Job ID = 10845227 sra ファイルのダウンロード中... Completed: 137216K bytes transferred in 4 seconds (234473K 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 2873014 spots for /home/okishinya/chipatlas/results/dm3/SRX3937189/SRR7004609.sra Written 2873014 spots for /home/okishinya/chipatlas/results/dm3/SRX3937189/SRR7004609.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: 00:01:31 2873014 reads; of these: 2873014 (100.00%) were unpaired; of these: 742020 (25.83%) aligned 0 times 1550968 (53.98%) aligned exactly 1 time 580026 (20.19%) aligned >1 times 74.17% overall alignment rate Time searching: 00:01:31 Overall time: 00:01:31 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] 54609 / 2130994 = 0.0256 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 09:32:43: # Command line: callpeak -t SRX3937189.bam -f BAM -g dm -n SRX3937189.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3937189.10 # format = BAM # ChIP-seq file = ['SRX3937189.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 09:32:43: #1 read tag files... INFO @ Wed, 04 Jul 2018 09:32:43: #1 read treatment tags... INFO @ Wed, 04 Jul 2018 09:32:43: # Command line: callpeak -t SRX3937189.bam -f BAM -g dm -n SRX3937189.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3937189.20 # format = BAM # ChIP-seq file = ['SRX3937189.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 09:32:43: #1 read tag files... INFO @ Wed, 04 Jul 2018 09:32:43: #1 read treatment tags... INFO @ Wed, 04 Jul 2018 09:32:43: # Command line: callpeak -t SRX3937189.bam -f BAM -g dm -n SRX3937189.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3937189.05 # format = BAM # ChIP-seq file = ['SRX3937189.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 09:32:43: #1 read tag files... INFO @ Wed, 04 Jul 2018 09:32:43: #1 read treatment tags... INFO @ Wed, 04 Jul 2018 09:32:52: 1000000 INFO @ Wed, 04 Jul 2018 09:32:52: 1000000 INFO @ Wed, 04 Jul 2018 09:32:52: 1000000 INFO @ Wed, 04 Jul 2018 09:33:00: 2000000 INFO @ Wed, 04 Jul 2018 09:33:01: #1 tag size is determined as 100 bps INFO @ Wed, 04 Jul 2018 09:33:01: #1 tag size = 100 INFO @ Wed, 04 Jul 2018 09:33:01: #1 total tags in treatment: 2076385 INFO @ Wed, 04 Jul 2018 09:33:01: #1 user defined the maximum tags... INFO @ Wed, 04 Jul 2018 09:33:01: #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 09:33:01: #1 tags after filtering in treatment: 2076385 INFO @ Wed, 04 Jul 2018 09:33:01: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 04 Jul 2018 09:33:01: #1 finished! INFO @ Wed, 04 Jul 2018 09:33:01: #2 Build Peak Model... INFO @ Wed, 04 Jul 2018 09:33:01: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 04 Jul 2018 09:33:01: #2 number of paired peaks: 238 WARNING @ Wed, 04 Jul 2018 09:33:01: Fewer paired peaks (238) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 238 pairs to build model! INFO @ Wed, 04 Jul 2018 09:33:01: start model_add_line... INFO @ Wed, 04 Jul 2018 09:33:01: start X-correlation... INFO @ Wed, 04 Jul 2018 09:33:01: end of X-cor INFO @ Wed, 04 Jul 2018 09:33:01: #2 finished! INFO @ Wed, 04 Jul 2018 09:33:01: #2 predicted fragment length is 99 bps INFO @ Wed, 04 Jul 2018 09:33:01: #2 alternative fragment length(s) may be 99,570 bps INFO @ Wed, 04 Jul 2018 09:33:01: #2.2 Generate R script for model : SRX3937189.20_model.r WARNING @ Wed, 04 Jul 2018 09:33:01: #2 Since the d (99) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 04 Jul 2018 09:33:01: #2 You may need to consider one of the other alternative d(s): 99,570 WARNING @ Wed, 04 Jul 2018 09:33:01: #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 09:33:01: #3 Call peaks... INFO @ Wed, 04 Jul 2018 09:33:01: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 04 Jul 2018 09:33:01: 2000000 INFO @ Wed, 04 Jul 2018 09:33:01: 2000000 INFO @ Wed, 04 Jul 2018 09:33:02: #1 tag size is determined as 100 bps INFO @ Wed, 04 Jul 2018 09:33:02: #1 tag size = 100 INFO @ Wed, 04 Jul 2018 09:33:02: #1 total tags in treatment: 2076385 INFO @ Wed, 04 Jul 2018 09:33:02: #1 user defined the maximum tags... INFO @ Wed, 04 Jul 2018 09:33:02: #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 09:33:02: #1 tag size is determined as 100 bps INFO @ Wed, 04 Jul 2018 09:33:02: #1 tag size = 100 INFO @ Wed, 04 Jul 2018 09:33:02: #1 total tags in treatment: 2076385 INFO @ Wed, 04 Jul 2018 09:33:02: #1 user defined the maximum tags... INFO @ Wed, 04 Jul 2018 09:33:02: #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 09:33:02: #1 tags after filtering in treatment: 2076385 INFO @ Wed, 04 Jul 2018 09:33:02: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 04 Jul 2018 09:33:02: #1 finished! INFO @ Wed, 04 Jul 2018 09:33:02: #2 Build Peak Model... INFO @ Wed, 04 Jul 2018 09:33:02: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 04 Jul 2018 09:33:02: #1 tags after filtering in treatment: 2076385 INFO @ Wed, 04 Jul 2018 09:33:02: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 04 Jul 2018 09:33:02: #1 finished! INFO @ Wed, 04 Jul 2018 09:33:02: #2 Build Peak Model... INFO @ Wed, 04 Jul 2018 09:33:02: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 04 Jul 2018 09:33:02: #2 number of paired peaks: 238 WARNING @ Wed, 04 Jul 2018 09:33:02: Fewer paired peaks (238) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 238 pairs to build model! INFO @ Wed, 04 Jul 2018 09:33:02: start model_add_line... INFO @ Wed, 04 Jul 2018 09:33:02: #2 number of paired peaks: 238 WARNING @ Wed, 04 Jul 2018 09:33:02: Fewer paired peaks (238) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 238 pairs to build model! INFO @ Wed, 04 Jul 2018 09:33:02: start X-correlation... INFO @ Wed, 04 Jul 2018 09:33:02: start model_add_line... INFO @ Wed, 04 Jul 2018 09:33:02: end of X-cor INFO @ Wed, 04 Jul 2018 09:33:02: #2 finished! INFO @ Wed, 04 Jul 2018 09:33:02: #2 predicted fragment length is 99 bps INFO @ Wed, 04 Jul 2018 09:33:02: #2 alternative fragment length(s) may be 99,570 bps INFO @ Wed, 04 Jul 2018 09:33:02: #2.2 Generate R script for model : SRX3937189.10_model.r WARNING @ Wed, 04 Jul 2018 09:33:02: #2 Since the d (99) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 04 Jul 2018 09:33:02: #2 You may need to consider one of the other alternative d(s): 99,570 WARNING @ Wed, 04 Jul 2018 09:33:02: #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 09:33:02: #3 Call peaks... INFO @ Wed, 04 Jul 2018 09:33:02: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 04 Jul 2018 09:33:02: start X-correlation... INFO @ Wed, 04 Jul 2018 09:33:02: end of X-cor INFO @ Wed, 04 Jul 2018 09:33:02: #2 finished! INFO @ Wed, 04 Jul 2018 09:33:02: #2 predicted fragment length is 99 bps INFO @ Wed, 04 Jul 2018 09:33:02: #2 alternative fragment length(s) may be 99,570 bps INFO @ Wed, 04 Jul 2018 09:33:02: #2.2 Generate R script for model : SRX3937189.05_model.r WARNING @ Wed, 04 Jul 2018 09:33:02: #2 Since the d (99) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 04 Jul 2018 09:33:02: #2 You may need to consider one of the other alternative d(s): 99,570 WARNING @ Wed, 04 Jul 2018 09:33:02: #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 09:33:02: #3 Call peaks... INFO @ Wed, 04 Jul 2018 09:33:02: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 04 Jul 2018 09:33:06: #3 Call peaks for each chromosome... INFO @ Wed, 04 Jul 2018 09:33:07: #3 Call peaks for each chromosome... INFO @ Wed, 04 Jul 2018 09:33:07: #3 Call peaks for each chromosome... INFO @ Wed, 04 Jul 2018 09:33:08: #4 Write output xls file... SRX3937189.20_peaks.xls INFO @ Wed, 04 Jul 2018 09:33:08: #4 Write peak in narrowPeak format file... SRX3937189.20_peaks.narrowPeak INFO @ Wed, 04 Jul 2018 09:33:08: #4 Write summits bed file... SRX3937189.20_summits.bed INFO @ Wed, 04 Jul 2018 09:33:08: Done! pass1 - making usageList (3 chroms): 0 millis pass2 - checking and writing primary data (104 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 04 Jul 2018 09:33:09: #4 Write output xls file... SRX3937189.10_peaks.xls INFO @ Wed, 04 Jul 2018 09:33:10: #4 Write peak in narrowPeak format file... SRX3937189.10_peaks.narrowPeak INFO @ Wed, 04 Jul 2018 09:33:10: #4 Write summits bed file... SRX3937189.10_summits.bed INFO @ Wed, 04 Jul 2018 09:33:10: Done! pass1 - making usageList (5 chroms): 0 millis pass2 - checking and writing primary data (227 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Wed, 04 Jul 2018 09:33:10: #4 Write output xls file... SRX3937189.05_peaks.xls INFO @ Wed, 04 Jul 2018 09:33:10: #4 Write peak in narrowPeak format file... SRX3937189.05_peaks.narrowPeak INFO @ Wed, 04 Jul 2018 09:33:10: #4 Write summits bed file... SRX3937189.05_summits.bed INFO @ Wed, 04 Jul 2018 09:33:10: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (389 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。