Job ID = 11633944 sra ファイルのダウンロード中... Completed: 184482K bytes transferred in 5 seconds (294751K 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 4965490 spots for /home/okishinya/chipatlas/results/sacCer3/ERX1424531/ERR1353056.sra Written 4965490 spots for /home/okishinya/chipatlas/results/sacCer3/ERX1424531/ERR1353056.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: 00:00:57 4965490 reads; of these: 4965490 (100.00%) were unpaired; of these: 423767 (8.53%) aligned 0 times 3498579 (70.46%) aligned exactly 1 time 1043144 (21.01%) aligned >1 times 91.47% overall alignment rate Time searching: 00:00:57 Overall time: 00:00:57 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 17 sequences. [bam_rmdupse_core] 2103984 / 4541723 = 0.4633 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 09:21:11: # Command line: callpeak -t ERX1424531.bam -f BAM -g 12100000 -n ERX1424531.05 -q 1e-05 # ARGUMENTS LIST: # name = ERX1424531.05 # format = BAM # ChIP-seq file = ['ERX1424531.bam'] # control file = None # effective genome size = 1.21e+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 @ Fri, 15 Feb 2019 09:21:11: #1 read tag files... INFO @ Fri, 15 Feb 2019 09:21:11: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 09:21:11: # Command line: callpeak -t ERX1424531.bam -f BAM -g 12100000 -n ERX1424531.10 -q 1e-10 # ARGUMENTS LIST: # name = ERX1424531.10 # format = BAM # ChIP-seq file = ['ERX1424531.bam'] # control file = None # effective genome size = 1.21e+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 @ Fri, 15 Feb 2019 09:21:11: #1 read tag files... INFO @ Fri, 15 Feb 2019 09:21:11: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 09:21:11: # Command line: callpeak -t ERX1424531.bam -f BAM -g 12100000 -n ERX1424531.20 -q 1e-20 # ARGUMENTS LIST: # name = ERX1424531.20 # format = BAM # ChIP-seq file = ['ERX1424531.bam'] # control file = None # effective genome size = 1.21e+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 @ Fri, 15 Feb 2019 09:21:11: #1 read tag files... INFO @ Fri, 15 Feb 2019 09:21:11: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 09:21:18: 1000000 INFO @ Fri, 15 Feb 2019 09:21:18: 1000000 INFO @ Fri, 15 Feb 2019 09:21:18: 1000000 INFO @ Fri, 15 Feb 2019 09:21:24: 2000000 INFO @ Fri, 15 Feb 2019 09:21:24: 2000000 INFO @ Fri, 15 Feb 2019 09:21:25: 2000000 INFO @ Fri, 15 Feb 2019 09:21:27: #1 tag size is determined as 50 bps INFO @ Fri, 15 Feb 2019 09:21:27: #1 tag size = 50 INFO @ Fri, 15 Feb 2019 09:21:27: #1 total tags in treatment: 2437739 INFO @ Fri, 15 Feb 2019 09:21:27: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 09:21:27: #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 09:21:27: #1 tags after filtering in treatment: 2437739 INFO @ Fri, 15 Feb 2019 09:21:27: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 09:21:27: #1 finished! INFO @ Fri, 15 Feb 2019 09:21:27: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 09:21:27: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 09:21:27: #1 tag size is determined as 50 bps INFO @ Fri, 15 Feb 2019 09:21:27: #1 tag size = 50 INFO @ Fri, 15 Feb 2019 09:21:27: #1 total tags in treatment: 2437739 INFO @ Fri, 15 Feb 2019 09:21:27: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 09:21:27: #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 09:21:27: #1 tags after filtering in treatment: 2437739 INFO @ Fri, 15 Feb 2019 09:21:27: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 09:21:27: #1 finished! INFO @ Fri, 15 Feb 2019 09:21:27: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 09:21:27: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 09:21:28: #2 number of paired peaks: 337 WARNING @ Fri, 15 Feb 2019 09:21:28: Fewer paired peaks (337) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 337 pairs to build model! INFO @ Fri, 15 Feb 2019 09:21:28: start model_add_line... INFO @ Fri, 15 Feb 2019 09:21:28: start X-correlation... INFO @ Fri, 15 Feb 2019 09:21:28: end of X-cor INFO @ Fri, 15 Feb 2019 09:21:28: #2 finished! INFO @ Fri, 15 Feb 2019 09:21:28: #2 predicted fragment length is 158 bps INFO @ Fri, 15 Feb 2019 09:21:28: #2 alternative fragment length(s) may be 158 bps INFO @ Fri, 15 Feb 2019 09:21:28: #2.2 Generate R script for model : ERX1424531.20_model.r INFO @ Fri, 15 Feb 2019 09:21:28: #3 Call peaks... INFO @ Fri, 15 Feb 2019 09:21:28: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 09:21:28: #2 number of paired peaks: 337 WARNING @ Fri, 15 Feb 2019 09:21:28: Fewer paired peaks (337) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 337 pairs to build model! INFO @ Fri, 15 Feb 2019 09:21:28: start model_add_line... INFO @ Fri, 15 Feb 2019 09:21:28: start X-correlation... INFO @ Fri, 15 Feb 2019 09:21:28: end of X-cor INFO @ Fri, 15 Feb 2019 09:21:28: #2 finished! INFO @ Fri, 15 Feb 2019 09:21:28: #2 predicted fragment length is 158 bps INFO @ Fri, 15 Feb 2019 09:21:28: #2 alternative fragment length(s) may be 158 bps INFO @ Fri, 15 Feb 2019 09:21:28: #2.2 Generate R script for model : ERX1424531.10_model.r INFO @ Fri, 15 Feb 2019 09:21:28: #3 Call peaks... INFO @ Fri, 15 Feb 2019 09:21:28: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 09:21:28: #1 tag size is determined as 50 bps INFO @ Fri, 15 Feb 2019 09:21:28: #1 tag size = 50 INFO @ Fri, 15 Feb 2019 09:21:28: #1 total tags in treatment: 2437739 INFO @ Fri, 15 Feb 2019 09:21:28: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 09:21:28: #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 09:21:28: #1 tags after filtering in treatment: 2437739 INFO @ Fri, 15 Feb 2019 09:21:28: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 09:21:28: #1 finished! INFO @ Fri, 15 Feb 2019 09:21:28: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 09:21:28: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 09:21:28: #2 number of paired peaks: 337 WARNING @ Fri, 15 Feb 2019 09:21:28: Fewer paired peaks (337) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 337 pairs to build model! INFO @ Fri, 15 Feb 2019 09:21:28: start model_add_line... INFO @ Fri, 15 Feb 2019 09:21:28: start X-correlation... INFO @ Fri, 15 Feb 2019 09:21:28: end of X-cor INFO @ Fri, 15 Feb 2019 09:21:28: #2 finished! INFO @ Fri, 15 Feb 2019 09:21:28: #2 predicted fragment length is 158 bps INFO @ Fri, 15 Feb 2019 09:21:28: #2 alternative fragment length(s) may be 158 bps INFO @ Fri, 15 Feb 2019 09:21:28: #2.2 Generate R script for model : ERX1424531.05_model.r INFO @ Fri, 15 Feb 2019 09:21:28: #3 Call peaks... INFO @ Fri, 15 Feb 2019 09:21:28: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 09:21:38: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 09:21:38: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 09:21:39: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 09:21:41: #4 Write output xls file... ERX1424531.10_peaks.xls INFO @ Fri, 15 Feb 2019 09:21:41: #4 Write output xls file... ERX1424531.20_peaks.xls INFO @ Fri, 15 Feb 2019 09:21:41: #4 Write peak in narrowPeak format file... ERX1424531.10_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 09:21:41: #4 Write peak in narrowPeak format file... ERX1424531.20_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 09:21:41: #4 Write summits bed file... ERX1424531.20_summits.bed INFO @ Fri, 15 Feb 2019 09:21:41: #4 Write summits bed file... ERX1424531.10_summits.bed INFO @ Fri, 15 Feb 2019 09:21:41: Done! INFO @ Fri, 15 Feb 2019 09:21:41: Done! pass1 - making usageList (16 chroms): 3 millis pass2 - checking and writing primary data (1738 records, 4 fields): 7 millis pass1 - making usageList (16 chroms): 9 millis pass2 - checking and writing primary data (2851 records, 4 fields): 14 millis CompletedMACS2peakCalling CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 09:21:42: #4 Write output xls file... ERX1424531.05_peaks.xls INFO @ Fri, 15 Feb 2019 09:21:42: #4 Write peak in narrowPeak format file... ERX1424531.05_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 09:21:43: #4 Write summits bed file... ERX1424531.05_summits.bed INFO @ Fri, 15 Feb 2019 09:21:43: Done! pass1 - making usageList (16 chroms): 3 millis pass2 - checking and writing primary data (3856 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。