Job ID = 11633467 sra ファイルのダウンロード中... Completed: 113305K bytes transferred in 4 seconds (206954K 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 1983540 spots for /home/okishinya/chipatlas/results/sacCer3/ERX1236244/ERR1162837.sra Written 1983540 spots for /home/okishinya/chipatlas/results/sacCer3/ERX1236244/ERR1162837.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: 00:01:40 1983540 reads; of these: 1983540 (100.00%) were paired; of these: 44997 (2.27%) aligned concordantly 0 times 1765292 (89.00%) aligned concordantly exactly 1 time 173251 (8.73%) aligned concordantly >1 times ---- 44997 pairs aligned concordantly 0 times; of these: 5053 (11.23%) aligned discordantly 1 time ---- 39944 pairs aligned 0 times concordantly or discordantly; of these: 79888 mates make up the pairs; of these: 72814 (91.15%) aligned 0 times 5037 (6.31%) aligned exactly 1 time 2037 (2.55%) aligned >1 times 98.16% overall alignment rate Time searching: 00:01:40 Overall time: 00:01:40 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] 96628 / 1942789 = 0.0497 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 09:06:18: # Command line: callpeak -t ERX1236244.bam -f BAM -g 12100000 -n ERX1236244.10 -q 1e-10 # ARGUMENTS LIST: # name = ERX1236244.10 # format = BAM # ChIP-seq file = ['ERX1236244.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 09:06:18: #1 read tag files... INFO @ Fri, 15 Feb 2019 09:06:18: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 09:06:18: # Command line: callpeak -t ERX1236244.bam -f BAM -g 12100000 -n ERX1236244.20 -q 1e-20 # ARGUMENTS LIST: # name = ERX1236244.20 # format = BAM # ChIP-seq file = ['ERX1236244.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 09:06:18: #1 read tag files... INFO @ Fri, 15 Feb 2019 09:06:18: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 09:06:18: # Command line: callpeak -t ERX1236244.bam -f BAM -g 12100000 -n ERX1236244.05 -q 1e-05 # ARGUMENTS LIST: # name = ERX1236244.05 # format = BAM # ChIP-seq file = ['ERX1236244.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 09:06:18: #1 read tag files... INFO @ Fri, 15 Feb 2019 09:06:18: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 09:06:24: 1000000 INFO @ Fri, 15 Feb 2019 09:06:24: 1000000 INFO @ Fri, 15 Feb 2019 09:06:25: 1000000 INFO @ Fri, 15 Feb 2019 09:06:29: 2000000 INFO @ Fri, 15 Feb 2019 09:06:29: 2000000 INFO @ Fri, 15 Feb 2019 09:06:31: 2000000 INFO @ Fri, 15 Feb 2019 09:06:35: 3000000 INFO @ Fri, 15 Feb 2019 09:06:35: 3000000 INFO @ Fri, 15 Feb 2019 09:06:36: 3000000 INFO @ Fri, 15 Feb 2019 09:06:38: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 09:06:38: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 09:06:38: #1 total tags in treatment: 1842086 INFO @ Fri, 15 Feb 2019 09:06:38: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 09:06:38: #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 09:06:39: #1 tags after filtering in treatment: 1692117 INFO @ Fri, 15 Feb 2019 09:06:39: #1 Redundant rate of treatment: 0.08 INFO @ Fri, 15 Feb 2019 09:06:39: #1 finished! INFO @ Fri, 15 Feb 2019 09:06:39: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 09:06:39: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 09:06:39: #2 number of paired peaks: 180 WARNING @ Fri, 15 Feb 2019 09:06:39: Fewer paired peaks (180) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 180 pairs to build model! INFO @ Fri, 15 Feb 2019 09:06:39: start model_add_line... INFO @ Fri, 15 Feb 2019 09:06:39: start X-correlation... INFO @ Fri, 15 Feb 2019 09:06:39: end of X-cor INFO @ Fri, 15 Feb 2019 09:06:39: #2 finished! INFO @ Fri, 15 Feb 2019 09:06:39: #2 predicted fragment length is 135 bps INFO @ Fri, 15 Feb 2019 09:06:39: #2 alternative fragment length(s) may be 3,79,95,135,147,169,226 bps INFO @ Fri, 15 Feb 2019 09:06:39: #2.2 Generate R script for model : ERX1236244.20_model.r INFO @ Fri, 15 Feb 2019 09:06:39: #3 Call peaks... INFO @ Fri, 15 Feb 2019 09:06:39: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 09:06:39: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 09:06:39: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 09:06:39: #1 total tags in treatment: 1842086 INFO @ Fri, 15 Feb 2019 09:06:39: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 09:06:39: #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 09:06:39: #1 tags after filtering in treatment: 1692117 INFO @ Fri, 15 Feb 2019 09:06:39: #1 Redundant rate of treatment: 0.08 INFO @ Fri, 15 Feb 2019 09:06:39: #1 finished! INFO @ Fri, 15 Feb 2019 09:06:39: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 09:06:39: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 09:06:39: #2 number of paired peaks: 180 WARNING @ Fri, 15 Feb 2019 09:06:39: Fewer paired peaks (180) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 180 pairs to build model! INFO @ Fri, 15 Feb 2019 09:06:39: start model_add_line... INFO @ Fri, 15 Feb 2019 09:06:39: start X-correlation... INFO @ Fri, 15 Feb 2019 09:06:39: end of X-cor INFO @ Fri, 15 Feb 2019 09:06:39: #2 finished! INFO @ Fri, 15 Feb 2019 09:06:39: #2 predicted fragment length is 135 bps INFO @ Fri, 15 Feb 2019 09:06:39: #2 alternative fragment length(s) may be 3,79,95,135,147,169,226 bps INFO @ Fri, 15 Feb 2019 09:06:39: #2.2 Generate R script for model : ERX1236244.10_model.r INFO @ Fri, 15 Feb 2019 09:06:39: #3 Call peaks... INFO @ Fri, 15 Feb 2019 09:06:39: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 09:06:40: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 09:06:40: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 09:06:40: #1 total tags in treatment: 1842086 INFO @ Fri, 15 Feb 2019 09:06:40: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 09:06:40: #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 09:06:40: #1 tags after filtering in treatment: 1692117 INFO @ Fri, 15 Feb 2019 09:06:40: #1 Redundant rate of treatment: 0.08 INFO @ Fri, 15 Feb 2019 09:06:40: #1 finished! INFO @ Fri, 15 Feb 2019 09:06:40: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 09:06:40: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 09:06:40: #2 number of paired peaks: 180 WARNING @ Fri, 15 Feb 2019 09:06:40: Fewer paired peaks (180) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 180 pairs to build model! INFO @ Fri, 15 Feb 2019 09:06:40: start model_add_line... INFO @ Fri, 15 Feb 2019 09:06:40: start X-correlation... INFO @ Fri, 15 Feb 2019 09:06:40: end of X-cor INFO @ Fri, 15 Feb 2019 09:06:40: #2 finished! INFO @ Fri, 15 Feb 2019 09:06:40: #2 predicted fragment length is 135 bps INFO @ Fri, 15 Feb 2019 09:06:40: #2 alternative fragment length(s) may be 3,79,95,135,147,169,226 bps INFO @ Fri, 15 Feb 2019 09:06:40: #2.2 Generate R script for model : ERX1236244.05_model.r INFO @ Fri, 15 Feb 2019 09:06:40: #3 Call peaks... INFO @ Fri, 15 Feb 2019 09:06:40: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 09:06:43: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 09:06:44: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 09:06:45: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 09:06:45: #4 Write output xls file... ERX1236244.20_peaks.xls INFO @ Fri, 15 Feb 2019 09:06:45: #4 Write peak in narrowPeak format file... ERX1236244.20_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 09:06:45: #4 Write summits bed file... ERX1236244.20_summits.bed INFO @ Fri, 15 Feb 2019 09:06:45: Done! pass1 - making usageList (16 chroms): 3 millis pass2 - checking and writing primary data (209 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 09:06:46: #4 Write output xls file... ERX1236244.10_peaks.xls INFO @ Fri, 15 Feb 2019 09:06:46: #4 Write peak in narrowPeak format file... ERX1236244.10_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 09:06:46: #4 Write summits bed file... ERX1236244.10_summits.bed INFO @ Fri, 15 Feb 2019 09:06:46: Done! pass1 - making usageList (16 chroms): 3 millis pass2 - checking and writing primary data (366 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 09:06:47: #4 Write output xls file... ERX1236244.05_peaks.xls INFO @ Fri, 15 Feb 2019 09:06:47: #4 Write peak in narrowPeak format file... ERX1236244.05_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 09:06:47: #4 Write summits bed file... ERX1236244.05_summits.bed INFO @ Fri, 15 Feb 2019 09:06:47: Done! pass1 - making usageList (16 chroms): 3 millis pass2 - checking and writing primary data (584 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。