Job ID = 10845232 sra ファイルのダウンロード中... Completed: 161202K bytes transferred in 4 seconds (291181K bits/sec), in 1 file. sra ファイルのダウンロードが完了しました。 Read layout: SINGLE fastq に変換中... Read 3384442 spots for /home/okishinya/chipatlas/results/dm3/SRX3937194/SRR7004614.sra Written 3384442 spots for /home/okishinya/chipatlas/results/dm3/SRX3937194/SRR7004614.sra rm: cannot remove `[DSE]RX*': そのようなファイルやディレクトリはありません rm: cannot remove `[DSE]RR*.fastq': そのようなファイルやディレクトリはありません 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: 00:02:06 3384442 reads; of these: 3384442 (100.00%) were unpaired; of these: 770562 (22.77%) aligned 0 times 1764661 (52.14%) aligned exactly 1 time 849219 (25.09%) aligned >1 times 77.23% overall alignment rate Time searching: 00:02:07 Overall time: 00:02:07 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] 120082 / 2613880 = 0.0459 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 @ Wed, 04 Jul 2018 09:33:49: # Command line: callpeak -t SRX3937194.bam -f BAM -g dm -n SRX3937194.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3937194.05 # format = BAM # ChIP-seq file = ['SRX3937194.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 @ Wed, 04 Jul 2018 09:33:49: #1 read tag files... INFO @ Wed, 04 Jul 2018 09:33:49: #1 read treatment tags... INFO @ Wed, 04 Jul 2018 09:33:49: # Command line: callpeak -t SRX3937194.bam -f BAM -g dm -n SRX3937194.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3937194.10 # format = BAM # ChIP-seq file = ['SRX3937194.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 @ Wed, 04 Jul 2018 09:33:49: #1 read tag files... INFO @ Wed, 04 Jul 2018 09:33:49: #1 read treatment tags... INFO @ Wed, 04 Jul 2018 09:33:49: # Command line: callpeak -t SRX3937194.bam -f BAM -g dm -n SRX3937194.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3937194.20 # format = BAM # ChIP-seq file = ['SRX3937194.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 @ Wed, 04 Jul 2018 09:33:49: #1 read tag files... INFO @ Wed, 04 Jul 2018 09:33:49: #1 read treatment tags... INFO @ Wed, 04 Jul 2018 09:33:58: 1000000 INFO @ Wed, 04 Jul 2018 09:33:58: 1000000 INFO @ Wed, 04 Jul 2018 09:33:58: 1000000 INFO @ Wed, 04 Jul 2018 09:34:06: 2000000 INFO @ Wed, 04 Jul 2018 09:34:08: 2000000 INFO @ Wed, 04 Jul 2018 09:34:08: 2000000 INFO @ Wed, 04 Jul 2018 09:34:11: #1 tag size is determined as 100 bps INFO @ Wed, 04 Jul 2018 09:34:11: #1 tag size = 100 INFO @ Wed, 04 Jul 2018 09:34:11: #1 total tags in treatment: 2493798 INFO @ Wed, 04 Jul 2018 09:34:11: #1 user defined the maximum tags... INFO @ Wed, 04 Jul 2018 09:34:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 04 Jul 2018 09:34:11: #1 tags after filtering in treatment: 2493798 INFO @ Wed, 04 Jul 2018 09:34:11: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 04 Jul 2018 09:34:11: #1 finished! INFO @ Wed, 04 Jul 2018 09:34:11: #2 Build Peak Model... INFO @ Wed, 04 Jul 2018 09:34:11: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 04 Jul 2018 09:34:11: #2 number of paired peaks: 300 WARNING @ Wed, 04 Jul 2018 09:34:11: Fewer paired peaks (300) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 300 pairs to build model! INFO @ Wed, 04 Jul 2018 09:34:11: start model_add_line... INFO @ Wed, 04 Jul 2018 09:34:11: start X-correlation... INFO @ Wed, 04 Jul 2018 09:34:11: end of X-cor INFO @ Wed, 04 Jul 2018 09:34:11: #2 finished! INFO @ Wed, 04 Jul 2018 09:34:11: #2 predicted fragment length is 97 bps INFO @ Wed, 04 Jul 2018 09:34:11: #2 alternative fragment length(s) may be 97 bps INFO @ Wed, 04 Jul 2018 09:34:11: #2.2 Generate R script for model : SRX3937194.20_model.r WARNING @ Wed, 04 Jul 2018 09:34:11: #2 Since the d (97) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 04 Jul 2018 09:34:11: #2 You may need to consider one of the other alternative d(s): 97 WARNING @ Wed, 04 Jul 2018 09:34:11: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 04 Jul 2018 09:34:11: #3 Call peaks... INFO @ Wed, 04 Jul 2018 09:34:11: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 04 Jul 2018 09:34:13: #1 tag size is determined as 100 bps INFO @ Wed, 04 Jul 2018 09:34:13: #1 tag size = 100 INFO @ Wed, 04 Jul 2018 09:34:13: #1 total tags in treatment: 2493798 INFO @ Wed, 04 Jul 2018 09:34:13: #1 user defined the maximum tags... INFO @ Wed, 04 Jul 2018 09:34:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 04 Jul 2018 09:34:13: #1 tag size is determined as 100 bps INFO @ Wed, 04 Jul 2018 09:34:13: #1 tag size = 100 INFO @ Wed, 04 Jul 2018 09:34:13: #1 total tags in treatment: 2493798 INFO @ Wed, 04 Jul 2018 09:34:13: #1 user defined the maximum tags... INFO @ Wed, 04 Jul 2018 09:34:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 04 Jul 2018 09:34:13: #1 tags after filtering in treatment: 2493798 INFO @ Wed, 04 Jul 2018 09:34:13: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 04 Jul 2018 09:34:13: #1 finished! INFO @ Wed, 04 Jul 2018 09:34:13: #2 Build Peak Model... INFO @ Wed, 04 Jul 2018 09:34:13: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 04 Jul 2018 09:34:13: #1 tags after filtering in treatment: 2493798 INFO @ Wed, 04 Jul 2018 09:34:13: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 04 Jul 2018 09:34:13: #1 finished! INFO @ Wed, 04 Jul 2018 09:34:13: #2 Build Peak Model... INFO @ Wed, 04 Jul 2018 09:34:13: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 04 Jul 2018 09:34:13: #2 number of paired peaks: 300 WARNING @ Wed, 04 Jul 2018 09:34:13: Fewer paired peaks (300) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 300 pairs to build model! INFO @ Wed, 04 Jul 2018 09:34:13: start model_add_line... INFO @ Wed, 04 Jul 2018 09:34:13: #2 number of paired peaks: 300 WARNING @ Wed, 04 Jul 2018 09:34:13: Fewer paired peaks (300) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 300 pairs to build model! INFO @ Wed, 04 Jul 2018 09:34:13: start model_add_line... INFO @ Wed, 04 Jul 2018 09:34:13: start X-correlation... INFO @ Wed, 04 Jul 2018 09:34:13: end of X-cor INFO @ Wed, 04 Jul 2018 09:34:13: #2 finished! INFO @ Wed, 04 Jul 2018 09:34:13: #2 predicted fragment length is 97 bps INFO @ Wed, 04 Jul 2018 09:34:13: #2 alternative fragment length(s) may be 97 bps INFO @ Wed, 04 Jul 2018 09:34:13: #2.2 Generate R script for model : SRX3937194.10_model.r INFO @ Wed, 04 Jul 2018 09:34:13: start X-correlation... INFO @ Wed, 04 Jul 2018 09:34:13: end of X-cor INFO @ Wed, 04 Jul 2018 09:34:13: #2 finished! INFO @ Wed, 04 Jul 2018 09:34:13: #2 predicted fragment length is 97 bps INFO @ Wed, 04 Jul 2018 09:34:13: #2 alternative fragment length(s) may be 97 bps INFO @ Wed, 04 Jul 2018 09:34:13: #2.2 Generate R script for model : SRX3937194.05_model.r WARNING @ Wed, 04 Jul 2018 09:34:13: #2 Since the d (97) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 04 Jul 2018 09:34:13: #2 You may need to consider one of the other alternative d(s): 97 WARNING @ Wed, 04 Jul 2018 09:34:13: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 04 Jul 2018 09:34:13: #3 Call peaks... INFO @ Wed, 04 Jul 2018 09:34:13: #3 Pre-compute pvalue-qvalue table... WARNING @ Wed, 04 Jul 2018 09:34:13: #2 Since the d (97) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 04 Jul 2018 09:34:13: #2 You may need to consider one of the other alternative d(s): 97 WARNING @ Wed, 04 Jul 2018 09:34:13: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 04 Jul 2018 09:34:13: #3 Call peaks... INFO @ Wed, 04 Jul 2018 09:34:13: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 04 Jul 2018 09:34:17: #3 Call peaks for each chromosome... INFO @ Wed, 04 Jul 2018 09:34:19: #3 Call peaks for each chromosome... INFO @ Wed, 04 Jul 2018 09:34:19: #3 Call peaks for each chromosome... INFO @ Wed, 04 Jul 2018 09:34:20: #4 Write output xls file... SRX3937194.20_peaks.xls INFO @ Wed, 04 Jul 2018 09:34:20: #4 Write peak in narrowPeak format file... SRX3937194.20_peaks.narrowPeak INFO @ Wed, 04 Jul 2018 09:34:20: #4 Write summits bed file... SRX3937194.20_summits.bed INFO @ Wed, 04 Jul 2018 09:34:20: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (253 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 04 Jul 2018 09:34:22: #4 Write output xls file... SRX3937194.05_peaks.xls INFO @ Wed, 04 Jul 2018 09:34:22: #4 Write peak in narrowPeak format file... SRX3937194.05_peaks.narrowPeak INFO @ Wed, 04 Jul 2018 09:34:22: #4 Write summits bed file... SRX3937194.05_summits.bed INFO @ Wed, 04 Jul 2018 09:34:22: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (644 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 04 Jul 2018 09:34:22: #4 Write output xls file... SRX3937194.10_peaks.xls INFO @ Wed, 04 Jul 2018 09:34:22: #4 Write peak in narrowPeak format file... SRX3937194.10_peaks.narrowPeak INFO @ Wed, 04 Jul 2018 09:34:22: #4 Write summits bed file... SRX3937194.10_summits.bed INFO @ Wed, 04 Jul 2018 09:34:22: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (425 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。