Job ID = 10480672 sra ファイルのダウンロード中... Completed: 370470K bytes transferred in 9 seconds (327707K 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... Written 10673586 spots for /home/okishinya/chipatlas/results/dm3/SRX3009514/SRR5832215.sra Written 10673586 spots total 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: 00:02:49 10673586 reads; of these: 10673586 (100.00%) were unpaired; of these: 4931326 (46.20%) aligned 0 times 4282653 (40.12%) aligned exactly 1 time 1459607 (13.67%) aligned >1 times 53.80% overall alignment rate Time searching: 00:02:49 Overall time: 00:02:49 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] 1332222 / 5742260 = 0.2320 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 @ Fri, 16 Mar 2018 07:33:35: # Command line: callpeak -t SRX3009514.bam -f BAM -g dm -n SRX3009514.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3009514.05 # format = BAM # ChIP-seq file = ['SRX3009514.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 @ Fri, 16 Mar 2018 07:33:35: #1 read tag files... INFO @ Fri, 16 Mar 2018 07:33:35: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 07:33:35: # Command line: callpeak -t SRX3009514.bam -f BAM -g dm -n SRX3009514.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3009514.10 # format = BAM # ChIP-seq file = ['SRX3009514.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 @ Fri, 16 Mar 2018 07:33:35: #1 read tag files... INFO @ Fri, 16 Mar 2018 07:33:35: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 07:33:35: # Command line: callpeak -t SRX3009514.bam -f BAM -g dm -n SRX3009514.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3009514.20 # format = BAM # ChIP-seq file = ['SRX3009514.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 @ Fri, 16 Mar 2018 07:33:35: #1 read tag files... INFO @ Fri, 16 Mar 2018 07:33:35: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 07:33:42: 1000000 INFO @ Fri, 16 Mar 2018 07:33:43: 1000000 INFO @ Fri, 16 Mar 2018 07:33:43: 1000000 INFO @ Fri, 16 Mar 2018 07:33:49: 2000000 INFO @ Fri, 16 Mar 2018 07:33:51: 2000000 INFO @ Fri, 16 Mar 2018 07:33:51: 2000000 INFO @ Fri, 16 Mar 2018 07:33:56: 3000000 INFO @ Fri, 16 Mar 2018 07:33:59: 3000000 INFO @ Fri, 16 Mar 2018 07:33:59: 3000000 INFO @ Fri, 16 Mar 2018 07:34:03: 4000000 INFO @ Fri, 16 Mar 2018 07:34:06: #1 tag size is determined as 51 bps INFO @ Fri, 16 Mar 2018 07:34:06: #1 tag size = 51 INFO @ Fri, 16 Mar 2018 07:34:06: #1 total tags in treatment: 4410038 INFO @ Fri, 16 Mar 2018 07:34:06: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 07:34:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Mar 2018 07:34:06: #1 tags after filtering in treatment: 4410038 INFO @ Fri, 16 Mar 2018 07:34:06: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 07:34:06: #1 finished! INFO @ Fri, 16 Mar 2018 07:34:06: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 07:34:06: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 07:34:06: #2 number of paired peaks: 642 WARNING @ Fri, 16 Mar 2018 07:34:06: Fewer paired peaks (642) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 642 pairs to build model! INFO @ Fri, 16 Mar 2018 07:34:06: start model_add_line... INFO @ Fri, 16 Mar 2018 07:34:06: start X-correlation... INFO @ Fri, 16 Mar 2018 07:34:06: end of X-cor INFO @ Fri, 16 Mar 2018 07:34:06: #2 finished! INFO @ Fri, 16 Mar 2018 07:34:06: #2 predicted fragment length is 55 bps INFO @ Fri, 16 Mar 2018 07:34:06: #2 alternative fragment length(s) may be 55 bps INFO @ Fri, 16 Mar 2018 07:34:06: #2.2 Generate R script for model : SRX3009514.20_model.r WARNING @ Fri, 16 Mar 2018 07:34:06: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 16 Mar 2018 07:34:06: #2 You may need to consider one of the other alternative d(s): 55 WARNING @ Fri, 16 Mar 2018 07:34:06: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 16 Mar 2018 07:34:06: #3 Call peaks... INFO @ Fri, 16 Mar 2018 07:34:06: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 07:34:06: 4000000 INFO @ Fri, 16 Mar 2018 07:34:06: 4000000 INFO @ Fri, 16 Mar 2018 07:34:09: #1 tag size is determined as 51 bps INFO @ Fri, 16 Mar 2018 07:34:09: #1 tag size = 51 INFO @ Fri, 16 Mar 2018 07:34:09: #1 total tags in treatment: 4410038 INFO @ Fri, 16 Mar 2018 07:34:09: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 07:34:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Mar 2018 07:34:09: #1 tag size is determined as 51 bps INFO @ Fri, 16 Mar 2018 07:34:09: #1 tag size = 51 INFO @ Fri, 16 Mar 2018 07:34:09: #1 total tags in treatment: 4410038 INFO @ Fri, 16 Mar 2018 07:34:09: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 07:34:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Mar 2018 07:34:10: #1 tags after filtering in treatment: 4410038 INFO @ Fri, 16 Mar 2018 07:34:10: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 07:34:10: #1 finished! INFO @ Fri, 16 Mar 2018 07:34:10: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 07:34:10: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 07:34:10: #1 tags after filtering in treatment: 4410038 INFO @ Fri, 16 Mar 2018 07:34:10: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 07:34:10: #1 finished! INFO @ Fri, 16 Mar 2018 07:34:10: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 07:34:10: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 07:34:10: #2 number of paired peaks: 642 WARNING @ Fri, 16 Mar 2018 07:34:10: Fewer paired peaks (642) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 642 pairs to build model! INFO @ Fri, 16 Mar 2018 07:34:10: start model_add_line... INFO @ Fri, 16 Mar 2018 07:34:10: #2 number of paired peaks: 642 WARNING @ Fri, 16 Mar 2018 07:34:10: Fewer paired peaks (642) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 642 pairs to build model! INFO @ Fri, 16 Mar 2018 07:34:10: start model_add_line... INFO @ Fri, 16 Mar 2018 07:34:10: start X-correlation... INFO @ Fri, 16 Mar 2018 07:34:10: end of X-cor INFO @ Fri, 16 Mar 2018 07:34:10: #2 finished! INFO @ Fri, 16 Mar 2018 07:34:10: #2 predicted fragment length is 55 bps INFO @ Fri, 16 Mar 2018 07:34:10: #2 alternative fragment length(s) may be 55 bps INFO @ Fri, 16 Mar 2018 07:34:10: #2.2 Generate R script for model : SRX3009514.10_model.r INFO @ Fri, 16 Mar 2018 07:34:10: start X-correlation... INFO @ Fri, 16 Mar 2018 07:34:10: end of X-cor INFO @ Fri, 16 Mar 2018 07:34:10: #2 finished! INFO @ Fri, 16 Mar 2018 07:34:10: #2 predicted fragment length is 55 bps INFO @ Fri, 16 Mar 2018 07:34:10: #2 alternative fragment length(s) may be 55 bps INFO @ Fri, 16 Mar 2018 07:34:10: #2.2 Generate R script for model : SRX3009514.05_model.r WARNING @ Fri, 16 Mar 2018 07:34:10: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 16 Mar 2018 07:34:10: #2 You may need to consider one of the other alternative d(s): 55 WARNING @ Fri, 16 Mar 2018 07:34:10: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 16 Mar 2018 07:34:10: #3 Call peaks... INFO @ Fri, 16 Mar 2018 07:34:10: #3 Pre-compute pvalue-qvalue table... WARNING @ Fri, 16 Mar 2018 07:34:10: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 16 Mar 2018 07:34:10: #2 You may need to consider one of the other alternative d(s): 55 WARNING @ Fri, 16 Mar 2018 07:34:10: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 16 Mar 2018 07:34:10: #3 Call peaks... INFO @ Fri, 16 Mar 2018 07:34:10: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 07:34:17: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 07:34:20: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 07:34:20: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 07:34:22: #4 Write output xls file... SRX3009514.20_peaks.xls INFO @ Fri, 16 Mar 2018 07:34:22: #4 Write peak in narrowPeak format file... SRX3009514.20_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 07:34:22: #4 Write summits bed file... SRX3009514.20_summits.bed INFO @ Fri, 16 Mar 2018 07:34:22: Done! pass1 - making usageList (8 chroms): 0 millis pass2 - checking and writing primary data (719 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 16 Mar 2018 07:34:26: #4 Write output xls file... SRX3009514.05_peaks.xls INFO @ Fri, 16 Mar 2018 07:34:26: #4 Write peak in narrowPeak format file... SRX3009514.05_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 07:34:26: #4 Write summits bed file... SRX3009514.05_summits.bed INFO @ Fri, 16 Mar 2018 07:34:26: Done! INFO @ Fri, 16 Mar 2018 07:34:26: #4 Write output xls file... SRX3009514.10_peaks.xls INFO @ Fri, 16 Mar 2018 07:34:26: #4 Write peak in narrowPeak format file... SRX3009514.10_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 07:34:26: #4 Write summits bed file... SRX3009514.10_summits.bed INFO @ Fri, 16 Mar 2018 07:34:26: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (1239 records, 4 fields): 4 millis CompletedMACS2peakCalling pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (951 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。