Job ID = 11245020 sra ファイルのダウンロード中... Completed: 240886K bytes transferred in 6 seconds (286599K 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 7719704 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4554733/SRR7696405.sra Written 7719704 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4554733/SRR7696405.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: 00:03:36 7719704 reads; of these: 7719704 (100.00%) were paired; of these: 5282055 (68.42%) aligned concordantly 0 times 2141935 (27.75%) aligned concordantly exactly 1 time 295714 (3.83%) aligned concordantly >1 times ---- 5282055 pairs aligned concordantly 0 times; of these: 5994 (0.11%) aligned discordantly 1 time ---- 5276061 pairs aligned 0 times concordantly or discordantly; of these: 10552122 mates make up the pairs; of these: 8597069 (81.47%) aligned 0 times 1700162 (16.11%) aligned exactly 1 time 254891 (2.42%) aligned >1 times 44.32% overall alignment rate Time searching: 00:03:36 Overall time: 00:03:36 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] 320510 / 2442936 = 0.1312 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 @ Tue, 09 Oct 2018 23:14:46: # Command line: callpeak -t SRX4554733.bam -f BAM -g 12100000 -n SRX4554733.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4554733.05 # format = BAM # ChIP-seq file = ['SRX4554733.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 @ Tue, 09 Oct 2018 23:14:46: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:14:46: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:14:46: # Command line: callpeak -t SRX4554733.bam -f BAM -g 12100000 -n SRX4554733.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4554733.10 # format = BAM # ChIP-seq file = ['SRX4554733.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 @ Tue, 09 Oct 2018 23:14:46: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:14:46: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:14:46: # Command line: callpeak -t SRX4554733.bam -f BAM -g 12100000 -n SRX4554733.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4554733.20 # format = BAM # ChIP-seq file = ['SRX4554733.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 @ Tue, 09 Oct 2018 23:14:46: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:14:46: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:14:51: 1000000 INFO @ Tue, 09 Oct 2018 23:14:52: 1000000 INFO @ Tue, 09 Oct 2018 23:14:52: 1000000 INFO @ Tue, 09 Oct 2018 23:14:57: 2000000 INFO @ Tue, 09 Oct 2018 23:14:59: 2000000 INFO @ Tue, 09 Oct 2018 23:14:59: 2000000 INFO @ Tue, 09 Oct 2018 23:15:03: 3000000 INFO @ Tue, 09 Oct 2018 23:15:05: 3000000 INFO @ Tue, 09 Oct 2018 23:15:07: 3000000 INFO @ Tue, 09 Oct 2018 23:15:09: 4000000 INFO @ Tue, 09 Oct 2018 23:15:12: 4000000 INFO @ Tue, 09 Oct 2018 23:15:13: 4000000 INFO @ Tue, 09 Oct 2018 23:15:15: 5000000 INFO @ Tue, 09 Oct 2018 23:15:18: 5000000 INFO @ Tue, 09 Oct 2018 23:15:19: 5000000 INFO @ Tue, 09 Oct 2018 23:15:21: 6000000 INFO @ Tue, 09 Oct 2018 23:15:22: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 23:15:22: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 23:15:22: #1 total tags in treatment: 2117234 INFO @ Tue, 09 Oct 2018 23:15:22: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:15:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 09 Oct 2018 23:15:22: #1 tags after filtering in treatment: 1155803 INFO @ Tue, 09 Oct 2018 23:15:22: #1 Redundant rate of treatment: 0.45 INFO @ Tue, 09 Oct 2018 23:15:22: #1 finished! INFO @ Tue, 09 Oct 2018 23:15:22: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:15:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:15:22: #2 number of paired peaks: 790 WARNING @ Tue, 09 Oct 2018 23:15:22: Fewer paired peaks (790) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 790 pairs to build model! INFO @ Tue, 09 Oct 2018 23:15:22: start model_add_line... INFO @ Tue, 09 Oct 2018 23:15:22: start X-correlation... INFO @ Tue, 09 Oct 2018 23:15:22: end of X-cor INFO @ Tue, 09 Oct 2018 23:15:22: #2 finished! INFO @ Tue, 09 Oct 2018 23:15:22: #2 predicted fragment length is 219 bps INFO @ Tue, 09 Oct 2018 23:15:22: #2 alternative fragment length(s) may be 0,25,56,145,183,200,219,233,260,490,522,562,580,598 bps INFO @ Tue, 09 Oct 2018 23:15:22: #2.2 Generate R script for model : SRX4554733.05_model.r INFO @ Tue, 09 Oct 2018 23:15:22: #3 Call peaks... INFO @ Tue, 09 Oct 2018 23:15:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 09 Oct 2018 23:15:24: 6000000 INFO @ Tue, 09 Oct 2018 23:15:25: 6000000 INFO @ Tue, 09 Oct 2018 23:15:25: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 23:15:25: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 23:15:25: #1 total tags in treatment: 2117234 INFO @ Tue, 09 Oct 2018 23:15:25: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:15:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 09 Oct 2018 23:15:25: #1 tags after filtering in treatment: 1155803 INFO @ Tue, 09 Oct 2018 23:15:25: #1 Redundant rate of treatment: 0.45 INFO @ Tue, 09 Oct 2018 23:15:25: #1 finished! INFO @ Tue, 09 Oct 2018 23:15:25: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:15:25: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:15:26: #2 number of paired peaks: 790 WARNING @ Tue, 09 Oct 2018 23:15:26: Fewer paired peaks (790) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 790 pairs to build model! INFO @ Tue, 09 Oct 2018 23:15:26: start model_add_line... INFO @ Tue, 09 Oct 2018 23:15:26: start X-correlation... INFO @ Tue, 09 Oct 2018 23:15:26: end of X-cor INFO @ Tue, 09 Oct 2018 23:15:26: #2 finished! INFO @ Tue, 09 Oct 2018 23:15:26: #2 predicted fragment length is 219 bps INFO @ Tue, 09 Oct 2018 23:15:26: #2 alternative fragment length(s) may be 0,25,56,145,183,200,219,233,260,490,522,562,580,598 bps INFO @ Tue, 09 Oct 2018 23:15:26: #2.2 Generate R script for model : SRX4554733.10_model.r INFO @ Tue, 09 Oct 2018 23:15:26: #3 Call peaks... INFO @ Tue, 09 Oct 2018 23:15:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 09 Oct 2018 23:15:26: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 23:15:26: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 23:15:26: #1 total tags in treatment: 2117234 INFO @ Tue, 09 Oct 2018 23:15:26: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:15:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 09 Oct 2018 23:15:26: #1 tags after filtering in treatment: 1155803 INFO @ Tue, 09 Oct 2018 23:15:26: #1 Redundant rate of treatment: 0.45 INFO @ Tue, 09 Oct 2018 23:15:26: #1 finished! INFO @ Tue, 09 Oct 2018 23:15:26: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:15:26: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:15:26: #2 number of paired peaks: 790 WARNING @ Tue, 09 Oct 2018 23:15:26: Fewer paired peaks (790) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 790 pairs to build model! INFO @ Tue, 09 Oct 2018 23:15:26: start model_add_line... INFO @ Tue, 09 Oct 2018 23:15:26: start X-correlation... INFO @ Tue, 09 Oct 2018 23:15:26: end of X-cor INFO @ Tue, 09 Oct 2018 23:15:26: #2 finished! INFO @ Tue, 09 Oct 2018 23:15:26: #2 predicted fragment length is 219 bps INFO @ Tue, 09 Oct 2018 23:15:26: #2 alternative fragment length(s) may be 0,25,56,145,183,200,219,233,260,490,522,562,580,598 bps INFO @ Tue, 09 Oct 2018 23:15:26: #2.2 Generate R script for model : SRX4554733.20_model.r INFO @ Tue, 09 Oct 2018 23:15:26: #3 Call peaks... INFO @ Tue, 09 Oct 2018 23:15:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 09 Oct 2018 23:15:30: #3 Call peaks for each chromosome... INFO @ Tue, 09 Oct 2018 23:15:31: #4 Write output xls file... SRX4554733.05_peaks.xls INFO @ Tue, 09 Oct 2018 23:15:31: #4 Write peak in narrowPeak format file... SRX4554733.05_peaks.narrowPeak INFO @ Tue, 09 Oct 2018 23:15:31: #4 Write summits bed file... SRX4554733.05_summits.bed INFO @ Tue, 09 Oct 2018 23:15:31: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (415 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 09 Oct 2018 23:15:33: #3 Call peaks for each chromosome... INFO @ Tue, 09 Oct 2018 23:15:33: #3 Call peaks for each chromosome... INFO @ Tue, 09 Oct 2018 23:15:35: #4 Write output xls file... SRX4554733.10_peaks.xls INFO @ Tue, 09 Oct 2018 23:15:35: #4 Write peak in narrowPeak format file... SRX4554733.10_peaks.narrowPeak INFO @ Tue, 09 Oct 2018 23:15:35: #4 Write summits bed file... SRX4554733.10_summits.bed INFO @ Tue, 09 Oct 2018 23:15:35: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (352 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 09 Oct 2018 23:15:35: #4 Write output xls file... SRX4554733.20_peaks.xls INFO @ Tue, 09 Oct 2018 23:15:35: #4 Write peak in narrowPeak format file... SRX4554733.20_peaks.narrowPeak INFO @ Tue, 09 Oct 2018 23:15:35: #4 Write summits bed file... SRX4554733.20_summits.bed INFO @ Tue, 09 Oct 2018 23:15:35: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (255 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。