Job ID = 11244897 sra ファイルのダウンロード中... Completed: 105187K bytes transferred in 4 seconds (199015K 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 2096285 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4456767/SRR7591552.sra Written 2096285 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4456767/SRR7591552.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: 00:01:41 2096285 reads; of these: 2096285 (100.00%) were paired; of these: 394656 (18.83%) aligned concordantly 0 times 1550035 (73.94%) aligned concordantly exactly 1 time 151594 (7.23%) aligned concordantly >1 times ---- 394656 pairs aligned concordantly 0 times; of these: 38083 (9.65%) aligned discordantly 1 time ---- 356573 pairs aligned 0 times concordantly or discordantly; of these: 713146 mates make up the pairs; of these: 676644 (94.88%) aligned 0 times 23217 (3.26%) aligned exactly 1 time 13285 (1.86%) aligned >1 times 83.86% overall alignment rate Time searching: 00:01:41 Overall time: 00:01:41 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] 22352 / 1737886 = 0.0129 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 @ Tue, 09 Oct 2018 22:42:15: # Command line: callpeak -t SRX4456767.bam -f BAM -g 12100000 -n SRX4456767.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4456767.05 # format = BAM # ChIP-seq file = ['SRX4456767.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 @ Tue, 09 Oct 2018 22:42:15: #1 read tag files... INFO @ Tue, 09 Oct 2018 22:42:15: # Command line: callpeak -t SRX4456767.bam -f BAM -g 12100000 -n SRX4456767.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4456767.10 # format = BAM # ChIP-seq file = ['SRX4456767.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 @ Tue, 09 Oct 2018 22:42:15: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 22:42:15: #1 read tag files... INFO @ Tue, 09 Oct 2018 22:42:15: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 22:42:15: # Command line: callpeak -t SRX4456767.bam -f BAM -g 12100000 -n SRX4456767.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4456767.20 # format = BAM # ChIP-seq file = ['SRX4456767.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 @ Tue, 09 Oct 2018 22:42:15: #1 read tag files... INFO @ Tue, 09 Oct 2018 22:42:15: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 22:42:22: 1000000 INFO @ Tue, 09 Oct 2018 22:42:22: 1000000 INFO @ Tue, 09 Oct 2018 22:42:22: 1000000 INFO @ Tue, 09 Oct 2018 22:42:29: 2000000 INFO @ Tue, 09 Oct 2018 22:42:29: 2000000 INFO @ Tue, 09 Oct 2018 22:42:29: 2000000 INFO @ Tue, 09 Oct 2018 22:42:35: 3000000 INFO @ Tue, 09 Oct 2018 22:42:37: 3000000 INFO @ Tue, 09 Oct 2018 22:42:37: 3000000 INFO @ Tue, 09 Oct 2018 22:42:38: #1 tag size is determined as 50 bps INFO @ Tue, 09 Oct 2018 22:42:38: #1 tag size = 50 INFO @ Tue, 09 Oct 2018 22:42:38: #1 total tags in treatment: 1679381 INFO @ Tue, 09 Oct 2018 22:42:38: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 22:42:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 09 Oct 2018 22:42:38: #1 tags after filtering in treatment: 1483502 INFO @ Tue, 09 Oct 2018 22:42:38: #1 Redundant rate of treatment: 0.12 INFO @ Tue, 09 Oct 2018 22:42:38: #1 finished! INFO @ Tue, 09 Oct 2018 22:42:38: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 22:42:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 22:42:39: #2 number of paired peaks: 165 WARNING @ Tue, 09 Oct 2018 22:42:39: Fewer paired peaks (165) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 165 pairs to build model! INFO @ Tue, 09 Oct 2018 22:42:39: start model_add_line... INFO @ Tue, 09 Oct 2018 22:42:39: start X-correlation... INFO @ Tue, 09 Oct 2018 22:42:39: end of X-cor INFO @ Tue, 09 Oct 2018 22:42:39: #2 finished! INFO @ Tue, 09 Oct 2018 22:42:39: #2 predicted fragment length is 245 bps INFO @ Tue, 09 Oct 2018 22:42:39: #2 alternative fragment length(s) may be 245 bps INFO @ Tue, 09 Oct 2018 22:42:39: #2.2 Generate R script for model : SRX4456767.20_model.r INFO @ Tue, 09 Oct 2018 22:42:39: #3 Call peaks... INFO @ Tue, 09 Oct 2018 22:42:39: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 09 Oct 2018 22:42:40: #1 tag size is determined as 50 bps INFO @ Tue, 09 Oct 2018 22:42:40: #1 tag size = 50 INFO @ Tue, 09 Oct 2018 22:42:40: #1 total tags in treatment: 1679381 INFO @ Tue, 09 Oct 2018 22:42:40: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 22:42:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 09 Oct 2018 22:42:40: #1 tag size is determined as 50 bps INFO @ Tue, 09 Oct 2018 22:42:40: #1 tag size = 50 INFO @ Tue, 09 Oct 2018 22:42:40: #1 total tags in treatment: 1679381 INFO @ Tue, 09 Oct 2018 22:42:40: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 22:42:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 09 Oct 2018 22:42:40: #1 tags after filtering in treatment: 1483502 INFO @ Tue, 09 Oct 2018 22:42:40: #1 Redundant rate of treatment: 0.12 INFO @ Tue, 09 Oct 2018 22:42:40: #1 finished! INFO @ Tue, 09 Oct 2018 22:42:40: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 22:42:40: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 22:42:40: #1 tags after filtering in treatment: 1483502 INFO @ Tue, 09 Oct 2018 22:42:40: #1 Redundant rate of treatment: 0.12 INFO @ Tue, 09 Oct 2018 22:42:40: #1 finished! INFO @ Tue, 09 Oct 2018 22:42:40: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 22:42:40: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 22:42:40: #2 number of paired peaks: 165 WARNING @ Tue, 09 Oct 2018 22:42:40: Fewer paired peaks (165) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 165 pairs to build model! INFO @ Tue, 09 Oct 2018 22:42:40: start model_add_line... INFO @ Tue, 09 Oct 2018 22:42:40: #2 number of paired peaks: 165 WARNING @ Tue, 09 Oct 2018 22:42:40: Fewer paired peaks (165) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 165 pairs to build model! INFO @ Tue, 09 Oct 2018 22:42:40: start model_add_line... INFO @ Tue, 09 Oct 2018 22:42:40: start X-correlation... INFO @ Tue, 09 Oct 2018 22:42:40: end of X-cor INFO @ Tue, 09 Oct 2018 22:42:40: #2 finished! INFO @ Tue, 09 Oct 2018 22:42:40: #2 predicted fragment length is 245 bps INFO @ Tue, 09 Oct 2018 22:42:40: #2 alternative fragment length(s) may be 245 bps INFO @ Tue, 09 Oct 2018 22:42:40: #2.2 Generate R script for model : SRX4456767.10_model.r INFO @ Tue, 09 Oct 2018 22:42:40: start X-correlation... INFO @ Tue, 09 Oct 2018 22:42:40: #3 Call peaks... INFO @ Tue, 09 Oct 2018 22:42:40: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 09 Oct 2018 22:42:40: end of X-cor INFO @ Tue, 09 Oct 2018 22:42:40: #2 finished! INFO @ Tue, 09 Oct 2018 22:42:40: #2 predicted fragment length is 245 bps INFO @ Tue, 09 Oct 2018 22:42:40: #2 alternative fragment length(s) may be 245 bps INFO @ Tue, 09 Oct 2018 22:42:40: #2.2 Generate R script for model : SRX4456767.05_model.r INFO @ Tue, 09 Oct 2018 22:42:40: #3 Call peaks... INFO @ Tue, 09 Oct 2018 22:42:40: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 09 Oct 2018 22:42:44: #3 Call peaks for each chromosome... INFO @ Tue, 09 Oct 2018 22:42:45: #3 Call peaks for each chromosome... INFO @ Tue, 09 Oct 2018 22:42:46: #3 Call peaks for each chromosome... INFO @ Tue, 09 Oct 2018 22:42:46: #4 Write output xls file... SRX4456767.20_peaks.xls INFO @ Tue, 09 Oct 2018 22:42:46: #4 Write peak in narrowPeak format file... SRX4456767.20_peaks.narrowPeak INFO @ Tue, 09 Oct 2018 22:42:46: #4 Write summits bed file... SRX4456767.20_summits.bed INFO @ Tue, 09 Oct 2018 22:42:46: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (333 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 09 Oct 2018 22:42:47: #4 Write output xls file... SRX4456767.05_peaks.xls INFO @ Tue, 09 Oct 2018 22:42:47: #4 Write peak in narrowPeak format file... SRX4456767.05_peaks.narrowPeak INFO @ Tue, 09 Oct 2018 22:42:47: #4 Write summits bed file... SRX4456767.05_summits.bed INFO @ Tue, 09 Oct 2018 22:42:47: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (997 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 09 Oct 2018 22:42:47: #4 Write output xls file... SRX4456767.10_peaks.xls INFO @ Tue, 09 Oct 2018 22:42:47: #4 Write peak in narrowPeak format file... SRX4456767.10_peaks.narrowPeak INFO @ Tue, 09 Oct 2018 22:42:47: #4 Write summits bed file... SRX4456767.10_summits.bed INFO @ Tue, 09 Oct 2018 22:42:47: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (693 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。