Job ID = 11633609 sra ファイルのダウンロード中... Completed: 177557K bytes transferred in 5 seconds (282700K 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 2526021 spots for /home/okishinya/chipatlas/results/sacCer3/ERX1420228/ERR1348704.sra Written 2526021 spots for /home/okishinya/chipatlas/results/sacCer3/ERX1420228/ERR1348704.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: 00:00:41 2526021 reads; of these: 2526021 (100.00%) were paired; of these: 2364895 (93.62%) aligned concordantly 0 times 144655 (5.73%) aligned concordantly exactly 1 time 16471 (0.65%) aligned concordantly >1 times ---- 2364895 pairs aligned concordantly 0 times; of these: 184378 (7.80%) aligned discordantly 1 time ---- 2180517 pairs aligned 0 times concordantly or discordantly; of these: 4361034 mates make up the pairs; of these: 4174068 (95.71%) aligned 0 times 142239 (3.26%) aligned exactly 1 time 44727 (1.03%) aligned >1 times 17.38% overall alignment rate Time searching: 00:00:41 Overall time: 00:00:41 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] 108336 / 221178 = 0.4898 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 09:11:20: # Command line: callpeak -t ERX1420228.bam -f BAM -g 12100000 -n ERX1420228.20 -q 1e-20 # ARGUMENTS LIST: # name = ERX1420228.20 # format = BAM # ChIP-seq file = ['ERX1420228.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 09:11:20: #1 read tag files... INFO @ Fri, 15 Feb 2019 09:11:20: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 09:11:20: # Command line: callpeak -t ERX1420228.bam -f BAM -g 12100000 -n ERX1420228.10 -q 1e-10 # ARGUMENTS LIST: # name = ERX1420228.10 # format = BAM # ChIP-seq file = ['ERX1420228.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 09:11:20: #1 read tag files... INFO @ Fri, 15 Feb 2019 09:11:20: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 09:11:20: # Command line: callpeak -t ERX1420228.bam -f BAM -g 12100000 -n ERX1420228.05 -q 1e-05 # ARGUMENTS LIST: # name = ERX1420228.05 # format = BAM # ChIP-seq file = ['ERX1420228.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 09:11:20: #1 read tag files... INFO @ Fri, 15 Feb 2019 09:11:20: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 09:11:24: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 09:11:24: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 09:11:24: #1 total tags in treatment: 82586 INFO @ Fri, 15 Feb 2019 09:11:24: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 09:11:24: #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 09:11:24: #1 tags after filtering in treatment: 78483 INFO @ Fri, 15 Feb 2019 09:11:24: #1 Redundant rate of treatment: 0.05 INFO @ Fri, 15 Feb 2019 09:11:24: #1 finished! INFO @ Fri, 15 Feb 2019 09:11:24: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 09:11:24: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 09:11:24: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 09:11:24: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 09:11:24: #1 total tags in treatment: 82586 INFO @ Fri, 15 Feb 2019 09:11:24: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 09:11:24: #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 09:11:24: #1 tags after filtering in treatment: 78483 INFO @ Fri, 15 Feb 2019 09:11:24: #1 Redundant rate of treatment: 0.05 INFO @ Fri, 15 Feb 2019 09:11:24: #1 finished! INFO @ Fri, 15 Feb 2019 09:11:24: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 09:11:24: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 09:11:24: #2 number of paired peaks: 143 WARNING @ Fri, 15 Feb 2019 09:11:24: Fewer paired peaks (143) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 143 pairs to build model! INFO @ Fri, 15 Feb 2019 09:11:24: start model_add_line... INFO @ Fri, 15 Feb 2019 09:11:24: start X-correlation... INFO @ Fri, 15 Feb 2019 09:11:24: end of X-cor INFO @ Fri, 15 Feb 2019 09:11:24: #2 finished! INFO @ Fri, 15 Feb 2019 09:11:24: #2 predicted fragment length is 287 bps INFO @ Fri, 15 Feb 2019 09:11:24: #2 alternative fragment length(s) may be 4,20,41,59,113,162,239,273,287,304,335 bps INFO @ Fri, 15 Feb 2019 09:11:24: #2.2 Generate R script for model : ERX1420228.20_model.r INFO @ Fri, 15 Feb 2019 09:11:24: #2 number of paired peaks: 143 WARNING @ Fri, 15 Feb 2019 09:11:24: Fewer paired peaks (143) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 143 pairs to build model! INFO @ Fri, 15 Feb 2019 09:11:24: start model_add_line... INFO @ Fri, 15 Feb 2019 09:11:24: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 09:11:24: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 09:11:24: #1 total tags in treatment: 82586 INFO @ Fri, 15 Feb 2019 09:11:24: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 09:11:24: #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 09:11:24: start X-correlation... INFO @ Fri, 15 Feb 2019 09:11:24: end of X-cor INFO @ Fri, 15 Feb 2019 09:11:24: #2 finished! INFO @ Fri, 15 Feb 2019 09:11:24: #2 predicted fragment length is 287 bps INFO @ Fri, 15 Feb 2019 09:11:24: #2 alternative fragment length(s) may be 4,20,41,59,113,162,239,273,287,304,335 bps INFO @ Fri, 15 Feb 2019 09:11:24: #2.2 Generate R script for model : ERX1420228.10_model.r INFO @ Fri, 15 Feb 2019 09:11:24: #3 Call peaks... INFO @ Fri, 15 Feb 2019 09:11:24: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 09:11:24: #1 tags after filtering in treatment: 78483 INFO @ Fri, 15 Feb 2019 09:11:24: #1 Redundant rate of treatment: 0.05 INFO @ Fri, 15 Feb 2019 09:11:24: #1 finished! INFO @ Fri, 15 Feb 2019 09:11:24: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 09:11:24: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 09:11:24: #3 Call peaks... INFO @ Fri, 15 Feb 2019 09:11:24: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 09:11:24: #2 number of paired peaks: 143 WARNING @ Fri, 15 Feb 2019 09:11:24: Fewer paired peaks (143) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 143 pairs to build model! INFO @ Fri, 15 Feb 2019 09:11:24: start model_add_line... INFO @ Fri, 15 Feb 2019 09:11:24: start X-correlation... INFO @ Fri, 15 Feb 2019 09:11:24: end of X-cor INFO @ Fri, 15 Feb 2019 09:11:24: #2 finished! INFO @ Fri, 15 Feb 2019 09:11:24: #2 predicted fragment length is 287 bps INFO @ Fri, 15 Feb 2019 09:11:24: #2 alternative fragment length(s) may be 4,20,41,59,113,162,239,273,287,304,335 bps INFO @ Fri, 15 Feb 2019 09:11:24: #2.2 Generate R script for model : ERX1420228.05_model.r INFO @ Fri, 15 Feb 2019 09:11:24: #3 Call peaks... INFO @ Fri, 15 Feb 2019 09:11:24: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 09:11:24: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 09:11:24: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 09:11:24: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 09:11:24: #4 Write output xls file... ERX1420228.20_peaks.xls INFO @ Fri, 15 Feb 2019 09:11:24: #4 Write peak in narrowPeak format file... ERX1420228.20_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 09:11:24: #4 Write summits bed file... ERX1420228.20_summits.bed INFO @ Fri, 15 Feb 2019 09:11:24: Done! INFO @ Fri, 15 Feb 2019 09:11:24: #4 Write output xls file... ERX1420228.05_peaks.xls INFO @ Fri, 15 Feb 2019 09:11:24: #4 Write output xls file... ERX1420228.10_peaks.xls INFO @ Fri, 15 Feb 2019 09:11:24: #4 Write peak in narrowPeak format file... ERX1420228.05_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 09:11:24: #4 Write peak in narrowPeak format file... ERX1420228.10_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 09:11:24: #4 Write summits bed file... ERX1420228.05_summits.bed INFO @ Fri, 15 Feb 2019 09:11:24: #4 Write summits bed file... ERX1420228.10_summits.bed INFO @ Fri, 15 Feb 2019 09:11:24: Done! INFO @ Fri, 15 Feb 2019 09:11:24: Done! pass1 - making usageList (0 chroms): 9 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) pass1 - making usageList (11 chroms): 26 millis pass2 - checking and writing primary data (41 records, 4 fields): 8 millis CompletedMACS2peakCalling pass1 - making usageList (3 chroms): 10 millis pass2 - checking and writing primary data (4 records, 4 fields): 7 millis CompletedMACS2peakCalling CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。