Job ID = 11193193 sra ファイルのダウンロード中... Completed: 181636K bytes transferred in 6 seconds (214693K 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 4146069 spots for /home/okishinya/chipatlas/results/sacCer3/SRX876283/SRR1802386.sra Written 4146069 spots for /home/okishinya/chipatlas/results/sacCer3/SRX876283/SRR1802386.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: 00:02:09 4146069 reads; of these: 4146069 (100.00%) were paired; of these: 1784254 (43.03%) aligned concordantly 0 times 2041370 (49.24%) aligned concordantly exactly 1 time 320445 (7.73%) aligned concordantly >1 times ---- 1784254 pairs aligned concordantly 0 times; of these: 54084 (3.03%) aligned discordantly 1 time ---- 1730170 pairs aligned 0 times concordantly or discordantly; of these: 3460340 mates make up the pairs; of these: 3329766 (96.23%) aligned 0 times 92488 (2.67%) aligned exactly 1 time 38086 (1.10%) aligned >1 times 59.84% overall alignment rate Time searching: 00:02:09 Overall time: 00:02:09 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] 2112964 / 2399909 = 0.8804 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 @ Sat, 15 Sep 2018 11:10:01: # Command line: callpeak -t SRX876283.bam -f BAM -g 12100000 -n SRX876283.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX876283.20 # format = BAM # ChIP-seq file = ['SRX876283.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 @ Sat, 15 Sep 2018 11:10:01: # Command line: callpeak -t SRX876283.bam -f BAM -g 12100000 -n SRX876283.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX876283.10 # format = BAM # ChIP-seq file = ['SRX876283.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 @ Sat, 15 Sep 2018 11:10:01: # Command line: callpeak -t SRX876283.bam -f BAM -g 12100000 -n SRX876283.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX876283.05 # format = BAM # ChIP-seq file = ['SRX876283.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 @ Sat, 15 Sep 2018 11:10:01: #1 read tag files... INFO @ Sat, 15 Sep 2018 11:10:01: #1 read tag files... INFO @ Sat, 15 Sep 2018 11:10:01: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 11:10:01: #1 read tag files... INFO @ Sat, 15 Sep 2018 11:10:01: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 11:10:01: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 11:10:06: #1 tag size is determined as 40 bps INFO @ Sat, 15 Sep 2018 11:10:06: #1 tag size = 40 INFO @ Sat, 15 Sep 2018 11:10:06: #1 total tags in treatment: 293791 INFO @ Sat, 15 Sep 2018 11:10:06: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 11:10:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 11:10:06: #1 tags after filtering in treatment: 262066 INFO @ Sat, 15 Sep 2018 11:10:06: #1 Redundant rate of treatment: 0.11 INFO @ Sat, 15 Sep 2018 11:10:06: #1 finished! INFO @ Sat, 15 Sep 2018 11:10:06: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 11:10:06: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 11:10:06: #2 number of paired peaks: 327 WARNING @ Sat, 15 Sep 2018 11:10:06: Fewer paired peaks (327) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 327 pairs to build model! INFO @ Sat, 15 Sep 2018 11:10:06: start model_add_line... INFO @ Sat, 15 Sep 2018 11:10:06: start X-correlation... INFO @ Sat, 15 Sep 2018 11:10:06: #1 tag size is determined as 40 bps INFO @ Sat, 15 Sep 2018 11:10:06: #1 tag size = 40 INFO @ Sat, 15 Sep 2018 11:10:06: #1 total tags in treatment: 293791 INFO @ Sat, 15 Sep 2018 11:10:06: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 11:10:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 11:10:06: #1 tags after filtering in treatment: 262066 INFO @ Sat, 15 Sep 2018 11:10:06: #1 Redundant rate of treatment: 0.11 INFO @ Sat, 15 Sep 2018 11:10:06: #1 finished! INFO @ Sat, 15 Sep 2018 11:10:06: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 11:10:06: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 11:10:06: end of X-cor INFO @ Sat, 15 Sep 2018 11:10:06: #2 finished! INFO @ Sat, 15 Sep 2018 11:10:06: #2 predicted fragment length is 136 bps INFO @ Sat, 15 Sep 2018 11:10:06: #2 alternative fragment length(s) may be 136,548,575,596 bps INFO @ Sat, 15 Sep 2018 11:10:06: #2.2 Generate R script for model : SRX876283.20_model.r INFO @ Sat, 15 Sep 2018 11:10:06: #3 Call peaks... INFO @ Sat, 15 Sep 2018 11:10:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 11:10:06: #2 number of paired peaks: 327 WARNING @ Sat, 15 Sep 2018 11:10:06: Fewer paired peaks (327) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 327 pairs to build model! INFO @ Sat, 15 Sep 2018 11:10:06: start model_add_line... INFO @ Sat, 15 Sep 2018 11:10:06: start X-correlation... INFO @ Sat, 15 Sep 2018 11:10:06: end of X-cor INFO @ Sat, 15 Sep 2018 11:10:06: #2 finished! INFO @ Sat, 15 Sep 2018 11:10:06: #2 predicted fragment length is 136 bps INFO @ Sat, 15 Sep 2018 11:10:06: #2 alternative fragment length(s) may be 136,548,575,596 bps INFO @ Sat, 15 Sep 2018 11:10:06: #2.2 Generate R script for model : SRX876283.10_model.r INFO @ Sat, 15 Sep 2018 11:10:06: #1 tag size is determined as 40 bps INFO @ Sat, 15 Sep 2018 11:10:06: #1 tag size = 40 INFO @ Sat, 15 Sep 2018 11:10:06: #1 total tags in treatment: 293791 INFO @ Sat, 15 Sep 2018 11:10:06: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 11:10:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 11:10:06: #3 Call peaks... INFO @ Sat, 15 Sep 2018 11:10:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 11:10:06: #1 tags after filtering in treatment: 262066 INFO @ Sat, 15 Sep 2018 11:10:06: #1 Redundant rate of treatment: 0.11 INFO @ Sat, 15 Sep 2018 11:10:06: #1 finished! INFO @ Sat, 15 Sep 2018 11:10:06: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 11:10:06: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 11:10:06: #2 number of paired peaks: 327 WARNING @ Sat, 15 Sep 2018 11:10:06: Fewer paired peaks (327) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 327 pairs to build model! INFO @ Sat, 15 Sep 2018 11:10:06: start model_add_line... INFO @ Sat, 15 Sep 2018 11:10:06: start X-correlation... INFO @ Sat, 15 Sep 2018 11:10:06: end of X-cor INFO @ Sat, 15 Sep 2018 11:10:06: #2 finished! INFO @ Sat, 15 Sep 2018 11:10:06: #2 predicted fragment length is 136 bps INFO @ Sat, 15 Sep 2018 11:10:06: #2 alternative fragment length(s) may be 136,548,575,596 bps INFO @ Sat, 15 Sep 2018 11:10:06: #2.2 Generate R script for model : SRX876283.05_model.r INFO @ Sat, 15 Sep 2018 11:10:06: #3 Call peaks... INFO @ Sat, 15 Sep 2018 11:10:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 11:10:07: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 11:10:07: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 11:10:07: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 11:10:07: #4 Write output xls file... SRX876283.20_peaks.xls INFO @ Sat, 15 Sep 2018 11:10:07: #4 Write peak in narrowPeak format file... SRX876283.20_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 11:10:07: #4 Write summits bed file... SRX876283.20_summits.bed INFO @ Sat, 15 Sep 2018 11:10:07: Done! pass1 - making usageList (6 chroms): 1 millis INFO @ Sat, 15 Sep 2018 11:10:07: #4 Write output xls file... SRX876283.10_peaks.xls INFO @ Sat, 15 Sep 2018 11:10:07: #4 Write peak in narrowPeak format file... SRX876283.10_peaks.narrowPeak pass2 - checking and writing primary data (6 records, 4 fields): 11 millis INFO @ Sat, 15 Sep 2018 11:10:07: #4 Write summits bed file... SRX876283.10_summits.bed INFO @ Sat, 15 Sep 2018 11:10:07: Done! CompletedMACS2peakCalling pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (73 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 15 Sep 2018 11:10:07: #4 Write output xls file... SRX876283.05_peaks.xls INFO @ Sat, 15 Sep 2018 11:10:07: #4 Write peak in narrowPeak format file... SRX876283.05_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 11:10:07: #4 Write summits bed file... SRX876283.05_summits.bed INFO @ Sat, 15 Sep 2018 11:10:07: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (291 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。