Job ID = 10536342 sra ファイルのダウンロード中... Completed: 786232K bytes transferred in 62 seconds (103104K 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 20543603 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3433209/SRR6333850.sra Written 20543603 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: 00:11:37 20543603 reads; of these: 20543603 (100.00%) were paired; of these: 7413215 (36.09%) aligned concordantly 0 times 11872667 (57.79%) aligned concordantly exactly 1 time 1257721 (6.12%) aligned concordantly >1 times ---- 7413215 pairs aligned concordantly 0 times; of these: 84448 (1.14%) aligned discordantly 1 time ---- 7328767 pairs aligned 0 times concordantly or discordantly; of these: 14657534 mates make up the pairs; of these: 14291520 (97.50%) aligned 0 times 311138 (2.12%) aligned exactly 1 time 54876 (0.37%) aligned >1 times 65.22% overall alignment rate Time searching: 00:11:37 Overall time: 00:11:37 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] 9542842 / 13138558 = 0.7263 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 08:58:55: # Command line: callpeak -t SRX3433209.bam -f BAM -g 12100000 -n SRX3433209.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3433209.10 # format = BAM # ChIP-seq file = ['SRX3433209.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 08:58:55: #1 read tag files... INFO @ Thu, 05 Apr 2018 08:58:55: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 08:58:55: # Command line: callpeak -t SRX3433209.bam -f BAM -g 12100000 -n SRX3433209.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3433209.05 # format = BAM # ChIP-seq file = ['SRX3433209.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 08:58:55: #1 read tag files... INFO @ Thu, 05 Apr 2018 08:58:55: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 08:58:55: # Command line: callpeak -t SRX3433209.bam -f BAM -g 12100000 -n SRX3433209.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3433209.20 # format = BAM # ChIP-seq file = ['SRX3433209.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 08:58:55: #1 read tag files... INFO @ Thu, 05 Apr 2018 08:58:55: #1 read treatment tags... INFO @ Thu, 05 Apr 2018 08:59:00: 1000000 INFO @ Thu, 05 Apr 2018 08:59:00: 1000000 INFO @ Thu, 05 Apr 2018 08:59:00: 1000000 INFO @ Thu, 05 Apr 2018 08:59:06: 2000000 INFO @ Thu, 05 Apr 2018 08:59:06: 2000000 INFO @ Thu, 05 Apr 2018 08:59:06: 2000000 INFO @ Thu, 05 Apr 2018 08:59:12: 3000000 INFO @ Thu, 05 Apr 2018 08:59:12: 3000000 INFO @ Thu, 05 Apr 2018 08:59:12: 3000000 INFO @ Thu, 05 Apr 2018 08:59:18: 4000000 INFO @ Thu, 05 Apr 2018 08:59:19: 4000000 INFO @ Thu, 05 Apr 2018 08:59:19: 4000000 INFO @ Thu, 05 Apr 2018 08:59:23: 5000000 INFO @ Thu, 05 Apr 2018 08:59:25: 5000000 INFO @ Thu, 05 Apr 2018 08:59:25: 5000000 INFO @ Thu, 05 Apr 2018 08:59:29: 6000000 INFO @ Thu, 05 Apr 2018 08:59:31: 6000000 INFO @ Thu, 05 Apr 2018 08:59:31: 6000000 INFO @ Thu, 05 Apr 2018 08:59:34: 7000000 INFO @ Thu, 05 Apr 2018 08:59:37: 7000000 INFO @ Thu, 05 Apr 2018 08:59:37: 7000000 INFO @ Thu, 05 Apr 2018 08:59:38: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 08:59:38: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 08:59:38: #1 total tags in treatment: 3592787 INFO @ Thu, 05 Apr 2018 08:59:38: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 08:59:38: #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 08:59:38: #1 tags after filtering in treatment: 2967185 INFO @ Thu, 05 Apr 2018 08:59:38: #1 Redundant rate of treatment: 0.17 INFO @ Thu, 05 Apr 2018 08:59:38: #1 finished! INFO @ Thu, 05 Apr 2018 08:59:38: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 08:59:38: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 08:59:38: #2 number of paired peaks: 112 WARNING @ Thu, 05 Apr 2018 08:59:38: Fewer paired peaks (112) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 112 pairs to build model! INFO @ Thu, 05 Apr 2018 08:59:38: start model_add_line... INFO @ Thu, 05 Apr 2018 08:59:38: start X-correlation... INFO @ Thu, 05 Apr 2018 08:59:38: end of X-cor INFO @ Thu, 05 Apr 2018 08:59:38: #2 finished! INFO @ Thu, 05 Apr 2018 08:59:38: #2 predicted fragment length is 148 bps INFO @ Thu, 05 Apr 2018 08:59:38: #2 alternative fragment length(s) may be 3,106,143,148,176 bps INFO @ Thu, 05 Apr 2018 08:59:38: #2.2 Generate R script for model : SRX3433209.05_model.r INFO @ Thu, 05 Apr 2018 08:59:38: #3 Call peaks... INFO @ Thu, 05 Apr 2018 08:59:39: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Apr 2018 08:59:41: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 08:59:41: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 08:59:41: #1 total tags in treatment: 3592787 INFO @ Thu, 05 Apr 2018 08:59:41: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 08:59:41: #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 08:59:41: #1 tag size is determined as 50 bps INFO @ Thu, 05 Apr 2018 08:59:41: #1 tag size = 50 INFO @ Thu, 05 Apr 2018 08:59:41: #1 total tags in treatment: 3592787 INFO @ Thu, 05 Apr 2018 08:59:41: #1 user defined the maximum tags... INFO @ Thu, 05 Apr 2018 08:59:41: #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 08:59:41: #1 tags after filtering in treatment: 2967185 INFO @ Thu, 05 Apr 2018 08:59:41: #1 Redundant rate of treatment: 0.17 INFO @ Thu, 05 Apr 2018 08:59:41: #1 finished! INFO @ Thu, 05 Apr 2018 08:59:41: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 08:59:41: #1 tags after filtering in treatment: 2967185 INFO @ Thu, 05 Apr 2018 08:59:41: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 08:59:41: #1 Redundant rate of treatment: 0.17 INFO @ Thu, 05 Apr 2018 08:59:41: #1 finished! INFO @ Thu, 05 Apr 2018 08:59:41: #2 Build Peak Model... INFO @ Thu, 05 Apr 2018 08:59:41: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Apr 2018 08:59:41: #2 number of paired peaks: 112 WARNING @ Thu, 05 Apr 2018 08:59:41: Fewer paired peaks (112) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 112 pairs to build model! INFO @ Thu, 05 Apr 2018 08:59:41: start model_add_line... INFO @ Thu, 05 Apr 2018 08:59:41: #2 number of paired peaks: 112 WARNING @ Thu, 05 Apr 2018 08:59:41: Fewer paired peaks (112) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 112 pairs to build model! INFO @ Thu, 05 Apr 2018 08:59:41: start model_add_line... INFO @ Thu, 05 Apr 2018 08:59:41: start X-correlation... INFO @ Thu, 05 Apr 2018 08:59:41: end of X-cor INFO @ Thu, 05 Apr 2018 08:59:41: #2 finished! INFO @ Thu, 05 Apr 2018 08:59:41: #2 predicted fragment length is 148 bps INFO @ Thu, 05 Apr 2018 08:59:41: #2 alternative fragment length(s) may be 3,106,143,148,176 bps INFO @ Thu, 05 Apr 2018 08:59:41: #2.2 Generate R script for model : SRX3433209.20_model.r INFO @ Thu, 05 Apr 2018 08:59:41: #3 Call peaks... INFO @ Thu, 05 Apr 2018 08:59:41: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Apr 2018 08:59:41: start X-correlation... INFO @ Thu, 05 Apr 2018 08:59:41: end of X-cor INFO @ Thu, 05 Apr 2018 08:59:41: #2 finished! INFO @ Thu, 05 Apr 2018 08:59:41: #2 predicted fragment length is 148 bps INFO @ Thu, 05 Apr 2018 08:59:41: #2 alternative fragment length(s) may be 3,106,143,148,176 bps INFO @ Thu, 05 Apr 2018 08:59:41: #2.2 Generate R script for model : SRX3433209.10_model.r INFO @ Thu, 05 Apr 2018 08:59:41: #3 Call peaks... INFO @ Thu, 05 Apr 2018 08:59:41: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Apr 2018 08:59:48: #3 Call peaks for each chromosome... INFO @ Thu, 05 Apr 2018 08:59:51: #3 Call peaks for each chromosome... INFO @ Thu, 05 Apr 2018 08:59:51: #3 Call peaks for each chromosome... INFO @ Thu, 05 Apr 2018 08:59:51: #4 Write output xls file... SRX3433209.05_peaks.xls INFO @ Thu, 05 Apr 2018 08:59:51: #4 Write peak in narrowPeak format file... SRX3433209.05_peaks.narrowPeak INFO @ Thu, 05 Apr 2018 08:59:51: #4 Write summits bed file... SRX3433209.05_summits.bed INFO @ Thu, 05 Apr 2018 08:59:51: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (1198 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 05 Apr 2018 08:59:54: #4 Write output xls file... SRX3433209.10_peaks.xls INFO @ Thu, 05 Apr 2018 08:59:54: #4 Write peak in narrowPeak format file... SRX3433209.10_peaks.narrowPeak INFO @ Thu, 05 Apr 2018 08:59:54: #4 Write summits bed file... SRX3433209.10_summits.bed INFO @ Thu, 05 Apr 2018 08:59:54: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (730 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 05 Apr 2018 08:59:54: #4 Write output xls file... SRX3433209.20_peaks.xls INFO @ Thu, 05 Apr 2018 08:59:54: #4 Write peak in narrowPeak format file... SRX3433209.20_peaks.narrowPeak INFO @ Thu, 05 Apr 2018 08:59:55: #4 Write summits bed file... SRX3433209.20_summits.bed INFO @ Thu, 05 Apr 2018 08:59:55: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (398 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。