Job ID = 11171318 sra ファイルのダウンロード中... Completed: 562627K bytes transferred in 12 seconds (368769K 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 12669853 spots for /home/okishinya/chipatlas/results/dm3/SRX3511949/SRR6418934.sra Written 12669853 spots for /home/okishinya/chipatlas/results/dm3/SRX3511949/SRR6418934.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: 00:07:57 12669853 reads; of these: 12669853 (100.00%) were unpaired; of these: 1154182 (9.11%) aligned 0 times 8593237 (67.82%) aligned exactly 1 time 2922434 (23.07%) aligned >1 times 90.89% overall alignment rate Time searching: 00:07:57 Overall time: 00:07:57 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] 667293 / 11515671 = 0.0579 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 @ Sat, 08 Sep 2018 13:55:19: # Command line: callpeak -t SRX3511949.bam -f BAM -g dm -n SRX3511949.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3511949.05 # format = BAM # ChIP-seq file = ['SRX3511949.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 @ Sat, 08 Sep 2018 13:55:19: #1 read tag files... INFO @ Sat, 08 Sep 2018 13:55:19: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 13:55:19: # Command line: callpeak -t SRX3511949.bam -f BAM -g dm -n SRX3511949.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3511949.10 # format = BAM # ChIP-seq file = ['SRX3511949.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 @ Sat, 08 Sep 2018 13:55:19: #1 read tag files... INFO @ Sat, 08 Sep 2018 13:55:19: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 13:55:19: # Command line: callpeak -t SRX3511949.bam -f BAM -g dm -n SRX3511949.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3511949.20 # format = BAM # ChIP-seq file = ['SRX3511949.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 @ Sat, 08 Sep 2018 13:55:19: #1 read tag files... INFO @ Sat, 08 Sep 2018 13:55:19: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 13:55:27: 1000000 INFO @ Sat, 08 Sep 2018 13:55:27: 1000000 INFO @ Sat, 08 Sep 2018 13:55:27: 1000000 INFO @ Sat, 08 Sep 2018 13:55:34: 2000000 INFO @ Sat, 08 Sep 2018 13:55:34: 2000000 INFO @ Sat, 08 Sep 2018 13:55:34: 2000000 INFO @ Sat, 08 Sep 2018 13:55:42: 3000000 INFO @ Sat, 08 Sep 2018 13:55:42: 3000000 INFO @ Sat, 08 Sep 2018 13:55:42: 3000000 INFO @ Sat, 08 Sep 2018 13:55:49: 4000000 INFO @ Sat, 08 Sep 2018 13:55:49: 4000000 INFO @ Sat, 08 Sep 2018 13:55:50: 4000000 INFO @ Sat, 08 Sep 2018 13:55:56: 5000000 INFO @ Sat, 08 Sep 2018 13:55:57: 5000000 INFO @ Sat, 08 Sep 2018 13:55:57: 5000000 INFO @ Sat, 08 Sep 2018 13:56:04: 6000000 INFO @ Sat, 08 Sep 2018 13:56:05: 6000000 INFO @ Sat, 08 Sep 2018 13:56:05: 6000000 INFO @ Sat, 08 Sep 2018 13:56:12: 7000000 INFO @ Sat, 08 Sep 2018 13:56:12: 7000000 INFO @ Sat, 08 Sep 2018 13:56:12: 7000000 INFO @ Sat, 08 Sep 2018 13:56:20: 8000000 INFO @ Sat, 08 Sep 2018 13:56:20: 8000000 INFO @ Sat, 08 Sep 2018 13:56:20: 8000000 INFO @ Sat, 08 Sep 2018 13:56:28: 9000000 INFO @ Sat, 08 Sep 2018 13:56:28: 9000000 INFO @ Sat, 08 Sep 2018 13:56:28: 9000000 INFO @ Sat, 08 Sep 2018 13:56:35: 10000000 INFO @ Sat, 08 Sep 2018 13:56:36: 10000000 INFO @ Sat, 08 Sep 2018 13:56:37: 10000000 INFO @ Sat, 08 Sep 2018 13:56:42: #1 tag size is determined as 100 bps INFO @ Sat, 08 Sep 2018 13:56:42: #1 tag size = 100 INFO @ Sat, 08 Sep 2018 13:56:42: #1 total tags in treatment: 10848378 INFO @ Sat, 08 Sep 2018 13:56:42: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 13:56:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 13:56:42: #1 tags after filtering in treatment: 10848378 INFO @ Sat, 08 Sep 2018 13:56:42: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 13:56:42: #1 finished! INFO @ Sat, 08 Sep 2018 13:56:42: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 13:56:42: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 13:56:42: #1 tag size is determined as 100 bps INFO @ Sat, 08 Sep 2018 13:56:42: #1 tag size = 100 INFO @ Sat, 08 Sep 2018 13:56:42: #1 total tags in treatment: 10848378 INFO @ Sat, 08 Sep 2018 13:56:42: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 13:56:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 13:56:43: #1 tags after filtering in treatment: 10848378 INFO @ Sat, 08 Sep 2018 13:56:43: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 13:56:43: #1 finished! INFO @ Sat, 08 Sep 2018 13:56:43: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 13:56:43: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 13:56:43: #2 number of paired peaks: 101 WARNING @ Sat, 08 Sep 2018 13:56:43: Fewer paired peaks (101) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 101 pairs to build model! INFO @ Sat, 08 Sep 2018 13:56:43: start model_add_line... INFO @ Sat, 08 Sep 2018 13:56:43: start X-correlation... INFO @ Sat, 08 Sep 2018 13:56:43: end of X-cor INFO @ Sat, 08 Sep 2018 13:56:43: #2 finished! INFO @ Sat, 08 Sep 2018 13:56:43: #2 predicted fragment length is 112 bps INFO @ Sat, 08 Sep 2018 13:56:43: #2 alternative fragment length(s) may be 112 bps INFO @ Sat, 08 Sep 2018 13:56:43: #2.2 Generate R script for model : SRX3511949.10_model.r WARNING @ Sat, 08 Sep 2018 13:56:43: #2 Since the d (112) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 13:56:43: #2 You may need to consider one of the other alternative d(s): 112 WARNING @ Sat, 08 Sep 2018 13:56:43: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Sep 2018 13:56:43: #3 Call peaks... INFO @ Sat, 08 Sep 2018 13:56:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 13:56:43: #2 number of paired peaks: 101 WARNING @ Sat, 08 Sep 2018 13:56:43: Fewer paired peaks (101) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 101 pairs to build model! INFO @ Sat, 08 Sep 2018 13:56:43: start model_add_line... INFO @ Sat, 08 Sep 2018 13:56:43: start X-correlation... INFO @ Sat, 08 Sep 2018 13:56:43: end of X-cor INFO @ Sat, 08 Sep 2018 13:56:43: #2 finished! INFO @ Sat, 08 Sep 2018 13:56:43: #2 predicted fragment length is 112 bps INFO @ Sat, 08 Sep 2018 13:56:43: #2 alternative fragment length(s) may be 112 bps INFO @ Sat, 08 Sep 2018 13:56:43: #2.2 Generate R script for model : SRX3511949.05_model.r WARNING @ Sat, 08 Sep 2018 13:56:43: #2 Since the d (112) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 13:56:43: #2 You may need to consider one of the other alternative d(s): 112 WARNING @ Sat, 08 Sep 2018 13:56:43: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Sep 2018 13:56:43: #3 Call peaks... INFO @ Sat, 08 Sep 2018 13:56:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 13:56:44: #1 tag size is determined as 100 bps INFO @ Sat, 08 Sep 2018 13:56:44: #1 tag size = 100 INFO @ Sat, 08 Sep 2018 13:56:44: #1 total tags in treatment: 10848378 INFO @ Sat, 08 Sep 2018 13:56:44: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 13:56:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 13:56:44: #1 tags after filtering in treatment: 10848378 INFO @ Sat, 08 Sep 2018 13:56:44: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 13:56:44: #1 finished! INFO @ Sat, 08 Sep 2018 13:56:44: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 13:56:44: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 13:56:45: #2 number of paired peaks: 101 WARNING @ Sat, 08 Sep 2018 13:56:45: Fewer paired peaks (101) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 101 pairs to build model! INFO @ Sat, 08 Sep 2018 13:56:45: start model_add_line... INFO @ Sat, 08 Sep 2018 13:56:45: start X-correlation... INFO @ Sat, 08 Sep 2018 13:56:45: end of X-cor INFO @ Sat, 08 Sep 2018 13:56:45: #2 finished! INFO @ Sat, 08 Sep 2018 13:56:45: #2 predicted fragment length is 112 bps INFO @ Sat, 08 Sep 2018 13:56:45: #2 alternative fragment length(s) may be 112 bps INFO @ Sat, 08 Sep 2018 13:56:45: #2.2 Generate R script for model : SRX3511949.20_model.r WARNING @ Sat, 08 Sep 2018 13:56:45: #2 Since the d (112) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 13:56:45: #2 You may need to consider one of the other alternative d(s): 112 WARNING @ Sat, 08 Sep 2018 13:56:45: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Sep 2018 13:56:45: #3 Call peaks... INFO @ Sat, 08 Sep 2018 13:56:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 13:57:05: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 13:57:06: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 13:57:07: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 13:57:18: #4 Write output xls file... SRX3511949.10_peaks.xls INFO @ Sat, 08 Sep 2018 13:57:18: #4 Write peak in narrowPeak format file... SRX3511949.10_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 13:57:18: #4 Write summits bed file... SRX3511949.10_summits.bed INFO @ Sat, 08 Sep 2018 13:57:18: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (458 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 13:57:19: #4 Write output xls file... SRX3511949.05_peaks.xls INFO @ Sat, 08 Sep 2018 13:57:19: #4 Write peak in narrowPeak format file... SRX3511949.05_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 13:57:19: #4 Write summits bed file... SRX3511949.05_summits.bed INFO @ Sat, 08 Sep 2018 13:57:19: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (762 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 13:57:22: #4 Write output xls file... SRX3511949.20_peaks.xls INFO @ Sat, 08 Sep 2018 13:57:22: #4 Write peak in narrowPeak format file... SRX3511949.20_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 13:57:22: #4 Write summits bed file... SRX3511949.20_summits.bed INFO @ Sat, 08 Sep 2018 13:57:22: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (254 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。