Job ID = 11633548 sra ファイルのダウンロード中... Completed: 73319K bytes transferred in 4 seconds (146821K 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 1218762 spots for /home/okishinya/chipatlas/results/sacCer3/ERX1236325/ERR1162918.sra Written 1218762 spots for /home/okishinya/chipatlas/results/sacCer3/ERX1236325/ERR1162918.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:00:50 1218762 reads; of these: 1218762 (100.00%) were paired; of these: 287576 (23.60%) aligned concordantly 0 times 834919 (68.51%) aligned concordantly exactly 1 time 96267 (7.90%) aligned concordantly >1 times ---- 287576 pairs aligned concordantly 0 times; of these: 21555 (7.50%) aligned discordantly 1 time ---- 266021 pairs aligned 0 times concordantly or discordantly; of these: 532042 mates make up the pairs; of these: 521083 (97.94%) aligned 0 times 5742 (1.08%) aligned exactly 1 time 5217 (0.98%) aligned >1 times 78.62% overall alignment rate Time searching: 00:00:51 Overall time: 00:00:51 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] 219358 / 952579 = 0.2303 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 09:07:19: # Command line: callpeak -t ERX1236325.bam -f BAM -g 12100000 -n ERX1236325.10 -q 1e-10 # ARGUMENTS LIST: # name = ERX1236325.10 # format = BAM # ChIP-seq file = ['ERX1236325.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 09:07:19: #1 read tag files... INFO @ Fri, 15 Feb 2019 09:07:19: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 09:07:19: # Command line: callpeak -t ERX1236325.bam -f BAM -g 12100000 -n ERX1236325.05 -q 1e-05 # ARGUMENTS LIST: # name = ERX1236325.05 # format = BAM # ChIP-seq file = ['ERX1236325.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 09:07:19: #1 read tag files... INFO @ Fri, 15 Feb 2019 09:07:19: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 09:07:19: # Command line: callpeak -t ERX1236325.bam -f BAM -g 12100000 -n ERX1236325.20 -q 1e-20 # ARGUMENTS LIST: # name = ERX1236325.20 # format = BAM # ChIP-seq file = ['ERX1236325.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 09:07:19: #1 read tag files... INFO @ Fri, 15 Feb 2019 09:07:19: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 09:07:26: 1000000 INFO @ Fri, 15 Feb 2019 09:07:27: 1000000 INFO @ Fri, 15 Feb 2019 09:07:27: 1000000 INFO @ Fri, 15 Feb 2019 09:07:29: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 09:07:29: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 09:07:29: #1 total tags in treatment: 716819 INFO @ Fri, 15 Feb 2019 09:07:29: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 09:07:29: #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 09:07:29: #1 tags after filtering in treatment: 684362 INFO @ Fri, 15 Feb 2019 09:07:29: #1 Redundant rate of treatment: 0.05 INFO @ Fri, 15 Feb 2019 09:07:29: #1 finished! INFO @ Fri, 15 Feb 2019 09:07:29: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 09:07:29: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 09:07:29: #2 number of paired peaks: 257 WARNING @ Fri, 15 Feb 2019 09:07:29: Fewer paired peaks (257) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 257 pairs to build model! INFO @ Fri, 15 Feb 2019 09:07:29: start model_add_line... INFO @ Fri, 15 Feb 2019 09:07:29: start X-correlation... INFO @ Fri, 15 Feb 2019 09:07:29: end of X-cor INFO @ Fri, 15 Feb 2019 09:07:29: #2 finished! INFO @ Fri, 15 Feb 2019 09:07:29: #2 predicted fragment length is 182 bps INFO @ Fri, 15 Feb 2019 09:07:29: #2 alternative fragment length(s) may be 111,166,182 bps INFO @ Fri, 15 Feb 2019 09:07:29: #2.2 Generate R script for model : ERX1236325.20_model.r INFO @ Fri, 15 Feb 2019 09:07:29: #3 Call peaks... INFO @ Fri, 15 Feb 2019 09:07:29: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 09:07:30: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 09:07:30: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 09:07:30: #1 total tags in treatment: 716819 INFO @ Fri, 15 Feb 2019 09:07:30: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 09:07:30: #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 09:07:30: #1 tags after filtering in treatment: 684362 INFO @ Fri, 15 Feb 2019 09:07:30: #1 Redundant rate of treatment: 0.05 INFO @ Fri, 15 Feb 2019 09:07:30: #1 finished! INFO @ Fri, 15 Feb 2019 09:07:30: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 09:07:30: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 09:07:30: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 09:07:30: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 09:07:30: #1 total tags in treatment: 716819 INFO @ Fri, 15 Feb 2019 09:07:30: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 09:07:30: #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 09:07:30: #1 tags after filtering in treatment: 684362 INFO @ Fri, 15 Feb 2019 09:07:30: #1 Redundant rate of treatment: 0.05 INFO @ Fri, 15 Feb 2019 09:07:30: #1 finished! INFO @ Fri, 15 Feb 2019 09:07:30: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 09:07:30: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 09:07:31: #2 number of paired peaks: 257 WARNING @ Fri, 15 Feb 2019 09:07:31: Fewer paired peaks (257) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 257 pairs to build model! INFO @ Fri, 15 Feb 2019 09:07:31: start model_add_line... INFO @ Fri, 15 Feb 2019 09:07:31: start X-correlation... INFO @ Fri, 15 Feb 2019 09:07:31: end of X-cor INFO @ Fri, 15 Feb 2019 09:07:31: #2 finished! INFO @ Fri, 15 Feb 2019 09:07:31: #2 predicted fragment length is 182 bps INFO @ Fri, 15 Feb 2019 09:07:31: #2 alternative fragment length(s) may be 111,166,182 bps INFO @ Fri, 15 Feb 2019 09:07:31: #2.2 Generate R script for model : ERX1236325.10_model.r INFO @ Fri, 15 Feb 2019 09:07:31: #2 number of paired peaks: 257 WARNING @ Fri, 15 Feb 2019 09:07:31: Fewer paired peaks (257) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 257 pairs to build model! INFO @ Fri, 15 Feb 2019 09:07:31: start model_add_line... INFO @ Fri, 15 Feb 2019 09:07:31: #3 Call peaks... INFO @ Fri, 15 Feb 2019 09:07:31: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 09:07:31: start X-correlation... INFO @ Fri, 15 Feb 2019 09:07:31: end of X-cor INFO @ Fri, 15 Feb 2019 09:07:31: #2 finished! INFO @ Fri, 15 Feb 2019 09:07:31: #2 predicted fragment length is 182 bps INFO @ Fri, 15 Feb 2019 09:07:31: #2 alternative fragment length(s) may be 111,166,182 bps INFO @ Fri, 15 Feb 2019 09:07:31: #2.2 Generate R script for model : ERX1236325.05_model.r INFO @ Fri, 15 Feb 2019 09:07:31: #3 Call peaks... INFO @ Fri, 15 Feb 2019 09:07:31: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 09:07:31: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 09:07:32: #4 Write output xls file... ERX1236325.20_peaks.xls INFO @ Fri, 15 Feb 2019 09:07:32: #4 Write peak in narrowPeak format file... ERX1236325.20_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 09:07:32: #4 Write summits bed file... ERX1236325.20_summits.bed INFO @ Fri, 15 Feb 2019 09:07:32: Done! pass1 - making usageList (16 chroms): 2 millis pass2 - checking and writing primary data (158 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 09:07:33: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 09:07:33: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 09:07:34: #4 Write output xls file... ERX1236325.10_peaks.xls INFO @ Fri, 15 Feb 2019 09:07:34: #4 Write peak in narrowPeak format file... ERX1236325.10_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 09:07:34: #4 Write summits bed file... ERX1236325.10_summits.bed INFO @ Fri, 15 Feb 2019 09:07:34: Done! pass1 - making usageList (16 chroms): 4 millis pass2 - checking and writing primary data (272 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 09:07:34: #4 Write output xls file... ERX1236325.05_peaks.xls INFO @ Fri, 15 Feb 2019 09:07:34: #4 Write peak in narrowPeak format file... ERX1236325.05_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 09:07:34: #4 Write summits bed file... ERX1236325.05_summits.bed INFO @ Fri, 15 Feb 2019 09:07:34: Done! pass1 - making usageList (16 chroms): 4 millis pass2 - checking and writing primary data (431 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。