Job ID = 10536356 sra ファイルのダウンロード中... Completed: 1039813K bytes transferred in 71 seconds (119601K 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 29784527 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3433219/SRR6333860.sra Written 29784527 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: 00:10:10 29784527 reads; of these: 29784527 (100.00%) were paired; of these: 18832404 (63.23%) aligned concordantly 0 times 9958022 (33.43%) aligned concordantly exactly 1 time 994101 (3.34%) aligned concordantly >1 times ---- 18832404 pairs aligned concordantly 0 times; of these: 73166 (0.39%) aligned discordantly 1 time ---- 18759238 pairs aligned 0 times concordantly or discordantly; of these: 37518476 mates make up the pairs; of these: 37296217 (99.41%) aligned 0 times 182903 (0.49%) aligned exactly 1 time 39356 (0.10%) aligned >1 times 37.39% overall alignment rate Time searching: 00:10:10 Overall time: 00:10:10 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 12 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] 8696869 / 10961169 = 0.7934 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 09:07:19: # Command line: callpeak -t SRX3433219.bam -f BAM -g 12100000 -n SRX3433219.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3433219.10 # format = BAM # ChIP-seq file = ['SRX3433219.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 09:07:19: #1 read tag files... INFO @ Thu, 05 Apr 2018 09:07:19: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 09:07:19: # Command line: callpeak -t SRX3433219.bam -f BAM -g 12100000 -n SRX3433219.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3433219.05 # format = BAM # ChIP-seq file = ['SRX3433219.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 09:07:19: #1 read tag files... INFO @ Thu, 05 Apr 2018 09:07:19: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 09:07:19: # Command line: callpeak -t SRX3433219.bam -f BAM -g 12100000 -n SRX3433219.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3433219.20 # format = BAM # ChIP-seq file = ['SRX3433219.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 09:07:19: #1 read tag files... INFO @ Thu, 05 Apr 2018 09:07:19: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 09:07:24: 1000000 INFO @ Thu, 05 Apr 2018 09:07:24: 1000000 INFO @ Thu, 05 Apr 2018 09:07:24: 1000000 INFO @ Thu, 05 Apr 2018 09:07:29: 2000000 INFO @ Thu, 05 Apr 2018 09:07:30: 2000000 INFO @ Thu, 05 Apr 2018 09:07:30: 2000000 INFO @ Thu, 05 Apr 2018 09:07:34: 3000000 INFO @ Thu, 05 Apr 2018 09:07:35: 3000000 INFO @ Thu, 05 Apr 2018 09:07:35: 3000000 INFO @ Thu, 05 Apr 2018 09:07:39: 4000000 INFO @ Thu, 05 Apr 2018 09:07:41: 4000000 INFO @ Thu, 05 Apr 2018 09:07:41: 4000000 INFO @ Thu, 05 Apr 2018 09:07:44: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 09:07:44: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 09:07:44: #1 total tags in treatment: 2262535 INFO @ Thu, 05 Apr 2018 09:07:44: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 09:07:44: #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 09:07:44: #1 tags after filtering in treatment: 1998711 INFO @ Thu, 05 Apr 2018 09:07:44: #1 Redundant rate of treatment: 0.12 INFO @ Thu, 05 Apr 2018 09:07:44: #1 finished! INFO @ Thu, 05 Apr 2018 09:07:44: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 09:07:44: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 09:07:44: #2 number of paired peaks: 162 WARNING @ Thu, 05 Apr 2018 09:07:44: Fewer paired peaks (162) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 162 pairs to build model! INFO @ Thu, 05 Apr 2018 09:07:44: start model_add_line... INFO @ Thu, 05 Apr 2018 09:07:44: start X-correlation... INFO @ Thu, 05 Apr 2018 09:07:44: end of X-cor INFO @ Thu, 05 Apr 2018 09:07:44: #2 finished! INFO @ Thu, 05 Apr 2018 09:07:44: #2 predicted fragment length is 141 bps INFO @ Thu, 05 Apr 2018 09:07:44: #2 alternative fragment length(s) may be 4,103,141,174 bps INFO @ Thu, 05 Apr 2018 09:07:44: #2.2 Generate R script for model : SRX3433219.10_model.r INFO @ Thu, 05 Apr 2018 09:07:44: #3 Call peaks... INFO @ Thu, 05 Apr 2018 09:07:44: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Apr 2018 09:07:46: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 09:07:46: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 09:07:46: #1 total tags in treatment: 2262535 INFO @ Thu, 05 Apr 2018 09:07:46: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 09:07:46: #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 09:07:46: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 09:07:46: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 09:07:46: #1 total tags in treatment: 2262535 INFO @ Thu, 05 Apr 2018 09:07:46: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 09:07:46: #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 09:07:46: #1 tags after filtering in treatment: 1998711 INFO @ Thu, 05 Apr 2018 09:07:46: #1 Redundant rate of treatment: 0.12 INFO @ Thu, 05 Apr 2018 09:07:46: #1 finished! INFO @ Thu, 05 Apr 2018 09:07:46: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 09:07:46: #1 tags after filtering in treatment: 1998711 INFO @ Thu, 05 Apr 2018 09:07:46: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 09:07:46: #1 Redundant rate of treatment: 0.12 INFO @ Thu, 05 Apr 2018 09:07:46: #1 finished! INFO @ Thu, 05 Apr 2018 09:07:46: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 09:07:46: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 09:07:46: #2 number of paired peaks: 162 WARNING @ Thu, 05 Apr 2018 09:07:46: Fewer paired peaks (162) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 162 pairs to build model! INFO @ Thu, 05 Apr 2018 09:07:46: start model_add_line... INFO @ Thu, 05 Apr 2018 09:07:46: start X-correlation... INFO @ Thu, 05 Apr 2018 09:07:46: end of X-cor INFO @ Thu, 05 Apr 2018 09:07:46: #2 finished! INFO @ Thu, 05 Apr 2018 09:07:46: #2 predicted fragment length is 141 bps INFO @ Thu, 05 Apr 2018 09:07:46: #2 alternative fragment length(s) may be 4,103,141,174 bps INFO @ Thu, 05 Apr 2018 09:07:46: #2.2 Generate R script for model : SRX3433219.05_model.r INFO @ Thu, 05 Apr 2018 09:07:46: #3 Call peaks... INFO @ Thu, 05 Apr 2018 09:07:46: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Apr 2018 09:07:46: #2 number of paired peaks: 162 WARNING @ Thu, 05 Apr 2018 09:07:46: Fewer paired peaks (162) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 162 pairs to build model! INFO @ Thu, 05 Apr 2018 09:07:46: start model_add_line... INFO @ Thu, 05 Apr 2018 09:07:46: start X-correlation... INFO @ Thu, 05 Apr 2018 09:07:46: end of X-cor INFO @ Thu, 05 Apr 2018 09:07:46: #2 finished! INFO @ Thu, 05 Apr 2018 09:07:46: #2 predicted fragment length is 141 bps INFO @ Thu, 05 Apr 2018 09:07:46: #2 alternative fragment length(s) may be 4,103,141,174 bps INFO @ Thu, 05 Apr 2018 09:07:46: #2.2 Generate R script for model : SRX3433219.20_model.r INFO @ Thu, 05 Apr 2018 09:07:46: #3 Call peaks... INFO @ Thu, 05 Apr 2018 09:07:46: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Apr 2018 09:07:50: #3 Call peaks for each chromosome... INFO @ Thu, 05 Apr 2018 09:07:52: #3 Call peaks for each chromosome... INFO @ Thu, 05 Apr 2018 09:07:52: #3 Call peaks for each chromosome... INFO @ Thu, 05 Apr 2018 09:07:52: #4 Write output xls file... SRX3433219.10_peaks.xls INFO @ Thu, 05 Apr 2018 09:07:52: #4 Write peak in narrowPeak format file... SRX3433219.10_peaks.narrowPeak INFO @ Thu, 05 Apr 2018 09:07:52: #4 Write summits bed file... SRX3433219.10_summits.bed INFO @ Thu, 05 Apr 2018 09:07:52: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (578 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Thu, 05 Apr 2018 09:07:54: #4 Write output xls file... SRX3433219.05_peaks.xls INFO @ Thu, 05 Apr 2018 09:07:54: #4 Write peak in narrowPeak format file... SRX3433219.05_peaks.narrowPeak INFO @ Thu, 05 Apr 2018 09:07:54: #4 Write summits bed file... SRX3433219.05_summits.bed INFO @ Thu, 05 Apr 2018 09:07:54: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (988 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 05 Apr 2018 09:07:54: #4 Write output xls file... SRX3433219.20_peaks.xls INFO @ Thu, 05 Apr 2018 09:07:54: #4 Write peak in narrowPeak format file... SRX3433219.20_peaks.narrowPeak INFO @ Thu, 05 Apr 2018 09:07:54: #4 Write summits bed file... SRX3433219.20_summits.bed INFO @ Thu, 05 Apr 2018 09:07:54: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (303 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。