Job ID = 11633500 sra ファイルのダウンロード中... Completed: 222431K bytes transferred in 5 seconds (322285K 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 4000000 spots for /home/okishinya/chipatlas/results/sacCer3/ERX1236277/ERR1162870.sra Written 4000000 spots for /home/okishinya/chipatlas/results/sacCer3/ERX1236277/ERR1162870.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: 00:03:04 4000000 reads; of these: 4000000 (100.00%) were paired; of these: 646054 (16.15%) aligned concordantly 0 times 2968777 (74.22%) aligned concordantly exactly 1 time 385169 (9.63%) aligned concordantly >1 times ---- 646054 pairs aligned concordantly 0 times; of these: 122139 (18.91%) aligned discordantly 1 time ---- 523915 pairs aligned 0 times concordantly or discordantly; of these: 1047830 mates make up the pairs; of these: 985765 (94.08%) aligned 0 times 29436 (2.81%) aligned exactly 1 time 32629 (3.11%) aligned >1 times 87.68% overall alignment rate Time searching: 00:03:04 Overall time: 00:03:04 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] 1194376 / 3474858 = 0.3437 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 09:02:55: # Command line: callpeak -t ERX1236277.bam -f BAM -g 12100000 -n ERX1236277.20 -q 1e-20 # ARGUMENTS LIST: # name = ERX1236277.20 # format = BAM # ChIP-seq file = ['ERX1236277.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 09:02:55: #1 read tag files... INFO @ Fri, 15 Feb 2019 09:02:55: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 09:02:55: # Command line: callpeak -t ERX1236277.bam -f BAM -g 12100000 -n ERX1236277.10 -q 1e-10 # ARGUMENTS LIST: # name = ERX1236277.10 # format = BAM # ChIP-seq file = ['ERX1236277.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 09:02:55: #1 read tag files... INFO @ Fri, 15 Feb 2019 09:02:55: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 09:02:55: # Command line: callpeak -t ERX1236277.bam -f BAM -g 12100000 -n ERX1236277.05 -q 1e-05 # ARGUMENTS LIST: # name = ERX1236277.05 # format = BAM # ChIP-seq file = ['ERX1236277.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 09:02:55: #1 read tag files... INFO @ Fri, 15 Feb 2019 09:02:55: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 09:03:00: 1000000 INFO @ Fri, 15 Feb 2019 09:03:01: 1000000 INFO @ Fri, 15 Feb 2019 09:03:01: 1000000 INFO @ Fri, 15 Feb 2019 09:03:06: 2000000 INFO @ Fri, 15 Feb 2019 09:03:06: 2000000 INFO @ Fri, 15 Feb 2019 09:03:07: 2000000 INFO @ Fri, 15 Feb 2019 09:03:12: 3000000 INFO @ Fri, 15 Feb 2019 09:03:12: 3000000 INFO @ Fri, 15 Feb 2019 09:03:13: 3000000 INFO @ Fri, 15 Feb 2019 09:03:18: 4000000 INFO @ Fri, 15 Feb 2019 09:03:18: 4000000 INFO @ Fri, 15 Feb 2019 09:03:19: 4000000 INFO @ Fri, 15 Feb 2019 09:03:22: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 09:03:22: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 09:03:22: #1 total tags in treatment: 2204496 INFO @ Fri, 15 Feb 2019 09:03:22: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 09:03:22: #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 09:03:22: #1 tags after filtering in treatment: 1954010 INFO @ Fri, 15 Feb 2019 09:03:22: #1 Redundant rate of treatment: 0.11 INFO @ Fri, 15 Feb 2019 09:03:22: #1 finished! INFO @ Fri, 15 Feb 2019 09:03:22: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 09:03:22: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 09:03:22: #2 number of paired peaks: 144 WARNING @ Fri, 15 Feb 2019 09:03:22: Fewer paired peaks (144) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 144 pairs to build model! INFO @ Fri, 15 Feb 2019 09:03:22: start model_add_line... INFO @ Fri, 15 Feb 2019 09:03:22: start X-correlation... INFO @ Fri, 15 Feb 2019 09:03:22: end of X-cor INFO @ Fri, 15 Feb 2019 09:03:22: #2 finished! INFO @ Fri, 15 Feb 2019 09:03:22: #2 predicted fragment length is 138 bps INFO @ Fri, 15 Feb 2019 09:03:22: #2 alternative fragment length(s) may be 4,99,117,122,138,174 bps INFO @ Fri, 15 Feb 2019 09:03:22: #2.2 Generate R script for model : ERX1236277.20_model.r INFO @ Fri, 15 Feb 2019 09:03:22: #3 Call peaks... INFO @ Fri, 15 Feb 2019 09:03:22: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 09:03:22: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 09:03:22: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 09:03:22: #1 total tags in treatment: 2204496 INFO @ Fri, 15 Feb 2019 09:03:22: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 09:03:22: #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 09:03:22: #1 tags after filtering in treatment: 1954010 INFO @ Fri, 15 Feb 2019 09:03:22: #1 Redundant rate of treatment: 0.11 INFO @ Fri, 15 Feb 2019 09:03:22: #1 finished! INFO @ Fri, 15 Feb 2019 09:03:22: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 09:03:22: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 09:03:22: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 09:03:22: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 09:03:22: #1 total tags in treatment: 2204496 INFO @ Fri, 15 Feb 2019 09:03:22: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 09:03:22: #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 09:03:22: #2 number of paired peaks: 144 WARNING @ Fri, 15 Feb 2019 09:03:22: Fewer paired peaks (144) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 144 pairs to build model! INFO @ Fri, 15 Feb 2019 09:03:22: start model_add_line... INFO @ Fri, 15 Feb 2019 09:03:22: start X-correlation... INFO @ Fri, 15 Feb 2019 09:03:22: end of X-cor INFO @ Fri, 15 Feb 2019 09:03:22: #2 finished! INFO @ Fri, 15 Feb 2019 09:03:22: #2 predicted fragment length is 138 bps INFO @ Fri, 15 Feb 2019 09:03:22: #2 alternative fragment length(s) may be 4,99,117,122,138,174 bps INFO @ Fri, 15 Feb 2019 09:03:22: #2.2 Generate R script for model : ERX1236277.10_model.r INFO @ Fri, 15 Feb 2019 09:03:22: #1 tags after filtering in treatment: 1954010 INFO @ Fri, 15 Feb 2019 09:03:22: #1 Redundant rate of treatment: 0.11 INFO @ Fri, 15 Feb 2019 09:03:22: #1 finished! INFO @ Fri, 15 Feb 2019 09:03:22: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 09:03:22: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 09:03:22: #3 Call peaks... INFO @ Fri, 15 Feb 2019 09:03:22: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 09:03:23: #2 number of paired peaks: 144 WARNING @ Fri, 15 Feb 2019 09:03:23: Fewer paired peaks (144) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 144 pairs to build model! INFO @ Fri, 15 Feb 2019 09:03:23: start model_add_line... INFO @ Fri, 15 Feb 2019 09:03:23: start X-correlation... INFO @ Fri, 15 Feb 2019 09:03:23: end of X-cor INFO @ Fri, 15 Feb 2019 09:03:23: #2 finished! INFO @ Fri, 15 Feb 2019 09:03:23: #2 predicted fragment length is 138 bps INFO @ Fri, 15 Feb 2019 09:03:23: #2 alternative fragment length(s) may be 4,99,117,122,138,174 bps INFO @ Fri, 15 Feb 2019 09:03:23: #2.2 Generate R script for model : ERX1236277.05_model.r INFO @ Fri, 15 Feb 2019 09:03:23: #3 Call peaks... INFO @ Fri, 15 Feb 2019 09:03:23: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 09:03:28: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 09:03:28: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 09:03:28: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 09:03:30: #4 Write output xls file... ERX1236277.20_peaks.xls INFO @ Fri, 15 Feb 2019 09:03:30: #4 Write peak in narrowPeak format file... ERX1236277.20_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 09:03:30: #4 Write summits bed file... ERX1236277.20_summits.bed INFO @ Fri, 15 Feb 2019 09:03:30: Done! pass1 - making usageList (16 chroms): 4 millis pass2 - checking and writing primary data (208 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 09:03:30: #4 Write output xls file... ERX1236277.05_peaks.xls INFO @ Fri, 15 Feb 2019 09:03:30: #4 Write output xls file... ERX1236277.10_peaks.xls INFO @ Fri, 15 Feb 2019 09:03:30: #4 Write peak in narrowPeak format file... ERX1236277.05_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 09:03:30: #4 Write peak in narrowPeak format file... ERX1236277.10_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 09:03:30: #4 Write summits bed file... ERX1236277.05_summits.bed INFO @ Fri, 15 Feb 2019 09:03:30: #4 Write summits bed file... ERX1236277.10_summits.bed INFO @ Fri, 15 Feb 2019 09:03:30: Done! INFO @ Fri, 15 Feb 2019 09:03:30: Done! pass1 - making usageList (16 chroms): 5 millis pass2 - checking and writing primary data (604 records, 4 fields): 4 millis pass1 - making usageList (16 chroms): 6 millis pass2 - checking and writing primary data (375 records, 4 fields): 17 millis CompletedMACS2peakCalling CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。