Job ID = 10536364 sra ファイルのダウンロード中... Completed: 1672633K bytes transferred in 118 seconds (116098K 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... Written 45974422 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3433226/SRR6333867.sra Written 45974422 spots total 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: 00:15:05 45974422 reads; of these: 45974422 (100.00%) were paired; of these: 31473926 (68.46%) aligned concordantly 0 times 10883521 (23.67%) aligned concordantly exactly 1 time 3616975 (7.87%) aligned concordantly >1 times ---- 31473926 pairs aligned concordantly 0 times; of these: 76093 (0.24%) aligned discordantly 1 time ---- 31397833 pairs aligned 0 times concordantly or discordantly; of these: 62795666 mates make up the pairs; of these: 62480168 (99.50%) aligned 0 times 209162 (0.33%) aligned exactly 1 time 106336 (0.17%) aligned >1 times 32.05% overall alignment rate Time searching: 00:15:05 Overall time: 00:15:05 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 16 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] 10592168 / 14519741 = 0.7295 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 @ Thu, 05 Apr 2018 09:26:24: # Command line: callpeak -t SRX3433226.bam -f BAM -g 12100000 -n SRX3433226.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3433226.20 # format = BAM # ChIP-seq file = ['SRX3433226.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 @ Thu, 05 Apr 2018 09:26:24: #1 read tag files... INFO @ Thu, 05 Apr 2018 09:26:24: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 09:26:24: # Command line: callpeak -t SRX3433226.bam -f BAM -g 12100000 -n SRX3433226.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3433226.10 # format = BAM # ChIP-seq file = ['SRX3433226.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 @ Thu, 05 Apr 2018 09:26:24: #1 read tag files... INFO @ Thu, 05 Apr 2018 09:26:24: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 09:26:24: # Command line: callpeak -t SRX3433226.bam -f BAM -g 12100000 -n SRX3433226.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3433226.05 # format = BAM # ChIP-seq file = ['SRX3433226.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 @ Thu, 05 Apr 2018 09:26:24: #1 read tag files... INFO @ Thu, 05 Apr 2018 09:26:24: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 09:26:31: 1000000 INFO @ Thu, 05 Apr 2018 09:26:31: 1000000 INFO @ Thu, 05 Apr 2018 09:26:31: 1000000 INFO @ Thu, 05 Apr 2018 09:26:37: 2000000 INFO @ Thu, 05 Apr 2018 09:26:38: 2000000 INFO @ Thu, 05 Apr 2018 09:26:38: 2000000 INFO @ Thu, 05 Apr 2018 09:26:44: 3000000 INFO @ Thu, 05 Apr 2018 09:26:45: 3000000 INFO @ Thu, 05 Apr 2018 09:26:45: 3000000 INFO @ Thu, 05 Apr 2018 09:26:51: 4000000 INFO @ Thu, 05 Apr 2018 09:26:51: 4000000 INFO @ Thu, 05 Apr 2018 09:26:51: 4000000 INFO @ Thu, 05 Apr 2018 09:26:57: 5000000 INFO @ Thu, 05 Apr 2018 09:26:58: 5000000 INFO @ Thu, 05 Apr 2018 09:26:58: 5000000 INFO @ Thu, 05 Apr 2018 09:27:04: 6000000 INFO @ Thu, 05 Apr 2018 09:27:04: 6000000 INFO @ Thu, 05 Apr 2018 09:27:04: 6000000 INFO @ Thu, 05 Apr 2018 09:27:11: 7000000 INFO @ Thu, 05 Apr 2018 09:27:11: 7000000 INFO @ Thu, 05 Apr 2018 09:27:11: 7000000 INFO @ Thu, 05 Apr 2018 09:27:17: 8000000 INFO @ Thu, 05 Apr 2018 09:27:17: 8000000 INFO @ Thu, 05 Apr 2018 09:27:18: 8000000 INFO @ Thu, 05 Apr 2018 09:27:19: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 09:27:19: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 09:27:19: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 09:27:19: #1 total tags in treatment: 3933133 INFO @ Thu, 05 Apr 2018 09:27:19: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 09:27:19: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 09:27:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Apr 2018 09:27:19: #1 total tags in treatment: 3933133 INFO @ Thu, 05 Apr 2018 09:27:19: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 09:27:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Apr 2018 09:27:19: #1 tags after filtering in treatment: 3151745 INFO @ Thu, 05 Apr 2018 09:27:19: #1 Redundant rate of treatment: 0.20 INFO @ Thu, 05 Apr 2018 09:27:19: #1 finished! INFO @ Thu, 05 Apr 2018 09:27:19: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 09:27:19: #1 tags after filtering in treatment: 3151745 INFO @ Thu, 05 Apr 2018 09:27:19: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 09:27:19: #1 Redundant rate of treatment: 0.20 INFO @ Thu, 05 Apr 2018 09:27:19: #1 finished! INFO @ Thu, 05 Apr 2018 09:27:19: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 09:27:19: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 09:27:19: #2 number of paired peaks: 157 WARNING @ Thu, 05 Apr 2018 09:27:19: Fewer paired peaks (157) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 157 pairs to build model! INFO @ Thu, 05 Apr 2018 09:27:19: start model_add_line... INFO @ Thu, 05 Apr 2018 09:27:19: #2 number of paired peaks: 157 WARNING @ Thu, 05 Apr 2018 09:27:19: Fewer paired peaks (157) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 157 pairs to build model! INFO @ Thu, 05 Apr 2018 09:27:19: start model_add_line... INFO @ Thu, 05 Apr 2018 09:27:19: start X-correlation... INFO @ Thu, 05 Apr 2018 09:27:19: start X-correlation... INFO @ Thu, 05 Apr 2018 09:27:19: end of X-cor INFO @ Thu, 05 Apr 2018 09:27:19: end of X-cor INFO @ Thu, 05 Apr 2018 09:27:19: #2 finished! INFO @ Thu, 05 Apr 2018 09:27:19: #2 finished! INFO @ Thu, 05 Apr 2018 09:27:19: #2 predicted fragment length is 2 bps INFO @ Thu, 05 Apr 2018 09:27:19: #2 predicted fragment length is 2 bps INFO @ Thu, 05 Apr 2018 09:27:19: #2 alternative fragment length(s) may be 2,33,55,74 bps INFO @ Thu, 05 Apr 2018 09:27:19: #2 alternative fragment length(s) may be 2,33,55,74 bps INFO @ Thu, 05 Apr 2018 09:27:19: #2.2 Generate R script for model : SRX3433226.10_model.r INFO @ Thu, 05 Apr 2018 09:27:19: #2.2 Generate R script for model : SRX3433226.05_model.r WARNING @ Thu, 05 Apr 2018 09:27:19: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Apr 2018 09:27:19: #2 You may need to consider one of the other alternative d(s): 2,33,55,74 WARNING @ Thu, 05 Apr 2018 09:27:19: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Apr 2018 09:27:19: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. WARNING @ Thu, 05 Apr 2018 09:27:19: #2 You may need to consider one of the other alternative d(s): 2,33,55,74 INFO @ Thu, 05 Apr 2018 09:27:19: #3 Call peaks... WARNING @ Thu, 05 Apr 2018 09:27:19: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 05 Apr 2018 09:27:19: #3 Call peaks... INFO @ Thu, 05 Apr 2018 09:27:19: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Apr 2018 09:27:19: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Apr 2018 09:27:20: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 09:27:20: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 09:27:20: #1 total tags in treatment: 3933133 INFO @ Thu, 05 Apr 2018 09:27:20: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 09:27:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Apr 2018 09:27:20: #1 tags after filtering in treatment: 3151745 INFO @ Thu, 05 Apr 2018 09:27:20: #1 Redundant rate of treatment: 0.20 INFO @ Thu, 05 Apr 2018 09:27:20: #1 finished! INFO @ Thu, 05 Apr 2018 09:27:20: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 09:27:20: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 09:27:20: #2 number of paired peaks: 157 WARNING @ Thu, 05 Apr 2018 09:27:20: Fewer paired peaks (157) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 157 pairs to build model! INFO @ Thu, 05 Apr 2018 09:27:20: start model_add_line... INFO @ Thu, 05 Apr 2018 09:27:20: start X-correlation... INFO @ Thu, 05 Apr 2018 09:27:20: end of X-cor INFO @ Thu, 05 Apr 2018 09:27:20: #2 finished! INFO @ Thu, 05 Apr 2018 09:27:20: #2 predicted fragment length is 2 bps INFO @ Thu, 05 Apr 2018 09:27:20: #2 alternative fragment length(s) may be 2,33,55,74 bps INFO @ Thu, 05 Apr 2018 09:27:20: #2.2 Generate R script for model : SRX3433226.20_model.r WARNING @ Thu, 05 Apr 2018 09:27:20: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Apr 2018 09:27:20: #2 You may need to consider one of the other alternative d(s): 2,33,55,74 WARNING @ Thu, 05 Apr 2018 09:27:20: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 05 Apr 2018 09:27:20: #3 Call peaks... INFO @ Thu, 05 Apr 2018 09:27:20: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Apr 2018 09:27:24: #3 Call peaks for each chromosome... INFO @ Thu, 05 Apr 2018 09:27:24: #3 Call peaks for each chromosome... INFO @ Thu, 05 Apr 2018 09:27:25: #3 Call peaks for each chromosome... INFO @ Thu, 05 Apr 2018 09:27:26: #4 Write output xls file... SRX3433226.05_peaks.xls INFO @ Thu, 05 Apr 2018 09:27:26: #4 Write peak in narrowPeak format file... SRX3433226.05_peaks.narrowPeak INFO @ Thu, 05 Apr 2018 09:27:26: #4 Write summits bed file... SRX3433226.05_summits.bed INFO @ Thu, 05 Apr 2018 09:27:26: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Thu, 05 Apr 2018 09:27:27: #4 Write output xls file... SRX3433226.10_peaks.xls INFO @ Thu, 05 Apr 2018 09:27:27: #4 Write peak in narrowPeak format file... SRX3433226.10_peaks.narrowPeak INFO @ Thu, 05 Apr 2018 09:27:27: #4 Write summits bed file... SRX3433226.10_summits.bed INFO @ Thu, 05 Apr 2018 09:27:27: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Thu, 05 Apr 2018 09:27:27: #4 Write output xls file... SRX3433226.20_peaks.xls INFO @ Thu, 05 Apr 2018 09:27:27: #4 Write peak in narrowPeak format file... SRX3433226.20_peaks.narrowPeak INFO @ Thu, 05 Apr 2018 09:27:27: #4 Write summits bed file... SRX3433226.20_summits.bed INFO @ Thu, 05 Apr 2018 09:27:27: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。