Job ID = 11293689 sra ファイルのダウンロード中... Completed: 276465K bytes transferred in 13 seconds (163287K 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 7824634 spots for /home/okishinya/chipatlas/results/dm3/SRX4375851/SRR7506505.sra Written 7824634 spots for /home/okishinya/chipatlas/results/dm3/SRX4375851/SRR7506505.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: 00:02:41 7824634 reads; of these: 7824634 (100.00%) were unpaired; of these: 1261693 (16.12%) aligned 0 times 5173994 (66.12%) aligned exactly 1 time 1388947 (17.75%) aligned >1 times 83.88% overall alignment rate Time searching: 00:02:41 Overall time: 00:02:41 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] 3338145 / 6562941 = 0.5086 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 @ Sun, 04 Nov 2018 17:51:55: # Command line: callpeak -t SRX4375851.bam -f BAM -g dm -n SRX4375851.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4375851.20 # format = BAM # ChIP-seq file = ['SRX4375851.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 @ Sun, 04 Nov 2018 17:51:55: # Command line: callpeak -t SRX4375851.bam -f BAM -g dm -n SRX4375851.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4375851.10 # format = BAM # ChIP-seq file = ['SRX4375851.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 @ Sun, 04 Nov 2018 17:51:55: # Command line: callpeak -t SRX4375851.bam -f BAM -g dm -n SRX4375851.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4375851.05 # format = BAM # ChIP-seq file = ['SRX4375851.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 @ Sun, 04 Nov 2018 17:51:55: #1 read tag files... INFO @ Sun, 04 Nov 2018 17:51:55: #1 read tag files... INFO @ Sun, 04 Nov 2018 17:51:55: #1 read tag files... INFO @ Sun, 04 Nov 2018 17:51:55: #1 read treatment tags... INFO @ Sun, 04 Nov 2018 17:51:55: #1 read treatment tags... INFO @ Sun, 04 Nov 2018 17:51:55: #1 read treatment tags... INFO @ Sun, 04 Nov 2018 17:52:01: 1000000 INFO @ Sun, 04 Nov 2018 17:52:01: 1000000 INFO @ Sun, 04 Nov 2018 17:52:02: 1000000 INFO @ Sun, 04 Nov 2018 17:52:08: 2000000 INFO @ Sun, 04 Nov 2018 17:52:08: 2000000 INFO @ Sun, 04 Nov 2018 17:52:09: 2000000 INFO @ Sun, 04 Nov 2018 17:52:15: 3000000 INFO @ Sun, 04 Nov 2018 17:52:15: 3000000 INFO @ Sun, 04 Nov 2018 17:52:16: 3000000 INFO @ Sun, 04 Nov 2018 17:52:17: #1 tag size is determined as 51 bps INFO @ Sun, 04 Nov 2018 17:52:17: #1 tag size = 51 INFO @ Sun, 04 Nov 2018 17:52:17: #1 total tags in treatment: 3224796 INFO @ Sun, 04 Nov 2018 17:52:17: #1 user defined the maximum tags... INFO @ Sun, 04 Nov 2018 17:52:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Nov 2018 17:52:17: #1 tag size is determined as 51 bps INFO @ Sun, 04 Nov 2018 17:52:17: #1 tag size = 51 INFO @ Sun, 04 Nov 2018 17:52:17: #1 total tags in treatment: 3224796 INFO @ Sun, 04 Nov 2018 17:52:17: #1 user defined the maximum tags... INFO @ Sun, 04 Nov 2018 17:52:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Nov 2018 17:52:17: #1 tags after filtering in treatment: 3224796 INFO @ Sun, 04 Nov 2018 17:52:17: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Nov 2018 17:52:17: #1 finished! INFO @ Sun, 04 Nov 2018 17:52:17: #2 Build Peak Model... INFO @ Sun, 04 Nov 2018 17:52:17: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 04 Nov 2018 17:52:17: #1 tags after filtering in treatment: 3224796 INFO @ Sun, 04 Nov 2018 17:52:17: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Nov 2018 17:52:17: #1 finished! INFO @ Sun, 04 Nov 2018 17:52:17: #2 Build Peak Model... INFO @ Sun, 04 Nov 2018 17:52:17: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 04 Nov 2018 17:52:17: #2 number of paired peaks: 939 WARNING @ Sun, 04 Nov 2018 17:52:17: Fewer paired peaks (939) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 939 pairs to build model! INFO @ Sun, 04 Nov 2018 17:52:17: start model_add_line... INFO @ Sun, 04 Nov 2018 17:52:17: start X-correlation... INFO @ Sun, 04 Nov 2018 17:52:17: #2 number of paired peaks: 939 WARNING @ Sun, 04 Nov 2018 17:52:17: Fewer paired peaks (939) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 939 pairs to build model! INFO @ Sun, 04 Nov 2018 17:52:17: start model_add_line... INFO @ Sun, 04 Nov 2018 17:52:17: start X-correlation... INFO @ Sun, 04 Nov 2018 17:52:17: end of X-cor INFO @ Sun, 04 Nov 2018 17:52:17: end of X-cor INFO @ Sun, 04 Nov 2018 17:52:17: #2 finished! INFO @ Sun, 04 Nov 2018 17:52:17: #2 finished! INFO @ Sun, 04 Nov 2018 17:52:17: #2 predicted fragment length is 55 bps INFO @ Sun, 04 Nov 2018 17:52:17: #2 predicted fragment length is 55 bps INFO @ Sun, 04 Nov 2018 17:52:17: #2 alternative fragment length(s) may be 55 bps INFO @ Sun, 04 Nov 2018 17:52:17: #2 alternative fragment length(s) may be 55 bps INFO @ Sun, 04 Nov 2018 17:52:17: #2.2 Generate R script for model : SRX4375851.20_model.r INFO @ Sun, 04 Nov 2018 17:52:17: #2.2 Generate R script for model : SRX4375851.10_model.r WARNING @ Sun, 04 Nov 2018 17:52:17: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 04 Nov 2018 17:52:17: #2 You may need to consider one of the other alternative d(s): 55 WARNING @ Sun, 04 Nov 2018 17:52:17: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 04 Nov 2018 17:52:17: #3 Call peaks... INFO @ Sun, 04 Nov 2018 17:52:17: #3 Pre-compute pvalue-qvalue table... WARNING @ Sun, 04 Nov 2018 17:52:17: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 04 Nov 2018 17:52:17: #2 You may need to consider one of the other alternative d(s): 55 WARNING @ Sun, 04 Nov 2018 17:52:17: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 04 Nov 2018 17:52:17: #3 Call peaks... INFO @ Sun, 04 Nov 2018 17:52:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Nov 2018 17:52:17: #1 tag size is determined as 51 bps INFO @ Sun, 04 Nov 2018 17:52:17: #1 tag size = 51 INFO @ Sun, 04 Nov 2018 17:52:17: #1 total tags in treatment: 3224796 INFO @ Sun, 04 Nov 2018 17:52:17: #1 user defined the maximum tags... INFO @ Sun, 04 Nov 2018 17:52:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Nov 2018 17:52:17: #1 tags after filtering in treatment: 3224796 INFO @ Sun, 04 Nov 2018 17:52:17: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Nov 2018 17:52:17: #1 finished! INFO @ Sun, 04 Nov 2018 17:52:17: #2 Build Peak Model... INFO @ Sun, 04 Nov 2018 17:52:17: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 04 Nov 2018 17:52:18: #2 number of paired peaks: 939 WARNING @ Sun, 04 Nov 2018 17:52:18: Fewer paired peaks (939) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 939 pairs to build model! INFO @ Sun, 04 Nov 2018 17:52:18: start model_add_line... INFO @ Sun, 04 Nov 2018 17:52:18: start X-correlation... INFO @ Sun, 04 Nov 2018 17:52:18: end of X-cor INFO @ Sun, 04 Nov 2018 17:52:18: #2 finished! INFO @ Sun, 04 Nov 2018 17:52:18: #2 predicted fragment length is 55 bps INFO @ Sun, 04 Nov 2018 17:52:18: #2 alternative fragment length(s) may be 55 bps INFO @ Sun, 04 Nov 2018 17:52:18: #2.2 Generate R script for model : SRX4375851.05_model.r WARNING @ Sun, 04 Nov 2018 17:52:18: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 04 Nov 2018 17:52:18: #2 You may need to consider one of the other alternative d(s): 55 WARNING @ Sun, 04 Nov 2018 17:52:18: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 04 Nov 2018 17:52:18: #3 Call peaks... INFO @ Sun, 04 Nov 2018 17:52:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Nov 2018 17:52:25: #3 Call peaks for each chromosome... INFO @ Sun, 04 Nov 2018 17:52:25: #3 Call peaks for each chromosome... INFO @ Sun, 04 Nov 2018 17:52:25: #3 Call peaks for each chromosome... INFO @ Sun, 04 Nov 2018 17:52:29: #4 Write output xls file... SRX4375851.20_peaks.xls INFO @ Sun, 04 Nov 2018 17:52:29: #4 Write peak in narrowPeak format file... SRX4375851.20_peaks.narrowPeak INFO @ Sun, 04 Nov 2018 17:52:29: #4 Write summits bed file... SRX4375851.20_summits.bed INFO @ Sun, 04 Nov 2018 17:52:29: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (703 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 04 Nov 2018 17:52:29: #4 Write output xls file... SRX4375851.10_peaks.xls INFO @ Sun, 04 Nov 2018 17:52:29: #4 Write peak in narrowPeak format file... SRX4375851.10_peaks.narrowPeak INFO @ Sun, 04 Nov 2018 17:52:29: #4 Write summits bed file... SRX4375851.10_summits.bed INFO @ Sun, 04 Nov 2018 17:52:29: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (966 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 04 Nov 2018 17:52:30: #4 Write output xls file... SRX4375851.05_peaks.xls INFO @ Sun, 04 Nov 2018 17:52:30: #4 Write peak in narrowPeak format file... SRX4375851.05_peaks.narrowPeak INFO @ Sun, 04 Nov 2018 17:52:30: #4 Write summits bed file... SRX4375851.05_summits.bed INFO @ Sun, 04 Nov 2018 17:52:30: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1476 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。