Job ID = 11192874 sra ファイルのダウンロード中... Completed: 769197K bytes transferred in 23 seconds (269802K 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 6226153 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2767194/SRR5483850.sra Written 6226153 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2767194/SRR5483850.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: 00:11:16 6226153 reads; of these: 6226153 (100.00%) were paired; of these: 451633 (7.25%) aligned concordantly 0 times 4767537 (76.57%) aligned concordantly exactly 1 time 1006983 (16.17%) aligned concordantly >1 times ---- 451633 pairs aligned concordantly 0 times; of these: 40942 (9.07%) aligned discordantly 1 time ---- 410691 pairs aligned 0 times concordantly or discordantly; of these: 821382 mates make up the pairs; of these: 653449 (79.55%) aligned 0 times 116514 (14.19%) aligned exactly 1 time 51419 (6.26%) aligned >1 times 94.75% overall alignment rate Time searching: 00:11:16 Overall time: 00:11:16 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_sort_core] merging from 12 files... [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] 5520182 / 5574843 = 0.9902 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 10:27:17: # Command line: callpeak -t SRX2767194.bam -f BAM -g 12100000 -n SRX2767194.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2767194.10 # format = BAM # ChIP-seq file = ['SRX2767194.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 10:27:17: #1 read tag files... INFO @ Sat, 15 Sep 2018 10:27:17: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 10:27:17: # Command line: callpeak -t SRX2767194.bam -f BAM -g 12100000 -n SRX2767194.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2767194.20 # format = BAM # ChIP-seq file = ['SRX2767194.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 10:27:17: # Command line: callpeak -t SRX2767194.bam -f BAM -g 12100000 -n SRX2767194.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2767194.05 # format = BAM # ChIP-seq file = ['SRX2767194.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 10:27:17: #1 read tag files... INFO @ Sat, 15 Sep 2018 10:27:17: #1 read tag files... INFO @ Sat, 15 Sep 2018 10:27:17: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 10:27:17: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Sep 2018 10:27:23: #1 tag size is determined as 121 bps INFO @ Sat, 15 Sep 2018 10:27:23: #1 tag size = 121 INFO @ Sat, 15 Sep 2018 10:27:23: #1 total tags in treatment: 288467 INFO @ Sat, 15 Sep 2018 10:27:23: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 10:27:23: #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 10:27:23: #1 tags after filtering in treatment: 60153 INFO @ Sat, 15 Sep 2018 10:27:23: #1 Redundant rate of treatment: 0.79 INFO @ Sat, 15 Sep 2018 10:27:23: #1 finished! INFO @ Sat, 15 Sep 2018 10:27:23: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 10:27:23: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 10:27:23: #2 number of paired peaks: 293 WARNING @ Sat, 15 Sep 2018 10:27:23: Fewer paired peaks (293) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 293 pairs to build model! INFO @ Sat, 15 Sep 2018 10:27:23: start model_add_line... INFO @ Sat, 15 Sep 2018 10:27:23: start X-correlation... INFO @ Sat, 15 Sep 2018 10:27:23: #1 tag size is determined as 121 bps INFO @ Sat, 15 Sep 2018 10:27:23: #1 tag size = 121 INFO @ Sat, 15 Sep 2018 10:27:23: #1 total tags in treatment: 288467 INFO @ Sat, 15 Sep 2018 10:27:23: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 10:27:23: #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 10:27:23: #1 tags after filtering in treatment: 60153 INFO @ Sat, 15 Sep 2018 10:27:23: #1 Redundant rate of treatment: 0.79 INFO @ Sat, 15 Sep 2018 10:27:23: #1 finished! INFO @ Sat, 15 Sep 2018 10:27:23: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 10:27:23: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 10:27:23: end of X-cor INFO @ Sat, 15 Sep 2018 10:27:23: #2 finished! INFO @ Sat, 15 Sep 2018 10:27:23: #2 predicted fragment length is 271 bps INFO @ Sat, 15 Sep 2018 10:27:23: #2 alternative fragment length(s) may be 14,89,109,142,173,201,223,244,271,297,361,396,421,470,493,521,556 bps INFO @ Sat, 15 Sep 2018 10:27:23: #2.2 Generate R script for model : SRX2767194.20_model.r INFO @ Sat, 15 Sep 2018 10:27:23: #3 Call peaks... INFO @ Sat, 15 Sep 2018 10:27:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 10:27:23: #2 number of paired peaks: 293 WARNING @ Sat, 15 Sep 2018 10:27:23: Fewer paired peaks (293) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 293 pairs to build model! INFO @ Sat, 15 Sep 2018 10:27:23: start model_add_line... INFO @ Sat, 15 Sep 2018 10:27:23: start X-correlation... INFO @ Sat, 15 Sep 2018 10:27:23: end of X-cor INFO @ Sat, 15 Sep 2018 10:27:23: #2 finished! INFO @ Sat, 15 Sep 2018 10:27:23: #2 predicted fragment length is 271 bps INFO @ Sat, 15 Sep 2018 10:27:23: #2 alternative fragment length(s) may be 14,89,109,142,173,201,223,244,271,297,361,396,421,470,493,521,556 bps INFO @ Sat, 15 Sep 2018 10:27:23: #2.2 Generate R script for model : SRX2767194.10_model.r INFO @ Sat, 15 Sep 2018 10:27:23: #3 Call peaks... INFO @ Sat, 15 Sep 2018 10:27:23: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 15 Sep 2018 10:27:23: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 10:27:23: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 10:27:23: #4 Write output xls file... SRX2767194.10_peaks.xls INFO @ Sat, 15 Sep 2018 10:27:23: #4 Write output xls file... SRX2767194.20_peaks.xls INFO @ Sat, 15 Sep 2018 10:27:23: #4 Write peak in narrowPeak format file... SRX2767194.20_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 10:27:23: #4 Write peak in narrowPeak format file... SRX2767194.10_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 10:27:23: #4 Write summits bed file... SRX2767194.20_summits.bed INFO @ Sat, 15 Sep 2018 10:27:23: #4 Write summits bed file... SRX2767194.10_summits.bed INFO @ Sat, 15 Sep 2018 10:27:23: Done! INFO @ Sat, 15 Sep 2018 10:27:23: Done! INFO @ Sat, 15 Sep 2018 10:27:23: #1 tag size is determined as 121 bps INFO @ Sat, 15 Sep 2018 10:27:23: #1 tag size = 121 INFO @ Sat, 15 Sep 2018 10:27:23: #1 total tags in treatment: 288467 INFO @ Sat, 15 Sep 2018 10:27:23: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 10:27:23: #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 10:27:23: #1 tags after filtering in treatment: 60153 INFO @ Sat, 15 Sep 2018 10:27:23: #1 Redundant rate of treatment: 0.79 INFO @ Sat, 15 Sep 2018 10:27:23: #1 finished! INFO @ Sat, 15 Sep 2018 10:27:23: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 10:27:23: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 10:27:23: #2 number of paired peaks: 293 WARNING @ Sat, 15 Sep 2018 10:27:23: Fewer paired peaks (293) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 293 pairs to build model! INFO @ Sat, 15 Sep 2018 10:27:23: start model_add_line... INFO @ Sat, 15 Sep 2018 10:27:23: start X-correlation... INFO @ Sat, 15 Sep 2018 10:27:23: end of X-cor INFO @ Sat, 15 Sep 2018 10:27:23: #2 finished! INFO @ Sat, 15 Sep 2018 10:27:23: #2 predicted fragment length is 271 bps INFO @ Sat, 15 Sep 2018 10:27:23: #2 alternative fragment length(s) may be 14,89,109,142,173,201,223,244,271,297,361,396,421,470,493,521,556 bps INFO @ Sat, 15 Sep 2018 10:27:23: #2.2 Generate R script for model : SRX2767194.05_model.r INFO @ Sat, 15 Sep 2018 10:27:23: #3 Call peaks... INFO @ Sat, 15 Sep 2018 10:27:23: #3 Pre-compute pvalue-qvalue table... pass1 - making usageList (3 chroms): 0 millis pass1 - making usageList (1 chroms): 1 millis pass2 - checking and writing primary data (4 records, 4 fields): 1 millis pass2 - checking and writing primary data (2 records, 4 fields): 1 millis CompletedMACS2peakCalling CompletedMACS2peakCalling INFO @ Sat, 15 Sep 2018 10:27:24: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 10:27:24: #4 Write output xls file... SRX2767194.05_peaks.xls INFO @ Sat, 15 Sep 2018 10:27:24: #4 Write peak in narrowPeak format file... SRX2767194.05_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 10:27:24: #4 Write summits bed file... SRX2767194.05_summits.bed INFO @ Sat, 15 Sep 2018 10:27:24: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (28 records, 4 fields): 3 millis CompletedMACS2peakCalling