFO @ Mon, 12 Aug 2019 23:58:32: 14000000 INFO @ Mon, 12 Aug 2019 23:58:33: 11000000 INFO @ Mon, 12 Aug 2019 23:58:36: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:58:36: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:58:36: #1 total tags in treatment: 14592994 INFO @ Mon, 12 Aug 2019 23:58:36: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:58:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 23:58:36: #1 tags after filtering in treatment: 14592994 INFO @ Mon, 12 Aug 2019 23:58:36: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:58:36: #1 finished! INFO @ Mon, 12 Aug 2019 23:58:36: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:58:36: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:58:38: #2 number of paired peaks: 776 WARNING @ Mon, 12 Aug 2019 23:58:38: Fewer paired peaks (776) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 776 pairs to build model! INFO @ Mon, 12 Aug 2019 23:58:38: start model_add_line... INFO @ Mon, 12 Aug 2019 23:58:38: start X-correlation... INFO @ Mon, 12 Aug 2019 23:58:38: end of X-cor INFO @ Mon, 12 Aug 2019 23:58:38: #2 finished! INFO @ Mon, 12 Aug 2019 23:58:38: #2 predicted fragment length is 47 bps INFO @ Mon, 12 Aug 2019 23:58:38: #2 alternative fragment length(s) may be 47 bps INFO @ Mon, 12 Aug 2019 23:58:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011083/SRX5011083.20_model.r WARNING @ Mon, 12 Aug 2019 23:58:38: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 23:58:38: #2 You may need to consider one of the other alternative d(s): 47 WARNING @ Mon, 12 Aug 2019 23:58:38: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 23:58:38: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:58:38: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:58:38: 14000000 INFO @ Mon, 12 Aug 2019 23:58:41: 12000000 INFO @ Mon, 12 Aug 2019 23:58:43: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:58:43: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:58:43: #1 total tags in treatment: 14592994 INFO @ Mon, 12 Aug 2019 23:58:43: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:58:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 23:58:43: #1 tags after filtering in treatment: 14592994 INFO @ Mon, 12 Aug 2019 23:58:43: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:58:43: #1 finished! INFO @ Mon, 12 Aug 2019 23:58:43: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:58:43: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:58:44: #2 number of paired peaks: 776 WARNING @ Mon, 12 Aug 2019 23:58:44: Fewer paired peaks (776) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 776 pairs to build model! INFO @ Mon, 12 Aug 2019 23:58:44: start model_add_line... INFO @ Mon, 12 Aug 2019 23:58:44: start X-correlation... INFO @ Mon, 12 Aug 2019 23:58:44: end of X-cor INFO @ Mon, 12 Aug 2019 23:58:44: #2 finished! INFO @ Mon, 12 Aug 2019 23:58:44: #2 predicted fragment length is 47 bps INFO @ Mon, 12 Aug 2019 23:58:44: #2 alternative fragment length(s) may be 47 bps INFO @ Mon, 12 Aug 2019 23:58:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011083/SRX5011083.10_model.r WARNING @ Mon, 12 Aug 2019 23:58:44: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 23:58:44: #2 You may need to consider one of the other alternative d(s): 47 WARNING @ Mon, 12 Aug 2019 23:58:44: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 23:58:44: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:58:44: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:58:49: 13000000 INFO @ Mon, 12 Aug 2019 23:58:58: 14000000 INFO @ Mon, 12 Aug 2019 23:59:03: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:59:03: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:59:03: #1 total tags in treatment: 14592994 INFO @ Mon, 12 Aug 2019 23:59:03: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:59:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 23:59:03: #1 tags after filtering in treatment: 14592994 INFO @ Mon, 12 Aug 2019 23:59:03: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:59:03: #1 finished! INFO @ Mon, 12 Aug 2019 23:59:03: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:59:03: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:59:04: #2 number of paired peaks: 776 WARNING @ Mon, 12 Aug 2019 23:59:04: Fewer paired peaks (776) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 776 pairs to build model! INFO @ Mon, 12 Aug 2019 23:59:04: start model_add_line... INFO @ Mon, 12 Aug 2019 23:59:04: start X-correlation... INFO @ Mon, 12 Aug 2019 23:59:04: end of X-cor INFO @ Mon, 12 Aug 2019 23:59:04: #2 finished! INFO @ Mon, 12 Aug 2019 23:59:04: #2 predicted fragment length is 47 bps INFO @ Mon, 12 Aug 2019 23:59:04: #2 alternative fragment length(s) may be 47 bps INFO @ Mon, 12 Aug 2019 23:59:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011083/SRX5011083.05_model.r WARNING @ Mon, 12 Aug 2019 23:59:04: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 23:59:04: #2 You may need to consider one of the other alternative d(s): 47 WARNING @ Mon, 12 Aug 2019 23:59:04: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 23:59:04: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:59:04: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:59:16: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:59:23: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:59:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011083/SRX5011083.20_peaks.xls INFO @ Mon, 12 Aug 2019 23:59:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011083/SRX5011083.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:59:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011083/SRX5011083.20_summits.bed INFO @ Mon, 12 Aug 2019 23:59:35: Done! pass1 - making usageList (11 chroms): 2 millis pass2 - checking and writing primary data (2223 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:59:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011083/SRX5011083.10_peaks.xls INFO @ Mon, 12 Aug 2019 23:59:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011083/SRX5011083.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:59:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011083/SRX5011083.10_summits.bed INFO @ Mon, 12 Aug 2019 23:59:42: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (3241 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:59:44: #3 Call peaks for each chromosome... INFO @ Tue, 13 Aug 2019 00:00:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011083/SRX5011083.05_peaks.xls INFO @ Tue, 13 Aug 2019 00:00:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011083/SRX5011083.05_peaks.narrowPeak INFO @ Tue, 13 Aug 2019 00:00:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011083/SRX5011083.05_summits.bed INFO @ Tue, 13 Aug 2019 00:00:03: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (4818 records, 4 fields): 11 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。