Job ID = 11192768 sra ファイルのダウンロード中... Completed: 30567K bytes transferred in 3 seconds (68052K 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 1017254 spots for /home/okishinya/chipatlas/results/sacCer3/SRX1924883/SRR3824914.sra Written 1017254 spots for /home/okishinya/chipatlas/results/sacCer3/SRX1924883/SRR3824914.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: 00:00:36 1017254 reads; of these: 1017254 (100.00%) were paired; of these: 110121 (10.83%) aligned concordantly 0 times 845671 (83.13%) aligned concordantly exactly 1 time 61462 (6.04%) aligned concordantly >1 times ---- 110121 pairs aligned concordantly 0 times; of these: 17662 (16.04%) aligned discordantly 1 time ---- 92459 pairs aligned 0 times concordantly or discordantly; of these: 184918 mates make up the pairs; of these: 143331 (77.51%) aligned 0 times 35772 (19.34%) aligned exactly 1 time 5815 (3.14%) aligned >1 times 92.96% overall alignment rate Time searching: 00:00:36 Overall time: 00:00:36 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] 750776 / 917877 = 0.8179 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 09:53:48: # Command line: callpeak -t SRX1924883.bam -f BAM -g 12100000 -n SRX1924883.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1924883.10 # format = BAM # ChIP-seq file = ['SRX1924883.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 09:53:48: #1 read tag files... INFO @ Sat, 15 Sep 2018 09:53:48: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 09:53:48: # Command line: callpeak -t SRX1924883.bam -f BAM -g 12100000 -n SRX1924883.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1924883.20 # format = BAM # ChIP-seq file = ['SRX1924883.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 09:53:48: #1 read tag files... INFO @ Sat, 15 Sep 2018 09:53:48: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 09:53:48: # Command line: callpeak -t SRX1924883.bam -f BAM -g 12100000 -n SRX1924883.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1924883.05 # format = BAM # ChIP-seq file = ['SRX1924883.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 09:53:48: #1 read tag files... INFO @ Sat, 15 Sep 2018 09:53:48: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 09:53:50: #1 tag size is determined as 38 bps INFO @ Sat, 15 Sep 2018 09:53:50: #1 tag size = 38 INFO @ Sat, 15 Sep 2018 09:53:50: #1 total tags in treatment: 163335 INFO @ Sat, 15 Sep 2018 09:53:50: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 09:53:50: #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 09:53:50: #1 tags after filtering in treatment: 156935 INFO @ Sat, 15 Sep 2018 09:53:50: #1 Redundant rate of treatment: 0.04 INFO @ Sat, 15 Sep 2018 09:53:50: #1 finished! INFO @ Sat, 15 Sep 2018 09:53:50: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 09:53:50: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 09:53:50: #2 number of paired peaks: 123 WARNING @ Sat, 15 Sep 2018 09:53:50: Fewer paired peaks (123) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 123 pairs to build model! INFO @ Sat, 15 Sep 2018 09:53:50: start model_add_line... INFO @ Sat, 15 Sep 2018 09:53:50: start X-correlation... INFO @ Sat, 15 Sep 2018 09:53:50: end of X-cor INFO @ Sat, 15 Sep 2018 09:53:50: #2 finished! INFO @ Sat, 15 Sep 2018 09:53:50: #2 predicted fragment length is 297 bps INFO @ Sat, 15 Sep 2018 09:53:50: #2 alternative fragment length(s) may be 18,37,170,196,230,258,297,317,334,374,390,414,465,481,509,583 bps INFO @ Sat, 15 Sep 2018 09:53:50: #2.2 Generate R script for model : SRX1924883.20_model.r INFO @ Sat, 15 Sep 2018 09:53:50: #3 Call peaks... INFO @ Sat, 15 Sep 2018 09:53:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 09:53:50: #1 tag size is determined as 38 bps INFO @ Sat, 15 Sep 2018 09:53:50: #1 tag size = 38 INFO @ Sat, 15 Sep 2018 09:53:50: #1 total tags in treatment: 163335 INFO @ Sat, 15 Sep 2018 09:53:50: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 09:53:50: #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 09:53:50: #1 tag size is determined as 38 bps INFO @ Sat, 15 Sep 2018 09:53:50: #1 tag size = 38 INFO @ Sat, 15 Sep 2018 09:53:50: #1 total tags in treatment: 163335 INFO @ Sat, 15 Sep 2018 09:53:50: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 09:53:50: #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 09:53:50: #1 tags after filtering in treatment: 156935 INFO @ Sat, 15 Sep 2018 09:53:50: #1 Redundant rate of treatment: 0.04 INFO @ Sat, 15 Sep 2018 09:53:50: #1 finished! INFO @ Sat, 15 Sep 2018 09:53:50: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 09:53:50: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 09:53:50: #1 tags after filtering in treatment: 156935 INFO @ Sat, 15 Sep 2018 09:53:50: #1 Redundant rate of treatment: 0.04 INFO @ Sat, 15 Sep 2018 09:53:50: #1 finished! INFO @ Sat, 15 Sep 2018 09:53:50: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 09:53:50: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 09:53:50: #2 number of paired peaks: 123 WARNING @ Sat, 15 Sep 2018 09:53:50: Fewer paired peaks (123) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 123 pairs to build model! INFO @ Sat, 15 Sep 2018 09:53:50: start model_add_line... INFO @ Sat, 15 Sep 2018 09:53:50: #2 number of paired peaks: 123 WARNING @ Sat, 15 Sep 2018 09:53:50: Fewer paired peaks (123) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 123 pairs to build model! INFO @ Sat, 15 Sep 2018 09:53:50: start model_add_line... INFO @ Sat, 15 Sep 2018 09:53:50: start X-correlation... INFO @ Sat, 15 Sep 2018 09:53:50: start X-correlation... INFO @ Sat, 15 Sep 2018 09:53:50: end of X-cor INFO @ Sat, 15 Sep 2018 09:53:50: #2 finished! INFO @ Sat, 15 Sep 2018 09:53:50: #2 predicted fragment length is 297 bps INFO @ Sat, 15 Sep 2018 09:53:50: #2 alternative fragment length(s) may be 18,37,170,196,230,258,297,317,334,374,390,414,465,481,509,583 bps INFO @ Sat, 15 Sep 2018 09:53:50: #2.2 Generate R script for model : SRX1924883.10_model.r INFO @ Sat, 15 Sep 2018 09:53:50: end of X-cor INFO @ Sat, 15 Sep 2018 09:53:50: #2 finished! INFO @ Sat, 15 Sep 2018 09:53:50: #2 predicted fragment length is 297 bps INFO @ Sat, 15 Sep 2018 09:53:50: #2 alternative fragment length(s) may be 18,37,170,196,230,258,297,317,334,374,390,414,465,481,509,583 bps INFO @ Sat, 15 Sep 2018 09:53:50: #2.2 Generate R script for model : SRX1924883.05_model.r INFO @ Sat, 15 Sep 2018 09:53:50: #3 Call peaks... INFO @ Sat, 15 Sep 2018 09:53:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 09:53:50: #3 Call peaks... INFO @ Sat, 15 Sep 2018 09:53:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 09:53:50: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 09:53:50: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 09:53:50: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 09:53:50: #4 Write output xls file... SRX1924883.20_peaks.xls INFO @ Sat, 15 Sep 2018 09:53:50: #4 Write peak in narrowPeak format file... SRX1924883.20_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 09:53:50: #4 Write summits bed file... SRX1924883.20_summits.bed INFO @ Sat, 15 Sep 2018 09:53:50: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sat, 15 Sep 2018 09:53:50: #4 Write output xls file... SRX1924883.10_peaks.xls INFO @ Sat, 15 Sep 2018 09:53:50: #4 Write peak in narrowPeak format file... SRX1924883.10_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 09:53:50: #4 Write summits bed file... SRX1924883.10_summits.bed INFO @ Sat, 15 Sep 2018 09:53:50: Done! INFO @ Sat, 15 Sep 2018 09:53:50: #4 Write output xls file... SRX1924883.05_peaks.xls INFO @ Sat, 15 Sep 2018 09:53:50: #4 Write peak in narrowPeak format file... SRX1924883.05_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 09:53:50: #4 Write summits bed file... SRX1924883.05_summits.bed INFO @ Sat, 15 Sep 2018 09:53:50: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (6 records, 4 fields): 1 millis CompletedMACS2peakCalling pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (38 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。