Job ID = 10937419 sra ファイルのダウンロード中... Completed: 87894K bytes transferred in 4 seconds (171698K 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 1701451 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2198722/SRR4304452.sra Written 1701451 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2198722/SRR4304452.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: 00:02:38 1701451 reads; of these: 1701451 (100.00%) were paired; of these: 912510 (53.63%) aligned concordantly 0 times 254358 (14.95%) aligned concordantly exactly 1 time 534583 (31.42%) aligned concordantly >1 times ---- 912510 pairs aligned concordantly 0 times; of these: 9740 (1.07%) aligned discordantly 1 time ---- 902770 pairs aligned 0 times concordantly or discordantly; of these: 1805540 mates make up the pairs; of these: 1528880 (84.68%) aligned 0 times 73854 (4.09%) aligned exactly 1 time 202806 (11.23%) aligned >1 times 55.07% overall alignment rate Time searching: 00:02:38 Overall time: 00:02:38 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] 10780 / 793928 = 0.0136 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 02:03:12: # Command line: callpeak -t SRX2198722.bam -f BAM -g 12100000 -n SRX2198722.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2198722.05 # format = BAM # ChIP-seq file = ['SRX2198722.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 02:03:12: #1 read tag files... INFO @ Fri, 10 Aug 2018 02:03:12: #1 read treatment tags... INFO @ Fri, 10 Aug 2018 02:03:12: # Command line: callpeak -t SRX2198722.bam -f BAM -g 12100000 -n SRX2198722.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2198722.20 # format = BAM # ChIP-seq file = ['SRX2198722.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 02:03:12: #1 read tag files... INFO @ Fri, 10 Aug 2018 02:03:12: #1 read treatment tags... INFO @ Fri, 10 Aug 2018 02:03:12: # Command line: callpeak -t SRX2198722.bam -f BAM -g 12100000 -n SRX2198722.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2198722.10 # format = BAM # ChIP-seq file = ['SRX2198722.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 02:03:12: #1 read tag files... INFO @ Fri, 10 Aug 2018 02:03:12: #1 read treatment tags... INFO @ Fri, 10 Aug 2018 02:03:18: 1000000 INFO @ Fri, 10 Aug 2018 02:03:18: 1000000 INFO @ Fri, 10 Aug 2018 02:03:20: 1000000 INFO @ Fri, 10 Aug 2018 02:03:23: #1 tag size is determined as 39 bps INFO @ Fri, 10 Aug 2018 02:03:23: #1 tag size = 39 INFO @ Fri, 10 Aug 2018 02:03:23: #1 total tags in treatment: 778173 INFO @ Fri, 10 Aug 2018 02:03:23: #1 user defined the maximum tags... INFO @ Fri, 10 Aug 2018 02:03:23: #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 02:03:23: #1 tag size is determined as 39 bps INFO @ Fri, 10 Aug 2018 02:03:23: #1 tag size = 39 INFO @ Fri, 10 Aug 2018 02:03:23: #1 total tags in treatment: 778173 INFO @ Fri, 10 Aug 2018 02:03:23: #1 user defined the maximum tags... INFO @ Fri, 10 Aug 2018 02:03:23: #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 02:03:23: #1 tags after filtering in treatment: 520550 INFO @ Fri, 10 Aug 2018 02:03:23: #1 Redundant rate of treatment: 0.33 INFO @ Fri, 10 Aug 2018 02:03:23: #1 finished! INFO @ Fri, 10 Aug 2018 02:03:23: #2 Build Peak Model... INFO @ Fri, 10 Aug 2018 02:03:23: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Aug 2018 02:03:23: #1 tags after filtering in treatment: 520550 INFO @ Fri, 10 Aug 2018 02:03:23: #1 Redundant rate of treatment: 0.33 INFO @ Fri, 10 Aug 2018 02:03:23: #1 finished! INFO @ Fri, 10 Aug 2018 02:03:23: #2 Build Peak Model... INFO @ Fri, 10 Aug 2018 02:03:23: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Aug 2018 02:03:23: #2 number of paired peaks: 444 WARNING @ Fri, 10 Aug 2018 02:03:23: Fewer paired peaks (444) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 444 pairs to build model! INFO @ Fri, 10 Aug 2018 02:03:23: start model_add_line... INFO @ Fri, 10 Aug 2018 02:03:23: #2 number of paired peaks: 444 WARNING @ Fri, 10 Aug 2018 02:03:23: Fewer paired peaks (444) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 444 pairs to build model! INFO @ Fri, 10 Aug 2018 02:03:23: start model_add_line... INFO @ Fri, 10 Aug 2018 02:03:23: start X-correlation... INFO @ Fri, 10 Aug 2018 02:03:23: start X-correlation... INFO @ Fri, 10 Aug 2018 02:03:23: end of X-cor INFO @ Fri, 10 Aug 2018 02:03:23: #2 finished! INFO @ Fri, 10 Aug 2018 02:03:23: end of X-cor INFO @ Fri, 10 Aug 2018 02:03:23: #2 predicted fragment length is 100 bps INFO @ Fri, 10 Aug 2018 02:03:23: #2 finished! INFO @ Fri, 10 Aug 2018 02:03:23: #2 alternative fragment length(s) may be 3,100,533,553 bps INFO @ Fri, 10 Aug 2018 02:03:23: #2.2 Generate R script for model : SRX2198722.05_model.r INFO @ Fri, 10 Aug 2018 02:03:23: #2 predicted fragment length is 100 bps INFO @ Fri, 10 Aug 2018 02:03:23: #2 alternative fragment length(s) may be 3,100,533,553 bps INFO @ Fri, 10 Aug 2018 02:03:23: #2.2 Generate R script for model : SRX2198722.20_model.r INFO @ Fri, 10 Aug 2018 02:03:23: #3 Call peaks... INFO @ Fri, 10 Aug 2018 02:03:23: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Aug 2018 02:03:23: #3 Call peaks... INFO @ Fri, 10 Aug 2018 02:03:23: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Aug 2018 02:03:26: #3 Call peaks for each chromosome... INFO @ Fri, 10 Aug 2018 02:03:26: #3 Call peaks for each chromosome... INFO @ Fri, 10 Aug 2018 02:03:26: #1 tag size is determined as 39 bps INFO @ Fri, 10 Aug 2018 02:03:26: #1 tag size = 39 INFO @ Fri, 10 Aug 2018 02:03:26: #1 total tags in treatment: 778173 INFO @ Fri, 10 Aug 2018 02:03:26: #1 user defined the maximum tags... INFO @ Fri, 10 Aug 2018 02:03:26: #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 02:03:26: #1 tags after filtering in treatment: 520550 INFO @ Fri, 10 Aug 2018 02:03:26: #1 Redundant rate of treatment: 0.33 INFO @ Fri, 10 Aug 2018 02:03:26: #1 finished! INFO @ Fri, 10 Aug 2018 02:03:26: #2 Build Peak Model... INFO @ Fri, 10 Aug 2018 02:03:26: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Aug 2018 02:03:26: #4 Write output xls file... SRX2198722.20_peaks.xls INFO @ Fri, 10 Aug 2018 02:03:26: #4 Write peak in narrowPeak format file... SRX2198722.20_peaks.narrowPeak INFO @ Fri, 10 Aug 2018 02:03:26: #4 Write summits bed file... SRX2198722.20_summits.bed INFO @ Fri, 10 Aug 2018 02:03:26: Done! INFO @ Fri, 10 Aug 2018 02:03:26: #4 Write output xls file... SRX2198722.05_peaks.xls INFO @ Fri, 10 Aug 2018 02:03:26: #4 Write peak in narrowPeak format file... SRX2198722.05_peaks.narrowPeak INFO @ Fri, 10 Aug 2018 02:03:26: #4 Write summits bed file... SRX2198722.05_summits.bed INFO @ Fri, 10 Aug 2018 02:03:26: Done! pass1 - making usageList (16 chroms): 2 millis pass2 - checking and writing primary data (102 records, 4 fields): 2 millis CompletedMACS2peakCalling pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (226 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 10 Aug 2018 02:03:26: #2 number of paired peaks: 444 WARNING @ Fri, 10 Aug 2018 02:03:26: Fewer paired peaks (444) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 444 pairs to build model! INFO @ Fri, 10 Aug 2018 02:03:26: start model_add_line... INFO @ Fri, 10 Aug 2018 02:03:26: start X-correlation... INFO @ Fri, 10 Aug 2018 02:03:26: end of X-cor INFO @ Fri, 10 Aug 2018 02:03:26: #2 finished! INFO @ Fri, 10 Aug 2018 02:03:26: #2 predicted fragment length is 100 bps INFO @ Fri, 10 Aug 2018 02:03:26: #2 alternative fragment length(s) may be 3,100,533,553 bps INFO @ Fri, 10 Aug 2018 02:03:26: #2.2 Generate R script for model : SRX2198722.10_model.r INFO @ Fri, 10 Aug 2018 02:03:26: #3 Call peaks... INFO @ Fri, 10 Aug 2018 02:03:26: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Aug 2018 02:03:29: #3 Call peaks for each chromosome... INFO @ Fri, 10 Aug 2018 02:03:29: #4 Write output xls file... SRX2198722.10_peaks.xls INFO @ Fri, 10 Aug 2018 02:03:29: #4 Write peak in narrowPeak format file... SRX2198722.10_peaks.narrowPeak INFO @ Fri, 10 Aug 2018 02:03:29: #4 Write summits bed file... SRX2198722.10_summits.bed INFO @ Fri, 10 Aug 2018 02:03:29: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (166 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。