Job ID = 11633488 sra ファイルのダウンロード中... Completed: 35230K bytes transferred in 3 seconds (88466K 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 598270 spots for /home/okishinya/chipatlas/results/sacCer3/ERX1236265/ERR1162858.sra Written 598270 spots for /home/okishinya/chipatlas/results/sacCer3/ERX1236265/ERR1162858.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: 00:00:28 598270 reads; of these: 598270 (100.00%) were paired; of these: 28648 (4.79%) aligned concordantly 0 times 523531 (87.51%) aligned concordantly exactly 1 time 46091 (7.70%) aligned concordantly >1 times ---- 28648 pairs aligned concordantly 0 times; of these: 10035 (35.03%) aligned discordantly 1 time ---- 18613 pairs aligned 0 times concordantly or discordantly; of these: 37226 mates make up the pairs; of these: 32868 (88.29%) aligned 0 times 2193 (5.89%) aligned exactly 1 time 2165 (5.82%) aligned >1 times 97.25% overall alignment rate Time searching: 00:00:28 Overall time: 00:00:28 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] 12754 / 579243 = 0.0220 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 08:57:57: # Command line: callpeak -t ERX1236265.bam -f BAM -g 12100000 -n ERX1236265.05 -q 1e-05 # ARGUMENTS LIST: # name = ERX1236265.05 # format = BAM # ChIP-seq file = ['ERX1236265.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 08:57:57: #1 read tag files... INFO @ Fri, 15 Feb 2019 08:57:57: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 08:57:57: # Command line: callpeak -t ERX1236265.bam -f BAM -g 12100000 -n ERX1236265.20 -q 1e-20 # ARGUMENTS LIST: # name = ERX1236265.20 # format = BAM # ChIP-seq file = ['ERX1236265.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 08:57:57: #1 read tag files... INFO @ Fri, 15 Feb 2019 08:57:57: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 08:57:57: # Command line: callpeak -t ERX1236265.bam -f BAM -g 12100000 -n ERX1236265.10 -q 1e-10 # ARGUMENTS LIST: # name = ERX1236265.10 # format = BAM # ChIP-seq file = ['ERX1236265.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 08:57:57: #1 read tag files... INFO @ Fri, 15 Feb 2019 08:57:57: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 08:58:04: 1000000 INFO @ Fri, 15 Feb 2019 08:58:04: 1000000 INFO @ Fri, 15 Feb 2019 08:58:04: 1000000 INFO @ Fri, 15 Feb 2019 08:58:05: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 08:58:05: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 08:58:05: #1 total tags in treatment: 557194 INFO @ Fri, 15 Feb 2019 08:58:05: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 08:58:05: #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 08:58:05: #1 tags after filtering in treatment: 543207 INFO @ Fri, 15 Feb 2019 08:58:05: #1 Redundant rate of treatment: 0.03 INFO @ Fri, 15 Feb 2019 08:58:05: #1 finished! INFO @ Fri, 15 Feb 2019 08:58:05: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 08:58:05: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 08:58:05: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 08:58:05: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 08:58:05: #1 total tags in treatment: 557194 INFO @ Fri, 15 Feb 2019 08:58:05: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 08:58:05: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 08:58:05: #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 08:58:05: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 08:58:05: #1 total tags in treatment: 557194 INFO @ Fri, 15 Feb 2019 08:58:05: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 08:58:05: #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 08:58:05: #1 tags after filtering in treatment: 543207 INFO @ Fri, 15 Feb 2019 08:58:05: #1 Redundant rate of treatment: 0.03 INFO @ Fri, 15 Feb 2019 08:58:05: #1 finished! INFO @ Fri, 15 Feb 2019 08:58:05: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 08:58:05: #1 tags after filtering in treatment: 543207 INFO @ Fri, 15 Feb 2019 08:58:05: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 08:58:05: #1 Redundant rate of treatment: 0.03 INFO @ Fri, 15 Feb 2019 08:58:05: #1 finished! INFO @ Fri, 15 Feb 2019 08:58:05: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 08:58:05: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 08:58:05: #2 number of paired peaks: 202 WARNING @ Fri, 15 Feb 2019 08:58:05: Fewer paired peaks (202) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 202 pairs to build model! INFO @ Fri, 15 Feb 2019 08:58:05: start model_add_line... INFO @ Fri, 15 Feb 2019 08:58:05: start X-correlation... INFO @ Fri, 15 Feb 2019 08:58:05: end of X-cor INFO @ Fri, 15 Feb 2019 08:58:05: #2 finished! INFO @ Fri, 15 Feb 2019 08:58:05: #2 predicted fragment length is 211 bps INFO @ Fri, 15 Feb 2019 08:58:05: #2 alternative fragment length(s) may be 4,191,211,230,268 bps INFO @ Fri, 15 Feb 2019 08:58:05: #2.2 Generate R script for model : ERX1236265.05_model.r INFO @ Fri, 15 Feb 2019 08:58:05: #3 Call peaks... INFO @ Fri, 15 Feb 2019 08:58:05: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 08:58:05: #2 number of paired peaks: 202 WARNING @ Fri, 15 Feb 2019 08:58:05: Fewer paired peaks (202) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 202 pairs to build model! INFO @ Fri, 15 Feb 2019 08:58:05: start model_add_line... INFO @ Fri, 15 Feb 2019 08:58:05: #2 number of paired peaks: 202 WARNING @ Fri, 15 Feb 2019 08:58:05: Fewer paired peaks (202) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 202 pairs to build model! INFO @ Fri, 15 Feb 2019 08:58:05: start model_add_line... INFO @ Fri, 15 Feb 2019 08:58:05: start X-correlation... INFO @ Fri, 15 Feb 2019 08:58:05: start X-correlation... INFO @ Fri, 15 Feb 2019 08:58:05: end of X-cor INFO @ Fri, 15 Feb 2019 08:58:05: #2 finished! INFO @ Fri, 15 Feb 2019 08:58:05: #2 predicted fragment length is 211 bps INFO @ Fri, 15 Feb 2019 08:58:05: #2 alternative fragment length(s) may be 4,191,211,230,268 bps INFO @ Fri, 15 Feb 2019 08:58:05: #2.2 Generate R script for model : ERX1236265.20_model.r INFO @ Fri, 15 Feb 2019 08:58:05: end of X-cor INFO @ Fri, 15 Feb 2019 08:58:05: #2 finished! INFO @ Fri, 15 Feb 2019 08:58:05: #2 predicted fragment length is 211 bps INFO @ Fri, 15 Feb 2019 08:58:05: #2 alternative fragment length(s) may be 4,191,211,230,268 bps INFO @ Fri, 15 Feb 2019 08:58:05: #2.2 Generate R script for model : ERX1236265.10_model.r INFO @ Fri, 15 Feb 2019 08:58:05: #3 Call peaks... INFO @ Fri, 15 Feb 2019 08:58:05: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 08:58:05: #3 Call peaks... INFO @ Fri, 15 Feb 2019 08:58:05: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 08:58:06: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 08:58:06: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 08:58:06: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 08:58:07: #4 Write output xls file... ERX1236265.05_peaks.xls INFO @ Fri, 15 Feb 2019 08:58:07: #4 Write peak in narrowPeak format file... ERX1236265.05_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 08:58:07: #4 Write summits bed file... ERX1236265.05_summits.bed INFO @ Fri, 15 Feb 2019 08:58:07: Done! pass1 - making usageList (16 chroms): 3 millis pass2 - checking and writing primary data (308 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 08:58:07: #4 Write output xls file... ERX1236265.10_peaks.xls INFO @ Fri, 15 Feb 2019 08:58:07: #4 Write peak in narrowPeak format file... ERX1236265.10_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 08:58:07: #4 Write summits bed file... ERX1236265.10_summits.bed INFO @ Fri, 15 Feb 2019 08:58:07: Done! INFO @ Fri, 15 Feb 2019 08:58:07: #4 Write output xls file... ERX1236265.20_peaks.xls INFO @ Fri, 15 Feb 2019 08:58:07: #4 Write peak in narrowPeak format file... ERX1236265.20_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 08:58:07: #4 Write summits bed file... ERX1236265.20_summits.bed INFO @ Fri, 15 Feb 2019 08:58:07: Done! pass1 - making usageList (16 chroms): 5 millis pass2 - checking and writing primary data (206 records, 4 fields): 6 millis CompletedMACS2peakCalling pass1 - making usageList (15 chroms): 6 millis pass2 - checking and writing primary data (75 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。