Job ID = 11633521 sra ファイルのダウンロード中... Completed: 237797K bytes transferred in 5 seconds (346575K 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/ERX1236298/ERR1162891.sra Written 4000000 spots for /home/okishinya/chipatlas/results/sacCer3/ERX1236298/ERR1162891.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: 00:03:00 4000000 reads; of these: 4000000 (100.00%) were paired; of these: 419966 (10.50%) aligned concordantly 0 times 3238312 (80.96%) aligned concordantly exactly 1 time 341722 (8.54%) aligned concordantly >1 times ---- 419966 pairs aligned concordantly 0 times; of these: 64176 (15.28%) aligned discordantly 1 time ---- 355790 pairs aligned 0 times concordantly or discordantly; of these: 711580 mates make up the pairs; of these: 683490 (96.05%) aligned 0 times 13449 (1.89%) aligned exactly 1 time 14641 (2.06%) aligned >1 times 91.46% overall alignment rate Time searching: 00:03:00 Overall time: 00:03:00 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] 1176457 / 3643036 = 0.3229 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 09:04:52: # Command line: callpeak -t ERX1236298.bam -f BAM -g 12100000 -n ERX1236298.20 -q 1e-20 # ARGUMENTS LIST: # name = ERX1236298.20 # format = BAM # ChIP-seq file = ['ERX1236298.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 09:04:52: #1 read tag files... INFO @ Fri, 15 Feb 2019 09:04:52: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 09:04:52: # Command line: callpeak -t ERX1236298.bam -f BAM -g 12100000 -n ERX1236298.10 -q 1e-10 # ARGUMENTS LIST: # name = ERX1236298.10 # format = BAM # ChIP-seq file = ['ERX1236298.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 09:04:52: #1 read tag files... INFO @ Fri, 15 Feb 2019 09:04:52: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 09:04:52: # Command line: callpeak -t ERX1236298.bam -f BAM -g 12100000 -n ERX1236298.05 -q 1e-05 # ARGUMENTS LIST: # name = ERX1236298.05 # format = BAM # ChIP-seq file = ['ERX1236298.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 09:04:52: #1 read tag files... INFO @ Fri, 15 Feb 2019 09:04:52: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 09:04:58: 1000000 INFO @ Fri, 15 Feb 2019 09:04:58: 1000000 INFO @ Fri, 15 Feb 2019 09:04:58: 1000000 INFO @ Fri, 15 Feb 2019 09:05:04: 2000000 INFO @ Fri, 15 Feb 2019 09:05:04: 2000000 INFO @ Fri, 15 Feb 2019 09:05:04: 2000000 INFO @ Fri, 15 Feb 2019 09:05:10: 3000000 INFO @ Fri, 15 Feb 2019 09:05:10: 3000000 INFO @ Fri, 15 Feb 2019 09:05:11: 3000000 INFO @ Fri, 15 Feb 2019 09:05:16: 4000000 INFO @ Fri, 15 Feb 2019 09:05:16: 4000000 INFO @ Fri, 15 Feb 2019 09:05:17: 4000000 INFO @ Fri, 15 Feb 2019 09:05:22: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 09:05:22: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 09:05:22: #1 total tags in treatment: 2423805 INFO @ Fri, 15 Feb 2019 09:05:22: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 09:05:22: #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 09:05:22: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 09:05:22: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 09:05:22: #1 total tags in treatment: 2423805 INFO @ Fri, 15 Feb 2019 09:05:22: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 09:05:22: #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 09:05:22: #1 tags after filtering in treatment: 2125449 INFO @ Fri, 15 Feb 2019 09:05:22: #1 Redundant rate of treatment: 0.12 INFO @ Fri, 15 Feb 2019 09:05:22: #1 finished! INFO @ Fri, 15 Feb 2019 09:05:22: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 09:05:22: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 09:05:22: #1 tags after filtering in treatment: 2125449 INFO @ Fri, 15 Feb 2019 09:05:22: #1 Redundant rate of treatment: 0.12 INFO @ Fri, 15 Feb 2019 09:05:22: #1 finished! INFO @ Fri, 15 Feb 2019 09:05:22: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 09:05:22: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 09:05:22: #2 number of paired peaks: 210 WARNING @ Fri, 15 Feb 2019 09:05:22: Fewer paired peaks (210) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 210 pairs to build model! INFO @ Fri, 15 Feb 2019 09:05:22: start model_add_line... INFO @ Fri, 15 Feb 2019 09:05:22: #2 number of paired peaks: 210 WARNING @ Fri, 15 Feb 2019 09:05:22: Fewer paired peaks (210) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 210 pairs to build model! INFO @ Fri, 15 Feb 2019 09:05:22: start model_add_line... INFO @ Fri, 15 Feb 2019 09:05:22: start X-correlation... INFO @ Fri, 15 Feb 2019 09:05:22: end of X-cor INFO @ Fri, 15 Feb 2019 09:05:22: #2 finished! INFO @ Fri, 15 Feb 2019 09:05:22: #2 predicted fragment length is 179 bps INFO @ Fri, 15 Feb 2019 09:05:22: #2 alternative fragment length(s) may be 4,179 bps INFO @ Fri, 15 Feb 2019 09:05:22: #2.2 Generate R script for model : ERX1236298.20_model.r INFO @ Fri, 15 Feb 2019 09:05:22: start X-correlation... INFO @ Fri, 15 Feb 2019 09:05:22: #3 Call peaks... INFO @ Fri, 15 Feb 2019 09:05:22: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 09:05:22: end of X-cor INFO @ Fri, 15 Feb 2019 09:05:22: #2 finished! INFO @ Fri, 15 Feb 2019 09:05:22: #2 predicted fragment length is 179 bps INFO @ Fri, 15 Feb 2019 09:05:22: #2 alternative fragment length(s) may be 4,179 bps INFO @ Fri, 15 Feb 2019 09:05:22: #2.2 Generate R script for model : ERX1236298.10_model.r INFO @ Fri, 15 Feb 2019 09:05:22: #3 Call peaks... INFO @ Fri, 15 Feb 2019 09:05:22: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 09:05:23: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 09:05:23: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 09:05:23: #1 total tags in treatment: 2423805 INFO @ Fri, 15 Feb 2019 09:05:23: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 09:05:23: #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 09:05:23: #1 tags after filtering in treatment: 2125449 INFO @ Fri, 15 Feb 2019 09:05:23: #1 Redundant rate of treatment: 0.12 INFO @ Fri, 15 Feb 2019 09:05:23: #1 finished! INFO @ Fri, 15 Feb 2019 09:05:23: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 09:05:23: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 09:05:23: #2 number of paired peaks: 210 WARNING @ Fri, 15 Feb 2019 09:05:23: Fewer paired peaks (210) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 210 pairs to build model! INFO @ Fri, 15 Feb 2019 09:05:23: start model_add_line... INFO @ Fri, 15 Feb 2019 09:05:24: start X-correlation... INFO @ Fri, 15 Feb 2019 09:05:24: end of X-cor INFO @ Fri, 15 Feb 2019 09:05:24: #2 finished! INFO @ Fri, 15 Feb 2019 09:05:24: #2 predicted fragment length is 179 bps INFO @ Fri, 15 Feb 2019 09:05:24: #2 alternative fragment length(s) may be 4,179 bps INFO @ Fri, 15 Feb 2019 09:05:24: #2.2 Generate R script for model : ERX1236298.05_model.r INFO @ Fri, 15 Feb 2019 09:05:24: #3 Call peaks... INFO @ Fri, 15 Feb 2019 09:05:24: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 09:05:29: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 09:05:29: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 09:05:30: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 09:05:31: #4 Write output xls file... ERX1236298.20_peaks.xls INFO @ Fri, 15 Feb 2019 09:05:31: #4 Write peak in narrowPeak format file... ERX1236298.20_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 09:05:31: #4 Write summits bed file... ERX1236298.20_summits.bed INFO @ Fri, 15 Feb 2019 09:05:31: Done! pass1 - making usageList (16 chroms): 4 millis pass2 - checking and writing primary data (303 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 09:05:32: #4 Write output xls file... ERX1236298.10_peaks.xls INFO @ Fri, 15 Feb 2019 09:05:32: #4 Write peak in narrowPeak format file... ERX1236298.10_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 09:05:32: #4 Write summits bed file... ERX1236298.10_summits.bed INFO @ Fri, 15 Feb 2019 09:05:32: Done! pass1 - making usageList (16 chroms): 7 millis pass2 - checking and writing primary data (525 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 09:05:33: #4 Write output xls file... ERX1236298.05_peaks.xls INFO @ Fri, 15 Feb 2019 09:05:33: #4 Write peak in narrowPeak format file... ERX1236298.05_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 09:05:33: #4 Write summits bed file... ERX1236298.05_summits.bed INFO @ Fri, 15 Feb 2019 09:05:33: Done! pass1 - making usageList (16 chroms): 6 millis pass2 - checking and writing primary data (889 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。