Job ID = 10714416 sra ファイルのダウンロード中... Completed: 187518K bytes transferred in 14 seconds (102488K 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 6486000 spots for /home/okishinya/chipatlas/results/ce10/SRX4082376/SRR7164194.sra Written 6486000 spots for /home/okishinya/chipatlas/results/ce10/SRX4082376/SRR7164194.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: 00:01:42 6486000 reads; of these: 6486000 (100.00%) were unpaired; of these: 589029 (9.08%) aligned 0 times 4494010 (69.29%) aligned exactly 1 time 1402961 (21.63%) aligned >1 times 90.92% overall alignment rate Time searching: 00:01:42 Overall time: 00:01:42 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] 1311390 / 5896971 = 0.2224 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, 03 Jun 2018 12:32:07: # Command line: callpeak -t SRX4082376.bam -f BAM -g ce -n SRX4082376.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4082376.05 # format = BAM # ChIP-seq file = ['SRX4082376.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, 03 Jun 2018 12:32:07: #1 read tag files... INFO @ Sun, 03 Jun 2018 12:32:07: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 12:32:07: # Command line: callpeak -t SRX4082376.bam -f BAM -g ce -n SRX4082376.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4082376.20 # format = BAM # ChIP-seq file = ['SRX4082376.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, 03 Jun 2018 12:32:07: #1 read tag files... INFO @ Sun, 03 Jun 2018 12:32:07: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 12:32:07: # Command line: callpeak -t SRX4082376.bam -f BAM -g ce -n SRX4082376.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4082376.10 # format = BAM # ChIP-seq file = ['SRX4082376.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, 03 Jun 2018 12:32:07: #1 read tag files... INFO @ Sun, 03 Jun 2018 12:32:07: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 12:32:14: 1000000 INFO @ Sun, 03 Jun 2018 12:32:14: 1000000 INFO @ Sun, 03 Jun 2018 12:32:14: 1000000 INFO @ Sun, 03 Jun 2018 12:32:20: 2000000 INFO @ Sun, 03 Jun 2018 12:32:20: 2000000 INFO @ Sun, 03 Jun 2018 12:32:21: 2000000 INFO @ Sun, 03 Jun 2018 12:32:26: 3000000 INFO @ Sun, 03 Jun 2018 12:32:27: 3000000 INFO @ Sun, 03 Jun 2018 12:32:27: 3000000 INFO @ Sun, 03 Jun 2018 12:32:33: 4000000 INFO @ Sun, 03 Jun 2018 12:32:34: 4000000 INFO @ Sun, 03 Jun 2018 12:32:34: 4000000 INFO @ Sun, 03 Jun 2018 12:32:36: #1 tag size is determined as 50 bps INFO @ Sun, 03 Jun 2018 12:32:36: #1 tag size = 50 INFO @ Sun, 03 Jun 2018 12:32:36: #1 total tags in treatment: 4585581 INFO @ Sun, 03 Jun 2018 12:32:36: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 12:32:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 12:32:36: #1 tags after filtering in treatment: 4585581 INFO @ Sun, 03 Jun 2018 12:32:36: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 12:32:36: #1 finished! INFO @ Sun, 03 Jun 2018 12:32:36: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 12:32:36: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 12:32:37: #2 number of paired peaks: 608 WARNING @ Sun, 03 Jun 2018 12:32:37: Fewer paired peaks (608) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 608 pairs to build model! INFO @ Sun, 03 Jun 2018 12:32:37: start model_add_line... INFO @ Sun, 03 Jun 2018 12:32:37: start X-correlation... INFO @ Sun, 03 Jun 2018 12:32:37: end of X-cor INFO @ Sun, 03 Jun 2018 12:32:37: #2 finished! INFO @ Sun, 03 Jun 2018 12:32:37: #2 predicted fragment length is 50 bps INFO @ Sun, 03 Jun 2018 12:32:37: #2 alternative fragment length(s) may be 4,50 bps INFO @ Sun, 03 Jun 2018 12:32:37: #2.2 Generate R script for model : SRX4082376.10_model.r WARNING @ Sun, 03 Jun 2018 12:32:37: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Jun 2018 12:32:37: #2 You may need to consider one of the other alternative d(s): 4,50 WARNING @ Sun, 03 Jun 2018 12:32:37: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 03 Jun 2018 12:32:37: #3 Call peaks... INFO @ Sun, 03 Jun 2018 12:32:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 12:32:38: #1 tag size is determined as 50 bps INFO @ Sun, 03 Jun 2018 12:32:38: #1 tag size = 50 INFO @ Sun, 03 Jun 2018 12:32:38: #1 total tags in treatment: 4585581 INFO @ Sun, 03 Jun 2018 12:32:38: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 12:32:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 12:32:38: #1 tags after filtering in treatment: 4585581 INFO @ Sun, 03 Jun 2018 12:32:38: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 12:32:38: #1 finished! INFO @ Sun, 03 Jun 2018 12:32:38: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 12:32:38: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 12:32:38: #2 number of paired peaks: 608 WARNING @ Sun, 03 Jun 2018 12:32:38: Fewer paired peaks (608) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 608 pairs to build model! INFO @ Sun, 03 Jun 2018 12:32:38: start model_add_line... INFO @ Sun, 03 Jun 2018 12:32:38: #1 tag size is determined as 50 bps INFO @ Sun, 03 Jun 2018 12:32:38: #1 tag size = 50 INFO @ Sun, 03 Jun 2018 12:32:38: #1 total tags in treatment: 4585581 INFO @ Sun, 03 Jun 2018 12:32:38: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 12:32:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 12:32:38: start X-correlation... INFO @ Sun, 03 Jun 2018 12:32:38: end of X-cor INFO @ Sun, 03 Jun 2018 12:32:38: #2 finished! INFO @ Sun, 03 Jun 2018 12:32:38: #2 predicted fragment length is 50 bps INFO @ Sun, 03 Jun 2018 12:32:38: #2 alternative fragment length(s) may be 4,50 bps INFO @ Sun, 03 Jun 2018 12:32:38: #2.2 Generate R script for model : SRX4082376.20_model.r WARNING @ Sun, 03 Jun 2018 12:32:38: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Jun 2018 12:32:38: #2 You may need to consider one of the other alternative d(s): 4,50 WARNING @ Sun, 03 Jun 2018 12:32:38: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 03 Jun 2018 12:32:38: #3 Call peaks... INFO @ Sun, 03 Jun 2018 12:32:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 12:32:38: #1 tags after filtering in treatment: 4585581 INFO @ Sun, 03 Jun 2018 12:32:38: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 12:32:38: #1 finished! INFO @ Sun, 03 Jun 2018 12:32:38: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 12:32:38: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 12:32:39: #2 number of paired peaks: 608 WARNING @ Sun, 03 Jun 2018 12:32:39: Fewer paired peaks (608) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 608 pairs to build model! INFO @ Sun, 03 Jun 2018 12:32:39: start model_add_line... INFO @ Sun, 03 Jun 2018 12:32:39: start X-correlation... INFO @ Sun, 03 Jun 2018 12:32:39: end of X-cor INFO @ Sun, 03 Jun 2018 12:32:39: #2 finished! INFO @ Sun, 03 Jun 2018 12:32:39: #2 predicted fragment length is 50 bps INFO @ Sun, 03 Jun 2018 12:32:39: #2 alternative fragment length(s) may be 4,50 bps INFO @ Sun, 03 Jun 2018 12:32:39: #2.2 Generate R script for model : SRX4082376.05_model.r WARNING @ Sun, 03 Jun 2018 12:32:39: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Jun 2018 12:32:39: #2 You may need to consider one of the other alternative d(s): 4,50 WARNING @ Sun, 03 Jun 2018 12:32:39: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 03 Jun 2018 12:32:39: #3 Call peaks... INFO @ Sun, 03 Jun 2018 12:32:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 12:32:47: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 12:32:49: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 12:32:50: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 12:32:53: #4 Write output xls file... SRX4082376.10_peaks.xls INFO @ Sun, 03 Jun 2018 12:32:53: #4 Write peak in narrowPeak format file... SRX4082376.10_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 12:32:53: #4 Write summits bed file... SRX4082376.10_summits.bed INFO @ Sun, 03 Jun 2018 12:32:53: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (429 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 12:32:55: #4 Write output xls file... SRX4082376.20_peaks.xls INFO @ Sun, 03 Jun 2018 12:32:55: #4 Write peak in narrowPeak format file... SRX4082376.20_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 12:32:55: #4 Write summits bed file... SRX4082376.20_summits.bed INFO @ Sun, 03 Jun 2018 12:32:55: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (185 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 12:32:56: #4 Write output xls file... SRX4082376.05_peaks.xls INFO @ Sun, 03 Jun 2018 12:32:56: #4 Write peak in narrowPeak format file... SRX4082376.05_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 12:32:56: #4 Write summits bed file... SRX4082376.05_summits.bed INFO @ Sun, 03 Jun 2018 12:32:56: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (652 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。