Job ID = 10937510 sra ファイルのダウンロード中... Completed: 397185K bytes transferred in 20 seconds (160390K bits/sec), in 1 file. Completed: 330955K bytes transferred in 30 seconds (90077K 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 3636128 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3010316/SRR5833312.sra Written 3636128 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3010316/SRR5833312.sra Read 4210866 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3010316/SRR5833311.sra Written 4210866 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3010316/SRR5833311.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 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: 00:02:55 7846994 reads; of these: 7846994 (100.00%) were paired; of these: 6685983 (85.20%) aligned concordantly 0 times 913441 (11.64%) aligned concordantly exactly 1 time 247570 (3.15%) aligned concordantly >1 times ---- 6685983 pairs aligned concordantly 0 times; of these: 6674 (0.10%) aligned discordantly 1 time ---- 6679309 pairs aligned 0 times concordantly or discordantly; of these: 13358618 mates make up the pairs; of these: 13324795 (99.75%) aligned 0 times 23438 (0.18%) aligned exactly 1 time 10385 (0.08%) aligned >1 times 15.10% overall alignment rate Time searching: 00:02:55 Overall time: 00:02:55 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] 67491 / 1166932 = 0.0578 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 02:30:20: # Command line: callpeak -t SRX3010316.bam -f BAM -g 12100000 -n SRX3010316.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3010316.20 # format = BAM # ChIP-seq file = ['SRX3010316.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 02:30:20: #1 read tag files... INFO @ Fri, 10 Aug 2018 02:30:20: #1 read treatment tags... INFO @ Fri, 10 Aug 2018 02:30:20: # Command line: callpeak -t SRX3010316.bam -f BAM -g 12100000 -n SRX3010316.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3010316.10 # format = BAM # ChIP-seq file = ['SRX3010316.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 02:30:20: #1 read tag files... INFO @ Fri, 10 Aug 2018 02:30:20: #1 read treatment tags... INFO @ Fri, 10 Aug 2018 02:30:20: # Command line: callpeak -t SRX3010316.bam -f BAM -g 12100000 -n SRX3010316.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3010316.05 # format = BAM # ChIP-seq file = ['SRX3010316.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 02:30:20: #1 read tag files... INFO @ Fri, 10 Aug 2018 02:30:20: #1 read treatment tags... INFO @ Fri, 10 Aug 2018 02:30:32: 1000000 INFO @ Fri, 10 Aug 2018 02:30:32: 1000000 INFO @ Fri, 10 Aug 2018 02:30:32: 1000000 INFO @ Fri, 10 Aug 2018 02:30:44: 2000000 INFO @ Fri, 10 Aug 2018 02:30:44: 2000000 INFO @ Fri, 10 Aug 2018 02:30:44: 2000000 INFO @ Fri, 10 Aug 2018 02:30:47: #1 tag size is determined as 101 bps INFO @ Fri, 10 Aug 2018 02:30:47: #1 tag size = 101 INFO @ Fri, 10 Aug 2018 02:30:47: #1 total tags in treatment: 1093666 INFO @ Fri, 10 Aug 2018 02:30:47: #1 user defined the maximum tags... INFO @ Fri, 10 Aug 2018 02:30:47: #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 02:30:47: #1 tag size is determined as 101 bps INFO @ Fri, 10 Aug 2018 02:30:47: #1 tag size = 101 INFO @ Fri, 10 Aug 2018 02:30:47: #1 total tags in treatment: 1093666 INFO @ Fri, 10 Aug 2018 02:30:47: #1 user defined the maximum tags... INFO @ Fri, 10 Aug 2018 02:30:47: #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 02:30:47: #1 tag size is determined as 101 bps INFO @ Fri, 10 Aug 2018 02:30:47: #1 tag size = 101 INFO @ Fri, 10 Aug 2018 02:30:47: #1 total tags in treatment: 1093666 INFO @ Fri, 10 Aug 2018 02:30:47: #1 user defined the maximum tags... INFO @ Fri, 10 Aug 2018 02:30:47: #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 02:30:47: #1 tags after filtering in treatment: 866604 INFO @ Fri, 10 Aug 2018 02:30:47: #1 Redundant rate of treatment: 0.21 INFO @ Fri, 10 Aug 2018 02:30:47: #1 finished! INFO @ Fri, 10 Aug 2018 02:30:47: #2 Build Peak Model... INFO @ Fri, 10 Aug 2018 02:30:47: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Aug 2018 02:30:47: #1 tags after filtering in treatment: 866604 INFO @ Fri, 10 Aug 2018 02:30:47: #1 Redundant rate of treatment: 0.21 INFO @ Fri, 10 Aug 2018 02:30:47: #1 finished! INFO @ Fri, 10 Aug 2018 02:30:47: #2 Build Peak Model... INFO @ Fri, 10 Aug 2018 02:30:47: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Aug 2018 02:30:47: #1 tags after filtering in treatment: 866604 INFO @ Fri, 10 Aug 2018 02:30:47: #1 Redundant rate of treatment: 0.21 INFO @ Fri, 10 Aug 2018 02:30:47: #1 finished! INFO @ Fri, 10 Aug 2018 02:30:47: #2 Build Peak Model... INFO @ Fri, 10 Aug 2018 02:30:47: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Aug 2018 02:30:47: #2 number of paired peaks: 274 WARNING @ Fri, 10 Aug 2018 02:30:47: Fewer paired peaks (274) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 274 pairs to build model! INFO @ Fri, 10 Aug 2018 02:30:47: start model_add_line... INFO @ Fri, 10 Aug 2018 02:30:47: #2 number of paired peaks: 274 WARNING @ Fri, 10 Aug 2018 02:30:47: Fewer paired peaks (274) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 274 pairs to build model! INFO @ Fri, 10 Aug 2018 02:30:47: start model_add_line... INFO @ Fri, 10 Aug 2018 02:30:47: start X-correlation... INFO @ Fri, 10 Aug 2018 02:30:47: #2 number of paired peaks: 274 WARNING @ Fri, 10 Aug 2018 02:30:47: Fewer paired peaks (274) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 274 pairs to build model! INFO @ Fri, 10 Aug 2018 02:30:47: start model_add_line... INFO @ Fri, 10 Aug 2018 02:30:47: end of X-cor INFO @ Fri, 10 Aug 2018 02:30:47: #2 finished! INFO @ Fri, 10 Aug 2018 02:30:47: #2 predicted fragment length is 195 bps INFO @ Fri, 10 Aug 2018 02:30:47: #2 alternative fragment length(s) may be 195 bps INFO @ Fri, 10 Aug 2018 02:30:47: #2.2 Generate R script for model : SRX3010316.05_model.r INFO @ Fri, 10 Aug 2018 02:30:47: start X-correlation... WARNING @ Fri, 10 Aug 2018 02:30:47: #2 Since the d (195) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Aug 2018 02:30:47: #2 You may need to consider one of the other alternative d(s): 195 WARNING @ Fri, 10 Aug 2018 02:30:47: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Aug 2018 02:30:47: #3 Call peaks... INFO @ Fri, 10 Aug 2018 02:30:47: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Aug 2018 02:30:47: start X-correlation... INFO @ Fri, 10 Aug 2018 02:30:47: end of X-cor INFO @ Fri, 10 Aug 2018 02:30:47: #2 finished! INFO @ Fri, 10 Aug 2018 02:30:47: #2 predicted fragment length is 195 bps INFO @ Fri, 10 Aug 2018 02:30:47: #2 alternative fragment length(s) may be 195 bps INFO @ Fri, 10 Aug 2018 02:30:47: #2.2 Generate R script for model : SRX3010316.20_model.r INFO @ Fri, 10 Aug 2018 02:30:47: end of X-cor INFO @ Fri, 10 Aug 2018 02:30:47: #2 finished! INFO @ Fri, 10 Aug 2018 02:30:47: #2 predicted fragment length is 195 bps INFO @ Fri, 10 Aug 2018 02:30:47: #2 alternative fragment length(s) may be 195 bps INFO @ Fri, 10 Aug 2018 02:30:47: #2.2 Generate R script for model : SRX3010316.10_model.r WARNING @ Fri, 10 Aug 2018 02:30:47: #2 Since the d (195) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Aug 2018 02:30:47: #2 You may need to consider one of the other alternative d(s): 195 WARNING @ Fri, 10 Aug 2018 02:30:47: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Aug 2018 02:30:47: #3 Call peaks... INFO @ Fri, 10 Aug 2018 02:30:47: #3 Pre-compute pvalue-qvalue table... WARNING @ Fri, 10 Aug 2018 02:30:47: #2 Since the d (195) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Aug 2018 02:30:47: #2 You may need to consider one of the other alternative d(s): 195 WARNING @ Fri, 10 Aug 2018 02:30:47: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Aug 2018 02:30:47: #3 Call peaks... INFO @ Fri, 10 Aug 2018 02:30:47: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Aug 2018 02:30:51: #3 Call peaks for each chromosome... INFO @ Fri, 10 Aug 2018 02:30:51: #3 Call peaks for each chromosome... INFO @ Fri, 10 Aug 2018 02:30:51: #3 Call peaks for each chromosome... INFO @ Fri, 10 Aug 2018 02:30:52: #4 Write output xls file... SRX3010316.10_peaks.xls INFO @ Fri, 10 Aug 2018 02:30:52: #4 Write peak in narrowPeak format file... SRX3010316.10_peaks.narrowPeak INFO @ Fri, 10 Aug 2018 02:30:52: #4 Write summits bed file... SRX3010316.10_summits.bed INFO @ Fri, 10 Aug 2018 02:30:52: Done! INFO @ Fri, 10 Aug 2018 02:30:52: #4 Write output xls file... SRX3010316.05_peaks.xls INFO @ Fri, 10 Aug 2018 02:30:52: #4 Write peak in narrowPeak format file... SRX3010316.05_peaks.narrowPeak INFO @ Fri, 10 Aug 2018 02:30:52: #4 Write summits bed file... SRX3010316.05_summits.bed INFO @ Fri, 10 Aug 2018 02:30:52: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (187 records, 4 fields): 2 millis CompletedMACS2peakCalling pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (260 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 10 Aug 2018 02:30:53: #4 Write output xls file... SRX3010316.20_peaks.xls INFO @ Fri, 10 Aug 2018 02:30:53: #4 Write peak in narrowPeak format file... SRX3010316.20_peaks.narrowPeak INFO @ Fri, 10 Aug 2018 02:30:53: #4 Write summits bed file... SRX3010316.20_summits.bed INFO @ Fri, 10 Aug 2018 02:30:53: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (160 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。