Job ID = 2590812 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 25,449,790 reads read : 50,899,580 reads written : 25,449,790 reads 0-length : 25,449,790 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: 00:10:56 25449790 reads; of these: 25449790 (100.00%) were unpaired; of these: 1480827 (5.82%) aligned 0 times 16778059 (65.93%) aligned exactly 1 time 7190904 (28.26%) aligned >1 times 94.18% overall alignment rate Time searching: 00:10:56 Overall time: 00:10:56 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] 11546772 / 23968963 = 0.4817 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 23:39:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011053/SRX5011053.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011053/SRX5011053.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011053/SRX5011053.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011053/SRX5011053.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 23:39:54: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:39:54: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:39:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011053/SRX5011053.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011053/SRX5011053.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011053/SRX5011053.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011053/SRX5011053.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 23:39:54: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:39:54: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:39:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011053/SRX5011053.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011053/SRX5011053.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011053/SRX5011053.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011053/SRX5011053.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 23:39:56: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:39:56: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:40:02: 1000000 INFO @ Mon, 12 Aug 2019 23:40:05: 1000000 INFO @ Mon, 12 Aug 2019 23:40:07: 1000000 INFO @ Mon, 12 Aug 2019 23:40:09: 2000000 INFO @ Mon, 12 Aug 2019 23:40:15: 2000000 INFO @ Mon, 12 Aug 2019 23:40:16: 3000000 INFO @ Mon, 12 Aug 2019 23:40:18: 2000000 INFO @ Mon, 12 Aug 2019 23:40:23: 4000000 INFO @ Mon, 12 Aug 2019 23:40:25: 3000000 INFO @ Mon, 12 Aug 2019 23:40:28: 3000000 INFO @ Mon, 12 Aug 2019 23:40:30: 5000000 INFO @ Mon, 12 Aug 2019 23:40:36: 4000000 INFO @ Mon, 12 Aug 2019 23:40:37: 6000000 INFO @ Mon, 12 Aug 2019 23:40:38: 4000000 INFO @ Mon, 12 Aug 2019 23:40:45: 7000000 INFO @ Mon, 12 Aug 2019 23:40:46: 5000000 INFO @ Mon, 12 Aug 2019 23:40:49: 5000000 INFO @ Mon, 12 Aug 2019 23:40:51: 8000000 INFO @ Mon, 12 Aug 2019 23:40:56: 6000000 INFO @ Mon, 12 Aug 2019 23:40:59: 9000000 INFO @ Mon, 12 Aug 2019 23:40:59: 6000000 INFO @ Mon, 12 Aug 2019 23:41:06: 10000000 INFO @ Mon, 12 Aug 2019 23:41:06: 7000000 INFO @ Mon, 12 Aug 2019 23:41:09: 7000000 INFO @ Mon, 12 Aug 2019 23:41:13: 11000000 INFO @ Mon, 12 Aug 2019 23:41:16: 8000000 INFO @ Mon, 12 Aug 2019 23:41:18: 8000000 INFO @ Mon, 12 Aug 2019 23:41:20: 12000000 INFO @ Mon, 12 Aug 2019 23:41:23: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:41:23: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:41:23: #1 total tags in treatment: 12422191 INFO @ Mon, 12 Aug 2019 23:41:23: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:41:23: #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 23:41:23: #1 tags after filtering in treatment: 12422191 INFO @ Mon, 12 Aug 2019 23:41:23: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:41:23: #1 finished! INFO @ Mon, 12 Aug 2019 23:41:23: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:41:23: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:41:25: #2 number of paired peaks: 779 WARNING @ Mon, 12 Aug 2019 23:41:25: Fewer paired peaks (779) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 779 pairs to build model! INFO @ Mon, 12 Aug 2019 23:41:25: start model_add_line... INFO @ Mon, 12 Aug 2019 23:41:25: start X-correlation... INFO @ Mon, 12 Aug 2019 23:41:25: end of X-cor INFO @ Mon, 12 Aug 2019 23:41:25: #2 finished! INFO @ Mon, 12 Aug 2019 23:41:25: #2 predicted fragment length is 51 bps INFO @ Mon, 12 Aug 2019 23:41:25: #2 alternative fragment length(s) may be 51 bps INFO @ Mon, 12 Aug 2019 23:41:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011053/SRX5011053.10_model.r WARNING @ Mon, 12 Aug 2019 23:41:25: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 23:41:25: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Mon, 12 Aug 2019 23:41:25: #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 23:41:25: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:41:25: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:41:26: 9000000 INFO @ Mon, 12 Aug 2019 23:41:28: 9000000 INFO @ Mon, 12 Aug 2019 23:41:35: 10000000 INFO @ Mon, 12 Aug 2019 23:41:38: 10000000 INFO @ Mon, 12 Aug 2019 23:41:45: 11000000 INFO @ Mon, 12 Aug 2019 23:41:47: 11000000 INFO @ Mon, 12 Aug 2019 23:41:54: 12000000 INFO @ Mon, 12 Aug 2019 23:41:57: 12000000 INFO @ Mon, 12 Aug 2019 23:41:58: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:41:58: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:41:58: #1 total tags in treatment: 12422191 INFO @ Mon, 12 Aug 2019 23:41:58: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:41:58: #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 23:41:59: #1 tags after filtering in treatment: 12422191 INFO @ Mon, 12 Aug 2019 23:41:59: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:41:59: #1 finished! INFO @ Mon, 12 Aug 2019 23:41:59: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:41:59: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:41:59: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:42:00: #2 number of paired peaks: 779 WARNING @ Mon, 12 Aug 2019 23:42:00: Fewer paired peaks (779) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 779 pairs to build model! INFO @ Mon, 12 Aug 2019 23:42:00: start model_add_line... INFO @ Mon, 12 Aug 2019 23:42:00: start X-correlation... INFO @ Mon, 12 Aug 2019 23:42:00: end of X-cor INFO @ Mon, 12 Aug 2019 23:42:00: #2 finished! INFO @ Mon, 12 Aug 2019 23:42:00: #2 predicted fragment length is 51 bps INFO @ Mon, 12 Aug 2019 23:42:00: #2 alternative fragment length(s) may be 51 bps INFO @ Mon, 12 Aug 2019 23:42:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011053/SRX5011053.05_model.r WARNING @ Mon, 12 Aug 2019 23:42:00: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 23:42:00: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Mon, 12 Aug 2019 23:42:00: #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 23:42:00: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:42:00: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:42:00: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:42:00: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:42:00: #1 total tags in treatment: 12422191 INFO @ Mon, 12 Aug 2019 23:42:00: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:42:00: #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 23:42:01: #1 tags after filtering in treatment: 12422191 INFO @ Mon, 12 Aug 2019 23:42:01: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:42:01: #1 finished! INFO @ Mon, 12 Aug 2019 23:42:01: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:42:01: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:42:02: #2 number of paired peaks: 779 WARNING @ Mon, 12 Aug 2019 23:42:02: Fewer paired peaks (779) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 779 pairs to build model! INFO @ Mon, 12 Aug 2019 23:42:02: start model_add_line... INFO @ Mon, 12 Aug 2019 23:42:02: start X-correlation... INFO @ Mon, 12 Aug 2019 23:42:02: end of X-cor INFO @ Mon, 12 Aug 2019 23:42:02: #2 finished! INFO @ Mon, 12 Aug 2019 23:42:02: #2 predicted fragment length is 51 bps INFO @ Mon, 12 Aug 2019 23:42:02: #2 alternative fragment length(s) may be 51 bps INFO @ Mon, 12 Aug 2019 23:42:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011053/SRX5011053.20_model.r WARNING @ Mon, 12 Aug 2019 23:42:02: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 23:42:02: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Mon, 12 Aug 2019 23:42:02: #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 23:42:02: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:42:02: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:42:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011053/SRX5011053.10_peaks.xls INFO @ Mon, 12 Aug 2019 23:42:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011053/SRX5011053.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:42:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011053/SRX5011053.10_summits.bed INFO @ Mon, 12 Aug 2019 23:42:15: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (2609 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:42:34: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:42:36: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:42:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011053/SRX5011053.05_peaks.xls INFO @ Mon, 12 Aug 2019 23:42:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011053/SRX5011053.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:42:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011053/SRX5011053.05_summits.bed INFO @ Mon, 12 Aug 2019 23:42:51: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (4295 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:42:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011053/SRX5011053.20_peaks.xls INFO @ Mon, 12 Aug 2019 23:42:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011053/SRX5011053.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:42:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011053/SRX5011053.20_summits.bed INFO @ Mon, 12 Aug 2019 23:42:53: Done! pass1 - making usageList (11 chroms): 2 millis pass2 - checking and writing primary data (1227 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。