Job ID = 10937399 sra ファイルのダウンロード中... Completed: 219938K bytes transferred in 4 seconds (367206K 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 3072894 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2198719/SRR4304449.sra Written 3072894 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2198719/SRR4304449.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: 00:02:17 3072894 reads; of these: 3072894 (100.00%) were paired; of these: 1040201 (33.85%) aligned concordantly 0 times 1716989 (55.88%) aligned concordantly exactly 1 time 315704 (10.27%) aligned concordantly >1 times ---- 1040201 pairs aligned concordantly 0 times; of these: 77412 (7.44%) aligned discordantly 1 time ---- 962789 pairs aligned 0 times concordantly or discordantly; of these: 1925578 mates make up the pairs; of these: 1797523 (93.35%) aligned 0 times 68603 (3.56%) aligned exactly 1 time 59452 (3.09%) aligned >1 times 70.75% overall alignment rate Time searching: 00:02:17 Overall time: 00:02:17 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] 1300325 / 2105904 = 0.6175 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 @ Fri, 10 Aug 2018 02:00:06: # Command line: callpeak -t SRX2198719.bam -f BAM -g 12100000 -n SRX2198719.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2198719.20 # format = BAM # ChIP-seq file = ['SRX2198719.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 @ Fri, 10 Aug 2018 02:00:06: #1 read tag files... INFO @ Fri, 10 Aug 2018 02:00:06: #1 read treatment tags... INFO @ Fri, 10 Aug 2018 02:00:06: # Command line: callpeak -t SRX2198719.bam -f BAM -g 12100000 -n SRX2198719.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2198719.10 # format = BAM # ChIP-seq file = ['SRX2198719.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 @ Fri, 10 Aug 2018 02:00:06: #1 read tag files... INFO @ Fri, 10 Aug 2018 02:00:06: #1 read treatment tags... INFO @ Fri, 10 Aug 2018 02:00:06: # Command line: callpeak -t SRX2198719.bam -f BAM -g 12100000 -n SRX2198719.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2198719.05 # format = BAM # ChIP-seq file = ['SRX2198719.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 @ Fri, 10 Aug 2018 02:00:06: #1 read tag files... INFO @ Fri, 10 Aug 2018 02:00:06: #1 read treatment tags... INFO @ Fri, 10 Aug 2018 02:00:13: 1000000 INFO @ Fri, 10 Aug 2018 02:00:13: 1000000 INFO @ Fri, 10 Aug 2018 02:00:13: 1000000 INFO @ Fri, 10 Aug 2018 02:00:17: #1 tag size is determined as 51 bps INFO @ Fri, 10 Aug 2018 02:00:17: #1 tag size = 51 INFO @ Fri, 10 Aug 2018 02:00:17: #1 total tags in treatment: 789330 INFO @ Fri, 10 Aug 2018 02:00:17: #1 user defined the maximum tags... INFO @ Fri, 10 Aug 2018 02:00:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Aug 2018 02:00:17: #1 tags after filtering in treatment: 362965 INFO @ Fri, 10 Aug 2018 02:00:17: #1 Redundant rate of treatment: 0.54 INFO @ Fri, 10 Aug 2018 02:00:17: #1 finished! INFO @ Fri, 10 Aug 2018 02:00:17: #2 Build Peak Model... INFO @ Fri, 10 Aug 2018 02:00:17: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Aug 2018 02:00:17: #2 number of paired peaks: 711 WARNING @ Fri, 10 Aug 2018 02:00:17: Fewer paired peaks (711) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 711 pairs to build model! INFO @ Fri, 10 Aug 2018 02:00:17: start model_add_line... INFO @ Fri, 10 Aug 2018 02:00:18: start X-correlation... INFO @ Fri, 10 Aug 2018 02:00:18: end of X-cor INFO @ Fri, 10 Aug 2018 02:00:18: #2 finished! INFO @ Fri, 10 Aug 2018 02:00:18: #2 predicted fragment length is 177 bps INFO @ Fri, 10 Aug 2018 02:00:18: #2 alternative fragment length(s) may be 1,75,105,177,202,213,231,249 bps INFO @ Fri, 10 Aug 2018 02:00:18: #2.2 Generate R script for model : SRX2198719.20_model.r INFO @ Fri, 10 Aug 2018 02:00:18: #3 Call peaks... INFO @ Fri, 10 Aug 2018 02:00:18: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Aug 2018 02:00:18: #1 tag size is determined as 51 bps INFO @ Fri, 10 Aug 2018 02:00:18: #1 tag size = 51 INFO @ Fri, 10 Aug 2018 02:00:18: #1 total tags in treatment: 789330 INFO @ Fri, 10 Aug 2018 02:00:18: #1 user defined the maximum tags... INFO @ Fri, 10 Aug 2018 02:00:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Aug 2018 02:00:18: #1 tags after filtering in treatment: 362965 INFO @ Fri, 10 Aug 2018 02:00:18: #1 Redundant rate of treatment: 0.54 INFO @ Fri, 10 Aug 2018 02:00:18: #1 finished! INFO @ Fri, 10 Aug 2018 02:00:18: #2 Build Peak Model... INFO @ Fri, 10 Aug 2018 02:00:18: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Aug 2018 02:00:18: #2 number of paired peaks: 711 WARNING @ Fri, 10 Aug 2018 02:00:18: Fewer paired peaks (711) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 711 pairs to build model! INFO @ Fri, 10 Aug 2018 02:00:18: start model_add_line... INFO @ Fri, 10 Aug 2018 02:00:18: start X-correlation... INFO @ Fri, 10 Aug 2018 02:00:18: end of X-cor INFO @ Fri, 10 Aug 2018 02:00:18: #2 finished! INFO @ Fri, 10 Aug 2018 02:00:18: #2 predicted fragment length is 177 bps INFO @ Fri, 10 Aug 2018 02:00:18: #2 alternative fragment length(s) may be 1,75,105,177,202,213,231,249 bps INFO @ Fri, 10 Aug 2018 02:00:18: #2.2 Generate R script for model : SRX2198719.05_model.r INFO @ Fri, 10 Aug 2018 02:00:18: #3 Call peaks... INFO @ Fri, 10 Aug 2018 02:00:18: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Aug 2018 02:00:18: #1 tag size is determined as 51 bps INFO @ Fri, 10 Aug 2018 02:00:18: #1 tag size = 51 INFO @ Fri, 10 Aug 2018 02:00:18: #1 total tags in treatment: 789330 INFO @ Fri, 10 Aug 2018 02:00:18: #1 user defined the maximum tags... INFO @ Fri, 10 Aug 2018 02:00:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Aug 2018 02:00:18: #1 tags after filtering in treatment: 362965 INFO @ Fri, 10 Aug 2018 02:00:18: #1 Redundant rate of treatment: 0.54 INFO @ Fri, 10 Aug 2018 02:00:18: #1 finished! INFO @ Fri, 10 Aug 2018 02:00:18: #2 Build Peak Model... INFO @ Fri, 10 Aug 2018 02:00:18: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Aug 2018 02:00:18: #2 number of paired peaks: 711 WARNING @ Fri, 10 Aug 2018 02:00:18: Fewer paired peaks (711) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 711 pairs to build model! INFO @ Fri, 10 Aug 2018 02:00:18: start model_add_line... INFO @ Fri, 10 Aug 2018 02:00:18: start X-correlation... INFO @ Fri, 10 Aug 2018 02:00:18: end of X-cor INFO @ Fri, 10 Aug 2018 02:00:18: #2 finished! INFO @ Fri, 10 Aug 2018 02:00:18: #2 predicted fragment length is 177 bps INFO @ Fri, 10 Aug 2018 02:00:18: #2 alternative fragment length(s) may be 1,75,105,177,202,213,231,249 bps INFO @ Fri, 10 Aug 2018 02:00:18: #2.2 Generate R script for model : SRX2198719.10_model.r INFO @ Fri, 10 Aug 2018 02:00:18: #3 Call peaks... INFO @ Fri, 10 Aug 2018 02:00:18: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Aug 2018 02:00:19: #3 Call peaks for each chromosome... INFO @ Fri, 10 Aug 2018 02:00:19: #3 Call peaks for each chromosome... INFO @ Fri, 10 Aug 2018 02:00:20: #3 Call peaks for each chromosome... INFO @ Fri, 10 Aug 2018 02:00:20: #4 Write output xls file... SRX2198719.20_peaks.xls INFO @ Fri, 10 Aug 2018 02:00:20: #4 Write peak in narrowPeak format file... SRX2198719.20_peaks.narrowPeak INFO @ Fri, 10 Aug 2018 02:00:20: #4 Write summits bed file... SRX2198719.20_summits.bed INFO @ Fri, 10 Aug 2018 02:00:20: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (25 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 10 Aug 2018 02:00:20: #4 Write output xls file... SRX2198719.05_peaks.xls INFO @ Fri, 10 Aug 2018 02:00:20: #4 Write peak in narrowPeak format file... SRX2198719.05_peaks.narrowPeak INFO @ Fri, 10 Aug 2018 02:00:20: #4 Write summits bed file... SRX2198719.05_summits.bed INFO @ Fri, 10 Aug 2018 02:00:20: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (214 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 10 Aug 2018 02:00:20: #4 Write output xls file... SRX2198719.10_peaks.xls INFO @ Fri, 10 Aug 2018 02:00:20: #4 Write peak in narrowPeak format file... SRX2198719.10_peaks.narrowPeak INFO @ Fri, 10 Aug 2018 02:00:20: #4 Write summits bed file... SRX2198719.10_summits.bed INFO @ Fri, 10 Aug 2018 02:00:20: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (97 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。