Job ID = 4178545 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 15,851,901 reads read : 31,703,802 reads written : 15,851,901 reads 0-length : 15,851,901 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: 00:00:00 Multiseed full-index search: 00:03:22 15851901 reads; of these: 15851901 (100.00%) were unpaired; of these: 6900648 (43.53%) aligned 0 times 6867651 (43.32%) aligned exactly 1 time 2083602 (13.14%) aligned >1 times 56.47% overall alignment rate Time searching: 00:03:22 Overall time: 00:03:22 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_rmdupse_core] 4678169 / 8951253 = 0.5226 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 05 Dec 2019 13:02:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5827817/SRX5827817.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5827817/SRX5827817.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5827817/SRX5827817.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5827817/SRX5827817.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 @ Thu, 05 Dec 2019 13:02:29: #1 read tag files... INFO @ Thu, 05 Dec 2019 13:02:29: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 13:02:35: 1000000 INFO @ Thu, 05 Dec 2019 13:02:42: 2000000 INFO @ Thu, 05 Dec 2019 13:02:48: 3000000 INFO @ Thu, 05 Dec 2019 13:02:54: 4000000 INFO @ Thu, 05 Dec 2019 13:02:56: #1 tag size is determined as 51 bps INFO @ Thu, 05 Dec 2019 13:02:56: #1 tag size = 51 INFO @ Thu, 05 Dec 2019 13:02:56: #1 total tags in treatment: 4273084 INFO @ Thu, 05 Dec 2019 13:02:56: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 13:02:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 13:02:56: #1 tags after filtering in treatment: 4273084 INFO @ Thu, 05 Dec 2019 13:02:56: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 13:02:56: #1 finished! INFO @ Thu, 05 Dec 2019 13:02:56: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 13:02:56: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 13:02:56: #2 number of paired peaks: 480 WARNING @ Thu, 05 Dec 2019 13:02:56: Fewer paired peaks (480) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 480 pairs to build model! INFO @ Thu, 05 Dec 2019 13:02:56: start model_add_line... INFO @ Thu, 05 Dec 2019 13:02:56: start X-correlation... INFO @ Thu, 05 Dec 2019 13:02:56: end of X-cor INFO @ Thu, 05 Dec 2019 13:02:56: #2 finished! INFO @ Thu, 05 Dec 2019 13:02:56: #2 predicted fragment length is 58 bps INFO @ Thu, 05 Dec 2019 13:02:56: #2 alternative fragment length(s) may be 58 bps INFO @ Thu, 05 Dec 2019 13:02:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5827817/SRX5827817.05_model.r WARNING @ Thu, 05 Dec 2019 13:02:56: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Dec 2019 13:02:56: #2 You may need to consider one of the other alternative d(s): 58 WARNING @ Thu, 05 Dec 2019 13:02:56: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 05 Dec 2019 13:02:56: #3 Call peaks... INFO @ Thu, 05 Dec 2019 13:02:56: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 13:02:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5827817/SRX5827817.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5827817/SRX5827817.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5827817/SRX5827817.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5827817/SRX5827817.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 @ Thu, 05 Dec 2019 13:02:59: #1 read tag files... INFO @ Thu, 05 Dec 2019 13:02:59: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 13:03:05: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 13:03:05: 1000000 INFO @ Thu, 05 Dec 2019 13:03:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5827817/SRX5827817.05_peaks.xls INFO @ Thu, 05 Dec 2019 13:03:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5827817/SRX5827817.05_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 13:03:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5827817/SRX5827817.05_summits.bed INFO @ Thu, 05 Dec 2019 13:03:09: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1307 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 13:03:11: 2000000 INFO @ Thu, 05 Dec 2019 13:03:17: 3000000 INFO @ Thu, 05 Dec 2019 13:03:23: 4000000 INFO @ Thu, 05 Dec 2019 13:03:25: #1 tag size is determined as 51 bps INFO @ Thu, 05 Dec 2019 13:03:25: #1 tag size = 51 INFO @ Thu, 05 Dec 2019 13:03:25: #1 total tags in treatment: 4273084 INFO @ Thu, 05 Dec 2019 13:03:25: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 13:03:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 13:03:25: #1 tags after filtering in treatment: 4273084 INFO @ Thu, 05 Dec 2019 13:03:25: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 13:03:25: #1 finished! INFO @ Thu, 05 Dec 2019 13:03:25: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 13:03:25: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 13:03:25: #2 number of paired peaks: 480 WARNING @ Thu, 05 Dec 2019 13:03:25: Fewer paired peaks (480) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 480 pairs to build model! INFO @ Thu, 05 Dec 2019 13:03:25: start model_add_line... INFO @ Thu, 05 Dec 2019 13:03:25: start X-correlation... INFO @ Thu, 05 Dec 2019 13:03:25: end of X-cor INFO @ Thu, 05 Dec 2019 13:03:25: #2 finished! INFO @ Thu, 05 Dec 2019 13:03:25: #2 predicted fragment length is 58 bps INFO @ Thu, 05 Dec 2019 13:03:25: #2 alternative fragment length(s) may be 58 bps INFO @ Thu, 05 Dec 2019 13:03:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5827817/SRX5827817.10_model.r WARNING @ Thu, 05 Dec 2019 13:03:25: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Dec 2019 13:03:25: #2 You may need to consider one of the other alternative d(s): 58 WARNING @ Thu, 05 Dec 2019 13:03:25: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 05 Dec 2019 13:03:25: #3 Call peaks... INFO @ Thu, 05 Dec 2019 13:03:25: #3 Pre-compute pvalue-qvalue table... BedGraph に変換中... INFO @ Thu, 05 Dec 2019 13:03:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5827817/SRX5827817.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5827817/SRX5827817.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5827817/SRX5827817.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5827817/SRX5827817.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 @ Thu, 05 Dec 2019 13:03:29: #1 read tag files... INFO @ Thu, 05 Dec 2019 13:03:29: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 13:03:33: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 13:03:35: 1000000 INFO @ Thu, 05 Dec 2019 13:03:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5827817/SRX5827817.10_peaks.xls INFO @ Thu, 05 Dec 2019 13:03:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5827817/SRX5827817.10_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 13:03:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5827817/SRX5827817.10_summits.bed INFO @ Thu, 05 Dec 2019 13:03:38: Done! pass1 - making usageList (9 chroms): 0 millis pass2 - checking and writing primary data (909 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 13:03:41: 2000000 INFO @ Thu, 05 Dec 2019 13:03:47: 3000000 INFO @ Thu, 05 Dec 2019 13:03:53: 4000000 INFO @ Thu, 05 Dec 2019 13:03:54: #1 tag size is determined as 51 bps INFO @ Thu, 05 Dec 2019 13:03:54: #1 tag size = 51 INFO @ Thu, 05 Dec 2019 13:03:54: #1 total tags in treatment: 4273084 INFO @ Thu, 05 Dec 2019 13:03:54: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 13:03:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 13:03:55: #1 tags after filtering in treatment: 4273084 INFO @ Thu, 05 Dec 2019 13:03:55: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 13:03:55: #1 finished! INFO @ Thu, 05 Dec 2019 13:03:55: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 13:03:55: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 13:03:55: #2 number of paired peaks: 480 WARNING @ Thu, 05 Dec 2019 13:03:55: Fewer paired peaks (480) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 480 pairs to build model! INFO @ Thu, 05 Dec 2019 13:03:55: start model_add_line... INFO @ Thu, 05 Dec 2019 13:03:55: start X-correlation... INFO @ Thu, 05 Dec 2019 13:03:55: end of X-cor INFO @ Thu, 05 Dec 2019 13:03:55: #2 finished! INFO @ Thu, 05 Dec 2019 13:03:55: #2 predicted fragment length is 58 bps INFO @ Thu, 05 Dec 2019 13:03:55: #2 alternative fragment length(s) may be 58 bps INFO @ Thu, 05 Dec 2019 13:03:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5827817/SRX5827817.20_model.r WARNING @ Thu, 05 Dec 2019 13:04:01: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Dec 2019 13:04:01: #2 You may need to consider one of the other alternative d(s): 58 WARNING @ Thu, 05 Dec 2019 13:04:01: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 05 Dec 2019 13:04:01: #3 Call peaks... INFO @ Thu, 05 Dec 2019 13:04:01: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 13:04:09: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 13:04:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5827817/SRX5827817.20_peaks.xls INFO @ Thu, 05 Dec 2019 13:04:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5827817/SRX5827817.20_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 13:04:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5827817/SRX5827817.20_summits.bed INFO @ Thu, 05 Dec 2019 13:04:14: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (506 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。