Job ID = 10536335 sra ファイルのダウンロード中... Completed: 1399751K bytes transferred in 26 seconds (432720K 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 22559478 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3433202/SRR6333843.sra Written 22559478 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: 00:12:51 22559478 reads; of these: 22559478 (100.00%) were paired; of these: 8299108 (36.79%) aligned concordantly 0 times 12407536 (55.00%) aligned concordantly exactly 1 time 1852834 (8.21%) aligned concordantly >1 times ---- 8299108 pairs aligned concordantly 0 times; of these: 15782 (0.19%) aligned discordantly 1 time ---- 8283326 pairs aligned 0 times concordantly or discordantly; of these: 16566652 mates make up the pairs; of these: 15895729 (95.95%) aligned 0 times 565721 (3.41%) aligned exactly 1 time 105202 (0.64%) aligned >1 times 64.77% overall alignment rate Time searching: 00:12:51 Overall time: 00:12:51 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] 13681592 / 14266707 = 0.9590 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 08:57:28: # Command line: callpeak -t SRX3433202.bam -f BAM -g 12100000 -n SRX3433202.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3433202.20 # format = BAM # ChIP-seq file = ['SRX3433202.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 08:57:28: #1 read tag files... INFO @ Thu, 05 Apr 2018 08:57:28: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 08:57:28: # Command line: callpeak -t SRX3433202.bam -f BAM -g 12100000 -n SRX3433202.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3433202.10 # format = BAM # ChIP-seq file = ['SRX3433202.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 08:57:28: #1 read tag files... INFO @ Thu, 05 Apr 2018 08:57:28: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 08:57:28: # Command line: callpeak -t SRX3433202.bam -f BAM -g 12100000 -n SRX3433202.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3433202.05 # format = BAM # ChIP-seq file = ['SRX3433202.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 08:57:28: #1 read tag files... INFO @ Thu, 05 Apr 2018 08:57:28: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 08:57:33: 1000000 INFO @ Thu, 05 Apr 2018 08:57:33: 1000000 INFO @ Thu, 05 Apr 2018 08:57:34: 1000000 INFO @ Thu, 05 Apr 2018 08:57:38: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 08:57:38: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 08:57:38: #1 total tags in treatment: 584952 INFO @ Thu, 05 Apr 2018 08:57:38: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 08:57:38: #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 08:57:38: #1 tags after filtering in treatment: 537455 INFO @ Thu, 05 Apr 2018 08:57:38: #1 Redundant rate of treatment: 0.08 INFO @ Thu, 05 Apr 2018 08:57:38: #1 finished! INFO @ Thu, 05 Apr 2018 08:57:38: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 08:57:38: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 08:57:38: #2 number of paired peaks: 205 WARNING @ Thu, 05 Apr 2018 08:57:38: Fewer paired peaks (205) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 205 pairs to build model! INFO @ Thu, 05 Apr 2018 08:57:38: start model_add_line... INFO @ Thu, 05 Apr 2018 08:57:38: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 08:57:38: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 08:57:38: #1 total tags in treatment: 584952 INFO @ Thu, 05 Apr 2018 08:57:38: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 08:57:38: #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 08:57:38: start X-correlation... INFO @ Thu, 05 Apr 2018 08:57:38: end of X-cor INFO @ Thu, 05 Apr 2018 08:57:38: #2 finished! INFO @ Thu, 05 Apr 2018 08:57:38: #2 predicted fragment length is 187 bps INFO @ Thu, 05 Apr 2018 08:57:38: #2 alternative fragment length(s) may be 38,85,118,141,187,231,264,291,303,428,451,520,561,582 bps INFO @ Thu, 05 Apr 2018 08:57:38: #2.2 Generate R script for model : SRX3433202.05_model.r INFO @ Thu, 05 Apr 2018 08:57:38: #1 tags after filtering in treatment: 537455 INFO @ Thu, 05 Apr 2018 08:57:38: #1 Redundant rate of treatment: 0.08 INFO @ Thu, 05 Apr 2018 08:57:38: #1 finished! INFO @ Thu, 05 Apr 2018 08:57:38: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 08:57:38: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 08:57:38: #3 Call peaks... INFO @ Thu, 05 Apr 2018 08:57:38: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Apr 2018 08:57:38: #2 number of paired peaks: 205 WARNING @ Thu, 05 Apr 2018 08:57:38: Fewer paired peaks (205) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 205 pairs to build model! INFO @ Thu, 05 Apr 2018 08:57:38: start model_add_line... INFO @ Thu, 05 Apr 2018 08:57:38: start X-correlation... INFO @ Thu, 05 Apr 2018 08:57:38: end of X-cor INFO @ Thu, 05 Apr 2018 08:57:38: #2 finished! INFO @ Thu, 05 Apr 2018 08:57:38: #2 predicted fragment length is 187 bps INFO @ Thu, 05 Apr 2018 08:57:38: #2 alternative fragment length(s) may be 38,85,118,141,187,231,264,291,303,428,451,520,561,582 bps INFO @ Thu, 05 Apr 2018 08:57:38: #2.2 Generate R script for model : SRX3433202.20_model.r INFO @ Thu, 05 Apr 2018 08:57:38: #3 Call peaks... INFO @ Thu, 05 Apr 2018 08:57:38: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Apr 2018 08:57:38: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 08:57:38: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 08:57:38: #1 total tags in treatment: 584952 INFO @ Thu, 05 Apr 2018 08:57:38: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 08:57:38: #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 08:57:38: #1 tags after filtering in treatment: 537455 INFO @ Thu, 05 Apr 2018 08:57:38: #1 Redundant rate of treatment: 0.08 INFO @ Thu, 05 Apr 2018 08:57:38: #1 finished! INFO @ Thu, 05 Apr 2018 08:57:38: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 08:57:38: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 08:57:38: #2 number of paired peaks: 205 WARNING @ Thu, 05 Apr 2018 08:57:38: Fewer paired peaks (205) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 205 pairs to build model! INFO @ Thu, 05 Apr 2018 08:57:38: start model_add_line... INFO @ Thu, 05 Apr 2018 08:57:38: start X-correlation... INFO @ Thu, 05 Apr 2018 08:57:38: end of X-cor INFO @ Thu, 05 Apr 2018 08:57:38: #2 finished! INFO @ Thu, 05 Apr 2018 08:57:38: #2 predicted fragment length is 187 bps INFO @ Thu, 05 Apr 2018 08:57:38: #2 alternative fragment length(s) may be 38,85,118,141,187,231,264,291,303,428,451,520,561,582 bps INFO @ Thu, 05 Apr 2018 08:57:38: #2.2 Generate R script for model : SRX3433202.10_model.r INFO @ Thu, 05 Apr 2018 08:57:38: #3 Call peaks... INFO @ Thu, 05 Apr 2018 08:57:38: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Apr 2018 08:57:40: #3 Call peaks for each chromosome... INFO @ Thu, 05 Apr 2018 08:57:40: #3 Call peaks for each chromosome... INFO @ Thu, 05 Apr 2018 08:57:40: #3 Call peaks for each chromosome... INFO @ Thu, 05 Apr 2018 08:57:40: #4 Write output xls file... SRX3433202.05_peaks.xls INFO @ Thu, 05 Apr 2018 08:57:40: #4 Write peak in narrowPeak format file... SRX3433202.05_peaks.narrowPeak INFO @ Thu, 05 Apr 2018 08:57:40: #4 Write summits bed file... SRX3433202.05_summits.bed INFO @ Thu, 05 Apr 2018 08:57:40: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (88 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 05 Apr 2018 08:57:41: #4 Write output xls file... SRX3433202.20_peaks.xls INFO @ Thu, 05 Apr 2018 08:57:41: #4 Write peak in narrowPeak format file... SRX3433202.20_peaks.narrowPeak INFO @ Thu, 05 Apr 2018 08:57:41: #4 Write summits bed file... SRX3433202.20_summits.bed INFO @ Thu, 05 Apr 2018 08:57:41: Done! pass1 - making usageList (3 chroms): 0 millis pass2 - checking and writing primary data (5 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 05 Apr 2018 08:57:41: #4 Write output xls file... SRX3433202.10_peaks.xls INFO @ Thu, 05 Apr 2018 08:57:41: #4 Write peak in narrowPeak format file... SRX3433202.10_peaks.narrowPeak INFO @ Thu, 05 Apr 2018 08:57:41: #4 Write summits bed file... SRX3433202.10_summits.bed INFO @ Thu, 05 Apr 2018 08:57:41: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (13 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。