Job ID = 11632733 sra ファイルのダウンロード中... Completed: 864494K bytes transferred in 12 seconds (574517K 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 50998149 spots for /home/okishinya/chipatlas/results/rn6/SRX4497203/SRR7633473.sra Written 50998149 spots for /home/okishinya/chipatlas/results/rn6/SRX4497203/SRR7633473.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: 00:00:00 Multiseed full-index search: 00:37:14 50998149 reads; of these: 50998149 (100.00%) were unpaired; of these: 16555279 (32.46%) aligned 0 times 24011585 (47.08%) aligned exactly 1 time 10431285 (20.45%) aligned >1 times 67.54% overall alignment rate Time searching: 00:37:18 Overall time: 00:37:18 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] 17658346 / 34442870 = 0.5127 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 08:08:27: # Command line: callpeak -t SRX4497203.bam -f BAM -g 2.15e9 -n SRX4497203.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4497203.05 # format = BAM # ChIP-seq file = ['SRX4497203.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 08:08:27: #1 read tag files... INFO @ Fri, 15 Feb 2019 08:08:27: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 08:08:27: # Command line: callpeak -t SRX4497203.bam -f BAM -g 2.15e9 -n SRX4497203.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4497203.10 # format = BAM # ChIP-seq file = ['SRX4497203.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 08:08:27: #1 read tag files... INFO @ Fri, 15 Feb 2019 08:08:27: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 08:08:28: # Command line: callpeak -t SRX4497203.bam -f BAM -g 2.15e9 -n SRX4497203.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4497203.20 # format = BAM # ChIP-seq file = ['SRX4497203.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 08:08:28: #1 read tag files... INFO @ Fri, 15 Feb 2019 08:08:28: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 08:08:34: 1000000 INFO @ Fri, 15 Feb 2019 08:08:34: 1000000 INFO @ Fri, 15 Feb 2019 08:08:34: 1000000 INFO @ Fri, 15 Feb 2019 08:08:40: 2000000 INFO @ Fri, 15 Feb 2019 08:08:40: 2000000 INFO @ Fri, 15 Feb 2019 08:08:40: 2000000 INFO @ Fri, 15 Feb 2019 08:08:46: 3000000 INFO @ Fri, 15 Feb 2019 08:08:46: 3000000 INFO @ Fri, 15 Feb 2019 08:08:46: 3000000 INFO @ Fri, 15 Feb 2019 08:08:52: 4000000 INFO @ Fri, 15 Feb 2019 08:08:52: 4000000 INFO @ Fri, 15 Feb 2019 08:08:52: 4000000 INFO @ Fri, 15 Feb 2019 08:08:58: 5000000 INFO @ Fri, 15 Feb 2019 08:08:58: 5000000 INFO @ Fri, 15 Feb 2019 08:08:58: 5000000 INFO @ Fri, 15 Feb 2019 08:09:04: 6000000 INFO @ Fri, 15 Feb 2019 08:09:04: 6000000 INFO @ Fri, 15 Feb 2019 08:09:04: 6000000 INFO @ Fri, 15 Feb 2019 08:09:10: 7000000 INFO @ Fri, 15 Feb 2019 08:09:10: 7000000 INFO @ Fri, 15 Feb 2019 08:09:10: 7000000 INFO @ Fri, 15 Feb 2019 08:09:16: 8000000 INFO @ Fri, 15 Feb 2019 08:09:16: 8000000 INFO @ Fri, 15 Feb 2019 08:09:16: 8000000 INFO @ Fri, 15 Feb 2019 08:09:22: 9000000 INFO @ Fri, 15 Feb 2019 08:09:22: 9000000 INFO @ Fri, 15 Feb 2019 08:09:22: 9000000 INFO @ Fri, 15 Feb 2019 08:09:28: 10000000 INFO @ Fri, 15 Feb 2019 08:09:28: 10000000 INFO @ Fri, 15 Feb 2019 08:09:28: 10000000 INFO @ Fri, 15 Feb 2019 08:09:34: 11000000 INFO @ Fri, 15 Feb 2019 08:09:34: 11000000 INFO @ Fri, 15 Feb 2019 08:09:34: 11000000 INFO @ Fri, 15 Feb 2019 08:09:40: 12000000 INFO @ Fri, 15 Feb 2019 08:09:40: 12000000 INFO @ Fri, 15 Feb 2019 08:09:41: 12000000 INFO @ Fri, 15 Feb 2019 08:09:46: 13000000 INFO @ Fri, 15 Feb 2019 08:09:46: 13000000 INFO @ Fri, 15 Feb 2019 08:09:47: 13000000 INFO @ Fri, 15 Feb 2019 08:09:52: 14000000 INFO @ Fri, 15 Feb 2019 08:09:52: 14000000 INFO @ Fri, 15 Feb 2019 08:09:53: 14000000 INFO @ Fri, 15 Feb 2019 08:09:58: 15000000 INFO @ Fri, 15 Feb 2019 08:09:59: 15000000 INFO @ Fri, 15 Feb 2019 08:09:59: 15000000 INFO @ Fri, 15 Feb 2019 08:10:04: 16000000 INFO @ Fri, 15 Feb 2019 08:10:05: 16000000 INFO @ Fri, 15 Feb 2019 08:10:05: 16000000 INFO @ Fri, 15 Feb 2019 08:10:09: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 08:10:09: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 08:10:09: #1 total tags in treatment: 16784524 INFO @ Fri, 15 Feb 2019 08:10:09: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 08:10:09: #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 08:10:09: #1 tags after filtering in treatment: 16784401 INFO @ Fri, 15 Feb 2019 08:10:09: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 08:10:09: #1 finished! INFO @ Fri, 15 Feb 2019 08:10:09: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 08:10:09: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 08:10:10: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 08:10:10: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 08:10:10: #1 total tags in treatment: 16784524 INFO @ Fri, 15 Feb 2019 08:10:10: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 08:10:10: #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 08:10:10: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 08:10:10: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 08:10:10: #1 total tags in treatment: 16784524 INFO @ Fri, 15 Feb 2019 08:10:10: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 08:10:10: #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 08:10:10: #1 tags after filtering in treatment: 16784401 INFO @ Fri, 15 Feb 2019 08:10:10: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 08:10:10: #1 finished! INFO @ Fri, 15 Feb 2019 08:10:10: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 08:10:10: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 08:10:11: #1 tags after filtering in treatment: 16784401 INFO @ Fri, 15 Feb 2019 08:10:11: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 08:10:11: #1 finished! INFO @ Fri, 15 Feb 2019 08:10:11: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 08:10:11: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 08:10:11: #2 number of paired peaks: 11039 INFO @ Fri, 15 Feb 2019 08:10:11: start model_add_line... INFO @ Fri, 15 Feb 2019 08:10:12: start X-correlation... INFO @ Fri, 15 Feb 2019 08:10:12: end of X-cor INFO @ Fri, 15 Feb 2019 08:10:12: #2 finished! INFO @ Fri, 15 Feb 2019 08:10:12: #2 predicted fragment length is 50 bps INFO @ Fri, 15 Feb 2019 08:10:12: #2 alternative fragment length(s) may be 50,224,403,542 bps INFO @ Fri, 15 Feb 2019 08:10:12: #2.2 Generate R script for model : SRX4497203.05_model.r WARNING @ Fri, 15 Feb 2019 08:10:12: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 15 Feb 2019 08:10:12: #2 You may need to consider one of the other alternative d(s): 50,224,403,542 WARNING @ Fri, 15 Feb 2019 08:10:12: #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 08:10:12: #3 Call peaks... INFO @ Fri, 15 Feb 2019 08:10:12: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 08:10:12: #2 number of paired peaks: 11039 INFO @ Fri, 15 Feb 2019 08:10:12: start model_add_line... INFO @ Fri, 15 Feb 2019 08:10:13: #2 number of paired peaks: 11039 INFO @ Fri, 15 Feb 2019 08:10:13: start model_add_line... INFO @ Fri, 15 Feb 2019 08:10:13: start X-correlation... INFO @ Fri, 15 Feb 2019 08:10:13: end of X-cor INFO @ Fri, 15 Feb 2019 08:10:13: #2 finished! INFO @ Fri, 15 Feb 2019 08:10:13: #2 predicted fragment length is 50 bps INFO @ Fri, 15 Feb 2019 08:10:13: #2 alternative fragment length(s) may be 50,224,403,542 bps INFO @ Fri, 15 Feb 2019 08:10:13: #2.2 Generate R script for model : SRX4497203.10_model.r WARNING @ Fri, 15 Feb 2019 08:10:13: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 15 Feb 2019 08:10:13: #2 You may need to consider one of the other alternative d(s): 50,224,403,542 WARNING @ Fri, 15 Feb 2019 08:10:13: #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 08:10:13: #3 Call peaks... INFO @ Fri, 15 Feb 2019 08:10:13: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 08:10:13: start X-correlation... INFO @ Fri, 15 Feb 2019 08:10:13: end of X-cor INFO @ Fri, 15 Feb 2019 08:10:13: #2 finished! INFO @ Fri, 15 Feb 2019 08:10:13: #2 predicted fragment length is 50 bps INFO @ Fri, 15 Feb 2019 08:10:13: #2 alternative fragment length(s) may be 50,224,403,542 bps INFO @ Fri, 15 Feb 2019 08:10:13: #2.2 Generate R script for model : SRX4497203.20_model.r WARNING @ Fri, 15 Feb 2019 08:10:13: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 15 Feb 2019 08:10:13: #2 You may need to consider one of the other alternative d(s): 50,224,403,542 WARNING @ Fri, 15 Feb 2019 08:10:13: #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 08:10:13: #3 Call peaks... INFO @ Fri, 15 Feb 2019 08:10:13: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 08:10:51: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 08:10:53: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 08:10:53: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 08:11:15: #4 Write output xls file... SRX4497203.20_peaks.xls INFO @ Fri, 15 Feb 2019 08:11:15: #4 Write peak in narrowPeak format file... SRX4497203.20_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 08:11:15: #4 Write summits bed file... SRX4497203.20_summits.bed INFO @ Fri, 15 Feb 2019 08:11:15: Done! pass1 - making usageList (41 chroms): 5 millis pass2 - checking and writing primary data (825 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 08:11:17: #4 Write output xls file... SRX4497203.10_peaks.xls INFO @ Fri, 15 Feb 2019 08:11:17: #4 Write peak in narrowPeak format file... SRX4497203.10_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 08:11:17: #4 Write summits bed file... SRX4497203.10_summits.bed INFO @ Fri, 15 Feb 2019 08:11:17: Done! pass1 - making usageList (55 chroms): 6 millis pass2 - checking and writing primary data (2270 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 08:11:23: #4 Write output xls file... SRX4497203.05_peaks.xls INFO @ Fri, 15 Feb 2019 08:11:23: #4 Write peak in narrowPeak format file... SRX4497203.05_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 08:11:23: #4 Write summits bed file... SRX4497203.05_summits.bed INFO @ Fri, 15 Feb 2019 08:11:23: Done! pass1 - making usageList (76 chroms): 7 millis pass2 - checking and writing primary data (4604 records, 4 fields): 13 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。