Job ID = 11633962 sra ファイルのダウンロード中... Completed: 736986K bytes transferred in 9 seconds (656039K 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 23347752 spots for /home/okishinya/chipatlas/results/sacCer3/ERX1424549/ERR1353074.sra Written 23347752 spots for /home/okishinya/chipatlas/results/sacCer3/ERX1424549/ERR1353074.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: 00:02:45 23347752 reads; of these: 23347752 (100.00%) were unpaired; of these: 14513676 (62.16%) aligned 0 times 6287951 (26.93%) aligned exactly 1 time 2546125 (10.91%) aligned >1 times 37.84% overall alignment rate Time searching: 00:02:45 Overall time: 00:02:45 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] 7472708 / 8834076 = 0.8459 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 09:23:55: # Command line: callpeak -t ERX1424549.bam -f BAM -g 12100000 -n ERX1424549.10 -q 1e-10 # ARGUMENTS LIST: # name = ERX1424549.10 # format = BAM # ChIP-seq file = ['ERX1424549.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 09:23:55: #1 read tag files... INFO @ Fri, 15 Feb 2019 09:23:55: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 09:23:55: # Command line: callpeak -t ERX1424549.bam -f BAM -g 12100000 -n ERX1424549.05 -q 1e-05 # ARGUMENTS LIST: # name = ERX1424549.05 # format = BAM # ChIP-seq file = ['ERX1424549.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 09:23:55: #1 read tag files... INFO @ Fri, 15 Feb 2019 09:23:55: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 09:23:55: # Command line: callpeak -t ERX1424549.bam -f BAM -g 12100000 -n ERX1424549.20 -q 1e-20 # ARGUMENTS LIST: # name = ERX1424549.20 # format = BAM # ChIP-seq file = ['ERX1424549.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 09:23:55: #1 read tag files... INFO @ Fri, 15 Feb 2019 09:23:55: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 09:24:01: 1000000 INFO @ Fri, 15 Feb 2019 09:24:01: 1000000 INFO @ Fri, 15 Feb 2019 09:24:02: 1000000 INFO @ Fri, 15 Feb 2019 09:24:04: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 09:24:04: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 09:24:04: #1 total tags in treatment: 1361368 INFO @ Fri, 15 Feb 2019 09:24:04: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 09:24:04: #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 09:24:04: #1 tags after filtering in treatment: 1361368 INFO @ Fri, 15 Feb 2019 09:24:04: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 09:24:04: #1 finished! INFO @ Fri, 15 Feb 2019 09:24:04: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 09:24:04: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 09:24:04: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 09:24:04: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 09:24:04: #1 total tags in treatment: 1361368 INFO @ Fri, 15 Feb 2019 09:24:04: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 09:24:04: #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 09:24:04: #1 tags after filtering in treatment: 1361368 INFO @ Fri, 15 Feb 2019 09:24:04: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 09:24:04: #1 finished! INFO @ Fri, 15 Feb 2019 09:24:04: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 09:24:04: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 09:24:04: #2 number of paired peaks: 450 WARNING @ Fri, 15 Feb 2019 09:24:04: Fewer paired peaks (450) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 450 pairs to build model! INFO @ Fri, 15 Feb 2019 09:24:04: start model_add_line... INFO @ Fri, 15 Feb 2019 09:24:04: start X-correlation... INFO @ Fri, 15 Feb 2019 09:24:04: end of X-cor INFO @ Fri, 15 Feb 2019 09:24:04: #2 finished! INFO @ Fri, 15 Feb 2019 09:24:04: #2 predicted fragment length is 166 bps INFO @ Fri, 15 Feb 2019 09:24:04: #2 alternative fragment length(s) may be 166 bps INFO @ Fri, 15 Feb 2019 09:24:04: #2.2 Generate R script for model : ERX1424549.05_model.r INFO @ Fri, 15 Feb 2019 09:24:04: #3 Call peaks... INFO @ Fri, 15 Feb 2019 09:24:04: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 09:24:04: #2 number of paired peaks: 450 WARNING @ Fri, 15 Feb 2019 09:24:04: Fewer paired peaks (450) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 450 pairs to build model! INFO @ Fri, 15 Feb 2019 09:24:04: start model_add_line... INFO @ Fri, 15 Feb 2019 09:24:04: start X-correlation... INFO @ Fri, 15 Feb 2019 09:24:04: end of X-cor INFO @ Fri, 15 Feb 2019 09:24:04: #2 finished! INFO @ Fri, 15 Feb 2019 09:24:04: #2 predicted fragment length is 166 bps INFO @ Fri, 15 Feb 2019 09:24:04: #2 alternative fragment length(s) may be 166 bps INFO @ Fri, 15 Feb 2019 09:24:04: #2.2 Generate R script for model : ERX1424549.20_model.r INFO @ Fri, 15 Feb 2019 09:24:04: #3 Call peaks... INFO @ Fri, 15 Feb 2019 09:24:04: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 09:24:05: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 09:24:05: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 09:24:05: #1 total tags in treatment: 1361368 INFO @ Fri, 15 Feb 2019 09:24:05: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 09:24:05: #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 09:24:05: #1 tags after filtering in treatment: 1361368 INFO @ Fri, 15 Feb 2019 09:24:05: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 09:24:05: #1 finished! INFO @ Fri, 15 Feb 2019 09:24:05: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 09:24:05: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 09:24:05: #2 number of paired peaks: 450 WARNING @ Fri, 15 Feb 2019 09:24:05: Fewer paired peaks (450) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 450 pairs to build model! INFO @ Fri, 15 Feb 2019 09:24:05: start model_add_line... INFO @ Fri, 15 Feb 2019 09:24:05: start X-correlation... INFO @ Fri, 15 Feb 2019 09:24:05: end of X-cor INFO @ Fri, 15 Feb 2019 09:24:05: #2 finished! INFO @ Fri, 15 Feb 2019 09:24:05: #2 predicted fragment length is 166 bps INFO @ Fri, 15 Feb 2019 09:24:05: #2 alternative fragment length(s) may be 166 bps INFO @ Fri, 15 Feb 2019 09:24:05: #2.2 Generate R script for model : ERX1424549.10_model.r INFO @ Fri, 15 Feb 2019 09:24:05: #3 Call peaks... INFO @ Fri, 15 Feb 2019 09:24:05: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 09:24:09: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 09:24:09: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 09:24:11: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 09:24:11: #4 Write output xls file... ERX1424549.20_peaks.xls INFO @ Fri, 15 Feb 2019 09:24:11: #4 Write peak in narrowPeak format file... ERX1424549.20_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 09:24:11: #4 Write summits bed file... ERX1424549.20_summits.bed INFO @ Fri, 15 Feb 2019 09:24:11: Done! INFO @ Fri, 15 Feb 2019 09:24:11: #4 Write output xls file... ERX1424549.05_peaks.xls INFO @ Fri, 15 Feb 2019 09:24:11: #4 Write peak in narrowPeak format file... ERX1424549.05_peaks.narrowPeak pass1 - making usageList (16 chroms): 2 millis INFO @ Fri, 15 Feb 2019 09:24:11: #4 Write summits bed file... ERX1424549.05_summits.bed pass2 - checking and writing primary data (1027 records, 4 fields): 5 millis INFO @ Fri, 15 Feb 2019 09:24:11: Done! CompletedMACS2peakCalling pass1 - making usageList (17 chroms): 5 millis pass2 - checking and writing primary data (2084 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 09:24:12: #4 Write output xls file... ERX1424549.10_peaks.xls INFO @ Fri, 15 Feb 2019 09:24:12: #4 Write peak in narrowPeak format file... ERX1424549.10_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 09:24:12: #4 Write summits bed file... ERX1424549.10_summits.bed INFO @ Fri, 15 Feb 2019 09:24:12: Done! pass1 - making usageList (17 chroms): 4 millis pass2 - checking and writing primary data (1510 records, 4 fields): 11 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。