Job ID = 11633438 sra ファイルのダウンロード中... Completed: 89798K bytes transferred in 4 seconds (162750K 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 1607200 spots for /home/okishinya/chipatlas/results/sacCer3/ERX1236215/ERR1162808.sra Written 1607200 spots for /home/okishinya/chipatlas/results/sacCer3/ERX1236215/ERR1162808.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: 00:01:15 1607200 reads; of these: 1607200 (100.00%) were paired; of these: 109140 (6.79%) aligned concordantly 0 times 1366680 (85.03%) aligned concordantly exactly 1 time 131380 (8.17%) aligned concordantly >1 times ---- 109140 pairs aligned concordantly 0 times; of these: 24843 (22.76%) aligned discordantly 1 time ---- 84297 pairs aligned 0 times concordantly or discordantly; of these: 168594 mates make up the pairs; of these: 150438 (89.23%) aligned 0 times 11696 (6.94%) aligned exactly 1 time 6460 (3.83%) aligned >1 times 95.32% overall alignment rate Time searching: 00:01:15 Overall time: 00:01:15 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] 115190 / 1520888 = 0.0757 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 08:57:34: # Command line: callpeak -t ERX1236215.bam -f BAM -g 12100000 -n ERX1236215.05 -q 1e-05 # ARGUMENTS LIST: # name = ERX1236215.05 # format = BAM # ChIP-seq file = ['ERX1236215.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 08:57:34: #1 read tag files... INFO @ Fri, 15 Feb 2019 08:57:34: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 08:57:34: # Command line: callpeak -t ERX1236215.bam -f BAM -g 12100000 -n ERX1236215.20 -q 1e-20 # ARGUMENTS LIST: # name = ERX1236215.20 # format = BAM # ChIP-seq file = ['ERX1236215.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 08:57:34: #1 read tag files... INFO @ Fri, 15 Feb 2019 08:57:34: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 08:57:34: # Command line: callpeak -t ERX1236215.bam -f BAM -g 12100000 -n ERX1236215.10 -q 1e-10 # ARGUMENTS LIST: # name = ERX1236215.10 # format = BAM # ChIP-seq file = ['ERX1236215.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 08:57:34: #1 read tag files... INFO @ Fri, 15 Feb 2019 08:57:34: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 08:57:40: 1000000 INFO @ Fri, 15 Feb 2019 08:57:40: 1000000 INFO @ Fri, 15 Feb 2019 08:57:40: 1000000 INFO @ Fri, 15 Feb 2019 08:57:46: 2000000 INFO @ Fri, 15 Feb 2019 08:57:46: 2000000 INFO @ Fri, 15 Feb 2019 08:57:46: 2000000 INFO @ Fri, 15 Feb 2019 08:57:51: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 08:57:51: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 08:57:51: #1 total tags in treatment: 1385422 INFO @ Fri, 15 Feb 2019 08:57:51: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 08:57:51: #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 08:57:51: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 08:57:51: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 08:57:51: #1 total tags in treatment: 1385422 INFO @ Fri, 15 Feb 2019 08:57:51: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 08:57:51: #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 08:57:51: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 08:57:51: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 08:57:51: #1 total tags in treatment: 1385422 INFO @ Fri, 15 Feb 2019 08:57:51: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 08:57:51: #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 08:57:51: #1 tags after filtering in treatment: 1296486 INFO @ Fri, 15 Feb 2019 08:57:51: #1 Redundant rate of treatment: 0.06 INFO @ Fri, 15 Feb 2019 08:57:51: #1 finished! INFO @ Fri, 15 Feb 2019 08:57:51: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 08:57:51: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 08:57:51: #1 tags after filtering in treatment: 1296486 INFO @ Fri, 15 Feb 2019 08:57:51: #1 Redundant rate of treatment: 0.06 INFO @ Fri, 15 Feb 2019 08:57:51: #1 finished! INFO @ Fri, 15 Feb 2019 08:57:51: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 08:57:51: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 08:57:51: #1 tags after filtering in treatment: 1296486 INFO @ Fri, 15 Feb 2019 08:57:51: #1 Redundant rate of treatment: 0.06 INFO @ Fri, 15 Feb 2019 08:57:51: #1 finished! INFO @ Fri, 15 Feb 2019 08:57:51: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 08:57:51: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 08:57:51: #2 number of paired peaks: 198 WARNING @ Fri, 15 Feb 2019 08:57:51: Fewer paired peaks (198) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 198 pairs to build model! INFO @ Fri, 15 Feb 2019 08:57:51: start model_add_line... INFO @ Fri, 15 Feb 2019 08:57:51: #2 number of paired peaks: 198 WARNING @ Fri, 15 Feb 2019 08:57:51: Fewer paired peaks (198) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 198 pairs to build model! INFO @ Fri, 15 Feb 2019 08:57:51: start model_add_line... INFO @ Fri, 15 Feb 2019 08:57:51: #2 number of paired peaks: 198 WARNING @ Fri, 15 Feb 2019 08:57:51: Fewer paired peaks (198) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 198 pairs to build model! INFO @ Fri, 15 Feb 2019 08:57:51: start model_add_line... INFO @ Fri, 15 Feb 2019 08:57:51: start X-correlation... INFO @ Fri, 15 Feb 2019 08:57:51: start X-correlation... INFO @ Fri, 15 Feb 2019 08:57:51: start X-correlation... INFO @ Fri, 15 Feb 2019 08:57:51: end of X-cor INFO @ Fri, 15 Feb 2019 08:57:51: end of X-cor INFO @ Fri, 15 Feb 2019 08:57:51: #2 finished! INFO @ Fri, 15 Feb 2019 08:57:51: #2 finished! INFO @ Fri, 15 Feb 2019 08:57:51: #2 predicted fragment length is 148 bps INFO @ Fri, 15 Feb 2019 08:57:51: #2 predicted fragment length is 148 bps INFO @ Fri, 15 Feb 2019 08:57:51: #2 alternative fragment length(s) may be 4,148,184 bps INFO @ Fri, 15 Feb 2019 08:57:51: #2 alternative fragment length(s) may be 4,148,184 bps INFO @ Fri, 15 Feb 2019 08:57:51: #2.2 Generate R script for model : ERX1236215.05_model.r INFO @ Fri, 15 Feb 2019 08:57:51: #2.2 Generate R script for model : ERX1236215.20_model.r INFO @ Fri, 15 Feb 2019 08:57:51: end of X-cor INFO @ Fri, 15 Feb 2019 08:57:51: #2 finished! INFO @ Fri, 15 Feb 2019 08:57:51: #2 predicted fragment length is 148 bps INFO @ Fri, 15 Feb 2019 08:57:51: #2 alternative fragment length(s) may be 4,148,184 bps INFO @ Fri, 15 Feb 2019 08:57:51: #2.2 Generate R script for model : ERX1236215.10_model.r INFO @ Fri, 15 Feb 2019 08:57:51: #3 Call peaks... INFO @ Fri, 15 Feb 2019 08:57:51: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 08:57:51: #3 Call peaks... INFO @ Fri, 15 Feb 2019 08:57:51: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 08:57:51: #3 Call peaks... INFO @ Fri, 15 Feb 2019 08:57:51: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 08:57:54: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 08:57:54: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 08:57:54: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 08:57:56: #4 Write output xls file... ERX1236215.20_peaks.xls INFO @ Fri, 15 Feb 2019 08:57:56: #4 Write peak in narrowPeak format file... ERX1236215.20_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 08:57:56: #4 Write summits bed file... ERX1236215.20_summits.bed INFO @ Fri, 15 Feb 2019 08:57:56: Done! pass1 - making usageList (16 chroms): 2 millis pass2 - checking and writing primary data (206 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 08:57:56: #4 Write output xls file... ERX1236215.05_peaks.xls INFO @ Fri, 15 Feb 2019 08:57:56: #4 Write peak in narrowPeak format file... ERX1236215.05_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 08:57:56: #4 Write summits bed file... ERX1236215.05_summits.bed INFO @ Fri, 15 Feb 2019 08:57:56: #4 Write output xls file... ERX1236215.10_peaks.xls INFO @ Fri, 15 Feb 2019 08:57:56: Done! INFO @ Fri, 15 Feb 2019 08:57:56: #4 Write peak in narrowPeak format file... ERX1236215.10_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 08:57:56: #4 Write summits bed file... ERX1236215.10_summits.bed INFO @ Fri, 15 Feb 2019 08:57:56: Done! pass1 - making usageList (16 chroms): 2 millis pass2 - checking and writing primary data (578 records, 4 fields): 4 millis pass1 - making usageList (16 chroms): 6 millis CompletedMACS2peakCalling pass2 - checking and writing primary data (351 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。