Job ID = 9157425 sra ファイルのダウンロード中... Completed: 248203K bytes transferred in 5 seconds (361696K bits/sec), in 1 file, 2 directories. 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 8786701 spots for /home/okishinya/chipatlas/results/ce10/SRX2144178/SRR4188782.sra Written 8786701 spots total 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: 00:02:23 8786701 reads; of these: 8786701 (100.00%) were unpaired; of these: 691775 (7.87%) aligned 0 times 6537006 (74.40%) aligned exactly 1 time 1557920 (17.73%) aligned >1 times 92.13% overall alignment rate Time searching: 00:02:23 Overall time: 00:02:23 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_rmdupse_core] 567784 / 8094926 = 0.0701 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 @ Tue, 27 Jun 2017 11:57:27: # Command line: callpeak -t SRX2144178.bam -f BAM -g ce -n SRX2144178.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2144178.05 # format = BAM # ChIP-seq file = ['SRX2144178.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Tue, 27 Jun 2017 11:57:27: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:57:27: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:57:27: # Command line: callpeak -t SRX2144178.bam -f BAM -g ce -n SRX2144178.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2144178.10 # format = BAM # ChIP-seq file = ['SRX2144178.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Tue, 27 Jun 2017 11:57:27: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:57:27: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:57:27: # Command line: callpeak -t SRX2144178.bam -f BAM -g ce -n SRX2144178.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2144178.20 # format = BAM # ChIP-seq file = ['SRX2144178.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Tue, 27 Jun 2017 11:57:27: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:57:27: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:57:33: 1000000 INFO @ Tue, 27 Jun 2017 11:57:34: 1000000 INFO @ Tue, 27 Jun 2017 11:57:34: 1000000 INFO @ Tue, 27 Jun 2017 11:57:40: 2000000 INFO @ Tue, 27 Jun 2017 11:57:41: 2000000 INFO @ Tue, 27 Jun 2017 11:57:41: 2000000 INFO @ Tue, 27 Jun 2017 11:57:47: 3000000 INFO @ Tue, 27 Jun 2017 11:57:48: 3000000 INFO @ Tue, 27 Jun 2017 11:57:48: 3000000 INFO @ Tue, 27 Jun 2017 11:57:53: 4000000 INFO @ Tue, 27 Jun 2017 11:57:56: 4000000 INFO @ Tue, 27 Jun 2017 11:57:56: 4000000 INFO @ Tue, 27 Jun 2017 11:58:00: 5000000 INFO @ Tue, 27 Jun 2017 11:58:03: 5000000 INFO @ Tue, 27 Jun 2017 11:58:03: 5000000 INFO @ Tue, 27 Jun 2017 11:58:07: 6000000 INFO @ Tue, 27 Jun 2017 11:58:11: 6000000 INFO @ Tue, 27 Jun 2017 11:58:11: 6000000 INFO @ Tue, 27 Jun 2017 11:58:14: 7000000 INFO @ Tue, 27 Jun 2017 11:58:17: #1 tag size is determined as 50 bps INFO @ Tue, 27 Jun 2017 11:58:17: #1 tag size = 50 INFO @ Tue, 27 Jun 2017 11:58:17: #1 total tags in treatment: 7527142 INFO @ Tue, 27 Jun 2017 11:58:17: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:58:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 11:58:18: #1 tags after filtering in treatment: 7527142 INFO @ Tue, 27 Jun 2017 11:58:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:58:18: #1 finished! INFO @ Tue, 27 Jun 2017 11:58:18: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:58:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:58:18: #2 number of paired peaks: 414 WARNING @ Tue, 27 Jun 2017 11:58:18: Fewer paired peaks (414) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 414 pairs to build model! INFO @ Tue, 27 Jun 2017 11:58:18: start model_add_line... INFO @ Tue, 27 Jun 2017 11:58:18: start X-correlation... INFO @ Tue, 27 Jun 2017 11:58:18: end of X-cor INFO @ Tue, 27 Jun 2017 11:58:18: #2 finished! INFO @ Tue, 27 Jun 2017 11:58:18: #2 predicted fragment length is 47 bps INFO @ Tue, 27 Jun 2017 11:58:18: #2 alternative fragment length(s) may be 4,47,521 bps INFO @ Tue, 27 Jun 2017 11:58:18: #2.2 Generate R script for model : SRX2144178.05_model.r WARNING @ Tue, 27 Jun 2017 11:58:18: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 11:58:18: #2 You may need to consider one of the other alternative d(s): 4,47,521 WARNING @ Tue, 27 Jun 2017 11:58:18: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 27 Jun 2017 11:58:18: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:58:18: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:58:19: 7000000 INFO @ Tue, 27 Jun 2017 11:58:19: 7000000 INFO @ Tue, 27 Jun 2017 11:58:23: #1 tag size is determined as 50 bps INFO @ Tue, 27 Jun 2017 11:58:23: #1 tag size = 50 INFO @ Tue, 27 Jun 2017 11:58:23: #1 total tags in treatment: 7527142 INFO @ Tue, 27 Jun 2017 11:58:23: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:58:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 11:58:23: #1 tag size is determined as 50 bps INFO @ Tue, 27 Jun 2017 11:58:23: #1 tag size = 50 INFO @ Tue, 27 Jun 2017 11:58:23: #1 total tags in treatment: 7527142 INFO @ Tue, 27 Jun 2017 11:58:23: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:58:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 11:58:23: #1 tags after filtering in treatment: 7527142 INFO @ Tue, 27 Jun 2017 11:58:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:58:23: #1 finished! INFO @ Tue, 27 Jun 2017 11:58:23: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:58:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:58:23: #1 tags after filtering in treatment: 7527142 INFO @ Tue, 27 Jun 2017 11:58:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:58:23: #1 finished! INFO @ Tue, 27 Jun 2017 11:58:23: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:58:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:58:23: #2 number of paired peaks: 414 WARNING @ Tue, 27 Jun 2017 11:58:23: Fewer paired peaks (414) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 414 pairs to build model! INFO @ Tue, 27 Jun 2017 11:58:23: start model_add_line... INFO @ Tue, 27 Jun 2017 11:58:23: #2 number of paired peaks: 414 WARNING @ Tue, 27 Jun 2017 11:58:23: Fewer paired peaks (414) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 414 pairs to build model! INFO @ Tue, 27 Jun 2017 11:58:23: start model_add_line... INFO @ Tue, 27 Jun 2017 11:58:24: start X-correlation... INFO @ Tue, 27 Jun 2017 11:58:24: end of X-cor INFO @ Tue, 27 Jun 2017 11:58:24: #2 finished! INFO @ Tue, 27 Jun 2017 11:58:24: #2 predicted fragment length is 47 bps INFO @ Tue, 27 Jun 2017 11:58:24: #2 alternative fragment length(s) may be 4,47,521 bps INFO @ Tue, 27 Jun 2017 11:58:24: #2.2 Generate R script for model : SRX2144178.20_model.r INFO @ Tue, 27 Jun 2017 11:58:24: start X-correlation... WARNING @ Tue, 27 Jun 2017 11:58:24: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 11:58:24: #2 You may need to consider one of the other alternative d(s): 4,47,521 WARNING @ Tue, 27 Jun 2017 11:58:24: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 27 Jun 2017 11:58:24: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:58:24: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:58:24: end of X-cor INFO @ Tue, 27 Jun 2017 11:58:24: #2 finished! INFO @ Tue, 27 Jun 2017 11:58:24: #2 predicted fragment length is 47 bps INFO @ Tue, 27 Jun 2017 11:58:24: #2 alternative fragment length(s) may be 4,47,521 bps INFO @ Tue, 27 Jun 2017 11:58:24: #2.2 Generate R script for model : SRX2144178.10_model.r WARNING @ Tue, 27 Jun 2017 11:58:24: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 11:58:24: #2 You may need to consider one of the other alternative d(s): 4,47,521 WARNING @ Tue, 27 Jun 2017 11:58:24: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 27 Jun 2017 11:58:24: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:58:24: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:58:34: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:58:40: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:58:41: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:58:43: #4 Write output xls file... SRX2144178.05_peaks.xls INFO @ Tue, 27 Jun 2017 11:58:43: #4 Write peak in narrowPeak format file... SRX2144178.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:58:43: #4 Write summits bed file... SRX2144178.05_summits.bed INFO @ Tue, 27 Jun 2017 11:58:43: Done! pass1 - making usageList (6 chroms): 4 millis pass2 - checking and writing primary data (644 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 11:58:50: #4 Write output xls file... SRX2144178.20_peaks.xls INFO @ Tue, 27 Jun 2017 11:58:50: #4 Write peak in narrowPeak format file... SRX2144178.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:58:50: #4 Write summits bed file... SRX2144178.20_summits.bed INFO @ Tue, 27 Jun 2017 11:58:50: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (170 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 11:58:51: #4 Write output xls file... SRX2144178.10_peaks.xls INFO @ Tue, 27 Jun 2017 11:58:51: #4 Write peak in narrowPeak format file... SRX2144178.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:58:51: #4 Write summits bed file... SRX2144178.10_summits.bed INFO @ Tue, 27 Jun 2017 11:58:51: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (395 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。