Job ID = 11162634 sra ファイルのダウンロード中... Completed: 13697K bytes transferred in 2 seconds (37745K 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 437626 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3709373/SRR6736425.sra Written 437626 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3709373/SRR6736425.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: 00:00:16 437626 reads; of these: 437626 (100.00%) were paired; of these: 157430 (35.97%) aligned concordantly 0 times 211974 (48.44%) aligned concordantly exactly 1 time 68222 (15.59%) aligned concordantly >1 times ---- 157430 pairs aligned concordantly 0 times; of these: 1077 (0.68%) aligned discordantly 1 time ---- 156353 pairs aligned 0 times concordantly or discordantly; of these: 312706 mates make up the pairs; of these: 245004 (78.35%) aligned 0 times 51927 (16.61%) aligned exactly 1 time 15775 (5.04%) aligned >1 times 72.01% overall alignment rate Time searching: 00:00:16 Overall time: 00:00:16 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] 230551 / 280805 = 0.8210 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 @ Wed, 05 Sep 2018 10:37:08: # Command line: callpeak -t SRX3709373.bam -f BAM -g 12100000 -n SRX3709373.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3709373.20 # format = BAM # ChIP-seq file = ['SRX3709373.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 @ Wed, 05 Sep 2018 10:37:08: #1 read tag files... INFO @ Wed, 05 Sep 2018 10:37:08: #1 read treatment tags... INFO @ Wed, 05 Sep 2018 10:37:09: # Command line: callpeak -t SRX3709373.bam -f BAM -g 12100000 -n SRX3709373.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3709373.10 # format = BAM # ChIP-seq file = ['SRX3709373.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 @ Wed, 05 Sep 2018 10:37:09: #1 read tag files... INFO @ Wed, 05 Sep 2018 10:37:09: #1 read treatment tags... INFO @ Wed, 05 Sep 2018 10:37:09: # Command line: callpeak -t SRX3709373.bam -f BAM -g 12100000 -n SRX3709373.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3709373.05 # format = BAM # ChIP-seq file = ['SRX3709373.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 @ Wed, 05 Sep 2018 10:37:09: #1 read tag files... INFO @ Wed, 05 Sep 2018 10:37:09: #1 read treatment tags... INFO @ Wed, 05 Sep 2018 10:37:09: #1 tag size is determined as 40 bps INFO @ Wed, 05 Sep 2018 10:37:09: #1 tag size = 40 INFO @ Wed, 05 Sep 2018 10:37:09: #1 total tags in treatment: 50129 INFO @ Wed, 05 Sep 2018 10:37:09: #1 user defined the maximum tags... INFO @ Wed, 05 Sep 2018 10:37:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 05 Sep 2018 10:37:09: #1 tags after filtering in treatment: 47039 INFO @ Wed, 05 Sep 2018 10:37:09: #1 Redundant rate of treatment: 0.06 INFO @ Wed, 05 Sep 2018 10:37:09: #1 finished! INFO @ Wed, 05 Sep 2018 10:37:09: #2 Build Peak Model... INFO @ Wed, 05 Sep 2018 10:37:09: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 05 Sep 2018 10:37:09: #2 number of paired peaks: 182 WARNING @ Wed, 05 Sep 2018 10:37:09: Fewer paired peaks (182) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 182 pairs to build model! INFO @ Wed, 05 Sep 2018 10:37:09: start model_add_line... INFO @ Wed, 05 Sep 2018 10:37:09: start X-correlation... INFO @ Wed, 05 Sep 2018 10:37:09: end of X-cor INFO @ Wed, 05 Sep 2018 10:37:09: #2 finished! INFO @ Wed, 05 Sep 2018 10:37:09: #2 predicted fragment length is 223 bps INFO @ Wed, 05 Sep 2018 10:37:09: #2 alternative fragment length(s) may be 87,107,146,174,202,223,243,260,284,298,340,398,415,462,516,557,583 bps INFO @ Wed, 05 Sep 2018 10:37:09: #2.2 Generate R script for model : SRX3709373.20_model.r INFO @ Wed, 05 Sep 2018 10:37:09: #1 tag size is determined as 40 bps INFO @ Wed, 05 Sep 2018 10:37:09: #1 tag size = 40 INFO @ Wed, 05 Sep 2018 10:37:09: #1 total tags in treatment: 50129 INFO @ Wed, 05 Sep 2018 10:37:09: #1 user defined the maximum tags... INFO @ Wed, 05 Sep 2018 10:37:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 05 Sep 2018 10:37:09: #1 tag size is determined as 40 bps INFO @ Wed, 05 Sep 2018 10:37:09: #1 tag size = 40 INFO @ Wed, 05 Sep 2018 10:37:09: #1 total tags in treatment: 50129 INFO @ Wed, 05 Sep 2018 10:37:09: #1 user defined the maximum tags... INFO @ Wed, 05 Sep 2018 10:37:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 05 Sep 2018 10:37:09: #3 Call peaks... INFO @ Wed, 05 Sep 2018 10:37:09: #1 tags after filtering in treatment: 47039 INFO @ Wed, 05 Sep 2018 10:37:09: #1 Redundant rate of treatment: 0.06 INFO @ Wed, 05 Sep 2018 10:37:09: #1 finished! INFO @ Wed, 05 Sep 2018 10:37:09: #2 Build Peak Model... INFO @ Wed, 05 Sep 2018 10:37:09: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 05 Sep 2018 10:37:09: #1 tags after filtering in treatment: 47039 INFO @ Wed, 05 Sep 2018 10:37:09: #1 Redundant rate of treatment: 0.06 INFO @ Wed, 05 Sep 2018 10:37:09: #1 finished! INFO @ Wed, 05 Sep 2018 10:37:09: #2 Build Peak Model... INFO @ Wed, 05 Sep 2018 10:37:09: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 05 Sep 2018 10:37:09: #2 number of paired peaks: 182 WARNING @ Wed, 05 Sep 2018 10:37:09: Fewer paired peaks (182) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 182 pairs to build model! INFO @ Wed, 05 Sep 2018 10:37:09: start model_add_line... INFO @ Wed, 05 Sep 2018 10:37:09: start X-correlation... INFO @ Wed, 05 Sep 2018 10:37:09: #2 number of paired peaks: 182 WARNING @ Wed, 05 Sep 2018 10:37:09: Fewer paired peaks (182) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 182 pairs to build model! INFO @ Wed, 05 Sep 2018 10:37:09: start model_add_line... INFO @ Wed, 05 Sep 2018 10:37:09: start X-correlation... INFO @ Wed, 05 Sep 2018 10:37:09: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 05 Sep 2018 10:37:09: end of X-cor INFO @ Wed, 05 Sep 2018 10:37:09: #2 finished! INFO @ Wed, 05 Sep 2018 10:37:09: #2 predicted fragment length is 223 bps INFO @ Wed, 05 Sep 2018 10:37:09: #2 alternative fragment length(s) may be 87,107,146,174,202,223,243,260,284,298,340,398,415,462,516,557,583 bps INFO @ Wed, 05 Sep 2018 10:37:09: #2.2 Generate R script for model : SRX3709373.10_model.r INFO @ Wed, 05 Sep 2018 10:37:09: end of X-cor INFO @ Wed, 05 Sep 2018 10:37:09: #2 finished! INFO @ Wed, 05 Sep 2018 10:37:09: #2 predicted fragment length is 223 bps INFO @ Wed, 05 Sep 2018 10:37:09: #2 alternative fragment length(s) may be 87,107,146,174,202,223,243,260,284,298,340,398,415,462,516,557,583 bps INFO @ Wed, 05 Sep 2018 10:37:09: #2.2 Generate R script for model : SRX3709373.05_model.r INFO @ Wed, 05 Sep 2018 10:37:09: #3 Call peaks... INFO @ Wed, 05 Sep 2018 10:37:09: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 05 Sep 2018 10:37:09: #3 Call peaks... INFO @ Wed, 05 Sep 2018 10:37:09: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 05 Sep 2018 10:37:10: #3 Call peaks for each chromosome... INFO @ Wed, 05 Sep 2018 10:37:10: #3 Call peaks for each chromosome... INFO @ Wed, 05 Sep 2018 10:37:10: #3 Call peaks for each chromosome... INFO @ Wed, 05 Sep 2018 10:37:10: #4 Write output xls file... SRX3709373.20_peaks.xls INFO @ Wed, 05 Sep 2018 10:37:10: #4 Write peak in narrowPeak format file... SRX3709373.20_peaks.narrowPeak INFO @ Wed, 05 Sep 2018 10:37:10: #4 Write summits bed file... SRX3709373.20_summits.bed INFO @ Wed, 05 Sep 2018 10:37:10: Done! INFO @ Wed, 05 Sep 2018 10:37:10: #4 Write output xls file... SRX3709373.05_peaks.xls INFO @ Wed, 05 Sep 2018 10:37:10: #4 Write peak in narrowPeak format file... SRX3709373.05_peaks.narrowPeak INFO @ Wed, 05 Sep 2018 10:37:10: #4 Write summits bed file... SRX3709373.05_summits.bed INFO @ Wed, 05 Sep 2018 10:37:10: Done! INFO @ Wed, 05 Sep 2018 10:37:10: #4 Write output xls file... SRX3709373.10_peaks.xls INFO @ Wed, 05 Sep 2018 10:37:10: #4 Write peak in narrowPeak format file... SRX3709373.10_peaks.narrowPeak INFO @ Wed, 05 Sep 2018 10:37:10: #4 Write summits bed file... SRX3709373.10_summits.bed INFO @ Wed, 05 Sep 2018 10:37:10: Done! pass1 - making usageList (1 chroms): 6 millis pass2 - checking and writing primary data (1 records, 4 fields): 4 millis pass1 - making usageList (3 chroms): 6 millis pass2 - checking and writing primary data (4 records, 4 fields): 5 millis CompletedMACS2peakCalling CompletedMACS2peakCalling pass1 - making usageList (1 chroms): 2 millis pass2 - checking and writing primary data (1 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。