Job ID = 11633499 sra ファイルのダウンロード中... Completed: 95875K bytes transferred in 4 seconds (182591K 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 1603576 spots for /home/okishinya/chipatlas/results/sacCer3/ERX1236276/ERR1162869.sra Written 1603576 spots for /home/okishinya/chipatlas/results/sacCer3/ERX1236276/ERR1162869.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: 00:01:13 1603576 reads; of these: 1603576 (100.00%) were paired; of these: 269318 (16.79%) aligned concordantly 0 times 1176267 (73.35%) aligned concordantly exactly 1 time 157991 (9.85%) aligned concordantly >1 times ---- 269318 pairs aligned concordantly 0 times; of these: 44173 (16.40%) aligned discordantly 1 time ---- 225145 pairs aligned 0 times concordantly or discordantly; of these: 450290 mates make up the pairs; of these: 431445 (95.81%) aligned 0 times 7195 (1.60%) aligned exactly 1 time 11650 (2.59%) aligned >1 times 86.55% overall alignment rate Time searching: 00:01:13 Overall time: 00:01:13 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] 310012 / 1378235 = 0.2249 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 08:59:43: # Command line: callpeak -t ERX1236276.bam -f BAM -g 12100000 -n ERX1236276.20 -q 1e-20 # ARGUMENTS LIST: # name = ERX1236276.20 # format = BAM # ChIP-seq file = ['ERX1236276.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 08:59:43: #1 read tag files... INFO @ Fri, 15 Feb 2019 08:59:43: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 08:59:43: # Command line: callpeak -t ERX1236276.bam -f BAM -g 12100000 -n ERX1236276.05 -q 1e-05 # ARGUMENTS LIST: # name = ERX1236276.05 # format = BAM # ChIP-seq file = ['ERX1236276.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 08:59:43: #1 read tag files... INFO @ Fri, 15 Feb 2019 08:59:43: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 08:59:43: # Command line: callpeak -t ERX1236276.bam -f BAM -g 12100000 -n ERX1236276.10 -q 1e-10 # ARGUMENTS LIST: # name = ERX1236276.10 # format = BAM # ChIP-seq file = ['ERX1236276.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 08:59:43: #1 read tag files... INFO @ Fri, 15 Feb 2019 08:59:43: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 08:59:48: 1000000 INFO @ Fri, 15 Feb 2019 08:59:49: 1000000 INFO @ Fri, 15 Feb 2019 08:59:49: 1000000 INFO @ Fri, 15 Feb 2019 08:59:54: 2000000 INFO @ Fri, 15 Feb 2019 08:59:55: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 08:59:55: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 08:59:55: #1 total tags in treatment: 1033707 INFO @ Fri, 15 Feb 2019 08:59:55: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 08:59:55: #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 08:59:55: #1 tags after filtering in treatment: 967000 INFO @ Fri, 15 Feb 2019 08:59:55: #1 Redundant rate of treatment: 0.06 INFO @ Fri, 15 Feb 2019 08:59:55: #1 finished! INFO @ Fri, 15 Feb 2019 08:59:55: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 08:59:55: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 08:59:55: #2 number of paired peaks: 168 WARNING @ Fri, 15 Feb 2019 08:59:55: Fewer paired peaks (168) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 168 pairs to build model! INFO @ Fri, 15 Feb 2019 08:59:55: start model_add_line... INFO @ Fri, 15 Feb 2019 08:59:55: start X-correlation... INFO @ Fri, 15 Feb 2019 08:59:55: end of X-cor INFO @ Fri, 15 Feb 2019 08:59:55: #2 finished! INFO @ Fri, 15 Feb 2019 08:59:55: #2 predicted fragment length is 166 bps INFO @ Fri, 15 Feb 2019 08:59:55: #2 alternative fragment length(s) may be 4,93,130,148,166 bps INFO @ Fri, 15 Feb 2019 08:59:55: #2.2 Generate R script for model : ERX1236276.10_model.r INFO @ Fri, 15 Feb 2019 08:59:55: #3 Call peaks... INFO @ Fri, 15 Feb 2019 08:59:55: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 08:59:55: 2000000 INFO @ Fri, 15 Feb 2019 08:59:55: 2000000 INFO @ Fri, 15 Feb 2019 08:59:56: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 08:59:56: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 08:59:56: #1 total tags in treatment: 1033707 INFO @ Fri, 15 Feb 2019 08:59:56: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 08:59:56: #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 08:59:56: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 08:59:56: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 08:59:56: #1 total tags in treatment: 1033707 INFO @ Fri, 15 Feb 2019 08:59:56: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 08:59:56: #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 08:59:56: #1 tags after filtering in treatment: 967000 INFO @ Fri, 15 Feb 2019 08:59:56: #1 Redundant rate of treatment: 0.06 INFO @ Fri, 15 Feb 2019 08:59:56: #1 finished! INFO @ Fri, 15 Feb 2019 08:59:56: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 08:59:56: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 08:59:56: #1 tags after filtering in treatment: 967000 INFO @ Fri, 15 Feb 2019 08:59:56: #1 Redundant rate of treatment: 0.06 INFO @ Fri, 15 Feb 2019 08:59:56: #1 finished! INFO @ Fri, 15 Feb 2019 08:59:56: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 08:59:56: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 08:59:56: #2 number of paired peaks: 168 WARNING @ Fri, 15 Feb 2019 08:59:56: Fewer paired peaks (168) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 168 pairs to build model! INFO @ Fri, 15 Feb 2019 08:59:56: start model_add_line... INFO @ Fri, 15 Feb 2019 08:59:56: #2 number of paired peaks: 168 WARNING @ Fri, 15 Feb 2019 08:59:56: Fewer paired peaks (168) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 168 pairs to build model! INFO @ Fri, 15 Feb 2019 08:59:56: start model_add_line... INFO @ Fri, 15 Feb 2019 08:59:56: start X-correlation... INFO @ Fri, 15 Feb 2019 08:59:56: start X-correlation... INFO @ Fri, 15 Feb 2019 08:59:56: end of X-cor INFO @ Fri, 15 Feb 2019 08:59:56: #2 finished! INFO @ Fri, 15 Feb 2019 08:59:56: #2 predicted fragment length is 166 bps INFO @ Fri, 15 Feb 2019 08:59:56: #2 alternative fragment length(s) may be 4,93,130,148,166 bps INFO @ Fri, 15 Feb 2019 08:59:56: #2.2 Generate R script for model : ERX1236276.05_model.r INFO @ Fri, 15 Feb 2019 08:59:56: end of X-cor INFO @ Fri, 15 Feb 2019 08:59:56: #2 finished! INFO @ Fri, 15 Feb 2019 08:59:56: #2 predicted fragment length is 166 bps INFO @ Fri, 15 Feb 2019 08:59:56: #2 alternative fragment length(s) may be 4,93,130,148,166 bps INFO @ Fri, 15 Feb 2019 08:59:56: #2.2 Generate R script for model : ERX1236276.20_model.r INFO @ Fri, 15 Feb 2019 08:59:56: #3 Call peaks... INFO @ Fri, 15 Feb 2019 08:59:56: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 08:59:56: #3 Call peaks... INFO @ Fri, 15 Feb 2019 08:59:56: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 08:59:58: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 08:59:59: #4 Write output xls file... ERX1236276.10_peaks.xls INFO @ Fri, 15 Feb 2019 08:59:59: #4 Write peak in narrowPeak format file... ERX1236276.10_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 08:59:59: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 08:59:59: #4 Write summits bed file... ERX1236276.10_summits.bed INFO @ Fri, 15 Feb 2019 08:59:59: Done! pass1 - making usageList (16 chroms): 4 millis pass2 - checking and writing primary data (265 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 08:59:59: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 09:00:00: #4 Write output xls file... ERX1236276.20_peaks.xls INFO @ Fri, 15 Feb 2019 09:00:00: #4 Write peak in narrowPeak format file... ERX1236276.20_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 09:00:00: #4 Write summits bed file... ERX1236276.20_summits.bed INFO @ Fri, 15 Feb 2019 09:00:00: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (110 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 09:00:00: #4 Write output xls file... ERX1236276.05_peaks.xls INFO @ Fri, 15 Feb 2019 09:00:00: #4 Write peak in narrowPeak format file... ERX1236276.05_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 09:00:00: #4 Write summits bed file... ERX1236276.05_summits.bed INFO @ Fri, 15 Feb 2019 09:00:00: Done! pass1 - making usageList (16 chroms): 2 millis pass2 - checking and writing primary data (426 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。