Job ID = 11633510 sra ファイルのダウンロード中... Completed: 123934K bytes transferred in 4 seconds (203174K 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: PAIRED fastq に変換中... Read 1994859 spots for /home/okishinya/chipatlas/results/sacCer3/ERX1236287/ERR1162880.sra Written 1994859 spots for /home/okishinya/chipatlas/results/sacCer3/ERX1236287/ERR1162880.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: 00:00:52 1994859 reads; of these: 1994859 (100.00%) were paired; of these: 1147031 (57.50%) aligned concordantly 0 times 750700 (37.63%) aligned concordantly exactly 1 time 97128 (4.87%) aligned concordantly >1 times ---- 1147031 pairs aligned concordantly 0 times; of these: 45790 (3.99%) aligned discordantly 1 time ---- 1101241 pairs aligned 0 times concordantly or discordantly; of these: 2202482 mates make up the pairs; of these: 2151862 (97.70%) aligned 0 times 34002 (1.54%) aligned exactly 1 time 16618 (0.75%) aligned >1 times 46.06% overall alignment rate Time searching: 00:00:52 Overall time: 00:00:52 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_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrIX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrVI... [bam_rmdup_core] processing reference chrVII... [bam_rmdup_core] processing reference chrVIII... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXI... [bam_rmdup_core] processing reference chrXII... [bam_rmdup_core] processing reference chrXIII... [bam_rmdup_core] processing reference chrXIV... [bam_rmdup_core] processing reference chrXV... [bam_rmdup_core] processing reference chrXVI... [bam_rmdup_core] 456424 / 893253 = 0.5110 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 09:01:05: # Command line: callpeak -t ERX1236287.bam -f BAM -g 12100000 -n ERX1236287.10 -q 1e-10 # ARGUMENTS LIST: # name = ERX1236287.10 # format = BAM # ChIP-seq file = ['ERX1236287.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 09:01:05: #1 read tag files... INFO @ Fri, 15 Feb 2019 09:01:05: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 09:01:05: # Command line: callpeak -t ERX1236287.bam -f BAM -g 12100000 -n ERX1236287.05 -q 1e-05 # ARGUMENTS LIST: # name = ERX1236287.05 # format = BAM # ChIP-seq file = ['ERX1236287.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 09:01:05: #1 read tag files... INFO @ Fri, 15 Feb 2019 09:01:05: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 09:01:05: # Command line: callpeak -t ERX1236287.bam -f BAM -g 12100000 -n ERX1236287.20 -q 1e-20 # ARGUMENTS LIST: # name = ERX1236287.20 # format = BAM # ChIP-seq file = ['ERX1236287.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 09:01:05: #1 read tag files... INFO @ Fri, 15 Feb 2019 09:01:05: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 09:01:10: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 09:01:10: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 09:01:10: #1 total tags in treatment: 412239 INFO @ Fri, 15 Feb 2019 09:01:10: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 09:01:10: #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 09:01:10: #1 tags after filtering in treatment: 397855 INFO @ Fri, 15 Feb 2019 09:01:10: #1 Redundant rate of treatment: 0.03 INFO @ Fri, 15 Feb 2019 09:01:10: #1 finished! INFO @ Fri, 15 Feb 2019 09:01:10: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 09:01:10: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 09:01:10: #2 number of paired peaks: 146 WARNING @ Fri, 15 Feb 2019 09:01:10: Fewer paired peaks (146) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 146 pairs to build model! INFO @ Fri, 15 Feb 2019 09:01:10: start model_add_line... INFO @ Fri, 15 Feb 2019 09:01:10: start X-correlation... INFO @ Fri, 15 Feb 2019 09:01:10: end of X-cor INFO @ Fri, 15 Feb 2019 09:01:10: #2 finished! INFO @ Fri, 15 Feb 2019 09:01:10: #2 predicted fragment length is 257 bps INFO @ Fri, 15 Feb 2019 09:01:10: #2 alternative fragment length(s) may be 3,164,186,217,257,288,304,322 bps INFO @ Fri, 15 Feb 2019 09:01:10: #2.2 Generate R script for model : ERX1236287.10_model.r INFO @ Fri, 15 Feb 2019 09:01:10: #3 Call peaks... INFO @ Fri, 15 Feb 2019 09:01:10: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 09:01:11: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 09:01:11: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 09:01:11: #1 total tags in treatment: 412239 INFO @ Fri, 15 Feb 2019 09:01:11: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 09:01:11: #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 09:01:11: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 09:01:11: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 09:01:11: #1 total tags in treatment: 412239 INFO @ Fri, 15 Feb 2019 09:01:11: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 09:01:11: #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 09:01:11: #1 tags after filtering in treatment: 397855 INFO @ Fri, 15 Feb 2019 09:01:11: #1 Redundant rate of treatment: 0.03 INFO @ Fri, 15 Feb 2019 09:01:11: #1 finished! INFO @ Fri, 15 Feb 2019 09:01:11: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 09:01:11: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 09:01:11: #1 tags after filtering in treatment: 397855 INFO @ Fri, 15 Feb 2019 09:01:11: #1 Redundant rate of treatment: 0.03 INFO @ Fri, 15 Feb 2019 09:01:11: #1 finished! INFO @ Fri, 15 Feb 2019 09:01:11: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 09:01:11: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 09:01:11: #2 number of paired peaks: 146 WARNING @ Fri, 15 Feb 2019 09:01:11: Fewer paired peaks (146) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 146 pairs to build model! INFO @ Fri, 15 Feb 2019 09:01:11: start model_add_line... INFO @ Fri, 15 Feb 2019 09:01:11: #2 number of paired peaks: 146 INFO @ Fri, 15 Feb 2019 09:01:11: start X-correlation... WARNING @ Fri, 15 Feb 2019 09:01:11: Fewer paired peaks (146) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 146 pairs to build model! INFO @ Fri, 15 Feb 2019 09:01:11: start model_add_line... INFO @ Fri, 15 Feb 2019 09:01:11: end of X-cor INFO @ Fri, 15 Feb 2019 09:01:11: #2 finished! INFO @ Fri, 15 Feb 2019 09:01:11: start X-correlation... INFO @ Fri, 15 Feb 2019 09:01:11: #2 predicted fragment length is 257 bps INFO @ Fri, 15 Feb 2019 09:01:11: #2 alternative fragment length(s) may be 3,164,186,217,257,288,304,322 bps INFO @ Fri, 15 Feb 2019 09:01:11: #2.2 Generate R script for model : ERX1236287.05_model.r INFO @ Fri, 15 Feb 2019 09:01:11: end of X-cor INFO @ Fri, 15 Feb 2019 09:01:11: #2 finished! INFO @ Fri, 15 Feb 2019 09:01:11: #2 predicted fragment length is 257 bps INFO @ Fri, 15 Feb 2019 09:01:11: #2 alternative fragment length(s) may be 3,164,186,217,257,288,304,322 bps INFO @ Fri, 15 Feb 2019 09:01:11: #2.2 Generate R script for model : ERX1236287.20_model.r INFO @ Fri, 15 Feb 2019 09:01:11: #3 Call peaks... INFO @ Fri, 15 Feb 2019 09:01:11: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 09:01:11: #3 Call peaks... INFO @ Fri, 15 Feb 2019 09:01:11: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 09:01:12: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 09:01:12: #4 Write output xls file... ERX1236287.10_peaks.xls INFO @ Fri, 15 Feb 2019 09:01:12: #4 Write peak in narrowPeak format file... ERX1236287.10_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 09:01:12: #4 Write summits bed file... ERX1236287.10_summits.bed INFO @ Fri, 15 Feb 2019 09:01:12: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (151 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 09:01:12: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 09:01:12: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 09:01:13: #4 Write output xls file... ERX1236287.05_peaks.xls INFO @ Fri, 15 Feb 2019 09:01:13: #4 Write output xls file... ERX1236287.20_peaks.xls INFO @ Fri, 15 Feb 2019 09:01:13: #4 Write peak in narrowPeak format file... ERX1236287.20_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 09:01:13: #4 Write peak in narrowPeak format file... ERX1236287.05_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 09:01:13: #4 Write summits bed file... ERX1236287.20_summits.bed INFO @ Fri, 15 Feb 2019 09:01:13: #4 Write summits bed file... ERX1236287.05_summits.bed INFO @ Fri, 15 Feb 2019 09:01:13: Done! INFO @ Fri, 15 Feb 2019 09:01:13: Done! pass1 - making usageList (13 chroms): 3 millis pass2 - checking and writing primary data (40 records, 4 fields): 3 millis pass1 - making usageList (16 chroms): 5 millis pass2 - checking and writing primary data (262 records, 4 fields): 5 millis CompletedMACS2peakCalling CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。