Job ID = 11633582 sra ファイルのダウンロード中... Completed: 105269K bytes transferred in 4 seconds (202842K 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 1942890 spots for /home/okishinya/chipatlas/results/sacCer3/ERX1303544/ERR1231605.sra Written 1942890 spots for /home/okishinya/chipatlas/results/sacCer3/ERX1303544/ERR1231605.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 1942890 reads; of these: 1942890 (100.00%) were paired; of these: 1565834 (80.59%) aligned concordantly 0 times 325295 (16.74%) aligned concordantly exactly 1 time 51761 (2.66%) aligned concordantly >1 times ---- 1565834 pairs aligned concordantly 0 times; of these: 585779 (37.41%) aligned discordantly 1 time ---- 980055 pairs aligned 0 times concordantly or discordantly; of these: 1960110 mates make up the pairs; of these: 1301508 (66.40%) aligned 0 times 495985 (25.30%) aligned exactly 1 time 162617 (8.30%) aligned >1 times 66.51% 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] 110954 / 523596 = 0.2119 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 09:09:12: # Command line: callpeak -t ERX1303544.bam -f BAM -g 12100000 -n ERX1303544.05 -q 1e-05 # ARGUMENTS LIST: # name = ERX1303544.05 # format = BAM # ChIP-seq file = ['ERX1303544.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 09:09:12: #1 read tag files... INFO @ Fri, 15 Feb 2019 09:09:12: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 09:09:12: # Command line: callpeak -t ERX1303544.bam -f BAM -g 12100000 -n ERX1303544.10 -q 1e-10 # ARGUMENTS LIST: # name = ERX1303544.10 # format = BAM # ChIP-seq file = ['ERX1303544.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 09:09:12: #1 read tag files... INFO @ Fri, 15 Feb 2019 09:09:12: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 09:09:12: # Command line: callpeak -t ERX1303544.bam -f BAM -g 12100000 -n ERX1303544.20 -q 1e-20 # ARGUMENTS LIST: # name = ERX1303544.20 # format = BAM # ChIP-seq file = ['ERX1303544.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 09:09:12: #1 read tag files... INFO @ Fri, 15 Feb 2019 09:09:12: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 09:09:17: 1000000 INFO @ Fri, 15 Feb 2019 09:09:17: 1000000 INFO @ Fri, 15 Feb 2019 09:09:17: 1000000 INFO @ Fri, 15 Feb 2019 09:09:22: 2000000 INFO @ Fri, 15 Feb 2019 09:09:22: 2000000 INFO @ Fri, 15 Feb 2019 09:09:23: 2000000 INFO @ Fri, 15 Feb 2019 09:09:24: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 09:09:24: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 09:09:24: #1 total tags in treatment: 295979 INFO @ Fri, 15 Feb 2019 09:09:24: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 09:09:24: #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 09:09:24: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 09:09:24: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 09:09:24: #1 total tags in treatment: 295979 INFO @ Fri, 15 Feb 2019 09:09:24: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 09:09:24: #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 09:09:24: #1 tags after filtering in treatment: 289443 INFO @ Fri, 15 Feb 2019 09:09:24: #1 Redundant rate of treatment: 0.02 INFO @ Fri, 15 Feb 2019 09:09:24: #1 finished! INFO @ Fri, 15 Feb 2019 09:09:24: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 09:09:24: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 09:09:24: #1 tags after filtering in treatment: 289443 INFO @ Fri, 15 Feb 2019 09:09:24: #1 Redundant rate of treatment: 0.02 INFO @ Fri, 15 Feb 2019 09:09:24: #1 finished! INFO @ Fri, 15 Feb 2019 09:09:24: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 09:09:24: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 09:09:24: #2 number of paired peaks: 156 WARNING @ Fri, 15 Feb 2019 09:09:24: Fewer paired peaks (156) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 156 pairs to build model! INFO @ Fri, 15 Feb 2019 09:09:24: start model_add_line... INFO @ Fri, 15 Feb 2019 09:09:24: start X-correlation... INFO @ Fri, 15 Feb 2019 09:09:24: #2 number of paired peaks: 156 WARNING @ Fri, 15 Feb 2019 09:09:24: Fewer paired peaks (156) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 156 pairs to build model! INFO @ Fri, 15 Feb 2019 09:09:24: start model_add_line... INFO @ Fri, 15 Feb 2019 09:09:24: end of X-cor INFO @ Fri, 15 Feb 2019 09:09:24: #2 finished! INFO @ Fri, 15 Feb 2019 09:09:24: #2 predicted fragment length is 320 bps INFO @ Fri, 15 Feb 2019 09:09:24: #2 alternative fragment length(s) may be 293,320,334,349 bps INFO @ Fri, 15 Feb 2019 09:09:24: #2.2 Generate R script for model : ERX1303544.05_model.r INFO @ Fri, 15 Feb 2019 09:09:24: start X-correlation... INFO @ Fri, 15 Feb 2019 09:09:24: end of X-cor INFO @ Fri, 15 Feb 2019 09:09:24: #2 finished! INFO @ Fri, 15 Feb 2019 09:09:24: #2 predicted fragment length is 320 bps INFO @ Fri, 15 Feb 2019 09:09:24: #2 alternative fragment length(s) may be 293,320,334,349 bps INFO @ Fri, 15 Feb 2019 09:09:24: #2.2 Generate R script for model : ERX1303544.10_model.r INFO @ Fri, 15 Feb 2019 09:09:24: #3 Call peaks... INFO @ Fri, 15 Feb 2019 09:09:24: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 09:09:24: #3 Call peaks... INFO @ Fri, 15 Feb 2019 09:09:24: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 09:09:25: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 09:09:25: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 09:09:25: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 09:09:25: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 09:09:25: #1 total tags in treatment: 295979 INFO @ Fri, 15 Feb 2019 09:09:25: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 09:09:25: #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 09:09:25: #1 tags after filtering in treatment: 289443 INFO @ Fri, 15 Feb 2019 09:09:25: #1 Redundant rate of treatment: 0.02 INFO @ Fri, 15 Feb 2019 09:09:25: #1 finished! INFO @ Fri, 15 Feb 2019 09:09:25: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 09:09:25: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 09:09:25: #4 Write output xls file... ERX1303544.05_peaks.xls INFO @ Fri, 15 Feb 2019 09:09:25: #2 number of paired peaks: 156 WARNING @ Fri, 15 Feb 2019 09:09:25: Fewer paired peaks (156) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 156 pairs to build model! INFO @ Fri, 15 Feb 2019 09:09:25: start model_add_line... INFO @ Fri, 15 Feb 2019 09:09:25: #4 Write peak in narrowPeak format file... ERX1303544.05_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 09:09:25: start X-correlation... INFO @ Fri, 15 Feb 2019 09:09:25: #4 Write summits bed file... ERX1303544.05_summits.bed INFO @ Fri, 15 Feb 2019 09:09:25: end of X-cor INFO @ Fri, 15 Feb 2019 09:09:25: #2 finished! INFO @ Fri, 15 Feb 2019 09:09:25: #2 predicted fragment length is 320 bps INFO @ Fri, 15 Feb 2019 09:09:25: #2 alternative fragment length(s) may be 293,320,334,349 bps INFO @ Fri, 15 Feb 2019 09:09:25: #2.2 Generate R script for model : ERX1303544.20_model.r INFO @ Fri, 15 Feb 2019 09:09:25: Done! INFO @ Fri, 15 Feb 2019 09:09:25: #3 Call peaks... INFO @ Fri, 15 Feb 2019 09:09:25: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 09:09:25: #4 Write output xls file... ERX1303544.10_peaks.xls INFO @ Fri, 15 Feb 2019 09:09:25: #4 Write peak in narrowPeak format file... ERX1303544.10_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 09:09:25: #4 Write summits bed file... ERX1303544.10_summits.bed INFO @ Fri, 15 Feb 2019 09:09:25: Done! pass1 - making usageList (16 chroms): 5 millis pass2 - checking and writing primary data (122 records, 4 fields): 7 millis pass1 - making usageList (15 chroms): 14 millis pass2 - checking and writing primary data (63 records, 4 fields): 7 millis CompletedMACS2peakCalling CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 09:09:26: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 09:09:26: #4 Write output xls file... ERX1303544.20_peaks.xls INFO @ Fri, 15 Feb 2019 09:09:26: #4 Write peak in narrowPeak format file... ERX1303544.20_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 09:09:26: #4 Write summits bed file... ERX1303544.20_summits.bed INFO @ Fri, 15 Feb 2019 09:09:26: Done! pass1 - making usageList (3 chroms): 3 millis pass2 - checking and writing primary data (6 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。