Job ID = 1294264 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 2,838,894 reads read : 5,677,788 reads written : 5,677,788 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: 00:06:24 2838894 reads; of these: 2838894 (100.00%) were paired; of these: 663713 (23.38%) aligned concordantly 0 times 1786838 (62.94%) aligned concordantly exactly 1 time 388343 (13.68%) aligned concordantly >1 times ---- 663713 pairs aligned concordantly 0 times; of these: 166635 (25.11%) aligned discordantly 1 time ---- 497078 pairs aligned 0 times concordantly or discordantly; of these: 994156 mates make up the pairs; of these: 622346 (62.60%) aligned 0 times 236170 (23.76%) aligned exactly 1 time 135640 (13.64%) aligned >1 times 89.04% overall alignment rate Time searching: 00:06:24 Overall time: 00:06:24 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_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 17536 / 2210670 = 0.0079 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 05:59:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX215627/SRX215627.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX215627/SRX215627.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX215627/SRX215627.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX215627/SRX215627.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 05:59:47: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:59:47: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:59:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX215627/SRX215627.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX215627/SRX215627.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX215627/SRX215627.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX215627/SRX215627.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 05:59:47: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:59:47: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:59:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX215627/SRX215627.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX215627/SRX215627.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX215627/SRX215627.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX215627/SRX215627.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 05:59:47: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:59:47: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:59:56: 1000000 INFO @ Mon, 03 Jun 2019 05:59:58: 1000000 INFO @ Mon, 03 Jun 2019 05:59:59: 1000000 INFO @ Mon, 03 Jun 2019 06:00:06: 2000000 INFO @ Mon, 03 Jun 2019 06:00:10: 2000000 INFO @ Mon, 03 Jun 2019 06:00:12: 2000000 INFO @ Mon, 03 Jun 2019 06:00:14: 3000000 INFO @ Mon, 03 Jun 2019 06:00:23: 4000000 INFO @ Mon, 03 Jun 2019 06:00:23: 3000000 INFO @ Mon, 03 Jun 2019 06:00:24: 3000000 INFO @ Mon, 03 Jun 2019 06:00:33: 5000000 INFO @ Mon, 03 Jun 2019 06:00:33: #1 tag size is determined as 70 bps INFO @ Mon, 03 Jun 2019 06:00:33: #1 tag size = 70 INFO @ Mon, 03 Jun 2019 06:00:33: #1 total tags in treatment: 2157718 INFO @ Mon, 03 Jun 2019 06:00:33: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 06:00:33: #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 06:00:33: #1 tags after filtering in treatment: 2107783 INFO @ Mon, 03 Jun 2019 06:00:33: #1 Redundant rate of treatment: 0.02 INFO @ Mon, 03 Jun 2019 06:00:33: #1 finished! INFO @ Mon, 03 Jun 2019 06:00:33: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 06:00:33: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 06:00:33: #2 number of paired peaks: 293 WARNING @ Mon, 03 Jun 2019 06:00:33: Fewer paired peaks (293) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 293 pairs to build model! INFO @ Mon, 03 Jun 2019 06:00:33: start model_add_line... INFO @ Mon, 03 Jun 2019 06:00:33: start X-correlation... INFO @ Mon, 03 Jun 2019 06:00:33: end of X-cor INFO @ Mon, 03 Jun 2019 06:00:33: #2 finished! INFO @ Mon, 03 Jun 2019 06:00:33: #2 predicted fragment length is 122 bps INFO @ Mon, 03 Jun 2019 06:00:33: #2 alternative fragment length(s) may be 122 bps INFO @ Mon, 03 Jun 2019 06:00:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX215627/SRX215627.20_model.r WARNING @ Mon, 03 Jun 2019 06:00:33: #2 Since the d (122) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 06:00:33: #2 You may need to consider one of the other alternative d(s): 122 WARNING @ Mon, 03 Jun 2019 06:00:33: #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 06:00:33: #3 Call peaks... INFO @ Mon, 03 Jun 2019 06:00:33: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 06:00:35: 4000000 INFO @ Mon, 03 Jun 2019 06:00:37: 4000000 INFO @ Mon, 03 Jun 2019 06:00:40: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 06:00:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX215627/SRX215627.20_peaks.xls INFO @ Mon, 03 Jun 2019 06:00:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX215627/SRX215627.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 06:00:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX215627/SRX215627.20_summits.bed INFO @ Mon, 03 Jun 2019 06:00:43: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (87 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 06:00:45: 5000000 INFO @ Mon, 03 Jun 2019 06:00:45: #1 tag size is determined as 70 bps INFO @ Mon, 03 Jun 2019 06:00:45: #1 tag size = 70 INFO @ Mon, 03 Jun 2019 06:00:45: #1 total tags in treatment: 2157718 INFO @ Mon, 03 Jun 2019 06:00:45: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 06:00:45: #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 06:00:46: #1 tags after filtering in treatment: 2107783 INFO @ Mon, 03 Jun 2019 06:00:46: #1 Redundant rate of treatment: 0.02 INFO @ Mon, 03 Jun 2019 06:00:46: #1 finished! INFO @ Mon, 03 Jun 2019 06:00:46: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 06:00:46: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 06:00:46: #2 number of paired peaks: 293 WARNING @ Mon, 03 Jun 2019 06:00:46: Fewer paired peaks (293) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 293 pairs to build model! INFO @ Mon, 03 Jun 2019 06:00:46: start model_add_line... INFO @ Mon, 03 Jun 2019 06:00:46: start X-correlation... INFO @ Mon, 03 Jun 2019 06:00:46: end of X-cor INFO @ Mon, 03 Jun 2019 06:00:46: #2 finished! INFO @ Mon, 03 Jun 2019 06:00:46: #2 predicted fragment length is 122 bps INFO @ Mon, 03 Jun 2019 06:00:46: #2 alternative fragment length(s) may be 122 bps INFO @ Mon, 03 Jun 2019 06:00:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX215627/SRX215627.05_model.r WARNING @ Mon, 03 Jun 2019 06:00:46: #2 Since the d (122) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 06:00:46: #2 You may need to consider one of the other alternative d(s): 122 WARNING @ Mon, 03 Jun 2019 06:00:46: #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 06:00:46: #3 Call peaks... INFO @ Mon, 03 Jun 2019 06:00:46: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 06:00:49: 5000000 INFO @ Mon, 03 Jun 2019 06:00:49: #1 tag size is determined as 70 bps INFO @ Mon, 03 Jun 2019 06:00:49: #1 tag size = 70 INFO @ Mon, 03 Jun 2019 06:00:49: #1 total tags in treatment: 2157718 INFO @ Mon, 03 Jun 2019 06:00:49: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 06:00:49: #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 06:00:49: #1 tags after filtering in treatment: 2107783 INFO @ Mon, 03 Jun 2019 06:00:49: #1 Redundant rate of treatment: 0.02 INFO @ Mon, 03 Jun 2019 06:00:49: #1 finished! INFO @ Mon, 03 Jun 2019 06:00:49: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 06:00:49: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 06:00:49: #2 number of paired peaks: 293 WARNING @ Mon, 03 Jun 2019 06:00:49: Fewer paired peaks (293) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 293 pairs to build model! INFO @ Mon, 03 Jun 2019 06:00:49: start model_add_line... INFO @ Mon, 03 Jun 2019 06:00:49: start X-correlation... INFO @ Mon, 03 Jun 2019 06:00:49: end of X-cor INFO @ Mon, 03 Jun 2019 06:00:49: #2 finished! INFO @ Mon, 03 Jun 2019 06:00:49: #2 predicted fragment length is 122 bps INFO @ Mon, 03 Jun 2019 06:00:49: #2 alternative fragment length(s) may be 122 bps INFO @ Mon, 03 Jun 2019 06:00:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX215627/SRX215627.10_model.r WARNING @ Mon, 03 Jun 2019 06:00:49: #2 Since the d (122) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 06:00:49: #2 You may need to consider one of the other alternative d(s): 122 WARNING @ Mon, 03 Jun 2019 06:00:49: #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 06:00:49: #3 Call peaks... INFO @ Mon, 03 Jun 2019 06:00:49: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 06:00:52: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 06:00:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX215627/SRX215627.05_peaks.xls INFO @ Mon, 03 Jun 2019 06:00:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX215627/SRX215627.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 06:00:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX215627/SRX215627.05_summits.bed INFO @ Mon, 03 Jun 2019 06:00:56: Done! INFO @ Mon, 03 Jun 2019 06:00:56: #3 Call peaks for each chromosome... pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (323 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 06:00:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX215627/SRX215627.10_peaks.xls INFO @ Mon, 03 Jun 2019 06:00:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX215627/SRX215627.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 06:00:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX215627/SRX215627.10_summits.bed INFO @ Mon, 03 Jun 2019 06:00:59: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (204 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。