Job ID = 11193141 sra ファイルのダウンロード中... Completed: 175053K bytes transferred in 15 seconds (90583K 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 4882256 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4337733/SRR7467870.sra Written 4882256 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4337733/SRR7467870.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: 00:00:49 4882256 reads; of these: 4882256 (100.00%) were paired; of these: 4711085 (96.49%) aligned concordantly 0 times 150686 (3.09%) aligned concordantly exactly 1 time 20485 (0.42%) aligned concordantly >1 times ---- 4711085 pairs aligned concordantly 0 times; of these: 54622 (1.16%) aligned discordantly 1 time ---- 4656463 pairs aligned 0 times concordantly or discordantly; of these: 9312926 mates make up the pairs; of these: 9089371 (97.60%) aligned 0 times 190004 (2.04%) aligned exactly 1 time 33551 (0.36%) aligned >1 times 6.91% overall alignment rate Time searching: 00:00:49 Overall time: 00:00:49 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] 87517 / 224670 = 0.3895 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 11:01:22: # Command line: callpeak -t SRX4337733.bam -f BAM -g 12100000 -n SRX4337733.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4337733.10 # format = BAM # ChIP-seq file = ['SRX4337733.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 11:01:22: # Command line: callpeak -t SRX4337733.bam -f BAM -g 12100000 -n SRX4337733.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4337733.20 # format = BAM # ChIP-seq file = ['SRX4337733.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 11:01:22: #1 read tag files... INFO @ Sat, 15 Sep 2018 11:01:22: #1 read tag files... INFO @ Sat, 15 Sep 2018 11:01:22: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 11:01:22: # Command line: callpeak -t SRX4337733.bam -f BAM -g 12100000 -n SRX4337733.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4337733.05 # format = BAM # ChIP-seq file = ['SRX4337733.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 11:01:22: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 11:01:22: #1 read tag files... INFO @ Sat, 15 Sep 2018 11:01:22: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 11:01:25: #1 tag size is determined as 43 bps INFO @ Sat, 15 Sep 2018 11:01:25: #1 tag size = 43 INFO @ Sat, 15 Sep 2018 11:01:25: #1 total tags in treatment: 104146 INFO @ Sat, 15 Sep 2018 11:01:25: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 11:01:25: #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 11:01:25: #1 tags after filtering in treatment: 101240 INFO @ Sat, 15 Sep 2018 11:01:25: #1 Redundant rate of treatment: 0.03 INFO @ Sat, 15 Sep 2018 11:01:25: #1 finished! INFO @ Sat, 15 Sep 2018 11:01:25: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 11:01:25: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 11:01:25: #2 number of paired peaks: 159 WARNING @ Sat, 15 Sep 2018 11:01:25: Fewer paired peaks (159) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 159 pairs to build model! INFO @ Sat, 15 Sep 2018 11:01:25: start model_add_line... INFO @ Sat, 15 Sep 2018 11:01:25: start X-correlation... INFO @ Sat, 15 Sep 2018 11:01:25: #1 tag size is determined as 43 bps INFO @ Sat, 15 Sep 2018 11:01:25: #1 tag size = 43 INFO @ Sat, 15 Sep 2018 11:01:25: #1 total tags in treatment: 104146 INFO @ Sat, 15 Sep 2018 11:01:25: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 11:01:25: #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 11:01:25: #1 tags after filtering in treatment: 101240 INFO @ Sat, 15 Sep 2018 11:01:25: #1 Redundant rate of treatment: 0.03 INFO @ Sat, 15 Sep 2018 11:01:25: #1 finished! INFO @ Sat, 15 Sep 2018 11:01:25: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 11:01:25: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 11:01:25: #2 number of paired peaks: 159 WARNING @ Sat, 15 Sep 2018 11:01:25: Fewer paired peaks (159) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 159 pairs to build model! INFO @ Sat, 15 Sep 2018 11:01:25: start model_add_line... INFO @ Sat, 15 Sep 2018 11:01:25: start X-correlation... INFO @ Sat, 15 Sep 2018 11:01:25: end of X-cor INFO @ Sat, 15 Sep 2018 11:01:25: end of X-cor INFO @ Sat, 15 Sep 2018 11:01:25: #2 finished! INFO @ Sat, 15 Sep 2018 11:01:25: #2 finished! INFO @ Sat, 15 Sep 2018 11:01:25: #2 predicted fragment length is 199 bps INFO @ Sat, 15 Sep 2018 11:01:25: #2 predicted fragment length is 199 bps INFO @ Sat, 15 Sep 2018 11:01:25: #2 alternative fragment length(s) may be 21,59,82,137,165,199,234,269,315,371,408,449,492,507,553,586 bps INFO @ Sat, 15 Sep 2018 11:01:25: #2 alternative fragment length(s) may be 21,59,82,137,165,199,234,269,315,371,408,449,492,507,553,586 bps INFO @ Sat, 15 Sep 2018 11:01:25: #2.2 Generate R script for model : SRX4337733.10_model.r INFO @ Sat, 15 Sep 2018 11:01:25: #2.2 Generate R script for model : SRX4337733.20_model.r INFO @ Sat, 15 Sep 2018 11:01:26: #3 Call peaks... INFO @ Sat, 15 Sep 2018 11:01:26: #3 Call peaks... INFO @ Sat, 15 Sep 2018 11:01:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 11:01:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 11:01:26: #1 tag size is determined as 43 bps INFO @ Sat, 15 Sep 2018 11:01:26: #1 tag size = 43 INFO @ Sat, 15 Sep 2018 11:01:26: #1 total tags in treatment: 104146 INFO @ Sat, 15 Sep 2018 11:01:26: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 11:01:26: #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 11:01:26: #1 tags after filtering in treatment: 101240 INFO @ Sat, 15 Sep 2018 11:01:26: #1 Redundant rate of treatment: 0.03 INFO @ Sat, 15 Sep 2018 11:01:26: #1 finished! INFO @ Sat, 15 Sep 2018 11:01:26: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 11:01:26: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 11:01:26: #2 number of paired peaks: 159 WARNING @ Sat, 15 Sep 2018 11:01:26: Fewer paired peaks (159) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 159 pairs to build model! INFO @ Sat, 15 Sep 2018 11:01:26: start model_add_line... INFO @ Sat, 15 Sep 2018 11:01:26: start X-correlation... INFO @ Sat, 15 Sep 2018 11:01:26: end of X-cor INFO @ Sat, 15 Sep 2018 11:01:26: #2 finished! INFO @ Sat, 15 Sep 2018 11:01:26: #2 predicted fragment length is 199 bps INFO @ Sat, 15 Sep 2018 11:01:26: #2 alternative fragment length(s) may be 21,59,82,137,165,199,234,269,315,371,408,449,492,507,553,586 bps INFO @ Sat, 15 Sep 2018 11:01:26: #2.2 Generate R script for model : SRX4337733.05_model.r INFO @ Sat, 15 Sep 2018 11:01:26: #3 Call peaks... INFO @ Sat, 15 Sep 2018 11:01:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 11:01:26: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 11:01:26: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 11:01:26: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 11:01:26: #4 Write output xls file... SRX4337733.20_peaks.xls INFO @ Sat, 15 Sep 2018 11:01:26: #4 Write peak in narrowPeak format file... SRX4337733.20_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 11:01:26: #4 Write output xls file... SRX4337733.05_peaks.xls INFO @ Sat, 15 Sep 2018 11:01:26: #4 Write output xls file... SRX4337733.10_peaks.xls INFO @ Sat, 15 Sep 2018 11:01:26: #4 Write summits bed file... SRX4337733.20_summits.bed INFO @ Sat, 15 Sep 2018 11:01:26: #4 Write peak in narrowPeak format file... SRX4337733.10_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 11:01:26: #4 Write peak in narrowPeak format file... SRX4337733.05_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 11:01:26: #4 Write summits bed file... SRX4337733.10_summits.bed INFO @ Sat, 15 Sep 2018 11:01:26: #4 Write summits bed file... SRX4337733.05_summits.bed INFO @ Sat, 15 Sep 2018 11:01:26: Done! INFO @ Sat, 15 Sep 2018 11:01:26: Done! INFO @ Sat, 15 Sep 2018 11:01:26: Done! pass1 - making usageList (7 chroms)pass1 - making usageList (2 chroms)pass1 - making usageList (0 chroms): 30 millis : 29 millis : 29 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling pass2 - checking and writing primary data (2 records, 4 fields): 53 millis pass2 - checking and writing primary data (8 records, 4 fields): 53 millis CompletedMACS2peakCalling CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。