Job ID = 11192695 sra ファイルのダウンロード中... Completed: 9122K bytes transferred in 2 seconds (26628K 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 292749 spots for /home/okishinya/chipatlas/results/sacCer3/SRX1924816/SRR3824847.sra Written 292749 spots for /home/okishinya/chipatlas/results/sacCer3/SRX1924816/SRR3824847.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: 00:00:13 292749 reads; of these: 292749 (100.00%) were paired; of these: 95967 (32.78%) aligned concordantly 0 times 183020 (62.52%) aligned concordantly exactly 1 time 13762 (4.70%) aligned concordantly >1 times ---- 95967 pairs aligned concordantly 0 times; of these: 22703 (23.66%) aligned discordantly 1 time ---- 73264 pairs aligned 0 times concordantly or discordantly; of these: 146528 mates make up the pairs; of these: 77231 (52.71%) aligned 0 times 61453 (41.94%) aligned exactly 1 time 7844 (5.35%) aligned >1 times 86.81% overall alignment rate Time searching: 00:00:13 Overall time: 00:00:13 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] 128801 / 208459 = 0.6179 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 09:47:10: # Command line: callpeak -t SRX1924816.bam -f BAM -g 12100000 -n SRX1924816.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1924816.05 # format = BAM # ChIP-seq file = ['SRX1924816.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 09:47:10: #1 read tag files... INFO @ Sat, 15 Sep 2018 09:47:10: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 09:47:10: # Command line: callpeak -t SRX1924816.bam -f BAM -g 12100000 -n SRX1924816.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1924816.20 # format = BAM # ChIP-seq file = ['SRX1924816.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 09:47:10: #1 read tag files... INFO @ Sat, 15 Sep 2018 09:47:10: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 09:47:10: # Command line: callpeak -t SRX1924816.bam -f BAM -g 12100000 -n SRX1924816.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1924816.10 # format = BAM # ChIP-seq file = ['SRX1924816.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 09:47:10: #1 read tag files... INFO @ Sat, 15 Sep 2018 09:47:10: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 09:47:12: #1 tag size is determined as 40 bps INFO @ Sat, 15 Sep 2018 09:47:12: #1 tag size is determined as 40 bps INFO @ Sat, 15 Sep 2018 09:47:12: #1 tag size = 40 INFO @ Sat, 15 Sep 2018 09:47:12: #1 tag size = 40 INFO @ Sat, 15 Sep 2018 09:47:12: #1 total tags in treatment: 73961 INFO @ Sat, 15 Sep 2018 09:47:12: #1 total tags in treatment: 73961 INFO @ Sat, 15 Sep 2018 09:47:12: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 09:47:12: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 09:47:12: #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 09:47:12: #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 09:47:12: #1 tags after filtering in treatment: 73051 INFO @ Sat, 15 Sep 2018 09:47:12: #1 Redundant rate of treatment: 0.01 INFO @ Sat, 15 Sep 2018 09:47:12: #1 tags after filtering in treatment: 73051 INFO @ Sat, 15 Sep 2018 09:47:12: #1 finished! INFO @ Sat, 15 Sep 2018 09:47:12: #1 Redundant rate of treatment: 0.01 INFO @ Sat, 15 Sep 2018 09:47:12: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 09:47:12: #1 finished! INFO @ Sat, 15 Sep 2018 09:47:12: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 09:47:12: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 09:47:12: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 09:47:12: #2 number of paired peaks: 114 WARNING @ Sat, 15 Sep 2018 09:47:12: Fewer paired peaks (114) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 114 pairs to build model! INFO @ Sat, 15 Sep 2018 09:47:12: start model_add_line... INFO @ Sat, 15 Sep 2018 09:47:12: #2 number of paired peaks: 114 WARNING @ Sat, 15 Sep 2018 09:47:12: Fewer paired peaks (114) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 114 pairs to build model! INFO @ Sat, 15 Sep 2018 09:47:12: start model_add_line... INFO @ Sat, 15 Sep 2018 09:47:12: start X-correlation... INFO @ Sat, 15 Sep 2018 09:47:12: start X-correlation... INFO @ Sat, 15 Sep 2018 09:47:12: end of X-cor INFO @ Sat, 15 Sep 2018 09:47:12: end of X-cor INFO @ Sat, 15 Sep 2018 09:47:12: #2 finished! INFO @ Sat, 15 Sep 2018 09:47:12: #2 finished! INFO @ Sat, 15 Sep 2018 09:47:12: #2 predicted fragment length is 235 bps INFO @ Sat, 15 Sep 2018 09:47:12: #2 predicted fragment length is 235 bps INFO @ Sat, 15 Sep 2018 09:47:12: #2 alternative fragment length(s) may be 10,45,63,85,115,148,209,235,255,278,309,343,365,436,449,462,464,490,534,554,568 bps INFO @ Sat, 15 Sep 2018 09:47:12: #2 alternative fragment length(s) may be 10,45,63,85,115,148,209,235,255,278,309,343,365,436,449,462,464,490,534,554,568 bps INFO @ Sat, 15 Sep 2018 09:47:12: #2.2 Generate R script for model : SRX1924816.05_model.r INFO @ Sat, 15 Sep 2018 09:47:12: #2.2 Generate R script for model : SRX1924816.20_model.r INFO @ Sat, 15 Sep 2018 09:47:12: #3 Call peaks... INFO @ Sat, 15 Sep 2018 09:47:12: #3 Call peaks... INFO @ Sat, 15 Sep 2018 09:47:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 09:47:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 09:47:12: #1 tag size is determined as 40 bps INFO @ Sat, 15 Sep 2018 09:47:12: #1 tag size = 40 INFO @ Sat, 15 Sep 2018 09:47:12: #1 total tags in treatment: 73961 INFO @ Sat, 15 Sep 2018 09:47:12: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 09:47:12: #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 09:47:12: #1 tags after filtering in treatment: 73051 INFO @ Sat, 15 Sep 2018 09:47:12: #1 Redundant rate of treatment: 0.01 INFO @ Sat, 15 Sep 2018 09:47:12: #1 finished! INFO @ Sat, 15 Sep 2018 09:47:12: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 09:47:12: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 09:47:12: #2 number of paired peaks: 114 WARNING @ Sat, 15 Sep 2018 09:47:12: Fewer paired peaks (114) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 114 pairs to build model! INFO @ Sat, 15 Sep 2018 09:47:12: start model_add_line... INFO @ Sat, 15 Sep 2018 09:47:12: start X-correlation... INFO @ Sat, 15 Sep 2018 09:47:12: end of X-cor INFO @ Sat, 15 Sep 2018 09:47:12: #2 finished! INFO @ Sat, 15 Sep 2018 09:47:12: #2 predicted fragment length is 235 bps INFO @ Sat, 15 Sep 2018 09:47:12: #2 alternative fragment length(s) may be 10,45,63,85,115,148,209,235,255,278,309,343,365,436,449,462,464,490,534,554,568 bps INFO @ Sat, 15 Sep 2018 09:47:12: #2.2 Generate R script for model : SRX1924816.10_model.r INFO @ Sat, 15 Sep 2018 09:47:12: #3 Call peaks... INFO @ Sat, 15 Sep 2018 09:47:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 09:47:12: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 09:47:12: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 09:47:12: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 09:47:12: #4 Write output xls file... SRX1924816.20_peaks.xls INFO @ Sat, 15 Sep 2018 09:47:12: #4 Write peak in narrowPeak format file... SRX1924816.20_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 09:47:12: #4 Write summits bed file... SRX1924816.20_summits.bed INFO @ Sat, 15 Sep 2018 09:47:12: Done! INFO @ Sat, 15 Sep 2018 09:47:12: #4 Write output xls file... SRX1924816.05_peaks.xls INFO @ Sat, 15 Sep 2018 09:47:12: #4 Write peak in narrowPeak format file... SRX1924816.05_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 09:47:12: #4 Write summits bed file... SRX1924816.05_summits.bed INFO @ Sat, 15 Sep 2018 09:47:12: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sat, 15 Sep 2018 09:47:12: #4 Write output xls file... SRX1924816.10_peaks.xls INFO @ Sat, 15 Sep 2018 09:47:12: #4 Write peak in narrowPeak format file... SRX1924816.10_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 09:47:12: #4 Write summits bed file... SRX1924816.10_summits.bed INFO @ Sat, 15 Sep 2018 09:47:12: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。