Job ID = 11193054 sra ファイルのダウンロード中... Completed: 45811K bytes transferred in 6 seconds (56711K 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 2328427 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4233892/SRR7360657.sra Written 2328427 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4233892/SRR7360657.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: 00:00:23 2328427 reads; of these: 2328427 (100.00%) were unpaired; of these: 308135 (13.23%) aligned 0 times 1768390 (75.95%) aligned exactly 1 time 251902 (10.82%) aligned >1 times 86.77% overall alignment rate Time searching: 00:00:23 Overall time: 00:00:23 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 17 sequences. [bam_rmdupse_core] 268020 / 2020292 = 0.1327 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 @ Sat, 15 Sep 2018 10:51:07: # Command line: callpeak -t SRX4233892.bam -f BAM -g 12100000 -n SRX4233892.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4233892.10 # format = BAM # ChIP-seq file = ['SRX4233892.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 @ Sat, 15 Sep 2018 10:51:07: #1 read tag files... INFO @ Sat, 15 Sep 2018 10:51:07: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 10:51:07: # Command line: callpeak -t SRX4233892.bam -f BAM -g 12100000 -n SRX4233892.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4233892.05 # format = BAM # ChIP-seq file = ['SRX4233892.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 @ Sat, 15 Sep 2018 10:51:07: #1 read tag files... INFO @ Sat, 15 Sep 2018 10:51:07: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 10:51:07: # Command line: callpeak -t SRX4233892.bam -f BAM -g 12100000 -n SRX4233892.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4233892.20 # format = BAM # ChIP-seq file = ['SRX4233892.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 @ Sat, 15 Sep 2018 10:51:07: #1 read tag files... INFO @ Sat, 15 Sep 2018 10:51:07: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 10:51:12: 1000000 INFO @ Sat, 15 Sep 2018 10:51:13: 1000000 INFO @ Sat, 15 Sep 2018 10:51:13: 1000000 INFO @ Sat, 15 Sep 2018 10:51:17: #1 tag size is determined as 49 bps INFO @ Sat, 15 Sep 2018 10:51:17: #1 tag size = 49 INFO @ Sat, 15 Sep 2018 10:51:17: #1 total tags in treatment: 1752272 INFO @ Sat, 15 Sep 2018 10:51:17: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 10:51:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 10:51:17: #1 tags after filtering in treatment: 1752272 INFO @ Sat, 15 Sep 2018 10:51:17: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 10:51:17: #1 finished! INFO @ Sat, 15 Sep 2018 10:51:17: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 10:51:17: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 10:51:17: #2 number of paired peaks: 134 WARNING @ Sat, 15 Sep 2018 10:51:17: Fewer paired peaks (134) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 134 pairs to build model! INFO @ Sat, 15 Sep 2018 10:51:17: start model_add_line... INFO @ Sat, 15 Sep 2018 10:51:17: start X-correlation... INFO @ Sat, 15 Sep 2018 10:51:17: end of X-cor INFO @ Sat, 15 Sep 2018 10:51:17: #2 finished! INFO @ Sat, 15 Sep 2018 10:51:17: #2 predicted fragment length is 362 bps INFO @ Sat, 15 Sep 2018 10:51:17: #2 alternative fragment length(s) may be 362 bps INFO @ Sat, 15 Sep 2018 10:51:17: #2.2 Generate R script for model : SRX4233892.10_model.r INFO @ Sat, 15 Sep 2018 10:51:17: #3 Call peaks... INFO @ Sat, 15 Sep 2018 10:51:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 10:51:18: #1 tag size is determined as 49 bps INFO @ Sat, 15 Sep 2018 10:51:18: #1 tag size = 49 INFO @ Sat, 15 Sep 2018 10:51:18: #1 total tags in treatment: 1752272 INFO @ Sat, 15 Sep 2018 10:51:18: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 10:51:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 10:51:18: #1 tag size is determined as 49 bps INFO @ Sat, 15 Sep 2018 10:51:18: #1 tag size = 49 INFO @ Sat, 15 Sep 2018 10:51:18: #1 total tags in treatment: 1752272 INFO @ Sat, 15 Sep 2018 10:51:18: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 10:51:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 10:51:18: #1 tags after filtering in treatment: 1752272 INFO @ Sat, 15 Sep 2018 10:51:18: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 10:51:18: #1 finished! INFO @ Sat, 15 Sep 2018 10:51:18: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 10:51:18: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 10:51:18: #1 tags after filtering in treatment: 1752272 INFO @ Sat, 15 Sep 2018 10:51:18: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 10:51:18: #1 finished! INFO @ Sat, 15 Sep 2018 10:51:18: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 10:51:18: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 10:51:18: #2 number of paired peaks: 134 WARNING @ Sat, 15 Sep 2018 10:51:18: Fewer paired peaks (134) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 134 pairs to build model! INFO @ Sat, 15 Sep 2018 10:51:18: start model_add_line... INFO @ Sat, 15 Sep 2018 10:51:18: start X-correlation... INFO @ Sat, 15 Sep 2018 10:51:18: end of X-cor INFO @ Sat, 15 Sep 2018 10:51:18: #2 finished! INFO @ Sat, 15 Sep 2018 10:51:18: #2 predicted fragment length is 362 bps INFO @ Sat, 15 Sep 2018 10:51:18: #2 alternative fragment length(s) may be 362 bps INFO @ Sat, 15 Sep 2018 10:51:18: #2.2 Generate R script for model : SRX4233892.20_model.r INFO @ Sat, 15 Sep 2018 10:51:18: #2 number of paired peaks: 134 WARNING @ Sat, 15 Sep 2018 10:51:18: Fewer paired peaks (134) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 134 pairs to build model! INFO @ Sat, 15 Sep 2018 10:51:18: start model_add_line... INFO @ Sat, 15 Sep 2018 10:51:18: #3 Call peaks... INFO @ Sat, 15 Sep 2018 10:51:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 10:51:18: start X-correlation... INFO @ Sat, 15 Sep 2018 10:51:18: end of X-cor INFO @ Sat, 15 Sep 2018 10:51:18: #2 finished! INFO @ Sat, 15 Sep 2018 10:51:18: #2 predicted fragment length is 362 bps INFO @ Sat, 15 Sep 2018 10:51:18: #2 alternative fragment length(s) may be 362 bps INFO @ Sat, 15 Sep 2018 10:51:18: #2.2 Generate R script for model : SRX4233892.05_model.r INFO @ Sat, 15 Sep 2018 10:51:18: #3 Call peaks... INFO @ Sat, 15 Sep 2018 10:51:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 10:51:23: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 10:51:23: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 10:51:24: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 10:51:25: #4 Write output xls file... SRX4233892.10_peaks.xls INFO @ Sat, 15 Sep 2018 10:51:25: #4 Write peak in narrowPeak format file... SRX4233892.10_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 10:51:25: #4 Write summits bed file... SRX4233892.10_summits.bed INFO @ Sat, 15 Sep 2018 10:51:25: Done! pass1 - making usageList (3 chroms): 0 millis pass2 - checking and writing primary data (29 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 15 Sep 2018 10:51:25: #4 Write output xls file... SRX4233892.05_peaks.xls INFO @ Sat, 15 Sep 2018 10:51:25: #4 Write peak in narrowPeak format file... SRX4233892.05_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 10:51:25: #4 Write summits bed file... SRX4233892.05_summits.bed INFO @ Sat, 15 Sep 2018 10:51:25: Done! pass1 - making usageList (3 chroms): 0 millis pass2 - checking and writing primary data (39 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 15 Sep 2018 10:51:26: #4 Write output xls file... SRX4233892.20_peaks.xls INFO @ Sat, 15 Sep 2018 10:51:26: #4 Write peak in narrowPeak format file... SRX4233892.20_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 10:51:26: #4 Write summits bed file... SRX4233892.20_summits.bed INFO @ Sat, 15 Sep 2018 10:51:26: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (21 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。