Job ID = 11633567 sra ファイルのダウンロード中... Completed: 195690K bytes transferred in 4 seconds (320873K 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 3591429 spots for /home/okishinya/chipatlas/results/sacCer3/ERX1303529/ERR1231590.sra Written 3591429 spots for /home/okishinya/chipatlas/results/sacCer3/ERX1303529/ERR1231590.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: 00:03:35 3591429 reads; of these: 3591429 (100.00%) were paired; of these: 2144848 (59.72%) aligned concordantly 0 times 725490 (20.20%) aligned concordantly exactly 1 time 721091 (20.08%) aligned concordantly >1 times ---- 2144848 pairs aligned concordantly 0 times; of these: 775648 (36.16%) aligned discordantly 1 time ---- 1369200 pairs aligned 0 times concordantly or discordantly; of these: 2738400 mates make up the pairs; of these: 1487186 (54.31%) aligned 0 times 651823 (23.80%) aligned exactly 1 time 599391 (21.89%) aligned >1 times 79.30% overall alignment rate Time searching: 00:03:35 Overall time: 00:03:35 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] 466182 / 1649306 = 0.2827 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, 15 Feb 2019 09:10:00: # Command line: callpeak -t ERX1303529.bam -f BAM -g 12100000 -n ERX1303529.20 -q 1e-20 # ARGUMENTS LIST: # name = ERX1303529.20 # format = BAM # ChIP-seq file = ['ERX1303529.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, 15 Feb 2019 09:10:00: #1 read tag files... INFO @ Fri, 15 Feb 2019 09:10:00: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 09:10:00: # Command line: callpeak -t ERX1303529.bam -f BAM -g 12100000 -n ERX1303529.10 -q 1e-10 # ARGUMENTS LIST: # name = ERX1303529.10 # format = BAM # ChIP-seq file = ['ERX1303529.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, 15 Feb 2019 09:10:00: #1 read tag files... INFO @ Fri, 15 Feb 2019 09:10:00: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 09:10:00: # Command line: callpeak -t ERX1303529.bam -f BAM -g 12100000 -n ERX1303529.05 -q 1e-05 # ARGUMENTS LIST: # name = ERX1303529.05 # format = BAM # ChIP-seq file = ['ERX1303529.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, 15 Feb 2019 09:10:00: #1 read tag files... INFO @ Fri, 15 Feb 2019 09:10:00: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 09:10:05: 1000000 INFO @ Fri, 15 Feb 2019 09:10:06: 1000000 INFO @ Fri, 15 Feb 2019 09:10:06: 1000000 INFO @ Fri, 15 Feb 2019 09:10:10: 2000000 INFO @ Fri, 15 Feb 2019 09:10:11: 2000000 INFO @ Fri, 15 Feb 2019 09:10:11: 2000000 INFO @ Fri, 15 Feb 2019 09:10:15: 3000000 INFO @ Fri, 15 Feb 2019 09:10:16: 3000000 INFO @ Fri, 15 Feb 2019 09:10:16: 3000000 INFO @ Fri, 15 Feb 2019 09:10:20: 4000000 INFO @ Fri, 15 Feb 2019 09:10:21: 4000000 INFO @ Fri, 15 Feb 2019 09:10:22: 4000000 INFO @ Fri, 15 Feb 2019 09:10:23: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 09:10:23: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 09:10:23: #1 total tags in treatment: 1039096 INFO @ Fri, 15 Feb 2019 09:10:23: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 09:10:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 09:10:23: #1 tags after filtering in treatment: 517236 INFO @ Fri, 15 Feb 2019 09:10:23: #1 Redundant rate of treatment: 0.50 INFO @ Fri, 15 Feb 2019 09:10:23: #1 finished! INFO @ Fri, 15 Feb 2019 09:10:23: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 09:10:23: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 09:10:23: #2 number of paired peaks: 383 WARNING @ Fri, 15 Feb 2019 09:10:23: Fewer paired peaks (383) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 383 pairs to build model! INFO @ Fri, 15 Feb 2019 09:10:23: start model_add_line... INFO @ Fri, 15 Feb 2019 09:10:23: start X-correlation... INFO @ Fri, 15 Feb 2019 09:10:23: end of X-cor INFO @ Fri, 15 Feb 2019 09:10:23: #2 finished! INFO @ Fri, 15 Feb 2019 09:10:23: #2 predicted fragment length is 280 bps INFO @ Fri, 15 Feb 2019 09:10:23: #2 alternative fragment length(s) may be 4,280 bps INFO @ Fri, 15 Feb 2019 09:10:23: #2.2 Generate R script for model : ERX1303529.10_model.r INFO @ Fri, 15 Feb 2019 09:10:23: #3 Call peaks... INFO @ Fri, 15 Feb 2019 09:10:23: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 09:10:25: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 09:10:25: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 09:10:25: #1 total tags in treatment: 1039096 INFO @ Fri, 15 Feb 2019 09:10:25: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 09:10:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 09:10:25: #1 tags after filtering in treatment: 517236 INFO @ Fri, 15 Feb 2019 09:10:25: #1 Redundant rate of treatment: 0.50 INFO @ Fri, 15 Feb 2019 09:10:25: #1 finished! INFO @ Fri, 15 Feb 2019 09:10:25: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 09:10:25: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 09:10:25: #2 number of paired peaks: 383 WARNING @ Fri, 15 Feb 2019 09:10:25: Fewer paired peaks (383) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 383 pairs to build model! INFO @ Fri, 15 Feb 2019 09:10:25: start model_add_line... INFO @ Fri, 15 Feb 2019 09:10:25: start X-correlation... INFO @ Fri, 15 Feb 2019 09:10:25: end of X-cor INFO @ Fri, 15 Feb 2019 09:10:25: #2 finished! INFO @ Fri, 15 Feb 2019 09:10:25: #2 predicted fragment length is 280 bps INFO @ Fri, 15 Feb 2019 09:10:25: #2 alternative fragment length(s) may be 4,280 bps INFO @ Fri, 15 Feb 2019 09:10:25: #2.2 Generate R script for model : ERX1303529.20_model.r INFO @ Fri, 15 Feb 2019 09:10:25: #3 Call peaks... INFO @ Fri, 15 Feb 2019 09:10:25: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 09:10:25: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 09:10:25: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 09:10:25: #1 total tags in treatment: 1039096 INFO @ Fri, 15 Feb 2019 09:10:25: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 09:10:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 09:10:25: #1 tags after filtering in treatment: 517236 INFO @ Fri, 15 Feb 2019 09:10:25: #1 Redundant rate of treatment: 0.50 INFO @ Fri, 15 Feb 2019 09:10:25: #1 finished! INFO @ Fri, 15 Feb 2019 09:10:25: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 09:10:25: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 09:10:25: #2 number of paired peaks: 383 WARNING @ Fri, 15 Feb 2019 09:10:25: Fewer paired peaks (383) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 383 pairs to build model! INFO @ Fri, 15 Feb 2019 09:10:25: start model_add_line... INFO @ Fri, 15 Feb 2019 09:10:25: start X-correlation... INFO @ Fri, 15 Feb 2019 09:10:25: end of X-cor INFO @ Fri, 15 Feb 2019 09:10:25: #2 finished! INFO @ Fri, 15 Feb 2019 09:10:25: #2 predicted fragment length is 280 bps INFO @ Fri, 15 Feb 2019 09:10:25: #2 alternative fragment length(s) may be 4,280 bps INFO @ Fri, 15 Feb 2019 09:10:25: #2.2 Generate R script for model : ERX1303529.05_model.r INFO @ Fri, 15 Feb 2019 09:10:25: #3 Call peaks... INFO @ Fri, 15 Feb 2019 09:10:25: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 09:10:26: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 09:10:27: #4 Write output xls file... ERX1303529.10_peaks.xls INFO @ Fri, 15 Feb 2019 09:10:27: #4 Write peak in narrowPeak format file... ERX1303529.10_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 09:10:27: #4 Write summits bed file... ERX1303529.10_summits.bed INFO @ Fri, 15 Feb 2019 09:10:27: Done! pass1 - making usageList (17 chroms): 2 millis pass2 - checking and writing primary data (154 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 09:10:28: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 09:10:28: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 09:10:29: #4 Write output xls file... ERX1303529.20_peaks.xls INFO @ Fri, 15 Feb 2019 09:10:29: #4 Write peak in narrowPeak format file... ERX1303529.20_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 09:10:29: #4 Write summits bed file... ERX1303529.20_summits.bed INFO @ Fri, 15 Feb 2019 09:10:29: Done! pass1 - making usageList (17 chroms): 4 millis pass2 - checking and writing primary data (86 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 09:10:29: #4 Write output xls file... ERX1303529.05_peaks.xls INFO @ Fri, 15 Feb 2019 09:10:29: #4 Write peak in narrowPeak format file... ERX1303529.05_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 09:10:29: #4 Write summits bed file... ERX1303529.05_summits.bed INFO @ Fri, 15 Feb 2019 09:10:29: Done! pass1 - making usageList (17 chroms): 3 millis pass2 - checking and writing primary data (249 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。