Job ID = 10937565 sra ファイルのダウンロード中... Completed: 539109K bytes transferred in 26 seconds (167915K bits/sec), in 1 file. Completed: 328041K bytes transferred in 31 seconds (86116K 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 3528490 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3010343/SRR5833346.sra Written 3528490 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3010343/SRR5833346.sra Read 5476996 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3010343/SRR5833345.sra Written 5476996 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3010343/SRR5833345.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: 00:02:43 9005486 reads; of these: 9005486 (100.00%) were paired; of these: 8045043 (89.33%) aligned concordantly 0 times 730409 (8.11%) aligned concordantly exactly 1 time 230034 (2.55%) aligned concordantly >1 times ---- 8045043 pairs aligned concordantly 0 times; of these: 7485 (0.09%) aligned discordantly 1 time ---- 8037558 pairs aligned 0 times concordantly or discordantly; of these: 16075116 mates make up the pairs; of these: 16057000 (99.89%) aligned 0 times 10105 (0.06%) aligned exactly 1 time 8011 (0.05%) aligned >1 times 10.85% overall alignment rate Time searching: 00:02:43 Overall time: 00:02:43 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] 104256 / 967571 = 0.1078 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 02:39:19: # Command line: callpeak -t SRX3010343.bam -f BAM -g 12100000 -n SRX3010343.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3010343.10 # format = BAM # ChIP-seq file = ['SRX3010343.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 02:39:19: #1 read tag files... INFO @ Fri, 10 Aug 2018 02:39:19: #1 read treatment tags... INFO @ Fri, 10 Aug 2018 02:39:19: # Command line: callpeak -t SRX3010343.bam -f BAM -g 12100000 -n SRX3010343.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3010343.05 # format = BAM # ChIP-seq file = ['SRX3010343.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 02:39:19: #1 read tag files... INFO @ Fri, 10 Aug 2018 02:39:19: #1 read treatment tags... INFO @ Fri, 10 Aug 2018 02:39:19: # Command line: callpeak -t SRX3010343.bam -f BAM -g 12100000 -n SRX3010343.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3010343.20 # format = BAM # ChIP-seq file = ['SRX3010343.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 02:39:19: #1 read tag files... INFO @ Fri, 10 Aug 2018 02:39:19: #1 read treatment tags... INFO @ Fri, 10 Aug 2018 02:39:29: 1000000 INFO @ Fri, 10 Aug 2018 02:39:31: 1000000 INFO @ Fri, 10 Aug 2018 02:39:31: 1000000 INFO @ Fri, 10 Aug 2018 02:39:36: #1 tag size is determined as 101 bps INFO @ Fri, 10 Aug 2018 02:39:36: #1 tag size = 101 INFO @ Fri, 10 Aug 2018 02:39:36: #1 total tags in treatment: 856599 INFO @ Fri, 10 Aug 2018 02:39:36: #1 user defined the maximum tags... INFO @ Fri, 10 Aug 2018 02:39:36: #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 02:39:36: #1 tags after filtering in treatment: 672575 INFO @ Fri, 10 Aug 2018 02:39:36: #1 Redundant rate of treatment: 0.21 INFO @ Fri, 10 Aug 2018 02:39:36: #1 finished! INFO @ Fri, 10 Aug 2018 02:39:36: #2 Build Peak Model... INFO @ Fri, 10 Aug 2018 02:39:36: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Aug 2018 02:39:36: #2 number of paired peaks: 259 WARNING @ Fri, 10 Aug 2018 02:39:36: Fewer paired peaks (259) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 259 pairs to build model! INFO @ Fri, 10 Aug 2018 02:39:36: start model_add_line... INFO @ Fri, 10 Aug 2018 02:39:36: start X-correlation... INFO @ Fri, 10 Aug 2018 02:39:36: end of X-cor INFO @ Fri, 10 Aug 2018 02:39:36: #2 finished! INFO @ Fri, 10 Aug 2018 02:39:36: #2 predicted fragment length is 207 bps INFO @ Fri, 10 Aug 2018 02:39:36: #2 alternative fragment length(s) may be 207 bps INFO @ Fri, 10 Aug 2018 02:39:36: #2.2 Generate R script for model : SRX3010343.20_model.r INFO @ Fri, 10 Aug 2018 02:39:36: #3 Call peaks... INFO @ Fri, 10 Aug 2018 02:39:36: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Aug 2018 02:39:39: #3 Call peaks for each chromosome... INFO @ Fri, 10 Aug 2018 02:39:40: #4 Write output xls file... SRX3010343.20_peaks.xls INFO @ Fri, 10 Aug 2018 02:39:40: #4 Write peak in narrowPeak format file... SRX3010343.20_peaks.narrowPeak INFO @ Fri, 10 Aug 2018 02:39:40: #4 Write summits bed file... SRX3010343.20_summits.bed INFO @ Fri, 10 Aug 2018 02:39:40: Done! pass1 - making usageList (17 chroms): 2 millis pass2 - checking and writing primary data (128 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 10 Aug 2018 02:39:40: #1 tag size is determined as 101 bps INFO @ Fri, 10 Aug 2018 02:39:40: #1 tag size = 101 INFO @ Fri, 10 Aug 2018 02:39:40: #1 total tags in treatment: 856599 INFO @ Fri, 10 Aug 2018 02:39:40: #1 user defined the maximum tags... INFO @ Fri, 10 Aug 2018 02:39:40: #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 02:39:40: #1 tag size is determined as 101 bps INFO @ Fri, 10 Aug 2018 02:39:40: #1 tag size = 101 INFO @ Fri, 10 Aug 2018 02:39:40: #1 total tags in treatment: 856599 INFO @ Fri, 10 Aug 2018 02:39:40: #1 user defined the maximum tags... INFO @ Fri, 10 Aug 2018 02:39:40: #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 02:39:40: #1 tags after filtering in treatment: 672575 INFO @ Fri, 10 Aug 2018 02:39:40: #1 Redundant rate of treatment: 0.21 INFO @ Fri, 10 Aug 2018 02:39:40: #1 finished! INFO @ Fri, 10 Aug 2018 02:39:40: #2 Build Peak Model... INFO @ Fri, 10 Aug 2018 02:39:40: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Aug 2018 02:39:40: #1 tags after filtering in treatment: 672575 INFO @ Fri, 10 Aug 2018 02:39:40: #1 Redundant rate of treatment: 0.21 INFO @ Fri, 10 Aug 2018 02:39:40: #1 finished! INFO @ Fri, 10 Aug 2018 02:39:40: #2 Build Peak Model... INFO @ Fri, 10 Aug 2018 02:39:40: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Aug 2018 02:39:40: #2 number of paired peaks: 259 WARNING @ Fri, 10 Aug 2018 02:39:40: Fewer paired peaks (259) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 259 pairs to build model! INFO @ Fri, 10 Aug 2018 02:39:40: start model_add_line... INFO @ Fri, 10 Aug 2018 02:39:40: #2 number of paired peaks: 259 WARNING @ Fri, 10 Aug 2018 02:39:40: Fewer paired peaks (259) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 259 pairs to build model! INFO @ Fri, 10 Aug 2018 02:39:40: start model_add_line... INFO @ Fri, 10 Aug 2018 02:39:40: start X-correlation... INFO @ Fri, 10 Aug 2018 02:39:40: start X-correlation... INFO @ Fri, 10 Aug 2018 02:39:40: end of X-cor INFO @ Fri, 10 Aug 2018 02:39:40: #2 finished! INFO @ Fri, 10 Aug 2018 02:39:40: #2 predicted fragment length is 207 bps INFO @ Fri, 10 Aug 2018 02:39:40: #2 alternative fragment length(s) may be 207 bps INFO @ Fri, 10 Aug 2018 02:39:40: #2.2 Generate R script for model : SRX3010343.10_model.r INFO @ Fri, 10 Aug 2018 02:39:40: end of X-cor INFO @ Fri, 10 Aug 2018 02:39:40: #2 finished! INFO @ Fri, 10 Aug 2018 02:39:40: #2 predicted fragment length is 207 bps INFO @ Fri, 10 Aug 2018 02:39:40: #2 alternative fragment length(s) may be 207 bps INFO @ Fri, 10 Aug 2018 02:39:40: #2.2 Generate R script for model : SRX3010343.05_model.r INFO @ Fri, 10 Aug 2018 02:39:40: #3 Call peaks... INFO @ Fri, 10 Aug 2018 02:39:40: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Aug 2018 02:39:40: #3 Call peaks... INFO @ Fri, 10 Aug 2018 02:39:40: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Aug 2018 02:39:43: #3 Call peaks for each chromosome... INFO @ Fri, 10 Aug 2018 02:39:43: #3 Call peaks for each chromosome... INFO @ Fri, 10 Aug 2018 02:39:44: #4 Write output xls file... SRX3010343.05_peaks.xls INFO @ Fri, 10 Aug 2018 02:39:44: #4 Write output xls file... SRX3010343.10_peaks.xls INFO @ Fri, 10 Aug 2018 02:39:44: #4 Write peak in narrowPeak format file... SRX3010343.10_peaks.narrowPeak INFO @ Fri, 10 Aug 2018 02:39:44: #4 Write peak in narrowPeak format file... SRX3010343.05_peaks.narrowPeak INFO @ Fri, 10 Aug 2018 02:39:44: #4 Write summits bed file... SRX3010343.10_summits.bed INFO @ Fri, 10 Aug 2018 02:39:44: #4 Write summits bed file... SRX3010343.05_summits.bed INFO @ Fri, 10 Aug 2018 02:39:44: Done! INFO @ Fri, 10 Aug 2018 02:39:44: Done! pass1 - making usageList (17 chroms): 2 millis pass2 - checking and writing primary data (175 records, 4 fields): 3 millis pass1 - making usageList (17 chroms): 1 millis CompletedMACS2peakCalling pass2 - checking and writing primary data (241 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。