Job ID = 11633540 sra ファイルのダウンロード中... Completed: 223305K bytes transferred in 5 seconds (335059K 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/ERX1236317/ERR1162910.sra Written 4000000 spots for /home/okishinya/chipatlas/results/sacCer3/ERX1236317/ERR1162910.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: 00:00:01 Multiseed full-index search: 00:02:58 4000000 reads; of these: 4000000 (100.00%) were paired; of these: 441364 (11.03%) aligned concordantly 0 times 3141653 (78.54%) aligned concordantly exactly 1 time 416983 (10.42%) aligned concordantly >1 times ---- 441364 pairs aligned concordantly 0 times; of these: 13276 (3.01%) aligned discordantly 1 time ---- 428088 pairs aligned 0 times concordantly or discordantly; of these: 856176 mates make up the pairs; of these: 827574 (96.66%) aligned 0 times 20176 (2.36%) aligned exactly 1 time 8426 (0.98%) aligned >1 times 89.66% overall alignment rate Time searching: 00:02:59 Overall time: 00:02:59 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] 1271126 / 3570615 = 0.3560 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 09:05:40: # Command line: callpeak -t ERX1236317.bam -f BAM -g 12100000 -n ERX1236317.20 -q 1e-20 # ARGUMENTS LIST: # name = ERX1236317.20 # format = BAM # ChIP-seq file = ['ERX1236317.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 09:05:40: #1 read tag files... INFO @ Fri, 15 Feb 2019 09:05:40: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 09:05:40: # Command line: callpeak -t ERX1236317.bam -f BAM -g 12100000 -n ERX1236317.10 -q 1e-10 # ARGUMENTS LIST: # name = ERX1236317.10 # format = BAM # ChIP-seq file = ['ERX1236317.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 09:05:40: #1 read tag files... INFO @ Fri, 15 Feb 2019 09:05:40: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 09:05:40: # Command line: callpeak -t ERX1236317.bam -f BAM -g 12100000 -n ERX1236317.05 -q 1e-05 # ARGUMENTS LIST: # name = ERX1236317.05 # format = BAM # ChIP-seq file = ['ERX1236317.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 09:05:40: #1 read tag files... INFO @ Fri, 15 Feb 2019 09:05:40: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 09:05:45: 1000000 INFO @ Fri, 15 Feb 2019 09:05:46: 1000000 INFO @ Fri, 15 Feb 2019 09:05:46: 1000000 INFO @ Fri, 15 Feb 2019 09:05:51: 2000000 INFO @ Fri, 15 Feb 2019 09:05:51: 2000000 INFO @ Fri, 15 Feb 2019 09:05:51: 2000000 INFO @ Fri, 15 Feb 2019 09:05:56: 3000000 INFO @ Fri, 15 Feb 2019 09:05:57: 3000000 INFO @ Fri, 15 Feb 2019 09:05:57: 3000000 INFO @ Fri, 15 Feb 2019 09:06:02: 4000000 INFO @ Fri, 15 Feb 2019 09:06:02: 4000000 INFO @ Fri, 15 Feb 2019 09:06:02: 4000000 INFO @ Fri, 15 Feb 2019 09:06:05: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 09:06:05: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 09:06:05: #1 total tags in treatment: 2292483 INFO @ Fri, 15 Feb 2019 09:06:05: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 09:06:05: #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 09:06:05: #1 tags after filtering in treatment: 2000303 INFO @ Fri, 15 Feb 2019 09:06:05: #1 Redundant rate of treatment: 0.13 INFO @ Fri, 15 Feb 2019 09:06:05: #1 finished! INFO @ Fri, 15 Feb 2019 09:06:05: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 09:06:05: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 09:06:05: #2 number of paired peaks: 179 WARNING @ Fri, 15 Feb 2019 09:06:05: Fewer paired peaks (179) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 179 pairs to build model! INFO @ Fri, 15 Feb 2019 09:06:05: start model_add_line... INFO @ Fri, 15 Feb 2019 09:06:05: start X-correlation... INFO @ Fri, 15 Feb 2019 09:06:05: end of X-cor INFO @ Fri, 15 Feb 2019 09:06:05: #2 finished! INFO @ Fri, 15 Feb 2019 09:06:05: #2 predicted fragment length is 174 bps INFO @ Fri, 15 Feb 2019 09:06:05: #2 alternative fragment length(s) may be 4,149,174,194 bps INFO @ Fri, 15 Feb 2019 09:06:05: #2.2 Generate R script for model : ERX1236317.20_model.r INFO @ Fri, 15 Feb 2019 09:06:05: #3 Call peaks... INFO @ Fri, 15 Feb 2019 09:06:05: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 09:06:05: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 09:06:05: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 09:06:05: #1 total tags in treatment: 2292483 INFO @ Fri, 15 Feb 2019 09:06:05: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 09:06:05: #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 09:06:06: #1 tags after filtering in treatment: 2000303 INFO @ Fri, 15 Feb 2019 09:06:06: #1 Redundant rate of treatment: 0.13 INFO @ Fri, 15 Feb 2019 09:06:06: #1 finished! INFO @ Fri, 15 Feb 2019 09:06:06: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 09:06:06: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 09:06:06: #2 number of paired peaks: 179 WARNING @ Fri, 15 Feb 2019 09:06:06: Fewer paired peaks (179) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 179 pairs to build model! INFO @ Fri, 15 Feb 2019 09:06:06: start model_add_line... INFO @ Fri, 15 Feb 2019 09:06:06: start X-correlation... INFO @ Fri, 15 Feb 2019 09:06:06: end of X-cor INFO @ Fri, 15 Feb 2019 09:06:06: #2 finished! INFO @ Fri, 15 Feb 2019 09:06:06: #2 predicted fragment length is 174 bps INFO @ Fri, 15 Feb 2019 09:06:06: #2 alternative fragment length(s) may be 4,149,174,194 bps INFO @ Fri, 15 Feb 2019 09:06:06: #2.2 Generate R script for model : ERX1236317.05_model.r INFO @ Fri, 15 Feb 2019 09:06:06: #3 Call peaks... INFO @ Fri, 15 Feb 2019 09:06:06: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 09:06:06: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 09:06:06: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 09:06:06: #1 total tags in treatment: 2292483 INFO @ Fri, 15 Feb 2019 09:06:06: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 09:06:06: #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 09:06:06: #1 tags after filtering in treatment: 2000303 INFO @ Fri, 15 Feb 2019 09:06:06: #1 Redundant rate of treatment: 0.13 INFO @ Fri, 15 Feb 2019 09:06:06: #1 finished! INFO @ Fri, 15 Feb 2019 09:06:06: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 09:06:06: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 09:06:06: #2 number of paired peaks: 179 WARNING @ Fri, 15 Feb 2019 09:06:06: Fewer paired peaks (179) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 179 pairs to build model! INFO @ Fri, 15 Feb 2019 09:06:06: start model_add_line... INFO @ Fri, 15 Feb 2019 09:06:06: start X-correlation... INFO @ Fri, 15 Feb 2019 09:06:06: end of X-cor INFO @ Fri, 15 Feb 2019 09:06:06: #2 finished! INFO @ Fri, 15 Feb 2019 09:06:06: #2 predicted fragment length is 174 bps INFO @ Fri, 15 Feb 2019 09:06:06: #2 alternative fragment length(s) may be 4,149,174,194 bps INFO @ Fri, 15 Feb 2019 09:06:06: #2.2 Generate R script for model : ERX1236317.10_model.r INFO @ Fri, 15 Feb 2019 09:06:06: #3 Call peaks... INFO @ Fri, 15 Feb 2019 09:06:06: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 09:06:12: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 09:06:12: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 09:06:12: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 09:06:14: #4 Write output xls file... ERX1236317.20_peaks.xls INFO @ Fri, 15 Feb 2019 09:06:14: #4 Write peak in narrowPeak format file... ERX1236317.20_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 09:06:14: #4 Write summits bed file... ERX1236317.20_summits.bed INFO @ Fri, 15 Feb 2019 09:06:14: Done! pass1 - making usageList (16 chroms): 5 millis pass2 - checking and writing primary data (266 records, 4 fields): 6 millis INFO @ Fri, 15 Feb 2019 09:06:14: #4 Write output xls file... ERX1236317.05_peaks.xls INFO @ Fri, 15 Feb 2019 09:06:14: #4 Write peak in narrowPeak format file... ERX1236317.05_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 09:06:14: #4 Write summits bed file... ERX1236317.05_summits.bed INFO @ Fri, 15 Feb 2019 09:06:14: Done! CompletedMACS2peakCalling pass1 - making usageList (16 chroms): 6 millis pass2 - checking and writing primary data (694 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 09:06:15: #4 Write output xls file... ERX1236317.10_peaks.xls INFO @ Fri, 15 Feb 2019 09:06:15: #4 Write peak in narrowPeak format file... ERX1236317.10_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 09:06:15: #4 Write summits bed file... ERX1236317.10_summits.bed INFO @ Fri, 15 Feb 2019 09:06:15: Done! pass1 - making usageList (16 chroms): 5 millis pass2 - checking and writing primary data (442 records, 4 fields): 9 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。