Job ID = 1295029 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 29,203,399 reads read : 29,203,399 reads written : 29,203,399 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: 00:11:33 29203399 reads; of these: 29203399 (100.00%) were unpaired; of these: 1571128 (5.38%) aligned 0 times 20237100 (69.30%) aligned exactly 1 time 7395171 (25.32%) aligned >1 times 94.62% overall alignment rate Time searching: 00:11:33 Overall time: 00:11:33 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 12 files... [bam_rmdupse_core] 3008889 / 27632271 = 0.1089 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 11:53:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX306196/SRX306196.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX306196/SRX306196.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX306196/SRX306196.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX306196/SRX306196.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 11:53:04: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:53:04: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:53:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX306196/SRX306196.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX306196/SRX306196.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX306196/SRX306196.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX306196/SRX306196.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 11:53:04: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:53:04: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:53:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX306196/SRX306196.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX306196/SRX306196.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX306196/SRX306196.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX306196/SRX306196.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 11:53:04: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:53:04: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:53:12: 1000000 INFO @ Mon, 03 Jun 2019 11:53:13: 1000000 INFO @ Mon, 03 Jun 2019 11:53:14: 1000000 INFO @ Mon, 03 Jun 2019 11:53:20: 2000000 INFO @ Mon, 03 Jun 2019 11:53:20: 2000000 INFO @ Mon, 03 Jun 2019 11:53:23: 2000000 INFO @ Mon, 03 Jun 2019 11:53:28: 3000000 INFO @ Mon, 03 Jun 2019 11:53:28: 3000000 INFO @ Mon, 03 Jun 2019 11:53:31: 3000000 INFO @ Mon, 03 Jun 2019 11:53:36: 4000000 INFO @ Mon, 03 Jun 2019 11:53:36: 4000000 INFO @ Mon, 03 Jun 2019 11:53:40: 4000000 INFO @ Mon, 03 Jun 2019 11:53:44: 5000000 INFO @ Mon, 03 Jun 2019 11:53:44: 5000000 INFO @ Mon, 03 Jun 2019 11:53:49: 5000000 INFO @ Mon, 03 Jun 2019 11:53:52: 6000000 INFO @ Mon, 03 Jun 2019 11:53:52: 6000000 INFO @ Mon, 03 Jun 2019 11:53:57: 6000000 INFO @ Mon, 03 Jun 2019 11:54:00: 7000000 INFO @ Mon, 03 Jun 2019 11:54:00: 7000000 INFO @ Mon, 03 Jun 2019 11:54:06: 7000000 INFO @ Mon, 03 Jun 2019 11:54:08: 8000000 INFO @ Mon, 03 Jun 2019 11:54:08: 8000000 INFO @ Mon, 03 Jun 2019 11:54:15: 8000000 INFO @ Mon, 03 Jun 2019 11:54:16: 9000000 INFO @ Mon, 03 Jun 2019 11:54:16: 9000000 INFO @ Mon, 03 Jun 2019 11:54:24: 9000000 INFO @ Mon, 03 Jun 2019 11:54:24: 10000000 INFO @ Mon, 03 Jun 2019 11:54:24: 10000000 INFO @ Mon, 03 Jun 2019 11:54:32: 11000000 INFO @ Mon, 03 Jun 2019 11:54:32: 11000000 INFO @ Mon, 03 Jun 2019 11:54:33: 10000000 INFO @ Mon, 03 Jun 2019 11:54:40: 12000000 INFO @ Mon, 03 Jun 2019 11:54:40: 12000000 INFO @ Mon, 03 Jun 2019 11:54:42: 11000000 INFO @ Mon, 03 Jun 2019 11:54:48: 13000000 INFO @ Mon, 03 Jun 2019 11:54:48: 13000000 INFO @ Mon, 03 Jun 2019 11:54:51: 12000000 INFO @ Mon, 03 Jun 2019 11:54:56: 14000000 INFO @ Mon, 03 Jun 2019 11:54:56: 14000000 INFO @ Mon, 03 Jun 2019 11:55:00: 13000000 INFO @ Mon, 03 Jun 2019 11:55:04: 15000000 INFO @ Mon, 03 Jun 2019 11:55:04: 15000000 INFO @ Mon, 03 Jun 2019 11:55:09: 14000000 INFO @ Mon, 03 Jun 2019 11:55:12: 16000000 INFO @ Mon, 03 Jun 2019 11:55:12: 16000000 INFO @ Mon, 03 Jun 2019 11:55:18: 15000000 INFO @ Mon, 03 Jun 2019 11:55:20: 17000000 INFO @ Mon, 03 Jun 2019 11:55:20: 17000000 INFO @ Mon, 03 Jun 2019 11:55:27: 16000000 INFO @ Mon, 03 Jun 2019 11:55:28: 18000000 INFO @ Mon, 03 Jun 2019 11:55:28: 18000000 INFO @ Mon, 03 Jun 2019 11:55:35: 19000000 INFO @ Mon, 03 Jun 2019 11:55:36: 19000000 INFO @ Mon, 03 Jun 2019 11:55:36: 17000000 INFO @ Mon, 03 Jun 2019 11:55:43: 20000000 INFO @ Mon, 03 Jun 2019 11:55:43: 20000000 INFO @ Mon, 03 Jun 2019 11:55:45: 18000000 INFO @ Mon, 03 Jun 2019 11:55:51: 21000000 INFO @ Mon, 03 Jun 2019 11:55:51: 21000000 INFO @ Mon, 03 Jun 2019 11:55:54: 19000000 INFO @ Mon, 03 Jun 2019 11:55:59: 22000000 INFO @ Mon, 03 Jun 2019 11:55:59: 22000000 INFO @ Mon, 03 Jun 2019 11:56:02: 20000000 INFO @ Mon, 03 Jun 2019 11:56:07: 23000000 INFO @ Mon, 03 Jun 2019 11:56:07: 23000000 INFO @ Mon, 03 Jun 2019 11:56:11: 21000000 INFO @ Mon, 03 Jun 2019 11:56:15: 24000000 INFO @ Mon, 03 Jun 2019 11:56:15: 24000000 INFO @ Mon, 03 Jun 2019 11:56:20: 22000000 INFO @ Mon, 03 Jun 2019 11:56:20: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 11:56:20: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 11:56:20: #1 total tags in treatment: 24623382 INFO @ Mon, 03 Jun 2019 11:56:20: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:56:20: #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 11:56:20: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 11:56:20: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 11:56:20: #1 total tags in treatment: 24623382 INFO @ Mon, 03 Jun 2019 11:56:20: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:56:20: #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 11:56:21: #1 tags after filtering in treatment: 24623382 INFO @ Mon, 03 Jun 2019 11:56:21: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:56:21: #1 finished! INFO @ Mon, 03 Jun 2019 11:56:21: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:56:21: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:56:21: #1 tags after filtering in treatment: 24623382 INFO @ Mon, 03 Jun 2019 11:56:21: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:56:21: #1 finished! INFO @ Mon, 03 Jun 2019 11:56:21: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:56:21: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:56:23: #2 number of paired peaks: 222 WARNING @ Mon, 03 Jun 2019 11:56:23: Fewer paired peaks (222) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 222 pairs to build model! INFO @ Mon, 03 Jun 2019 11:56:23: start model_add_line... INFO @ Mon, 03 Jun 2019 11:56:23: #2 number of paired peaks: 222 WARNING @ Mon, 03 Jun 2019 11:56:23: Fewer paired peaks (222) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 222 pairs to build model! INFO @ Mon, 03 Jun 2019 11:56:23: start model_add_line... INFO @ Mon, 03 Jun 2019 11:56:23: start X-correlation... INFO @ Mon, 03 Jun 2019 11:56:23: end of X-cor INFO @ Mon, 03 Jun 2019 11:56:23: #2 finished! INFO @ Mon, 03 Jun 2019 11:56:23: #2 predicted fragment length is 56 bps INFO @ Mon, 03 Jun 2019 11:56:23: #2 alternative fragment length(s) may be 3,56,69 bps INFO @ Mon, 03 Jun 2019 11:56:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX306196/SRX306196.05_model.r WARNING @ Mon, 03 Jun 2019 11:56:23: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 11:56:23: #2 You may need to consider one of the other alternative d(s): 3,56,69 WARNING @ Mon, 03 Jun 2019 11:56:23: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 11:56:23: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:56:23: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:56:23: start X-correlation... INFO @ Mon, 03 Jun 2019 11:56:23: end of X-cor INFO @ Mon, 03 Jun 2019 11:56:23: #2 finished! INFO @ Mon, 03 Jun 2019 11:56:23: #2 predicted fragment length is 56 bps INFO @ Mon, 03 Jun 2019 11:56:23: #2 alternative fragment length(s) may be 3,56,69 bps INFO @ Mon, 03 Jun 2019 11:56:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX306196/SRX306196.20_model.r WARNING @ Mon, 03 Jun 2019 11:56:23: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 11:56:23: #2 You may need to consider one of the other alternative d(s): 3,56,69 WARNING @ Mon, 03 Jun 2019 11:56:23: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 11:56:23: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:56:23: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:56:29: 23000000 INFO @ Mon, 03 Jun 2019 11:56:37: 24000000 INFO @ Mon, 03 Jun 2019 11:56:43: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 11:56:43: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 11:56:43: #1 total tags in treatment: 24623382 INFO @ Mon, 03 Jun 2019 11:56:43: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:56:43: #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 11:56:43: #1 tags after filtering in treatment: 24623382 INFO @ Mon, 03 Jun 2019 11:56:43: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:56:43: #1 finished! INFO @ Mon, 03 Jun 2019 11:56:43: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:56:43: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:56:45: #2 number of paired peaks: 222 WARNING @ Mon, 03 Jun 2019 11:56:45: Fewer paired peaks (222) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 222 pairs to build model! INFO @ Mon, 03 Jun 2019 11:56:45: start model_add_line... INFO @ Mon, 03 Jun 2019 11:56:45: start X-correlation... INFO @ Mon, 03 Jun 2019 11:56:46: end of X-cor INFO @ Mon, 03 Jun 2019 11:56:46: #2 finished! INFO @ Mon, 03 Jun 2019 11:56:46: #2 predicted fragment length is 56 bps INFO @ Mon, 03 Jun 2019 11:56:46: #2 alternative fragment length(s) may be 3,56,69 bps INFO @ Mon, 03 Jun 2019 11:56:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX306196/SRX306196.10_model.r WARNING @ Mon, 03 Jun 2019 11:56:46: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 11:56:46: #2 You may need to consider one of the other alternative d(s): 3,56,69 WARNING @ Mon, 03 Jun 2019 11:56:46: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 11:56:46: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:56:46: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:57:25: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:57:25: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:57:46: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:57:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX306196/SRX306196.05_peaks.xls INFO @ Mon, 03 Jun 2019 11:57:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX306196/SRX306196.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:57:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX306196/SRX306196.05_summits.bed INFO @ Mon, 03 Jun 2019 11:57:54: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (4690 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 11:57:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX306196/SRX306196.20_peaks.xls INFO @ Mon, 03 Jun 2019 11:57:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX306196/SRX306196.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:57:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX306196/SRX306196.20_summits.bed INFO @ Mon, 03 Jun 2019 11:57:54: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (1348 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 11:58:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX306196/SRX306196.10_peaks.xls INFO @ Mon, 03 Jun 2019 11:58:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX306196/SRX306196.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:58:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX306196/SRX306196.10_summits.bed INFO @ Mon, 03 Jun 2019 11:58:16: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2860 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。