Job ID = 1307758 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 14,881,875 reads read : 29,763,750 reads written : 14,881,875 reads 0-length : 14,881,875 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: 00:08:46 14881875 reads; of these: 14881875 (100.00%) were unpaired; of these: 713039 (4.79%) aligned 0 times 9556076 (64.21%) aligned exactly 1 time 4612760 (31.00%) aligned >1 times 95.21% overall alignment rate Time searching: 00:08:46 Overall time: 00:08:46 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 8 files... [bam_rmdupse_core] 1409867 / 14168836 = 0.0995 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 22:48:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5343117/SRX5343117.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5343117/SRX5343117.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5343117/SRX5343117.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5343117/SRX5343117.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 22:48:29: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:48:29: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:48:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5343117/SRX5343117.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5343117/SRX5343117.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5343117/SRX5343117.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5343117/SRX5343117.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 22:48:29: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:48:29: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:48:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5343117/SRX5343117.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5343117/SRX5343117.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5343117/SRX5343117.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5343117/SRX5343117.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 22:48:29: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:48:29: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:48:38: 1000000 INFO @ Mon, 03 Jun 2019 22:48:39: 1000000 INFO @ Mon, 03 Jun 2019 22:48:40: 1000000 INFO @ Mon, 03 Jun 2019 22:48:47: 2000000 INFO @ Mon, 03 Jun 2019 22:48:49: 2000000 INFO @ Mon, 03 Jun 2019 22:48:50: 2000000 INFO @ Mon, 03 Jun 2019 22:48:55: 3000000 INFO @ Mon, 03 Jun 2019 22:48:59: 3000000 INFO @ Mon, 03 Jun 2019 22:49:00: 3000000 INFO @ Mon, 03 Jun 2019 22:49:04: 4000000 INFO @ Mon, 03 Jun 2019 22:49:09: 4000000 INFO @ Mon, 03 Jun 2019 22:49:10: 4000000 INFO @ Mon, 03 Jun 2019 22:49:12: 5000000 INFO @ Mon, 03 Jun 2019 22:49:19: 5000000 INFO @ Mon, 03 Jun 2019 22:49:19: 5000000 INFO @ Mon, 03 Jun 2019 22:49:21: 6000000 INFO @ Mon, 03 Jun 2019 22:49:28: 6000000 INFO @ Mon, 03 Jun 2019 22:49:29: 7000000 INFO @ Mon, 03 Jun 2019 22:49:29: 6000000 INFO @ Mon, 03 Jun 2019 22:49:38: 8000000 INFO @ Mon, 03 Jun 2019 22:49:38: 7000000 INFO @ Mon, 03 Jun 2019 22:49:39: 7000000 INFO @ Mon, 03 Jun 2019 22:49:46: 9000000 INFO @ Mon, 03 Jun 2019 22:49:48: 8000000 INFO @ Mon, 03 Jun 2019 22:49:49: 8000000 INFO @ Mon, 03 Jun 2019 22:49:55: 10000000 INFO @ Mon, 03 Jun 2019 22:49:58: 9000000 INFO @ Mon, 03 Jun 2019 22:49:59: 9000000 INFO @ Mon, 03 Jun 2019 22:50:03: 11000000 INFO @ Mon, 03 Jun 2019 22:50:07: 10000000 INFO @ Mon, 03 Jun 2019 22:50:09: 10000000 INFO @ Mon, 03 Jun 2019 22:50:11: 12000000 INFO @ Mon, 03 Jun 2019 22:50:17: 11000000 INFO @ Mon, 03 Jun 2019 22:50:18: #1 tag size is determined as 65 bps INFO @ Mon, 03 Jun 2019 22:50:18: #1 tag size = 65 INFO @ Mon, 03 Jun 2019 22:50:18: #1 total tags in treatment: 12758969 INFO @ Mon, 03 Jun 2019 22:50:18: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:50:18: #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 22:50:18: #1 tags after filtering in treatment: 12758969 INFO @ Mon, 03 Jun 2019 22:50:18: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:50:18: #1 finished! INFO @ Mon, 03 Jun 2019 22:50:18: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:50:18: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:50:18: 11000000 INFO @ Mon, 03 Jun 2019 22:50:19: #2 number of paired peaks: 278 WARNING @ Mon, 03 Jun 2019 22:50:19: Fewer paired peaks (278) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 278 pairs to build model! INFO @ Mon, 03 Jun 2019 22:50:19: start model_add_line... INFO @ Mon, 03 Jun 2019 22:50:19: start X-correlation... INFO @ Mon, 03 Jun 2019 22:50:19: end of X-cor INFO @ Mon, 03 Jun 2019 22:50:19: #2 finished! INFO @ Mon, 03 Jun 2019 22:50:19: #2 predicted fragment length is 61 bps INFO @ Mon, 03 Jun 2019 22:50:19: #2 alternative fragment length(s) may be 61 bps INFO @ Mon, 03 Jun 2019 22:50:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5343117/SRX5343117.10_model.r WARNING @ Mon, 03 Jun 2019 22:50:19: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 22:50:19: #2 You may need to consider one of the other alternative d(s): 61 WARNING @ Mon, 03 Jun 2019 22:50:19: #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 22:50:19: #3 Call peaks... INFO @ Mon, 03 Jun 2019 22:50:19: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 22:50:26: 12000000 INFO @ Mon, 03 Jun 2019 22:50:28: 12000000 INFO @ Mon, 03 Jun 2019 22:50:34: #1 tag size is determined as 65 bps INFO @ Mon, 03 Jun 2019 22:50:34: #1 tag size = 65 INFO @ Mon, 03 Jun 2019 22:50:34: #1 total tags in treatment: 12758969 INFO @ Mon, 03 Jun 2019 22:50:34: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:50:34: #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 22:50:34: #1 tags after filtering in treatment: 12758969 INFO @ Mon, 03 Jun 2019 22:50:34: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:50:34: #1 finished! INFO @ Mon, 03 Jun 2019 22:50:34: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:50:34: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:50:35: #1 tag size is determined as 65 bps INFO @ Mon, 03 Jun 2019 22:50:35: #1 tag size = 65 INFO @ Mon, 03 Jun 2019 22:50:35: #1 total tags in treatment: 12758969 INFO @ Mon, 03 Jun 2019 22:50:35: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:50:35: #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 22:50:35: #2 number of paired peaks: 278 WARNING @ Mon, 03 Jun 2019 22:50:35: Fewer paired peaks (278) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 278 pairs to build model! INFO @ Mon, 03 Jun 2019 22:50:35: start model_add_line... INFO @ Mon, 03 Jun 2019 22:50:35: start X-correlation... INFO @ Mon, 03 Jun 2019 22:50:35: end of X-cor INFO @ Mon, 03 Jun 2019 22:50:35: #2 finished! INFO @ Mon, 03 Jun 2019 22:50:35: #2 predicted fragment length is 61 bps INFO @ Mon, 03 Jun 2019 22:50:35: #2 alternative fragment length(s) may be 61 bps INFO @ Mon, 03 Jun 2019 22:50:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5343117/SRX5343117.05_model.r WARNING @ Mon, 03 Jun 2019 22:50:35: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 22:50:35: #2 You may need to consider one of the other alternative d(s): 61 WARNING @ Mon, 03 Jun 2019 22:50:35: #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 22:50:35: #3 Call peaks... INFO @ Mon, 03 Jun 2019 22:50:35: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 22:50:35: #1 tags after filtering in treatment: 12758969 INFO @ Mon, 03 Jun 2019 22:50:35: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:50:35: #1 finished! INFO @ Mon, 03 Jun 2019 22:50:35: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:50:35: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:50:37: #2 number of paired peaks: 278 WARNING @ Mon, 03 Jun 2019 22:50:37: Fewer paired peaks (278) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 278 pairs to build model! INFO @ Mon, 03 Jun 2019 22:50:37: start model_add_line... INFO @ Mon, 03 Jun 2019 22:50:37: start X-correlation... INFO @ Mon, 03 Jun 2019 22:50:37: end of X-cor INFO @ Mon, 03 Jun 2019 22:50:37: #2 finished! INFO @ Mon, 03 Jun 2019 22:50:37: #2 predicted fragment length is 61 bps INFO @ Mon, 03 Jun 2019 22:50:37: #2 alternative fragment length(s) may be 61 bps INFO @ Mon, 03 Jun 2019 22:50:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5343117/SRX5343117.20_model.r WARNING @ Mon, 03 Jun 2019 22:50:37: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 22:50:37: #2 You may need to consider one of the other alternative d(s): 61 WARNING @ Mon, 03 Jun 2019 22:50:37: #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 22:50:37: #3 Call peaks... INFO @ Mon, 03 Jun 2019 22:50:37: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 22:50:55: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 22:51:11: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 22:51:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5343117/SRX5343117.10_peaks.xls INFO @ Mon, 03 Jun 2019 22:51:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5343117/SRX5343117.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 22:51:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5343117/SRX5343117.10_summits.bed INFO @ Mon, 03 Jun 2019 22:51:11: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1322 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 22:51:12: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 22:51:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5343117/SRX5343117.05_peaks.xls INFO @ Mon, 03 Jun 2019 22:51:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5343117/SRX5343117.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 22:51:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5343117/SRX5343117.05_summits.bed INFO @ Mon, 03 Jun 2019 22:51:28: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1640 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 22:51:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5343117/SRX5343117.20_peaks.xls INFO @ Mon, 03 Jun 2019 22:51:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5343117/SRX5343117.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 22:51:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5343117/SRX5343117.20_summits.bed INFO @ Mon, 03 Jun 2019 22:51:29: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (952 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。