Job ID = 11192749 sra ファイルのダウンロード中... Completed: 18845K bytes transferred in 3 seconds (50603K 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 608231 spots for /home/okishinya/chipatlas/results/sacCer3/SRX1924864/SRR3824895.sra Written 608231 spots for /home/okishinya/chipatlas/results/sacCer3/SRX1924864/SRR3824895.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: 00:00:27 608231 reads; of these: 608231 (100.00%) were paired; of these: 192886 (31.71%) aligned concordantly 0 times 378703 (62.26%) aligned concordantly exactly 1 time 36642 (6.02%) aligned concordantly >1 times ---- 192886 pairs aligned concordantly 0 times; of these: 52836 (27.39%) aligned discordantly 1 time ---- 140050 pairs aligned 0 times concordantly or discordantly; of these: 280100 mates make up the pairs; of these: 140905 (50.31%) aligned 0 times 117562 (41.97%) aligned exactly 1 time 21633 (7.72%) aligned >1 times 88.42% overall alignment rate Time searching: 00:00:27 Overall time: 00:00:27 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 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] 262323 / 435046 = 0.6030 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 @ Sat, 15 Sep 2018 09:51:48: # Command line: callpeak -t SRX1924864.bam -f BAM -g 12100000 -n SRX1924864.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1924864.20 # format = BAM # ChIP-seq file = ['SRX1924864.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 @ Sat, 15 Sep 2018 09:51:48: #1 read tag files... INFO @ Sat, 15 Sep 2018 09:51:48: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 09:51:48: # Command line: callpeak -t SRX1924864.bam -f BAM -g 12100000 -n SRX1924864.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1924864.05 # format = BAM # ChIP-seq file = ['SRX1924864.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 @ Sat, 15 Sep 2018 09:51:48: #1 read tag files... INFO @ Sat, 15 Sep 2018 09:51:48: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 09:51:48: # Command line: callpeak -t SRX1924864.bam -f BAM -g 12100000 -n SRX1924864.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1924864.10 # format = BAM # ChIP-seq file = ['SRX1924864.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 @ Sat, 15 Sep 2018 09:51:48: #1 read tag files... INFO @ Sat, 15 Sep 2018 09:51:48: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 09:51:51: #1 tag size is determined as 36 bps INFO @ Sat, 15 Sep 2018 09:51:51: #1 tag size = 36 INFO @ Sat, 15 Sep 2018 09:51:51: #1 total tags in treatment: 162203 INFO @ Sat, 15 Sep 2018 09:51:51: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 09:51:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 09:51:51: #1 tag size is determined as 36 bps INFO @ Sat, 15 Sep 2018 09:51:51: #1 tag size = 36 INFO @ Sat, 15 Sep 2018 09:51:51: #1 total tags in treatment: 162203 INFO @ Sat, 15 Sep 2018 09:51:51: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 09:51:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 09:51:51: #1 tags after filtering in treatment: 157149 INFO @ Sat, 15 Sep 2018 09:51:51: #1 Redundant rate of treatment: 0.03 INFO @ Sat, 15 Sep 2018 09:51:51: #1 finished! INFO @ Sat, 15 Sep 2018 09:51:51: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 09:51:51: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 09:51:51: #1 tags after filtering in treatment: 157149 INFO @ Sat, 15 Sep 2018 09:51:51: #1 Redundant rate of treatment: 0.03 INFO @ Sat, 15 Sep 2018 09:51:51: #1 finished! INFO @ Sat, 15 Sep 2018 09:51:51: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 09:51:51: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 09:51:51: #2 number of paired peaks: 178 WARNING @ Sat, 15 Sep 2018 09:51:51: Fewer paired peaks (178) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 178 pairs to build model! INFO @ Sat, 15 Sep 2018 09:51:51: start model_add_line... INFO @ Sat, 15 Sep 2018 09:51:51: start X-correlation... INFO @ Sat, 15 Sep 2018 09:51:51: #2 number of paired peaks: 178 WARNING @ Sat, 15 Sep 2018 09:51:51: Fewer paired peaks (178) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 178 pairs to build model! INFO @ Sat, 15 Sep 2018 09:51:51: start model_add_line... INFO @ Sat, 15 Sep 2018 09:51:51: end of X-cor INFO @ Sat, 15 Sep 2018 09:51:51: #2 finished! INFO @ Sat, 15 Sep 2018 09:51:51: start X-correlation... INFO @ Sat, 15 Sep 2018 09:51:51: #2 predicted fragment length is 296 bps INFO @ Sat, 15 Sep 2018 09:51:51: #2 alternative fragment length(s) may be 34,36,71,104,121,154,179,212,246,269,296,327,343,370,402,417,436,474,544,573 bps INFO @ Sat, 15 Sep 2018 09:51:51: #2.2 Generate R script for model : SRX1924864.20_model.r INFO @ Sat, 15 Sep 2018 09:51:51: end of X-cor INFO @ Sat, 15 Sep 2018 09:51:51: #2 finished! INFO @ Sat, 15 Sep 2018 09:51:51: #2 predicted fragment length is 296 bps INFO @ Sat, 15 Sep 2018 09:51:51: #2 alternative fragment length(s) may be 34,36,71,104,121,154,179,212,246,269,296,327,343,370,402,417,436,474,544,573 bps INFO @ Sat, 15 Sep 2018 09:51:51: #2.2 Generate R script for model : SRX1924864.05_model.r INFO @ Sat, 15 Sep 2018 09:51:51: #3 Call peaks... INFO @ Sat, 15 Sep 2018 09:51:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 09:51:51: #3 Call peaks... INFO @ Sat, 15 Sep 2018 09:51:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 09:51:51: #1 tag size is determined as 36 bps INFO @ Sat, 15 Sep 2018 09:51:51: #1 tag size = 36 INFO @ Sat, 15 Sep 2018 09:51:51: #1 total tags in treatment: 162203 INFO @ Sat, 15 Sep 2018 09:51:51: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 09:51:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 09:51:51: #1 tags after filtering in treatment: 157149 INFO @ Sat, 15 Sep 2018 09:51:51: #1 Redundant rate of treatment: 0.03 INFO @ Sat, 15 Sep 2018 09:51:51: #1 finished! INFO @ Sat, 15 Sep 2018 09:51:51: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 09:51:51: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 09:51:51: #2 number of paired peaks: 178 WARNING @ Sat, 15 Sep 2018 09:51:51: Fewer paired peaks (178) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 178 pairs to build model! INFO @ Sat, 15 Sep 2018 09:51:51: start model_add_line... INFO @ Sat, 15 Sep 2018 09:51:51: start X-correlation... INFO @ Sat, 15 Sep 2018 09:51:51: end of X-cor INFO @ Sat, 15 Sep 2018 09:51:51: #2 finished! INFO @ Sat, 15 Sep 2018 09:51:51: #2 predicted fragment length is 296 bps INFO @ Sat, 15 Sep 2018 09:51:51: #2 alternative fragment length(s) may be 34,36,71,104,121,154,179,212,246,269,296,327,343,370,402,417,436,474,544,573 bps INFO @ Sat, 15 Sep 2018 09:51:51: #2.2 Generate R script for model : SRX1924864.10_model.r INFO @ Sat, 15 Sep 2018 09:51:51: #3 Call peaks... INFO @ Sat, 15 Sep 2018 09:51:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 09:51:51: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 09:51:51: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 09:51:52: #4 Write output xls file... SRX1924864.05_peaks.xls INFO @ Sat, 15 Sep 2018 09:51:52: #4 Write peak in narrowPeak format file... SRX1924864.05_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 09:51:52: #4 Write output xls file... SRX1924864.20_peaks.xls INFO @ Sat, 15 Sep 2018 09:51:52: #4 Write summits bed file... SRX1924864.05_summits.bed INFO @ Sat, 15 Sep 2018 09:51:52: #4 Write peak in narrowPeak format file... SRX1924864.20_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 09:51:52: Done! INFO @ Sat, 15 Sep 2018 09:51:52: #4 Write summits bed file... SRX1924864.20_summits.bed INFO @ Sat, 15 Sep 2018 09:51:52: Done! pass1 - making usageList (14 chroms): 1 millis pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) pass2 - checking and writing primary data (33 records, 4 fields): 2 millis CompletedMACS2peakCalling CompletedMACS2peakCalling INFO @ Sat, 15 Sep 2018 09:51:52: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 09:51:52: #4 Write output xls file... SRX1924864.10_peaks.xls INFO @ Sat, 15 Sep 2018 09:51:52: #4 Write peak in narrowPeak format file... SRX1924864.10_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 09:51:52: #4 Write summits bed file... SRX1924864.10_summits.bed INFO @ Sat, 15 Sep 2018 09:51:52: Done! pass1 - making usageList (2 chroms): 0 millis pass2 - checking and writing primary data (2 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。