Job ID = 11597964 sra ファイルのダウンロード中... Completed: 511185K bytes transferred in 6 seconds (661893K 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 12540682 spots for /home/okishinya/chipatlas/results/dm3/SRX4520669/SRR7659067.sra Written 12540682 spots for /home/okishinya/chipatlas/results/dm3/SRX4520669/SRR7659067.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:05:16 12540682 reads; of these: 12540682 (100.00%) were unpaired; of these: 653431 (5.21%) aligned 0 times 7660115 (61.08%) aligned exactly 1 time 4227136 (33.71%) aligned >1 times 94.79% overall alignment rate Time searching: 00:05:17 Overall time: 00:05:17 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 8 files... [bam_rmdupse_core] 1097197 / 11887251 = 0.0923 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, 30 Jan 2019 16:40:10: # Command line: callpeak -t SRX4520669.bam -f BAM -g dm -n SRX4520669.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4520669.10 # format = BAM # ChIP-seq file = ['SRX4520669.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, 30 Jan 2019 16:40:10: #1 read tag files... INFO @ Wed, 30 Jan 2019 16:40:10: #1 read treatment tags... INFO @ Wed, 30 Jan 2019 16:40:10: # Command line: callpeak -t SRX4520669.bam -f BAM -g dm -n SRX4520669.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4520669.05 # format = BAM # ChIP-seq file = ['SRX4520669.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, 30 Jan 2019 16:40:10: #1 read tag files... INFO @ Wed, 30 Jan 2019 16:40:10: # Command line: callpeak -t SRX4520669.bam -f BAM -g dm -n SRX4520669.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4520669.20 # format = BAM # ChIP-seq file = ['SRX4520669.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, 30 Jan 2019 16:40:10: #1 read treatment tags... INFO @ Wed, 30 Jan 2019 16:40:10: #1 read tag files... INFO @ Wed, 30 Jan 2019 16:40:10: #1 read treatment tags... INFO @ Wed, 30 Jan 2019 16:40:17: 1000000 INFO @ Wed, 30 Jan 2019 16:40:17: 1000000 INFO @ Wed, 30 Jan 2019 16:40:17: 1000000 INFO @ Wed, 30 Jan 2019 16:40:25: 2000000 INFO @ Wed, 30 Jan 2019 16:40:25: 2000000 INFO @ Wed, 30 Jan 2019 16:40:25: 2000000 INFO @ Wed, 30 Jan 2019 16:40:32: 3000000 INFO @ Wed, 30 Jan 2019 16:40:32: 3000000 INFO @ Wed, 30 Jan 2019 16:40:32: 3000000 INFO @ Wed, 30 Jan 2019 16:40:40: 4000000 INFO @ Wed, 30 Jan 2019 16:40:40: 4000000 INFO @ Wed, 30 Jan 2019 16:40:40: 4000000 INFO @ Wed, 30 Jan 2019 16:40:47: 5000000 INFO @ Wed, 30 Jan 2019 16:40:47: 5000000 INFO @ Wed, 30 Jan 2019 16:40:47: 5000000 INFO @ Wed, 30 Jan 2019 16:40:55: 6000000 INFO @ Wed, 30 Jan 2019 16:40:55: 6000000 INFO @ Wed, 30 Jan 2019 16:40:55: 6000000 INFO @ Wed, 30 Jan 2019 16:41:02: 7000000 INFO @ Wed, 30 Jan 2019 16:41:02: 7000000 INFO @ Wed, 30 Jan 2019 16:41:02: 7000000 INFO @ Wed, 30 Jan 2019 16:41:09: 8000000 INFO @ Wed, 30 Jan 2019 16:41:10: 8000000 INFO @ Wed, 30 Jan 2019 16:41:10: 8000000 INFO @ Wed, 30 Jan 2019 16:41:17: 9000000 INFO @ Wed, 30 Jan 2019 16:41:17: 9000000 INFO @ Wed, 30 Jan 2019 16:41:17: 9000000 INFO @ Wed, 30 Jan 2019 16:41:24: 10000000 INFO @ Wed, 30 Jan 2019 16:41:25: 10000000 INFO @ Wed, 30 Jan 2019 16:41:25: 10000000 INFO @ Wed, 30 Jan 2019 16:41:30: #1 tag size is determined as 50 bps INFO @ Wed, 30 Jan 2019 16:41:30: #1 tag size = 50 INFO @ Wed, 30 Jan 2019 16:41:30: #1 total tags in treatment: 10790054 INFO @ Wed, 30 Jan 2019 16:41:30: #1 user defined the maximum tags... INFO @ Wed, 30 Jan 2019 16:41:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 30 Jan 2019 16:41:30: #1 tags after filtering in treatment: 10790054 INFO @ Wed, 30 Jan 2019 16:41:30: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 30 Jan 2019 16:41:30: #1 finished! INFO @ Wed, 30 Jan 2019 16:41:30: #2 Build Peak Model... INFO @ Wed, 30 Jan 2019 16:41:30: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 30 Jan 2019 16:41:30: #1 tag size is determined as 50 bps INFO @ Wed, 30 Jan 2019 16:41:30: #1 tag size = 50 INFO @ Wed, 30 Jan 2019 16:41:30: #1 total tags in treatment: 10790054 INFO @ Wed, 30 Jan 2019 16:41:30: #1 user defined the maximum tags... INFO @ Wed, 30 Jan 2019 16:41:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 30 Jan 2019 16:41:30: #1 tag size is determined as 50 bps INFO @ Wed, 30 Jan 2019 16:41:30: #1 tag size = 50 INFO @ Wed, 30 Jan 2019 16:41:30: #1 total tags in treatment: 10790054 INFO @ Wed, 30 Jan 2019 16:41:30: #1 user defined the maximum tags... INFO @ Wed, 30 Jan 2019 16:41:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 30 Jan 2019 16:41:31: #1 tags after filtering in treatment: 10790054 INFO @ Wed, 30 Jan 2019 16:41:31: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 30 Jan 2019 16:41:31: #1 finished! INFO @ Wed, 30 Jan 2019 16:41:31: #2 Build Peak Model... INFO @ Wed, 30 Jan 2019 16:41:31: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 30 Jan 2019 16:41:31: #1 tags after filtering in treatment: 10790054 INFO @ Wed, 30 Jan 2019 16:41:31: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 30 Jan 2019 16:41:31: #1 finished! INFO @ Wed, 30 Jan 2019 16:41:31: #2 Build Peak Model... INFO @ Wed, 30 Jan 2019 16:41:31: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 30 Jan 2019 16:41:31: #2 number of paired peaks: 708 WARNING @ Wed, 30 Jan 2019 16:41:31: Fewer paired peaks (708) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 708 pairs to build model! INFO @ Wed, 30 Jan 2019 16:41:31: start model_add_line... INFO @ Wed, 30 Jan 2019 16:41:31: start X-correlation... INFO @ Wed, 30 Jan 2019 16:41:31: end of X-cor INFO @ Wed, 30 Jan 2019 16:41:31: #2 finished! INFO @ Wed, 30 Jan 2019 16:41:31: #2 predicted fragment length is 57 bps INFO @ Wed, 30 Jan 2019 16:41:31: #2 alternative fragment length(s) may be 3,57 bps INFO @ Wed, 30 Jan 2019 16:41:31: #2.2 Generate R script for model : SRX4520669.05_model.r WARNING @ Wed, 30 Jan 2019 16:41:31: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 30 Jan 2019 16:41:31: #2 You may need to consider one of the other alternative d(s): 3,57 WARNING @ Wed, 30 Jan 2019 16:41:31: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 30 Jan 2019 16:41:31: #3 Call peaks... INFO @ Wed, 30 Jan 2019 16:41:31: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 30 Jan 2019 16:41:31: #2 number of paired peaks: 708 WARNING @ Wed, 30 Jan 2019 16:41:31: Fewer paired peaks (708) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 708 pairs to build model! INFO @ Wed, 30 Jan 2019 16:41:31: start model_add_line... INFO @ Wed, 30 Jan 2019 16:41:32: #2 number of paired peaks: 708 WARNING @ Wed, 30 Jan 2019 16:41:32: Fewer paired peaks (708) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 708 pairs to build model! INFO @ Wed, 30 Jan 2019 16:41:32: start model_add_line... INFO @ Wed, 30 Jan 2019 16:41:32: start X-correlation... INFO @ Wed, 30 Jan 2019 16:41:32: end of X-cor INFO @ Wed, 30 Jan 2019 16:41:32: #2 finished! INFO @ Wed, 30 Jan 2019 16:41:32: #2 predicted fragment length is 57 bps INFO @ Wed, 30 Jan 2019 16:41:32: #2 alternative fragment length(s) may be 3,57 bps INFO @ Wed, 30 Jan 2019 16:41:32: #2.2 Generate R script for model : SRX4520669.10_model.r WARNING @ Wed, 30 Jan 2019 16:41:32: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 30 Jan 2019 16:41:32: #2 You may need to consider one of the other alternative d(s): 3,57 WARNING @ Wed, 30 Jan 2019 16:41:32: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 30 Jan 2019 16:41:32: #3 Call peaks... INFO @ Wed, 30 Jan 2019 16:41:32: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 30 Jan 2019 16:41:32: start X-correlation... INFO @ Wed, 30 Jan 2019 16:41:32: end of X-cor INFO @ Wed, 30 Jan 2019 16:41:32: #2 finished! INFO @ Wed, 30 Jan 2019 16:41:32: #2 predicted fragment length is 57 bps INFO @ Wed, 30 Jan 2019 16:41:32: #2 alternative fragment length(s) may be 3,57 bps INFO @ Wed, 30 Jan 2019 16:41:32: #2.2 Generate R script for model : SRX4520669.20_model.r WARNING @ Wed, 30 Jan 2019 16:41:32: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 30 Jan 2019 16:41:32: #2 You may need to consider one of the other alternative d(s): 3,57 WARNING @ Wed, 30 Jan 2019 16:41:32: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 30 Jan 2019 16:41:32: #3 Call peaks... INFO @ Wed, 30 Jan 2019 16:41:32: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 30 Jan 2019 16:41:55: #3 Call peaks for each chromosome... INFO @ Wed, 30 Jan 2019 16:41:56: #3 Call peaks for each chromosome... INFO @ Wed, 30 Jan 2019 16:41:56: #3 Call peaks for each chromosome... INFO @ Wed, 30 Jan 2019 16:42:09: #4 Write output xls file... SRX4520669.05_peaks.xls INFO @ Wed, 30 Jan 2019 16:42:09: #4 Write peak in narrowPeak format file... SRX4520669.05_peaks.narrowPeak INFO @ Wed, 30 Jan 2019 16:42:09: #4 Write summits bed file... SRX4520669.05_summits.bed INFO @ Wed, 30 Jan 2019 16:42:09: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3172 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Wed, 30 Jan 2019 16:42:09: #4 Write output xls file... SRX4520669.10_peaks.xls INFO @ Wed, 30 Jan 2019 16:42:09: #4 Write peak in narrowPeak format file... SRX4520669.10_peaks.narrowPeak INFO @ Wed, 30 Jan 2019 16:42:09: #4 Write summits bed file... SRX4520669.10_summits.bed INFO @ Wed, 30 Jan 2019 16:42:09: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (2011 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Wed, 30 Jan 2019 16:42:10: #4 Write output xls file... SRX4520669.20_peaks.xls INFO @ Wed, 30 Jan 2019 16:42:10: #4 Write peak in narrowPeak format file... SRX4520669.20_peaks.narrowPeak INFO @ Wed, 30 Jan 2019 16:42:10: #4 Write summits bed file... SRX4520669.20_summits.bed INFO @ Wed, 30 Jan 2019 16:42:10: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (840 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。