Job ID = 1294261 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 3,024,243 reads read : 6,048,486 reads written : 6,048,486 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: 00:07:04 3024243 reads; of these: 3024243 (100.00%) were paired; of these: 669406 (22.13%) aligned concordantly 0 times 1958111 (64.75%) aligned concordantly exactly 1 time 396726 (13.12%) aligned concordantly >1 times ---- 669406 pairs aligned concordantly 0 times; of these: 172802 (25.81%) aligned discordantly 1 time ---- 496604 pairs aligned 0 times concordantly or discordantly; of these: 993208 mates make up the pairs; of these: 590175 (59.42%) aligned 0 times 262725 (26.45%) aligned exactly 1 time 140308 (14.13%) aligned >1 times 90.24% overall alignment rate Time searching: 00:07:04 Overall time: 00:07:04 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] 15453 / 2390249 = 0.0065 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 06:03:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX215625/SRX215625.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX215625/SRX215625.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX215625/SRX215625.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX215625/SRX215625.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 06:03:31: #1 read tag files... INFO @ Mon, 03 Jun 2019 06:03:31: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 06:03:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX215625/SRX215625.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX215625/SRX215625.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX215625/SRX215625.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX215625/SRX215625.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 06:03:31: #1 read tag files... INFO @ Mon, 03 Jun 2019 06:03:31: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 06:03:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX215625/SRX215625.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX215625/SRX215625.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX215625/SRX215625.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX215625/SRX215625.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 06:03:32: #1 read tag files... INFO @ Mon, 03 Jun 2019 06:03:32: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 06:03:41: 1000000 INFO @ Mon, 03 Jun 2019 06:03:41: 1000000 INFO @ Mon, 03 Jun 2019 06:03:43: 1000000 INFO @ Mon, 03 Jun 2019 06:03:49: 2000000 INFO @ Mon, 03 Jun 2019 06:03:49: 2000000 INFO @ Mon, 03 Jun 2019 06:03:54: 2000000 INFO @ Mon, 03 Jun 2019 06:03:56: 3000000 INFO @ Mon, 03 Jun 2019 06:03:58: 3000000 INFO @ Mon, 03 Jun 2019 06:04:03: 4000000 INFO @ Mon, 03 Jun 2019 06:04:05: 3000000 INFO @ Mon, 03 Jun 2019 06:04:07: 4000000 INFO @ Mon, 03 Jun 2019 06:04:11: 5000000 INFO @ Mon, 03 Jun 2019 06:04:14: #1 tag size is determined as 70 bps INFO @ Mon, 03 Jun 2019 06:04:14: #1 tag size = 70 INFO @ Mon, 03 Jun 2019 06:04:14: #1 total tags in treatment: 2339443 INFO @ Mon, 03 Jun 2019 06:04:14: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 06:04:14: #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 06:04:14: #1 tags after filtering in treatment: 2277027 INFO @ Mon, 03 Jun 2019 06:04:14: #1 Redundant rate of treatment: 0.03 INFO @ Mon, 03 Jun 2019 06:04:14: #1 finished! INFO @ Mon, 03 Jun 2019 06:04:14: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 06:04:14: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 06:04:14: #2 number of paired peaks: 194 WARNING @ Mon, 03 Jun 2019 06:04:14: Fewer paired peaks (194) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 194 pairs to build model! INFO @ Mon, 03 Jun 2019 06:04:14: start model_add_line... INFO @ Mon, 03 Jun 2019 06:04:14: start X-correlation... INFO @ Mon, 03 Jun 2019 06:04:14: end of X-cor INFO @ Mon, 03 Jun 2019 06:04:14: #2 finished! INFO @ Mon, 03 Jun 2019 06:04:14: #2 predicted fragment length is 105 bps INFO @ Mon, 03 Jun 2019 06:04:14: #2 alternative fragment length(s) may be 105,481,537 bps INFO @ Mon, 03 Jun 2019 06:04:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX215625/SRX215625.20_model.r WARNING @ Mon, 03 Jun 2019 06:04:14: #2 Since the d (105) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 06:04:14: #2 You may need to consider one of the other alternative d(s): 105,481,537 WARNING @ Mon, 03 Jun 2019 06:04:14: #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 06:04:14: #3 Call peaks... INFO @ Mon, 03 Jun 2019 06:04:14: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 06:04:15: 5000000 INFO @ Mon, 03 Jun 2019 06:04:16: 4000000 INFO @ Mon, 03 Jun 2019 06:04:18: #1 tag size is determined as 70 bps INFO @ Mon, 03 Jun 2019 06:04:18: #1 tag size = 70 INFO @ Mon, 03 Jun 2019 06:04:18: #1 total tags in treatment: 2339443 INFO @ Mon, 03 Jun 2019 06:04:18: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 06:04:18: #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 06:04:18: #1 tags after filtering in treatment: 2277027 INFO @ Mon, 03 Jun 2019 06:04:18: #1 Redundant rate of treatment: 0.03 INFO @ Mon, 03 Jun 2019 06:04:18: #1 finished! INFO @ Mon, 03 Jun 2019 06:04:18: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 06:04:18: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 06:04:18: #2 number of paired peaks: 194 WARNING @ Mon, 03 Jun 2019 06:04:18: Fewer paired peaks (194) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 194 pairs to build model! INFO @ Mon, 03 Jun 2019 06:04:18: start model_add_line... INFO @ Mon, 03 Jun 2019 06:04:18: start X-correlation... INFO @ Mon, 03 Jun 2019 06:04:19: end of X-cor INFO @ Mon, 03 Jun 2019 06:04:19: #2 finished! INFO @ Mon, 03 Jun 2019 06:04:19: #2 predicted fragment length is 105 bps INFO @ Mon, 03 Jun 2019 06:04:19: #2 alternative fragment length(s) may be 105,481,537 bps INFO @ Mon, 03 Jun 2019 06:04:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX215625/SRX215625.10_model.r WARNING @ Mon, 03 Jun 2019 06:04:19: #2 Since the d (105) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 06:04:19: #2 You may need to consider one of the other alternative d(s): 105,481,537 WARNING @ Mon, 03 Jun 2019 06:04:19: #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 06:04:19: #3 Call peaks... INFO @ Mon, 03 Jun 2019 06:04:19: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 06:04:21: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 06:04:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX215625/SRX215625.20_peaks.xls INFO @ Mon, 03 Jun 2019 06:04:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX215625/SRX215625.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 06:04:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX215625/SRX215625.20_summits.bed INFO @ Mon, 03 Jun 2019 06:04:25: Done! pass1 - making usageList (5 chroms): 1 millis pass2 - checking and writing primary data (49 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 06:04:26: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 06:04:26: 5000000 INFO @ Mon, 03 Jun 2019 06:04:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX215625/SRX215625.10_peaks.xls INFO @ Mon, 03 Jun 2019 06:04:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX215625/SRX215625.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 06:04:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX215625/SRX215625.10_summits.bed INFO @ Mon, 03 Jun 2019 06:04:29: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (100 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 06:04:30: #1 tag size is determined as 70 bps INFO @ Mon, 03 Jun 2019 06:04:30: #1 tag size = 70 INFO @ Mon, 03 Jun 2019 06:04:30: #1 total tags in treatment: 2339443 INFO @ Mon, 03 Jun 2019 06:04:30: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 06:04:30: #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 06:04:30: #1 tags after filtering in treatment: 2277027 INFO @ Mon, 03 Jun 2019 06:04:30: #1 Redundant rate of treatment: 0.03 INFO @ Mon, 03 Jun 2019 06:04:30: #1 finished! INFO @ Mon, 03 Jun 2019 06:04:30: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 06:04:30: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 06:04:31: #2 number of paired peaks: 194 WARNING @ Mon, 03 Jun 2019 06:04:31: Fewer paired peaks (194) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 194 pairs to build model! INFO @ Mon, 03 Jun 2019 06:04:31: start model_add_line... INFO @ Mon, 03 Jun 2019 06:04:31: start X-correlation... INFO @ Mon, 03 Jun 2019 06:04:31: end of X-cor INFO @ Mon, 03 Jun 2019 06:04:31: #2 finished! INFO @ Mon, 03 Jun 2019 06:04:31: #2 predicted fragment length is 105 bps INFO @ Mon, 03 Jun 2019 06:04:31: #2 alternative fragment length(s) may be 105,481,537 bps INFO @ Mon, 03 Jun 2019 06:04:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX215625/SRX215625.05_model.r WARNING @ Mon, 03 Jun 2019 06:04:31: #2 Since the d (105) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 06:04:31: #2 You may need to consider one of the other alternative d(s): 105,481,537 WARNING @ Mon, 03 Jun 2019 06:04:31: #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 06:04:31: #3 Call peaks... INFO @ Mon, 03 Jun 2019 06:04:31: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 06:04:38: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 06:04:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX215625/SRX215625.05_peaks.xls INFO @ Mon, 03 Jun 2019 06:04:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX215625/SRX215625.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 06:04:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX215625/SRX215625.05_summits.bed INFO @ Mon, 03 Jun 2019 06:04:41: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (162 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。