Job ID = 11240708 sra ファイルのダウンロード中... Completed: 141512K bytes transferred in 5 seconds (214095K 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 5330979 spots for /home/okishinya/chipatlas/results/ce10/SRX4456931/SRR7591872.sra Written 5330979 spots for /home/okishinya/chipatlas/results/ce10/SRX4456931/SRR7591872.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: 00:01:23 5330979 reads; of these: 5330979 (100.00%) were unpaired; of these: 609954 (11.44%) aligned 0 times 3385364 (63.50%) aligned exactly 1 time 1335661 (25.05%) aligned >1 times 88.56% overall alignment rate Time searching: 00:01:23 Overall time: 00:01:23 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] 453156 / 4721025 = 0.0960 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 @ Sun, 07 Oct 2018 20:30:45: # Command line: callpeak -t SRX4456931.bam -f BAM -g ce -n SRX4456931.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4456931.20 # format = BAM # ChIP-seq file = ['SRX4456931.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 @ Sun, 07 Oct 2018 20:30:45: #1 read tag files... INFO @ Sun, 07 Oct 2018 20:30:45: #1 read treatment tags... INFO @ Sun, 07 Oct 2018 20:30:45: # Command line: callpeak -t SRX4456931.bam -f BAM -g ce -n SRX4456931.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4456931.10 # format = BAM # ChIP-seq file = ['SRX4456931.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 @ Sun, 07 Oct 2018 20:30:45: #1 read tag files... INFO @ Sun, 07 Oct 2018 20:30:45: #1 read treatment tags... INFO @ Sun, 07 Oct 2018 20:30:45: # Command line: callpeak -t SRX4456931.bam -f BAM -g ce -n SRX4456931.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4456931.05 # format = BAM # ChIP-seq file = ['SRX4456931.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 @ Sun, 07 Oct 2018 20:30:45: #1 read tag files... INFO @ Sun, 07 Oct 2018 20:30:45: #1 read treatment tags... INFO @ Sun, 07 Oct 2018 20:30:51: 1000000 INFO @ Sun, 07 Oct 2018 20:30:51: 1000000 INFO @ Sun, 07 Oct 2018 20:30:51: 1000000 INFO @ Sun, 07 Oct 2018 20:30:57: 2000000 INFO @ Sun, 07 Oct 2018 20:30:57: 2000000 INFO @ Sun, 07 Oct 2018 20:30:58: 2000000 INFO @ Sun, 07 Oct 2018 20:31:03: 3000000 INFO @ Sun, 07 Oct 2018 20:31:04: 3000000 INFO @ Sun, 07 Oct 2018 20:31:04: 3000000 INFO @ Sun, 07 Oct 2018 20:31:08: 4000000 INFO @ Sun, 07 Oct 2018 20:31:10: #1 tag size is determined as 50 bps INFO @ Sun, 07 Oct 2018 20:31:10: #1 tag size = 50 INFO @ Sun, 07 Oct 2018 20:31:10: #1 total tags in treatment: 4267869 INFO @ Sun, 07 Oct 2018 20:31:10: #1 user defined the maximum tags... INFO @ Sun, 07 Oct 2018 20:31:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 07 Oct 2018 20:31:10: #1 tags after filtering in treatment: 4267869 INFO @ Sun, 07 Oct 2018 20:31:10: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 07 Oct 2018 20:31:10: #1 finished! INFO @ Sun, 07 Oct 2018 20:31:10: #2 Build Peak Model... INFO @ Sun, 07 Oct 2018 20:31:10: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 07 Oct 2018 20:31:10: 4000000 INFO @ Sun, 07 Oct 2018 20:31:11: #2 number of paired peaks: 1585 INFO @ Sun, 07 Oct 2018 20:31:11: start model_add_line... INFO @ Sun, 07 Oct 2018 20:31:11: start X-correlation... INFO @ Sun, 07 Oct 2018 20:31:11: end of X-cor INFO @ Sun, 07 Oct 2018 20:31:11: #2 finished! INFO @ Sun, 07 Oct 2018 20:31:11: #2 predicted fragment length is 60 bps INFO @ Sun, 07 Oct 2018 20:31:11: #2 alternative fragment length(s) may be 3,60 bps INFO @ Sun, 07 Oct 2018 20:31:11: #2.2 Generate R script for model : SRX4456931.05_model.r WARNING @ Sun, 07 Oct 2018 20:31:11: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 07 Oct 2018 20:31:11: #2 You may need to consider one of the other alternative d(s): 3,60 WARNING @ Sun, 07 Oct 2018 20:31:11: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 07 Oct 2018 20:31:11: #3 Call peaks... INFO @ Sun, 07 Oct 2018 20:31:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 07 Oct 2018 20:31:11: 4000000 INFO @ Sun, 07 Oct 2018 20:31:12: #1 tag size is determined as 50 bps INFO @ Sun, 07 Oct 2018 20:31:12: #1 tag size = 50 INFO @ Sun, 07 Oct 2018 20:31:12: #1 total tags in treatment: 4267869 INFO @ Sun, 07 Oct 2018 20:31:12: #1 user defined the maximum tags... INFO @ Sun, 07 Oct 2018 20:31:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 07 Oct 2018 20:31:12: #1 tags after filtering in treatment: 4267869 INFO @ Sun, 07 Oct 2018 20:31:12: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 07 Oct 2018 20:31:12: #1 finished! INFO @ Sun, 07 Oct 2018 20:31:12: #2 Build Peak Model... INFO @ Sun, 07 Oct 2018 20:31:12: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 07 Oct 2018 20:31:12: #2 number of paired peaks: 1585 INFO @ Sun, 07 Oct 2018 20:31:12: start model_add_line... INFO @ Sun, 07 Oct 2018 20:31:12: start X-correlation... INFO @ Sun, 07 Oct 2018 20:31:12: end of X-cor INFO @ Sun, 07 Oct 2018 20:31:12: #2 finished! INFO @ Sun, 07 Oct 2018 20:31:12: #2 predicted fragment length is 60 bps INFO @ Sun, 07 Oct 2018 20:31:12: #2 alternative fragment length(s) may be 3,60 bps INFO @ Sun, 07 Oct 2018 20:31:12: #2.2 Generate R script for model : SRX4456931.10_model.r WARNING @ Sun, 07 Oct 2018 20:31:12: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 07 Oct 2018 20:31:12: #2 You may need to consider one of the other alternative d(s): 3,60 WARNING @ Sun, 07 Oct 2018 20:31:12: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 07 Oct 2018 20:31:12: #3 Call peaks... INFO @ Sun, 07 Oct 2018 20:31:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 07 Oct 2018 20:31:13: #1 tag size is determined as 50 bps INFO @ Sun, 07 Oct 2018 20:31:13: #1 tag size = 50 INFO @ Sun, 07 Oct 2018 20:31:13: #1 total tags in treatment: 4267869 INFO @ Sun, 07 Oct 2018 20:31:13: #1 user defined the maximum tags... INFO @ Sun, 07 Oct 2018 20:31:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 07 Oct 2018 20:31:13: #1 tags after filtering in treatment: 4267869 INFO @ Sun, 07 Oct 2018 20:31:13: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 07 Oct 2018 20:31:13: #1 finished! INFO @ Sun, 07 Oct 2018 20:31:13: #2 Build Peak Model... INFO @ Sun, 07 Oct 2018 20:31:13: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 07 Oct 2018 20:31:13: #2 number of paired peaks: 1585 INFO @ Sun, 07 Oct 2018 20:31:13: start model_add_line... INFO @ Sun, 07 Oct 2018 20:31:14: start X-correlation... INFO @ Sun, 07 Oct 2018 20:31:14: end of X-cor INFO @ Sun, 07 Oct 2018 20:31:14: #2 finished! INFO @ Sun, 07 Oct 2018 20:31:14: #2 predicted fragment length is 60 bps INFO @ Sun, 07 Oct 2018 20:31:14: #2 alternative fragment length(s) may be 3,60 bps INFO @ Sun, 07 Oct 2018 20:31:14: #2.2 Generate R script for model : SRX4456931.20_model.r WARNING @ Sun, 07 Oct 2018 20:31:14: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 07 Oct 2018 20:31:14: #2 You may need to consider one of the other alternative d(s): 3,60 WARNING @ Sun, 07 Oct 2018 20:31:14: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 07 Oct 2018 20:31:14: #3 Call peaks... INFO @ Sun, 07 Oct 2018 20:31:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 07 Oct 2018 20:31:21: #3 Call peaks for each chromosome... INFO @ Sun, 07 Oct 2018 20:31:23: #3 Call peaks for each chromosome... INFO @ Sun, 07 Oct 2018 20:31:24: #3 Call peaks for each chromosome... INFO @ Sun, 07 Oct 2018 20:31:26: #4 Write output xls file... SRX4456931.05_peaks.xls INFO @ Sun, 07 Oct 2018 20:31:26: #4 Write peak in narrowPeak format file... SRX4456931.05_peaks.narrowPeak INFO @ Sun, 07 Oct 2018 20:31:26: #4 Write summits bed file... SRX4456931.05_summits.bed INFO @ Sun, 07 Oct 2018 20:31:26: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (582 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 07 Oct 2018 20:31:29: #4 Write output xls file... SRX4456931.10_peaks.xls INFO @ Sun, 07 Oct 2018 20:31:29: #4 Write peak in narrowPeak format file... SRX4456931.10_peaks.narrowPeak INFO @ Sun, 07 Oct 2018 20:31:29: #4 Write summits bed file... SRX4456931.10_summits.bed INFO @ Sun, 07 Oct 2018 20:31:29: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (356 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 07 Oct 2018 20:31:29: #4 Write output xls file... SRX4456931.20_peaks.xls INFO @ Sun, 07 Oct 2018 20:31:29: #4 Write peak in narrowPeak format file... SRX4456931.20_peaks.narrowPeak INFO @ Sun, 07 Oct 2018 20:31:29: #4 Write summits bed file... SRX4456931.20_summits.bed INFO @ Sun, 07 Oct 2018 20:31:29: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (167 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。