Job ID = 11633432 sra ファイルのダウンロード中... Completed: 222339K bytes transferred in 5 seconds (333413K 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/ERX1236209/ERR1162802.sra Written 4000000 spots for /home/okishinya/chipatlas/results/sacCer3/ERX1236209/ERR1162802.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: 00:03:06 4000000 reads; of these: 4000000 (100.00%) were paired; of these: 347239 (8.68%) aligned concordantly 0 times 3278158 (81.95%) aligned concordantly exactly 1 time 374603 (9.37%) aligned concordantly >1 times ---- 347239 pairs aligned concordantly 0 times; of these: 18173 (5.23%) aligned discordantly 1 time ---- 329066 pairs aligned 0 times concordantly or discordantly; of these: 658132 mates make up the pairs; of these: 621978 (94.51%) aligned 0 times 27553 (4.19%) aligned exactly 1 time 8601 (1.31%) aligned >1 times 92.23% overall alignment rate Time searching: 00:03:06 Overall time: 00:03:06 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] 599695 / 3665679 = 0.1636 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 08:57:57: # Command line: callpeak -t ERX1236209.bam -f BAM -g 12100000 -n ERX1236209.05 -q 1e-05 # ARGUMENTS LIST: # name = ERX1236209.05 # format = BAM # ChIP-seq file = ['ERX1236209.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 08:57:57: #1 read tag files... INFO @ Fri, 15 Feb 2019 08:57:57: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 08:57:57: # Command line: callpeak -t ERX1236209.bam -f BAM -g 12100000 -n ERX1236209.10 -q 1e-10 # ARGUMENTS LIST: # name = ERX1236209.10 # format = BAM # ChIP-seq file = ['ERX1236209.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 08:57:57: #1 read tag files... INFO @ Fri, 15 Feb 2019 08:57:57: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 08:57:57: # Command line: callpeak -t ERX1236209.bam -f BAM -g 12100000 -n ERX1236209.20 -q 1e-20 # ARGUMENTS LIST: # name = ERX1236209.20 # format = BAM # ChIP-seq file = ['ERX1236209.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 08:57:57: #1 read tag files... INFO @ Fri, 15 Feb 2019 08:57:57: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 08:58:02: 1000000 INFO @ Fri, 15 Feb 2019 08:58:03: 1000000 INFO @ Fri, 15 Feb 2019 08:58:03: 1000000 INFO @ Fri, 15 Feb 2019 08:58:08: 2000000 INFO @ Fri, 15 Feb 2019 08:58:09: 2000000 INFO @ Fri, 15 Feb 2019 08:58:09: 2000000 INFO @ Fri, 15 Feb 2019 08:58:14: 3000000 INFO @ Fri, 15 Feb 2019 08:58:14: 3000000 INFO @ Fri, 15 Feb 2019 08:58:14: 3000000 INFO @ Fri, 15 Feb 2019 08:58:20: 4000000 INFO @ Fri, 15 Feb 2019 08:58:20: 4000000 INFO @ Fri, 15 Feb 2019 08:58:20: 4000000 INFO @ Fri, 15 Feb 2019 08:58:25: 5000000 INFO @ Fri, 15 Feb 2019 08:58:26: 5000000 INFO @ Fri, 15 Feb 2019 08:58:26: 5000000 INFO @ Fri, 15 Feb 2019 08:58:31: 6000000 INFO @ Fri, 15 Feb 2019 08:58:32: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 08:58:32: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 08:58:32: #1 total tags in treatment: 3055620 INFO @ Fri, 15 Feb 2019 08:58:32: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 08:58:32: #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 08:58:32: #1 tags after filtering in treatment: 2606491 INFO @ Fri, 15 Feb 2019 08:58:32: #1 Redundant rate of treatment: 0.15 INFO @ Fri, 15 Feb 2019 08:58:32: #1 finished! INFO @ Fri, 15 Feb 2019 08:58:32: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 08:58:32: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 08:58:32: 6000000 INFO @ Fri, 15 Feb 2019 08:58:32: 6000000 INFO @ Fri, 15 Feb 2019 08:58:32: #2 number of paired peaks: 176 WARNING @ Fri, 15 Feb 2019 08:58:32: Fewer paired peaks (176) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 176 pairs to build model! INFO @ Fri, 15 Feb 2019 08:58:32: start model_add_line... INFO @ Fri, 15 Feb 2019 08:58:32: start X-correlation... INFO @ Fri, 15 Feb 2019 08:58:32: end of X-cor INFO @ Fri, 15 Feb 2019 08:58:32: #2 finished! INFO @ Fri, 15 Feb 2019 08:58:32: #2 predicted fragment length is 174 bps INFO @ Fri, 15 Feb 2019 08:58:32: #2 alternative fragment length(s) may be 4,135,157,174,197 bps INFO @ Fri, 15 Feb 2019 08:58:32: #2.2 Generate R script for model : ERX1236209.05_model.r INFO @ Fri, 15 Feb 2019 08:58:32: #3 Call peaks... INFO @ Fri, 15 Feb 2019 08:58:32: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 08:58:33: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 08:58:33: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 08:58:33: #1 total tags in treatment: 3055620 INFO @ Fri, 15 Feb 2019 08:58:33: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 08:58:33: #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 08:58:33: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 08:58:33: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 08:58:33: #1 total tags in treatment: 3055620 INFO @ Fri, 15 Feb 2019 08:58:33: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 08:58:33: #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 08:58:33: #1 tags after filtering in treatment: 2606491 INFO @ Fri, 15 Feb 2019 08:58:33: #1 Redundant rate of treatment: 0.15 INFO @ Fri, 15 Feb 2019 08:58:33: #1 finished! INFO @ Fri, 15 Feb 2019 08:58:33: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 08:58:33: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 08:58:33: #1 tags after filtering in treatment: 2606491 INFO @ Fri, 15 Feb 2019 08:58:33: #1 Redundant rate of treatment: 0.15 INFO @ Fri, 15 Feb 2019 08:58:33: #1 finished! INFO @ Fri, 15 Feb 2019 08:58:33: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 08:58:33: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 08:58:33: #2 number of paired peaks: 176 WARNING @ Fri, 15 Feb 2019 08:58:33: Fewer paired peaks (176) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 176 pairs to build model! INFO @ Fri, 15 Feb 2019 08:58:33: start model_add_line... INFO @ Fri, 15 Feb 2019 08:58:33: #2 number of paired peaks: 176 WARNING @ Fri, 15 Feb 2019 08:58:33: Fewer paired peaks (176) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 176 pairs to build model! INFO @ Fri, 15 Feb 2019 08:58:33: start model_add_line... INFO @ Fri, 15 Feb 2019 08:58:33: start X-correlation... INFO @ Fri, 15 Feb 2019 08:58:33: end of X-cor INFO @ Fri, 15 Feb 2019 08:58:33: #2 finished! INFO @ Fri, 15 Feb 2019 08:58:33: #2 predicted fragment length is 174 bps INFO @ Fri, 15 Feb 2019 08:58:33: #2 alternative fragment length(s) may be 4,135,157,174,197 bps INFO @ Fri, 15 Feb 2019 08:58:33: #2.2 Generate R script for model : ERX1236209.20_model.r INFO @ Fri, 15 Feb 2019 08:58:33: start X-correlation... INFO @ Fri, 15 Feb 2019 08:58:33: end of X-cor INFO @ Fri, 15 Feb 2019 08:58:33: #2 finished! INFO @ Fri, 15 Feb 2019 08:58:33: #2 predicted fragment length is 174 bps INFO @ Fri, 15 Feb 2019 08:58:33: #2 alternative fragment length(s) may be 4,135,157,174,197 bps INFO @ Fri, 15 Feb 2019 08:58:33: #2.2 Generate R script for model : ERX1236209.10_model.r INFO @ Fri, 15 Feb 2019 08:58:33: #3 Call peaks... INFO @ Fri, 15 Feb 2019 08:58:33: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 08:58:33: #3 Call peaks... INFO @ Fri, 15 Feb 2019 08:58:33: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 08:58:41: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 08:58:42: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 08:58:42: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 08:58:44: #4 Write output xls file... ERX1236209.05_peaks.xls INFO @ Fri, 15 Feb 2019 08:58:44: #4 Write peak in narrowPeak format file... ERX1236209.05_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 08:58:44: #4 Write summits bed file... ERX1236209.05_summits.bed INFO @ Fri, 15 Feb 2019 08:58:44: Done! pass1 - making usageList (17 chroms): 6 millis pass2 - checking and writing primary data (817 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 08:58:44: #4 Write output xls file... ERX1236209.20_peaks.xls INFO @ Fri, 15 Feb 2019 08:58:44: #4 Write peak in narrowPeak format file... ERX1236209.20_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 08:58:44: #4 Write summits bed file... ERX1236209.20_summits.bed INFO @ Fri, 15 Feb 2019 08:58:44: Done! pass1 - making usageList (16 chroms): 7 millis pass2 - checking and writing primary data (318 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 08:58:45: #4 Write output xls file... ERX1236209.10_peaks.xls INFO @ Fri, 15 Feb 2019 08:58:45: #4 Write peak in narrowPeak format file... ERX1236209.10_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 08:58:45: #4 Write summits bed file... ERX1236209.10_summits.bed INFO @ Fri, 15 Feb 2019 08:58:45: Done! pass1 - making usageList (17 chroms): 6 millis pass2 - checking and writing primary data (493 records, 4 fields): 11 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。