Job ID = 11633501 sra ファイルのダウンロード中... Completed: 103496K bytes transferred in 4 seconds (187368K 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 1835158 spots for /home/okishinya/chipatlas/results/sacCer3/ERX1236278/ERR1162871.sra Written 1835158 spots for /home/okishinya/chipatlas/results/sacCer3/ERX1236278/ERR1162871.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: 00:01:27 1835158 reads; of these: 1835158 (100.00%) were paired; of these: 296371 (16.15%) aligned concordantly 0 times 1362014 (74.22%) aligned concordantly exactly 1 time 176773 (9.63%) aligned concordantly >1 times ---- 296371 pairs aligned concordantly 0 times; of these: 56385 (19.03%) aligned discordantly 1 time ---- 239986 pairs aligned 0 times concordantly or discordantly; of these: 479972 mates make up the pairs; of these: 451458 (94.06%) aligned 0 times 13841 (2.88%) aligned exactly 1 time 14673 (3.06%) aligned >1 times 87.70% overall alignment rate Time searching: 00:01:27 Overall time: 00:01:27 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] 303411 / 1594677 = 0.1903 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 09:00:17: # Command line: callpeak -t ERX1236278.bam -f BAM -g 12100000 -n ERX1236278.10 -q 1e-10 # ARGUMENTS LIST: # name = ERX1236278.10 # format = BAM # ChIP-seq file = ['ERX1236278.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 09:00:17: #1 read tag files... INFO @ Fri, 15 Feb 2019 09:00:17: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 09:00:17: # Command line: callpeak -t ERX1236278.bam -f BAM -g 12100000 -n ERX1236278.20 -q 1e-20 # ARGUMENTS LIST: # name = ERX1236278.20 # format = BAM # ChIP-seq file = ['ERX1236278.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 09:00:17: #1 read tag files... INFO @ Fri, 15 Feb 2019 09:00:17: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 09:00:17: # Command line: callpeak -t ERX1236278.bam -f BAM -g 12100000 -n ERX1236278.05 -q 1e-05 # ARGUMENTS LIST: # name = ERX1236278.05 # format = BAM # ChIP-seq file = ['ERX1236278.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 09:00:17: #1 read tag files... INFO @ Fri, 15 Feb 2019 09:00:17: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 09:00:23: 1000000 INFO @ Fri, 15 Feb 2019 09:00:24: 1000000 INFO @ Fri, 15 Feb 2019 09:00:24: 1000000 INFO @ Fri, 15 Feb 2019 09:00:29: 2000000 INFO @ Fri, 15 Feb 2019 09:00:31: 2000000 INFO @ Fri, 15 Feb 2019 09:00:31: 2000000 INFO @ Fri, 15 Feb 2019 09:00:32: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 09:00:32: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 09:00:32: #1 total tags in treatment: 1246935 INFO @ Fri, 15 Feb 2019 09:00:32: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 09:00:32: #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 09:00:32: #1 tags after filtering in treatment: 1157982 INFO @ Fri, 15 Feb 2019 09:00:32: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 15 Feb 2019 09:00:32: #1 finished! INFO @ Fri, 15 Feb 2019 09:00:32: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 09:00:32: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 09:00:32: #2 number of paired peaks: 170 WARNING @ Fri, 15 Feb 2019 09:00:32: Fewer paired peaks (170) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 170 pairs to build model! INFO @ Fri, 15 Feb 2019 09:00:32: start model_add_line... INFO @ Fri, 15 Feb 2019 09:00:32: start X-correlation... INFO @ Fri, 15 Feb 2019 09:00:32: end of X-cor INFO @ Fri, 15 Feb 2019 09:00:32: #2 finished! INFO @ Fri, 15 Feb 2019 09:00:32: #2 predicted fragment length is 170 bps INFO @ Fri, 15 Feb 2019 09:00:32: #2 alternative fragment length(s) may be 4,135,170 bps INFO @ Fri, 15 Feb 2019 09:00:32: #2.2 Generate R script for model : ERX1236278.10_model.r INFO @ Fri, 15 Feb 2019 09:00:32: #3 Call peaks... INFO @ Fri, 15 Feb 2019 09:00:32: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 09:00:35: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 09:00:35: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 09:00:35: #1 total tags in treatment: 1246935 INFO @ Fri, 15 Feb 2019 09:00:35: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 09:00:35: #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 09:00:35: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 09:00:35: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 09:00:35: #1 total tags in treatment: 1246935 INFO @ Fri, 15 Feb 2019 09:00:35: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 09:00:35: #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 09:00:35: #1 tags after filtering in treatment: 1157982 INFO @ Fri, 15 Feb 2019 09:00:35: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 15 Feb 2019 09:00:35: #1 finished! INFO @ Fri, 15 Feb 2019 09:00:35: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 09:00:35: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 09:00:35: #1 tags after filtering in treatment: 1157982 INFO @ Fri, 15 Feb 2019 09:00:35: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 15 Feb 2019 09:00:35: #1 finished! INFO @ Fri, 15 Feb 2019 09:00:35: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 09:00:35: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 09:00:35: #2 number of paired peaks: 170 WARNING @ Fri, 15 Feb 2019 09:00:35: Fewer paired peaks (170) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 170 pairs to build model! INFO @ Fri, 15 Feb 2019 09:00:35: start model_add_line... INFO @ Fri, 15 Feb 2019 09:00:35: #2 number of paired peaks: 170 WARNING @ Fri, 15 Feb 2019 09:00:35: Fewer paired peaks (170) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 170 pairs to build model! INFO @ Fri, 15 Feb 2019 09:00:35: start model_add_line... INFO @ Fri, 15 Feb 2019 09:00:35: start X-correlation... INFO @ Fri, 15 Feb 2019 09:00:35: start X-correlation... INFO @ Fri, 15 Feb 2019 09:00:35: end of X-cor INFO @ Fri, 15 Feb 2019 09:00:35: #2 finished! INFO @ Fri, 15 Feb 2019 09:00:35: #2 predicted fragment length is 170 bps INFO @ Fri, 15 Feb 2019 09:00:35: end of X-cor INFO @ Fri, 15 Feb 2019 09:00:35: #2 alternative fragment length(s) may be 4,135,170 bps INFO @ Fri, 15 Feb 2019 09:00:35: #2.2 Generate R script for model : ERX1236278.20_model.r INFO @ Fri, 15 Feb 2019 09:00:35: #2 finished! INFO @ Fri, 15 Feb 2019 09:00:35: #2 predicted fragment length is 170 bps INFO @ Fri, 15 Feb 2019 09:00:35: #2 alternative fragment length(s) may be 4,135,170 bps INFO @ Fri, 15 Feb 2019 09:00:35: #2.2 Generate R script for model : ERX1236278.05_model.r INFO @ Fri, 15 Feb 2019 09:00:35: #3 Call peaks... INFO @ Fri, 15 Feb 2019 09:00:35: #3 Call peaks... INFO @ Fri, 15 Feb 2019 09:00:35: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 09:00:35: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 09:00:36: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 09:00:37: #4 Write output xls file... ERX1236278.10_peaks.xls INFO @ Fri, 15 Feb 2019 09:00:37: #4 Write peak in narrowPeak format file... ERX1236278.10_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 09:00:37: #4 Write summits bed file... ERX1236278.10_summits.bed INFO @ Fri, 15 Feb 2019 09:00:37: Done! pass1 - making usageList (16 chroms): 2 millis pass2 - checking and writing primary data (302 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 09:00:38: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 09:00:38: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 09:00:40: #4 Write output xls file... ERX1236278.05_peaks.xls INFO @ Fri, 15 Feb 2019 09:00:40: #4 Write peak in narrowPeak format file... ERX1236278.05_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 09:00:40: #4 Write summits bed file... ERX1236278.05_summits.bed INFO @ Fri, 15 Feb 2019 09:00:40: Done! INFO @ Fri, 15 Feb 2019 09:00:40: #4 Write output xls file... ERX1236278.20_peaks.xls INFO @ Fri, 15 Feb 2019 09:00:40: #4 Write peak in narrowPeak format file... ERX1236278.20_peaks.narrowPeak pass1 - making usageList (16 chroms): 2 millis INFO @ Fri, 15 Feb 2019 09:00:40: #4 Write summits bed file... ERX1236278.20_summits.bed pass2 - checking and writing primary data (467 records, 4 fields): 3 millis INFO @ Fri, 15 Feb 2019 09:00:40: Done! CompletedMACS2peakCalling pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (151 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。