Job ID = 10937499 sra ファイルのダウンロード中... Completed: 401074K bytes transferred in 23 seconds (141894K 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 4153883 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3010307/SRR5833300.sra Written 4153883 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3010307/SRR5833300.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:05:16 4153883 reads; of these: 4153883 (100.00%) were paired; of these: 426180 (10.26%) aligned concordantly 0 times 3177987 (76.51%) aligned concordantly exactly 1 time 549716 (13.23%) aligned concordantly >1 times ---- 426180 pairs aligned concordantly 0 times; of these: 70042 (16.43%) aligned discordantly 1 time ---- 356138 pairs aligned 0 times concordantly or discordantly; of these: 712276 mates make up the pairs; of these: 574040 (80.59%) aligned 0 times 92238 (12.95%) aligned exactly 1 time 45998 (6.46%) aligned >1 times 93.09% overall alignment rate Time searching: 00:05:17 Overall time: 00:05:17 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] 75847 / 3756218 = 0.0202 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 02:31:02: # Command line: callpeak -t SRX3010307.bam -f BAM -g 12100000 -n SRX3010307.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3010307.10 # format = BAM # ChIP-seq file = ['SRX3010307.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 02:31:02: #1 read tag files... INFO @ Fri, 10 Aug 2018 02:31:02: #1 read treatment tags... INFO @ Fri, 10 Aug 2018 02:31:02: # Command line: callpeak -t SRX3010307.bam -f BAM -g 12100000 -n SRX3010307.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3010307.05 # format = BAM # ChIP-seq file = ['SRX3010307.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 02:31:02: #1 read tag files... INFO @ Fri, 10 Aug 2018 02:31:02: #1 read treatment tags... INFO @ Fri, 10 Aug 2018 02:31:02: # Command line: callpeak -t SRX3010307.bam -f BAM -g 12100000 -n SRX3010307.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3010307.20 # format = BAM # ChIP-seq file = ['SRX3010307.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 02:31:02: #1 read tag files... INFO @ Fri, 10 Aug 2018 02:31:02: #1 read treatment tags... INFO @ Fri, 10 Aug 2018 02:31:09: 1000000 INFO @ Fri, 10 Aug 2018 02:31:09: 1000000 INFO @ Fri, 10 Aug 2018 02:31:10: 1000000 INFO @ Fri, 10 Aug 2018 02:31:15: 2000000 INFO @ Fri, 10 Aug 2018 02:31:16: 2000000 INFO @ Fri, 10 Aug 2018 02:31:18: 2000000 INFO @ Fri, 10 Aug 2018 02:31:22: 3000000 INFO @ Fri, 10 Aug 2018 02:31:22: 3000000 INFO @ Fri, 10 Aug 2018 02:31:26: 3000000 INFO @ Fri, 10 Aug 2018 02:31:28: 4000000 INFO @ Fri, 10 Aug 2018 02:31:29: 4000000 INFO @ Fri, 10 Aug 2018 02:31:34: 4000000 INFO @ Fri, 10 Aug 2018 02:31:35: 5000000 INFO @ Fri, 10 Aug 2018 02:31:35: 5000000 INFO @ Fri, 10 Aug 2018 02:31:41: 6000000 INFO @ Fri, 10 Aug 2018 02:31:42: 5000000 INFO @ Fri, 10 Aug 2018 02:31:42: 6000000 INFO @ Fri, 10 Aug 2018 02:31:48: 7000000 INFO @ Fri, 10 Aug 2018 02:31:49: 7000000 INFO @ Fri, 10 Aug 2018 02:31:50: 6000000 INFO @ Fri, 10 Aug 2018 02:31:52: #1 tag size is determined as 101 bps INFO @ Fri, 10 Aug 2018 02:31:52: #1 tag size = 101 INFO @ Fri, 10 Aug 2018 02:31:52: #1 total tags in treatment: 3652067 INFO @ Fri, 10 Aug 2018 02:31:52: #1 user defined the maximum tags... INFO @ Fri, 10 Aug 2018 02:31:52: #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 02:31:52: #1 tags after filtering in treatment: 2902855 INFO @ Fri, 10 Aug 2018 02:31:52: #1 Redundant rate of treatment: 0.21 INFO @ Fri, 10 Aug 2018 02:31:52: #1 finished! INFO @ Fri, 10 Aug 2018 02:31:52: #2 Build Peak Model... INFO @ Fri, 10 Aug 2018 02:31:52: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Aug 2018 02:31:52: #2 number of paired peaks: 157 WARNING @ Fri, 10 Aug 2018 02:31:52: Fewer paired peaks (157) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 157 pairs to build model! INFO @ Fri, 10 Aug 2018 02:31:52: start model_add_line... INFO @ Fri, 10 Aug 2018 02:31:52: start X-correlation... INFO @ Fri, 10 Aug 2018 02:31:52: end of X-cor INFO @ Fri, 10 Aug 2018 02:31:52: #2 finished! INFO @ Fri, 10 Aug 2018 02:31:52: #2 predicted fragment length is 217 bps INFO @ Fri, 10 Aug 2018 02:31:52: #2 alternative fragment length(s) may be 0,130,160,195,217,230,560,587 bps INFO @ Fri, 10 Aug 2018 02:31:52: #2.2 Generate R script for model : SRX3010307.20_model.r INFO @ Fri, 10 Aug 2018 02:31:52: #3 Call peaks... INFO @ Fri, 10 Aug 2018 02:31:52: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Aug 2018 02:31:53: #1 tag size is determined as 101 bps INFO @ Fri, 10 Aug 2018 02:31:53: #1 tag size = 101 INFO @ Fri, 10 Aug 2018 02:31:53: #1 total tags in treatment: 3652067 INFO @ Fri, 10 Aug 2018 02:31:53: #1 user defined the maximum tags... INFO @ Fri, 10 Aug 2018 02:31:53: #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 02:31:53: #1 tags after filtering in treatment: 2902855 INFO @ Fri, 10 Aug 2018 02:31:53: #1 Redundant rate of treatment: 0.21 INFO @ Fri, 10 Aug 2018 02:31:53: #1 finished! INFO @ Fri, 10 Aug 2018 02:31:53: #2 Build Peak Model... INFO @ Fri, 10 Aug 2018 02:31:53: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Aug 2018 02:31:53: #2 number of paired peaks: 157 WARNING @ Fri, 10 Aug 2018 02:31:53: Fewer paired peaks (157) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 157 pairs to build model! INFO @ Fri, 10 Aug 2018 02:31:53: start model_add_line... INFO @ Fri, 10 Aug 2018 02:31:53: start X-correlation... INFO @ Fri, 10 Aug 2018 02:31:53: end of X-cor INFO @ Fri, 10 Aug 2018 02:31:53: #2 finished! INFO @ Fri, 10 Aug 2018 02:31:53: #2 predicted fragment length is 217 bps INFO @ Fri, 10 Aug 2018 02:31:53: #2 alternative fragment length(s) may be 0,130,160,195,217,230,560,587 bps INFO @ Fri, 10 Aug 2018 02:31:53: #2.2 Generate R script for model : SRX3010307.10_model.r INFO @ Fri, 10 Aug 2018 02:31:53: #3 Call peaks... INFO @ Fri, 10 Aug 2018 02:31:53: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Aug 2018 02:31:58: 7000000 INFO @ Fri, 10 Aug 2018 02:31:59: #3 Call peaks for each chromosome... INFO @ Fri, 10 Aug 2018 02:31:59: #3 Call peaks for each chromosome... INFO @ Fri, 10 Aug 2018 02:32:01: #4 Write output xls file... SRX3010307.20_peaks.xls INFO @ Fri, 10 Aug 2018 02:32:01: #4 Write peak in narrowPeak format file... SRX3010307.20_peaks.narrowPeak INFO @ Fri, 10 Aug 2018 02:32:01: #4 Write summits bed file... SRX3010307.20_summits.bed INFO @ Fri, 10 Aug 2018 02:32:01: Done! pass1 - making usageList (5 chroms): 2 millis pass2 - checking and writing primary data (9 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 10 Aug 2018 02:32:02: #4 Write output xls file... SRX3010307.10_peaks.xls INFO @ Fri, 10 Aug 2018 02:32:02: #4 Write peak in narrowPeak format file... SRX3010307.10_peaks.narrowPeak INFO @ Fri, 10 Aug 2018 02:32:02: #4 Write summits bed file... SRX3010307.10_summits.bed INFO @ Fri, 10 Aug 2018 02:32:02: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (14 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 10 Aug 2018 02:32:02: #1 tag size is determined as 101 bps INFO @ Fri, 10 Aug 2018 02:32:02: #1 tag size = 101 INFO @ Fri, 10 Aug 2018 02:32:02: #1 total tags in treatment: 3652067 INFO @ Fri, 10 Aug 2018 02:32:02: #1 user defined the maximum tags... INFO @ Fri, 10 Aug 2018 02:32:02: #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 02:32:02: #1 tags after filtering in treatment: 2902855 INFO @ Fri, 10 Aug 2018 02:32:02: #1 Redundant rate of treatment: 0.21 INFO @ Fri, 10 Aug 2018 02:32:02: #1 finished! INFO @ Fri, 10 Aug 2018 02:32:02: #2 Build Peak Model... INFO @ Fri, 10 Aug 2018 02:32:02: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Aug 2018 02:32:03: #2 number of paired peaks: 157 WARNING @ Fri, 10 Aug 2018 02:32:03: Fewer paired peaks (157) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 157 pairs to build model! INFO @ Fri, 10 Aug 2018 02:32:03: start model_add_line... INFO @ Fri, 10 Aug 2018 02:32:03: start X-correlation... INFO @ Fri, 10 Aug 2018 02:32:03: end of X-cor INFO @ Fri, 10 Aug 2018 02:32:03: #2 finished! INFO @ Fri, 10 Aug 2018 02:32:03: #2 predicted fragment length is 217 bps INFO @ Fri, 10 Aug 2018 02:32:03: #2 alternative fragment length(s) may be 0,130,160,195,217,230,560,587 bps INFO @ Fri, 10 Aug 2018 02:32:03: #2.2 Generate R script for model : SRX3010307.05_model.r INFO @ Fri, 10 Aug 2018 02:32:03: #3 Call peaks... INFO @ Fri, 10 Aug 2018 02:32:03: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Aug 2018 02:32:10: #3 Call peaks for each chromosome... INFO @ Fri, 10 Aug 2018 02:32:12: #4 Write output xls file... SRX3010307.05_peaks.xls INFO @ Fri, 10 Aug 2018 02:32:12: #4 Write peak in narrowPeak format file... SRX3010307.05_peaks.narrowPeak INFO @ Fri, 10 Aug 2018 02:32:12: #4 Write summits bed file... SRX3010307.05_summits.bed INFO @ Fri, 10 Aug 2018 02:32:12: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (39 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。