Job ID = 10480673 sra ファイルのダウンロード中... Completed: 559682K bytes transferred in 18 seconds (254352K 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 16128026 spots for /home/okishinya/chipatlas/results/dm3/SRX3009515/SRR5832216.sra Written 16128026 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: 00:00:01 Multiseed full-index search: 00:06:22 16128026 reads; of these: 16128026 (100.00%) were unpaired; of these: 3541417 (21.96%) aligned 0 times 8694776 (53.91%) aligned exactly 1 time 3891833 (24.13%) aligned >1 times 78.04% overall alignment rate Time searching: 00:06:23 Overall time: 00:06:23 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] 3518400 / 12586609 = 0.2795 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 07:40:16: # Command line: callpeak -t SRX3009515.bam -f BAM -g dm -n SRX3009515.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3009515.05 # format = BAM # ChIP-seq file = ['SRX3009515.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 07:40:16: #1 read tag files... INFO @ Fri, 16 Mar 2018 07:40:16: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 07:40:16: # Command line: callpeak -t SRX3009515.bam -f BAM -g dm -n SRX3009515.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3009515.10 # format = BAM # ChIP-seq file = ['SRX3009515.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 07:40:16: #1 read tag files... INFO @ Fri, 16 Mar 2018 07:40:16: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 07:40:16: # Command line: callpeak -t SRX3009515.bam -f BAM -g dm -n SRX3009515.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3009515.20 # format = BAM # ChIP-seq file = ['SRX3009515.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 07:40:16: #1 read tag files... INFO @ Fri, 16 Mar 2018 07:40:16: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 07:40:23: 1000000 INFO @ Fri, 16 Mar 2018 07:40:23: 1000000 INFO @ Fri, 16 Mar 2018 07:40:23: 1000000 INFO @ Fri, 16 Mar 2018 07:40:29: 2000000 INFO @ Fri, 16 Mar 2018 07:40:29: 2000000 INFO @ Fri, 16 Mar 2018 07:40:30: 2000000 INFO @ Fri, 16 Mar 2018 07:40:35: 3000000 INFO @ Fri, 16 Mar 2018 07:40:36: 3000000 INFO @ Fri, 16 Mar 2018 07:40:36: 3000000 INFO @ Fri, 16 Mar 2018 07:40:42: 4000000 INFO @ Fri, 16 Mar 2018 07:40:42: 4000000 INFO @ Fri, 16 Mar 2018 07:40:43: 4000000 INFO @ Fri, 16 Mar 2018 07:40:48: 5000000 INFO @ Fri, 16 Mar 2018 07:40:49: 5000000 INFO @ Fri, 16 Mar 2018 07:40:50: 5000000 INFO @ Fri, 16 Mar 2018 07:40:54: 6000000 INFO @ Fri, 16 Mar 2018 07:40:55: 6000000 INFO @ Fri, 16 Mar 2018 07:40:57: 6000000 INFO @ Fri, 16 Mar 2018 07:41:01: 7000000 INFO @ Fri, 16 Mar 2018 07:41:02: 7000000 INFO @ Fri, 16 Mar 2018 07:41:04: 7000000 INFO @ Fri, 16 Mar 2018 07:41:07: 8000000 INFO @ Fri, 16 Mar 2018 07:41:09: 8000000 INFO @ Fri, 16 Mar 2018 07:41:11: 8000000 INFO @ Fri, 16 Mar 2018 07:41:14: 9000000 INFO @ Fri, 16 Mar 2018 07:41:15: #1 tag size is determined as 51 bps INFO @ Fri, 16 Mar 2018 07:41:15: #1 tag size = 51 INFO @ Fri, 16 Mar 2018 07:41:15: #1 total tags in treatment: 9068209 INFO @ Fri, 16 Mar 2018 07:41:15: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 07:41:15: #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 07:41:15: #1 tags after filtering in treatment: 9068209 INFO @ Fri, 16 Mar 2018 07:41:15: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 07:41:15: #1 finished! INFO @ Fri, 16 Mar 2018 07:41:15: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 07:41:15: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 07:41:15: #2 number of paired peaks: 640 WARNING @ Fri, 16 Mar 2018 07:41:15: Fewer paired peaks (640) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 640 pairs to build model! INFO @ Fri, 16 Mar 2018 07:41:15: start model_add_line... INFO @ Fri, 16 Mar 2018 07:41:15: start X-correlation... INFO @ Fri, 16 Mar 2018 07:41:16: 9000000 INFO @ Fri, 16 Mar 2018 07:41:16: end of X-cor INFO @ Fri, 16 Mar 2018 07:41:16: #2 finished! INFO @ Fri, 16 Mar 2018 07:41:16: #2 predicted fragment length is 53 bps INFO @ Fri, 16 Mar 2018 07:41:16: #2 alternative fragment length(s) may be 53 bps INFO @ Fri, 16 Mar 2018 07:41:16: #2.2 Generate R script for model : SRX3009515.10_model.r WARNING @ Fri, 16 Mar 2018 07:41:16: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 16 Mar 2018 07:41:16: #2 You may need to consider one of the other alternative d(s): 53 WARNING @ Fri, 16 Mar 2018 07:41:16: #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 07:41:16: #3 Call peaks... INFO @ Fri, 16 Mar 2018 07:41:16: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 07:41:16: #1 tag size is determined as 51 bps INFO @ Fri, 16 Mar 2018 07:41:16: #1 tag size = 51 INFO @ Fri, 16 Mar 2018 07:41:16: #1 total tags in treatment: 9068209 INFO @ Fri, 16 Mar 2018 07:41:16: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 07:41:16: #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 07:41:16: #1 tags after filtering in treatment: 9068209 INFO @ Fri, 16 Mar 2018 07:41:16: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 07:41:16: #1 finished! INFO @ Fri, 16 Mar 2018 07:41:16: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 07:41:16: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 07:41:17: #2 number of paired peaks: 640 WARNING @ Fri, 16 Mar 2018 07:41:17: Fewer paired peaks (640) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 640 pairs to build model! INFO @ Fri, 16 Mar 2018 07:41:17: start model_add_line... INFO @ Fri, 16 Mar 2018 07:41:17: start X-correlation... INFO @ Fri, 16 Mar 2018 07:41:17: end of X-cor INFO @ Fri, 16 Mar 2018 07:41:17: #2 finished! INFO @ Fri, 16 Mar 2018 07:41:17: #2 predicted fragment length is 53 bps INFO @ Fri, 16 Mar 2018 07:41:17: #2 alternative fragment length(s) may be 53 bps INFO @ Fri, 16 Mar 2018 07:41:17: #2.2 Generate R script for model : SRX3009515.05_model.r WARNING @ Fri, 16 Mar 2018 07:41:17: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 16 Mar 2018 07:41:17: #2 You may need to consider one of the other alternative d(s): 53 WARNING @ Fri, 16 Mar 2018 07:41:17: #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 07:41:17: #3 Call peaks... INFO @ Fri, 16 Mar 2018 07:41:17: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 07:41:18: 9000000 INFO @ Fri, 16 Mar 2018 07:41:19: #1 tag size is determined as 51 bps INFO @ Fri, 16 Mar 2018 07:41:19: #1 tag size = 51 INFO @ Fri, 16 Mar 2018 07:41:19: #1 total tags in treatment: 9068209 INFO @ Fri, 16 Mar 2018 07:41:19: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 07:41:19: #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 07:41:19: #1 tags after filtering in treatment: 9068209 INFO @ Fri, 16 Mar 2018 07:41:19: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 07:41:19: #1 finished! INFO @ Fri, 16 Mar 2018 07:41:19: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 07:41:19: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 07:41:19: #2 number of paired peaks: 640 WARNING @ Fri, 16 Mar 2018 07:41:19: Fewer paired peaks (640) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 640 pairs to build model! INFO @ Fri, 16 Mar 2018 07:41:19: start model_add_line... INFO @ Fri, 16 Mar 2018 07:41:20: start X-correlation... INFO @ Fri, 16 Mar 2018 07:41:20: end of X-cor INFO @ Fri, 16 Mar 2018 07:41:20: #2 finished! INFO @ Fri, 16 Mar 2018 07:41:20: #2 predicted fragment length is 53 bps INFO @ Fri, 16 Mar 2018 07:41:20: #2 alternative fragment length(s) may be 53 bps INFO @ Fri, 16 Mar 2018 07:41:20: #2.2 Generate R script for model : SRX3009515.20_model.r WARNING @ Fri, 16 Mar 2018 07:41:20: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 16 Mar 2018 07:41:20: #2 You may need to consider one of the other alternative d(s): 53 WARNING @ Fri, 16 Mar 2018 07:41:20: #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 07:41:20: #3 Call peaks... INFO @ Fri, 16 Mar 2018 07:41:20: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 07:41:36: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 07:41:37: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 07:41:40: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 07:41:46: #4 Write output xls file... SRX3009515.10_peaks.xls INFO @ Fri, 16 Mar 2018 07:41:46: #4 Write peak in narrowPeak format file... SRX3009515.10_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 07:41:46: #4 Write summits bed file... SRX3009515.10_summits.bed INFO @ Fri, 16 Mar 2018 07:41:47: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1474 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 16 Mar 2018 07:41:49: #4 Write output xls file... SRX3009515.05_peaks.xls INFO @ Fri, 16 Mar 2018 07:41:49: #4 Write peak in narrowPeak format file... SRX3009515.05_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 07:41:49: #4 Write summits bed file... SRX3009515.05_summits.bed INFO @ Fri, 16 Mar 2018 07:41:49: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2823 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 16 Mar 2018 07:41:50: #4 Write output xls file... SRX3009515.20_peaks.xls INFO @ Fri, 16 Mar 2018 07:41:50: #4 Write peak in narrowPeak format file... SRX3009515.20_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 07:41:50: #4 Write summits bed file... SRX3009515.20_summits.bed INFO @ Fri, 16 Mar 2018 07:41:50: Done! pass1 - making usageList (11 chroms): 0 millis pass2 - checking and writing primary data (1017 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。