Job ID = 11192802 sra ファイルのダウンロード中... Completed: 12709K bytes transferred in 2 seconds (35852K 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 413020 spots for /home/okishinya/chipatlas/results/sacCer3/SRX1924925/SRR3824956.sra Written 413020 spots for /home/okishinya/chipatlas/results/sacCer3/SRX1924925/SRR3824956.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: 00:00:17 413020 reads; of these: 413020 (100.00%) were paired; of these: 45668 (11.06%) aligned concordantly 0 times 348144 (84.29%) aligned concordantly exactly 1 time 19208 (4.65%) aligned concordantly >1 times ---- 45668 pairs aligned concordantly 0 times; of these: 13999 (30.65%) aligned discordantly 1 time ---- 31669 pairs aligned 0 times concordantly or discordantly; of these: 63338 mates make up the pairs; of these: 44312 (69.96%) aligned 0 times 16317 (25.76%) aligned exactly 1 time 2709 (4.28%) aligned >1 times 94.64% overall alignment rate Time searching: 00:00:17 Overall time: 00:00:17 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] 308185 / 377451 = 0.8165 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 09:55:33: # Command line: callpeak -t SRX1924925.bam -f BAM -g 12100000 -n SRX1924925.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1924925.10 # format = BAM # ChIP-seq file = ['SRX1924925.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 09:55:33: #1 read tag files... INFO @ Sat, 15 Sep 2018 09:55:33: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 09:55:33: # Command line: callpeak -t SRX1924925.bam -f BAM -g 12100000 -n SRX1924925.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1924925.20 # format = BAM # ChIP-seq file = ['SRX1924925.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 09:55:33: #1 read tag files... INFO @ Sat, 15 Sep 2018 09:55:33: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 09:55:33: # Command line: callpeak -t SRX1924925.bam -f BAM -g 12100000 -n SRX1924925.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1924925.05 # format = BAM # ChIP-seq file = ['SRX1924925.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 09:55:33: #1 read tag files... INFO @ Sat, 15 Sep 2018 09:55:33: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 09:55:34: #1 tag size is determined as 38 bps INFO @ Sat, 15 Sep 2018 09:55:34: #1 tag size = 38 INFO @ Sat, 15 Sep 2018 09:55:34: #1 total tags in treatment: 65670 INFO @ Sat, 15 Sep 2018 09:55:34: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 09:55:34: #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 09:55:34: #1 tags after filtering in treatment: 64547 INFO @ Sat, 15 Sep 2018 09:55:34: #1 Redundant rate of treatment: 0.02 INFO @ Sat, 15 Sep 2018 09:55:34: #1 finished! INFO @ Sat, 15 Sep 2018 09:55:34: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 09:55:34: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 09:55:34: #1 tag size is determined as 38 bps INFO @ Sat, 15 Sep 2018 09:55:34: #1 tag size = 38 INFO @ Sat, 15 Sep 2018 09:55:34: #1 total tags in treatment: 65670 INFO @ Sat, 15 Sep 2018 09:55:34: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 09:55:34: #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 09:55:34: #1 tag size is determined as 38 bps INFO @ Sat, 15 Sep 2018 09:55:34: #1 tag size = 38 INFO @ Sat, 15 Sep 2018 09:55:34: #1 total tags in treatment: 65670 INFO @ Sat, 15 Sep 2018 09:55:34: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 09:55:34: #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 09:55:34: #1 tags after filtering in treatment: 64547 INFO @ Sat, 15 Sep 2018 09:55:34: #1 Redundant rate of treatment: 0.02 INFO @ Sat, 15 Sep 2018 09:55:34: #1 finished! INFO @ Sat, 15 Sep 2018 09:55:34: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 09:55:34: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 09:55:34: #1 tags after filtering in treatment: 64547 INFO @ Sat, 15 Sep 2018 09:55:34: #1 Redundant rate of treatment: 0.02 INFO @ Sat, 15 Sep 2018 09:55:34: #1 finished! INFO @ Sat, 15 Sep 2018 09:55:34: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 09:55:34: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 09:55:34: #2 number of paired peaks: 105 WARNING @ Sat, 15 Sep 2018 09:55:34: Fewer paired peaks (105) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 105 pairs to build model! INFO @ Sat, 15 Sep 2018 09:55:34: start model_add_line... INFO @ Sat, 15 Sep 2018 09:55:34: start X-correlation... INFO @ Sat, 15 Sep 2018 09:55:34: #2 number of paired peaks: 105 WARNING @ Sat, 15 Sep 2018 09:55:34: Fewer paired peaks (105) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 105 pairs to build model! INFO @ Sat, 15 Sep 2018 09:55:34: start model_add_line... INFO @ Sat, 15 Sep 2018 09:55:34: start X-correlation... INFO @ Sat, 15 Sep 2018 09:55:34: #2 number of paired peaks: 105 WARNING @ Sat, 15 Sep 2018 09:55:34: Fewer paired peaks (105) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 105 pairs to build model! INFO @ Sat, 15 Sep 2018 09:55:34: start model_add_line... INFO @ Sat, 15 Sep 2018 09:55:34: start X-correlation... INFO @ Sat, 15 Sep 2018 09:55:34: end of X-cor INFO @ Sat, 15 Sep 2018 09:55:34: end of X-cor INFO @ Sat, 15 Sep 2018 09:55:34: end of X-cor INFO @ Sat, 15 Sep 2018 09:55:34: #2 finished! INFO @ Sat, 15 Sep 2018 09:55:34: #2 finished! INFO @ Sat, 15 Sep 2018 09:55:34: #2 finished! INFO @ Sat, 15 Sep 2018 09:55:34: #2 predicted fragment length is 310 bps INFO @ Sat, 15 Sep 2018 09:55:34: #2 predicted fragment length is 310 bps INFO @ Sat, 15 Sep 2018 09:55:34: #2 predicted fragment length is 310 bps INFO @ Sat, 15 Sep 2018 09:55:34: #2 alternative fragment length(s) may be 12,30,66,100,141,161,182,203,235,256,269,310,340,413,443,474,517,544,572,587 bps INFO @ Sat, 15 Sep 2018 09:55:34: #2 alternative fragment length(s) may be 12,30,66,100,141,161,182,203,235,256,269,310,340,413,443,474,517,544,572,587 bps INFO @ Sat, 15 Sep 2018 09:55:34: #2 alternative fragment length(s) may be 12,30,66,100,141,161,182,203,235,256,269,310,340,413,443,474,517,544,572,587 bps INFO @ Sat, 15 Sep 2018 09:55:34: #2.2 Generate R script for model : SRX1924925.05_model.r INFO @ Sat, 15 Sep 2018 09:55:34: #2.2 Generate R script for model : SRX1924925.20_model.r INFO @ Sat, 15 Sep 2018 09:55:34: #2.2 Generate R script for model : SRX1924925.10_model.r INFO @ Sat, 15 Sep 2018 09:55:34: #3 Call peaks... INFO @ Sat, 15 Sep 2018 09:55:34: #3 Call peaks... INFO @ Sat, 15 Sep 2018 09:55:34: #3 Call peaks... INFO @ Sat, 15 Sep 2018 09:55:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 09:55:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 09:55:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 09:55:34: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 09:55:34: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 09:55:34: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 09:55:34: #4 Write output xls file... SRX1924925.10_peaks.xls INFO @ Sat, 15 Sep 2018 09:55:34: #4 Write output xls file... SRX1924925.05_peaks.xls INFO @ Sat, 15 Sep 2018 09:55:34: #4 Write output xls file... SRX1924925.20_peaks.xls INFO @ Sat, 15 Sep 2018 09:55:34: #4 Write peak in narrowPeak format file... SRX1924925.20_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 09:55:34: #4 Write peak in narrowPeak format file... SRX1924925.10_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 09:55:34: #4 Write peak in narrowPeak format file... SRX1924925.05_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 09:55:34: #4 Write summits bed file... SRX1924925.20_summits.bed INFO @ Sat, 15 Sep 2018 09:55:34: #4 Write summits bed file... SRX1924925.10_summits.bed INFO @ Sat, 15 Sep 2018 09:55:34: #4 Write summits bed file... SRX1924925.05_summits.bed INFO @ Sat, 15 Sep 2018 09:55:34: Done! INFO @ Sat, 15 Sep 2018 09:55:34: Done! INFO @ Sat, 15 Sep 2018 09:55:34: Done! pass1 - making usageList (0 chroms): 1 millis pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling pass1 - making usageList (6 chroms): 0 millis CompletedMACS2peakCalling pass2 - checking and writing primary data (9 records, 4 fields): 27 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。