Job ID = 11633502 sra ファイルのダウンロード中... Completed: 235729K bytes transferred in 5 seconds (356270K 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 4000000 spots for /home/okishinya/chipatlas/results/sacCer3/ERX1236279/ERR1162872.sra Written 4000000 spots for /home/okishinya/chipatlas/results/sacCer3/ERX1236279/ERR1162872.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: 00:03:03 4000000 reads; of these: 4000000 (100.00%) were paired; of these: 384292 (9.61%) aligned concordantly 0 times 3224656 (80.62%) aligned concordantly exactly 1 time 391052 (9.78%) aligned concordantly >1 times ---- 384292 pairs aligned concordantly 0 times; of these: 13934 (3.63%) aligned discordantly 1 time ---- 370358 pairs aligned 0 times concordantly or discordantly; of these: 740716 mates make up the pairs; of these: 723946 (97.74%) aligned 0 times 11134 (1.50%) aligned exactly 1 time 5636 (0.76%) aligned >1 times 90.95% overall alignment rate Time searching: 00:03:03 Overall time: 00:03:03 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] 1575472 / 3628802 = 0.4342 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 09:04:00: # Command line: callpeak -t ERX1236279.bam -f BAM -g 12100000 -n ERX1236279.20 -q 1e-20 # ARGUMENTS LIST: # name = ERX1236279.20 # format = BAM # ChIP-seq file = ['ERX1236279.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 09:04:00: #1 read tag files... INFO @ Fri, 15 Feb 2019 09:04:00: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 09:04:00: # Command line: callpeak -t ERX1236279.bam -f BAM -g 12100000 -n ERX1236279.10 -q 1e-10 # ARGUMENTS LIST: # name = ERX1236279.10 # format = BAM # ChIP-seq file = ['ERX1236279.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 09:04:00: #1 read tag files... INFO @ Fri, 15 Feb 2019 09:04:00: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 09:04:00: # Command line: callpeak -t ERX1236279.bam -f BAM -g 12100000 -n ERX1236279.05 -q 1e-05 # ARGUMENTS LIST: # name = ERX1236279.05 # format = BAM # ChIP-seq file = ['ERX1236279.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 09:04:00: #1 read tag files... INFO @ Fri, 15 Feb 2019 09:04:00: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 09:04:06: 1000000 INFO @ Fri, 15 Feb 2019 09:04:06: 1000000 INFO @ Fri, 15 Feb 2019 09:04:06: 1000000 INFO @ Fri, 15 Feb 2019 09:04:12: 2000000 INFO @ Fri, 15 Feb 2019 09:04:13: 2000000 INFO @ Fri, 15 Feb 2019 09:04:13: 2000000 INFO @ Fri, 15 Feb 2019 09:04:18: 3000000 INFO @ Fri, 15 Feb 2019 09:04:19: 3000000 INFO @ Fri, 15 Feb 2019 09:04:19: 3000000 INFO @ Fri, 15 Feb 2019 09:04:25: 4000000 INFO @ Fri, 15 Feb 2019 09:04:25: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 09:04:25: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 09:04:25: #1 total tags in treatment: 2045236 INFO @ Fri, 15 Feb 2019 09:04:25: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 09:04:25: #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 09:04:25: #1 tags after filtering in treatment: 1831588 INFO @ Fri, 15 Feb 2019 09:04:25: #1 Redundant rate of treatment: 0.10 INFO @ Fri, 15 Feb 2019 09:04:25: #1 finished! INFO @ Fri, 15 Feb 2019 09:04:25: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 09:04:25: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 09:04:26: #2 number of paired peaks: 133 WARNING @ Fri, 15 Feb 2019 09:04:26: Fewer paired peaks (133) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 133 pairs to build model! INFO @ Fri, 15 Feb 2019 09:04:26: start model_add_line... INFO @ Fri, 15 Feb 2019 09:04:26: start X-correlation... INFO @ Fri, 15 Feb 2019 09:04:26: end of X-cor INFO @ Fri, 15 Feb 2019 09:04:26: #2 finished! INFO @ Fri, 15 Feb 2019 09:04:26: #2 predicted fragment length is 142 bps INFO @ Fri, 15 Feb 2019 09:04:26: #2 alternative fragment length(s) may be 4,123,142,182,185 bps INFO @ Fri, 15 Feb 2019 09:04:26: #2.2 Generate R script for model : ERX1236279.20_model.r INFO @ Fri, 15 Feb 2019 09:04:26: #3 Call peaks... INFO @ Fri, 15 Feb 2019 09:04:26: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 09:04:26: 4000000 INFO @ Fri, 15 Feb 2019 09:04:26: 4000000 INFO @ Fri, 15 Feb 2019 09:04:26: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 09:04:26: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 09:04:26: #1 total tags in treatment: 2045236 INFO @ Fri, 15 Feb 2019 09:04:26: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 09:04:26: #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 09:04:26: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 09:04:26: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 09:04:26: #1 total tags in treatment: 2045236 INFO @ Fri, 15 Feb 2019 09:04:26: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 09:04:26: #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 09:04:26: #1 tags after filtering in treatment: 1831588 INFO @ Fri, 15 Feb 2019 09:04:26: #1 Redundant rate of treatment: 0.10 INFO @ Fri, 15 Feb 2019 09:04:26: #1 finished! INFO @ Fri, 15 Feb 2019 09:04:26: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 09:04:26: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 09:04:26: #1 tags after filtering in treatment: 1831588 INFO @ Fri, 15 Feb 2019 09:04:26: #1 Redundant rate of treatment: 0.10 INFO @ Fri, 15 Feb 2019 09:04:26: #1 finished! INFO @ Fri, 15 Feb 2019 09:04:26: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 09:04:26: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 09:04:27: #2 number of paired peaks: 133 WARNING @ Fri, 15 Feb 2019 09:04:27: Fewer paired peaks (133) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 133 pairs to build model! INFO @ Fri, 15 Feb 2019 09:04:27: start model_add_line... INFO @ Fri, 15 Feb 2019 09:04:27: #2 number of paired peaks: 133 WARNING @ Fri, 15 Feb 2019 09:04:27: Fewer paired peaks (133) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 133 pairs to build model! INFO @ Fri, 15 Feb 2019 09:04:27: start model_add_line... INFO @ Fri, 15 Feb 2019 09:04:27: start X-correlation... INFO @ Fri, 15 Feb 2019 09:04:27: start X-correlation... INFO @ Fri, 15 Feb 2019 09:04:27: end of X-cor INFO @ Fri, 15 Feb 2019 09:04:27: #2 finished! INFO @ Fri, 15 Feb 2019 09:04:27: #2 predicted fragment length is 142 bps INFO @ Fri, 15 Feb 2019 09:04:27: #2 alternative fragment length(s) may be 4,123,142,182,185 bps INFO @ Fri, 15 Feb 2019 09:04:27: #2.2 Generate R script for model : ERX1236279.10_model.r INFO @ Fri, 15 Feb 2019 09:04:27: end of X-cor INFO @ Fri, 15 Feb 2019 09:04:27: #2 finished! INFO @ Fri, 15 Feb 2019 09:04:27: #2 predicted fragment length is 142 bps INFO @ Fri, 15 Feb 2019 09:04:27: #2 alternative fragment length(s) may be 4,123,142,182,185 bps INFO @ Fri, 15 Feb 2019 09:04:27: #2.2 Generate R script for model : ERX1236279.05_model.r INFO @ Fri, 15 Feb 2019 09:04:27: #3 Call peaks... INFO @ Fri, 15 Feb 2019 09:04:27: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 09:04:27: #3 Call peaks... INFO @ Fri, 15 Feb 2019 09:04:27: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 09:04:31: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 09:04:32: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 09:04:32: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 09:04:33: #4 Write output xls file... ERX1236279.20_peaks.xls INFO @ Fri, 15 Feb 2019 09:04:33: #4 Write peak in narrowPeak format file... ERX1236279.20_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 09:04:33: #4 Write summits bed file... ERX1236279.20_summits.bed INFO @ Fri, 15 Feb 2019 09:04:33: Done! pass1 - making usageList (16 chroms): 3 millis pass2 - checking and writing primary data (189 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 09:04:34: #4 Write output xls file... ERX1236279.10_peaks.xls INFO @ Fri, 15 Feb 2019 09:04:34: #4 Write peak in narrowPeak format file... ERX1236279.10_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 09:04:34: #4 Write summits bed file... ERX1236279.10_summits.bed INFO @ Fri, 15 Feb 2019 09:04:34: Done! INFO @ Fri, 15 Feb 2019 09:04:34: #4 Write output xls file... ERX1236279.05_peaks.xls INFO @ Fri, 15 Feb 2019 09:04:34: #4 Write peak in narrowPeak format file... ERX1236279.05_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 09:04:34: #4 Write summits bed file... ERX1236279.05_summits.bed INFO @ Fri, 15 Feb 2019 09:04:34: Done! pass1 - making usageList (16 chroms): 3 millis pass2 - checking and writing primary data (371 records, 4 fields): 4 millis CompletedMACS2peakCalling pass1 - making usageList (16 chroms): 3 millis pass2 - checking and writing primary data (622 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。