Job ID = 11632732 sra ファイルのダウンロード中... Completed: 573090K bytes transferred in 8 seconds (568547K 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 33514968 spots for /home/okishinya/chipatlas/results/rn6/SRX4497202/SRR7633472.sra Written 33514968 spots for /home/okishinya/chipatlas/results/rn6/SRX4497202/SRR7633472.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: 00:00:01 Time loading forward index: 00:00:03 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:25:36 33514968 reads; of these: 33514968 (100.00%) were unpaired; of these: 3028744 (9.04%) aligned 0 times 21744537 (64.88%) aligned exactly 1 time 8741687 (26.08%) aligned >1 times 90.96% overall alignment rate Time searching: 00:25:41 Overall time: 00:25:41 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 953 sequences. [bam_sort_core] merging from 16 files... [bam_rmdupse_core] 18001792 / 30486224 = 0.5905 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, 15 Feb 2019 07:48:48: # Command line: callpeak -t SRX4497202.bam -f BAM -g 2.15e9 -n SRX4497202.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4497202.05 # format = BAM # ChIP-seq file = ['SRX4497202.bam'] # control file = None # effective genome size = 2.15e+09 # 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, 15 Feb 2019 07:48:48: # Command line: callpeak -t SRX4497202.bam -f BAM -g 2.15e9 -n SRX4497202.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4497202.20 # format = BAM # ChIP-seq file = ['SRX4497202.bam'] # control file = None # effective genome size = 2.15e+09 # 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, 15 Feb 2019 07:48:48: #1 read tag files... INFO @ Fri, 15 Feb 2019 07:48:48: #1 read tag files... INFO @ Fri, 15 Feb 2019 07:48:48: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 07:48:48: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 07:48:48: # Command line: callpeak -t SRX4497202.bam -f BAM -g 2.15e9 -n SRX4497202.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4497202.10 # format = BAM # ChIP-seq file = ['SRX4497202.bam'] # control file = None # effective genome size = 2.15e+09 # 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, 15 Feb 2019 07:48:48: #1 read tag files... INFO @ Fri, 15 Feb 2019 07:48:48: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 07:48:54: 1000000 INFO @ Fri, 15 Feb 2019 07:48:54: 1000000 INFO @ Fri, 15 Feb 2019 07:48:54: 1000000 INFO @ Fri, 15 Feb 2019 07:49:01: 2000000 INFO @ Fri, 15 Feb 2019 07:49:01: 2000000 INFO @ Fri, 15 Feb 2019 07:49:01: 2000000 INFO @ Fri, 15 Feb 2019 07:49:07: 3000000 INFO @ Fri, 15 Feb 2019 07:49:07: 3000000 INFO @ Fri, 15 Feb 2019 07:49:07: 3000000 INFO @ Fri, 15 Feb 2019 07:49:14: 4000000 INFO @ Fri, 15 Feb 2019 07:49:14: 4000000 INFO @ Fri, 15 Feb 2019 07:49:14: 4000000 INFO @ Fri, 15 Feb 2019 07:49:20: 5000000 INFO @ Fri, 15 Feb 2019 07:49:20: 5000000 INFO @ Fri, 15 Feb 2019 07:49:21: 5000000 INFO @ Fri, 15 Feb 2019 07:49:27: 6000000 INFO @ Fri, 15 Feb 2019 07:49:27: 6000000 INFO @ Fri, 15 Feb 2019 07:49:27: 6000000 INFO @ Fri, 15 Feb 2019 07:49:33: 7000000 INFO @ Fri, 15 Feb 2019 07:49:34: 7000000 INFO @ Fri, 15 Feb 2019 07:49:34: 7000000 INFO @ Fri, 15 Feb 2019 07:49:40: 8000000 INFO @ Fri, 15 Feb 2019 07:49:40: 8000000 INFO @ Fri, 15 Feb 2019 07:49:41: 8000000 INFO @ Fri, 15 Feb 2019 07:49:46: 9000000 INFO @ Fri, 15 Feb 2019 07:49:47: 9000000 INFO @ Fri, 15 Feb 2019 07:49:48: 9000000 INFO @ Fri, 15 Feb 2019 07:49:53: 10000000 INFO @ Fri, 15 Feb 2019 07:49:53: 10000000 INFO @ Fri, 15 Feb 2019 07:49:55: 10000000 INFO @ Fri, 15 Feb 2019 07:49:59: 11000000 INFO @ Fri, 15 Feb 2019 07:50:00: 11000000 INFO @ Fri, 15 Feb 2019 07:50:02: 11000000 INFO @ Fri, 15 Feb 2019 07:50:06: 12000000 INFO @ Fri, 15 Feb 2019 07:50:07: 12000000 INFO @ Fri, 15 Feb 2019 07:50:09: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 07:50:09: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 07:50:09: #1 total tags in treatment: 12484432 INFO @ Fri, 15 Feb 2019 07:50:09: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 07:50:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 07:50:09: 12000000 INFO @ Fri, 15 Feb 2019 07:50:09: #1 tags after filtering in treatment: 12484308 INFO @ Fri, 15 Feb 2019 07:50:09: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 07:50:09: #1 finished! INFO @ Fri, 15 Feb 2019 07:50:09: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 07:50:09: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 07:50:10: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 07:50:10: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 07:50:10: #1 total tags in treatment: 12484432 INFO @ Fri, 15 Feb 2019 07:50:10: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 07:50:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 07:50:10: #1 tags after filtering in treatment: 12484308 INFO @ Fri, 15 Feb 2019 07:50:10: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 07:50:10: #1 finished! INFO @ Fri, 15 Feb 2019 07:50:10: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 07:50:10: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 07:50:11: #2 number of paired peaks: 15990 INFO @ Fri, 15 Feb 2019 07:50:11: start model_add_line... INFO @ Fri, 15 Feb 2019 07:50:11: start X-correlation... INFO @ Fri, 15 Feb 2019 07:50:11: end of X-cor INFO @ Fri, 15 Feb 2019 07:50:11: #2 finished! INFO @ Fri, 15 Feb 2019 07:50:11: #2 predicted fragment length is 51 bps INFO @ Fri, 15 Feb 2019 07:50:11: #2 alternative fragment length(s) may be 51,159,213 bps INFO @ Fri, 15 Feb 2019 07:50:11: #2.2 Generate R script for model : SRX4497202.10_model.r WARNING @ Fri, 15 Feb 2019 07:50:11: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 15 Feb 2019 07:50:11: #2 You may need to consider one of the other alternative d(s): 51,159,213 WARNING @ Fri, 15 Feb 2019 07:50:11: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 15 Feb 2019 07:50:11: #3 Call peaks... INFO @ Fri, 15 Feb 2019 07:50:12: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 07:50:12: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 07:50:12: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 07:50:12: #1 total tags in treatment: 12484432 INFO @ Fri, 15 Feb 2019 07:50:12: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 07:50:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 07:50:13: #2 number of paired peaks: 15990 INFO @ Fri, 15 Feb 2019 07:50:13: start model_add_line... INFO @ Fri, 15 Feb 2019 07:50:13: start X-correlation... INFO @ Fri, 15 Feb 2019 07:50:13: end of X-cor INFO @ Fri, 15 Feb 2019 07:50:13: #2 finished! INFO @ Fri, 15 Feb 2019 07:50:13: #2 predicted fragment length is 51 bps INFO @ Fri, 15 Feb 2019 07:50:13: #2 alternative fragment length(s) may be 51,159,213 bps INFO @ Fri, 15 Feb 2019 07:50:13: #2.2 Generate R script for model : SRX4497202.05_model.r WARNING @ Fri, 15 Feb 2019 07:50:13: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 15 Feb 2019 07:50:13: #2 You may need to consider one of the other alternative d(s): 51,159,213 WARNING @ Fri, 15 Feb 2019 07:50:13: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 15 Feb 2019 07:50:13: #3 Call peaks... INFO @ Fri, 15 Feb 2019 07:50:13: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 07:50:13: #1 tags after filtering in treatment: 12484308 INFO @ Fri, 15 Feb 2019 07:50:13: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 07:50:13: #1 finished! INFO @ Fri, 15 Feb 2019 07:50:13: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 07:50:13: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 07:50:15: #2 number of paired peaks: 15990 INFO @ Fri, 15 Feb 2019 07:50:15: start model_add_line... INFO @ Fri, 15 Feb 2019 07:50:15: start X-correlation... INFO @ Fri, 15 Feb 2019 07:50:15: end of X-cor INFO @ Fri, 15 Feb 2019 07:50:15: #2 finished! INFO @ Fri, 15 Feb 2019 07:50:15: #2 predicted fragment length is 51 bps INFO @ Fri, 15 Feb 2019 07:50:15: #2 alternative fragment length(s) may be 51,159,213 bps INFO @ Fri, 15 Feb 2019 07:50:15: #2.2 Generate R script for model : SRX4497202.20_model.r WARNING @ Fri, 15 Feb 2019 07:50:15: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 15 Feb 2019 07:50:15: #2 You may need to consider one of the other alternative d(s): 51,159,213 WARNING @ Fri, 15 Feb 2019 07:50:15: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 15 Feb 2019 07:50:15: #3 Call peaks... INFO @ Fri, 15 Feb 2019 07:50:15: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 07:50:40: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 07:50:43: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 07:50:45: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 07:50:56: #4 Write output xls file... SRX4497202.10_peaks.xls INFO @ Fri, 15 Feb 2019 07:50:56: #4 Write peak in narrowPeak format file... SRX4497202.10_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 07:50:56: #4 Write summits bed file... SRX4497202.10_summits.bed INFO @ Fri, 15 Feb 2019 07:50:56: Done! pass1 - making usageList (42 chroms): 12 millis pass2 - checking and writing primary data (830 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 07:51:00: #4 Write output xls file... SRX4497202.20_peaks.xls INFO @ Fri, 15 Feb 2019 07:51:00: #4 Write peak in narrowPeak format file... SRX4497202.20_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 07:51:00: #4 Write summits bed file... SRX4497202.20_summits.bed INFO @ Fri, 15 Feb 2019 07:51:00: Done! pass1 - making usageList (31 chroms): 3 millis pass2 - checking and writing primary data (376 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 07:51:02: #4 Write output xls file... SRX4497202.05_peaks.xls INFO @ Fri, 15 Feb 2019 07:51:02: #4 Write peak in narrowPeak format file... SRX4497202.05_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 07:51:02: #4 Write summits bed file... SRX4497202.05_summits.bed INFO @ Fri, 15 Feb 2019 07:51:02: Done! pass1 - making usageList (51 chroms): 5 millis pass2 - checking and writing primary data (1381 records, 4 fields): 15 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。