Job ID = 2011892 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 2,814,770 reads read : 5,629,540 reads written : 5,629,540 rm: cannot remove ‘[DSE]RR*’: No such file or directory 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: 00:01:51 2814770 reads; of these: 2814770 (100.00%) were paired; of these: 367938 (13.07%) aligned concordantly 0 times 2084276 (74.05%) aligned concordantly exactly 1 time 362556 (12.88%) aligned concordantly >1 times ---- 367938 pairs aligned concordantly 0 times; of these: 224038 (60.89%) aligned discordantly 1 time ---- 143900 pairs aligned 0 times concordantly or discordantly; of these: 287800 mates make up the pairs; of these: 143862 (49.99%) aligned 0 times 56999 (19.81%) aligned exactly 1 time 86939 (30.21%) aligned >1 times 97.44% overall alignment rate Time searching: 00:01:52 Overall time: 00:01:52 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] 75116 / 2669009 = 0.0281 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, 06 Jul 2019 03:06:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5383668/SRX5383668.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5383668/SRX5383668.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5383668/SRX5383668.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5383668/SRX5383668.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, 06 Jul 2019 03:06:13: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:06:13: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:06:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5383668/SRX5383668.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5383668/SRX5383668.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5383668/SRX5383668.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5383668/SRX5383668.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, 06 Jul 2019 03:06:13: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:06:13: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:06:20: 1000000 INFO @ Sat, 06 Jul 2019 03:06:21: 1000000 INFO @ Sat, 06 Jul 2019 03:06:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5383668/SRX5383668.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5383668/SRX5383668.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5383668/SRX5383668.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5383668/SRX5383668.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, 06 Jul 2019 03:06:23: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:06:23: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:06:28: 2000000 INFO @ Sat, 06 Jul 2019 03:06:28: 2000000 INFO @ Sat, 06 Jul 2019 03:06:30: 1000000 INFO @ Sat, 06 Jul 2019 03:06:35: 3000000 INFO @ Sat, 06 Jul 2019 03:06:36: 3000000 INFO @ Sat, 06 Jul 2019 03:06:38: 2000000 INFO @ Sat, 06 Jul 2019 03:06:43: 4000000 INFO @ Sat, 06 Jul 2019 03:06:44: 4000000 INFO @ Sat, 06 Jul 2019 03:06:45: 3000000 INFO @ Sat, 06 Jul 2019 03:06:50: 5000000 INFO @ Sat, 06 Jul 2019 03:06:51: 5000000 INFO @ Sat, 06 Jul 2019 03:06:53: 4000000 INFO @ Sat, 06 Jul 2019 03:06:53: #1 tag size is determined as 37 bps INFO @ Sat, 06 Jul 2019 03:06:53: #1 tag size = 37 INFO @ Sat, 06 Jul 2019 03:06:53: #1 total tags in treatment: 2376020 INFO @ Sat, 06 Jul 2019 03:06:53: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:06:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 03:06:53: #1 tags after filtering in treatment: 1999933 INFO @ Sat, 06 Jul 2019 03:06:53: #1 Redundant rate of treatment: 0.16 INFO @ Sat, 06 Jul 2019 03:06:53: #1 finished! INFO @ Sat, 06 Jul 2019 03:06:53: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:06:53: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:06:53: #2 number of paired peaks: 177 WARNING @ Sat, 06 Jul 2019 03:06:53: Fewer paired peaks (177) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 177 pairs to build model! INFO @ Sat, 06 Jul 2019 03:06:53: start model_add_line... INFO @ Sat, 06 Jul 2019 03:06:53: start X-correlation... INFO @ Sat, 06 Jul 2019 03:06:53: end of X-cor INFO @ Sat, 06 Jul 2019 03:06:53: #2 finished! INFO @ Sat, 06 Jul 2019 03:06:53: #2 predicted fragment length is 233 bps INFO @ Sat, 06 Jul 2019 03:06:53: #2 alternative fragment length(s) may be 0,39,72,105,159,196,233,273,279,306,333,376,424,450,486,528,541,561,591 bps INFO @ Sat, 06 Jul 2019 03:06:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5383668/SRX5383668.05_model.r INFO @ Sat, 06 Jul 2019 03:06:53: #3 Call peaks... INFO @ Sat, 06 Jul 2019 03:06:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 06 Jul 2019 03:06:53: #1 tag size is determined as 37 bps INFO @ Sat, 06 Jul 2019 03:06:53: #1 tag size = 37 INFO @ Sat, 06 Jul 2019 03:06:53: #1 total tags in treatment: 2376020 INFO @ Sat, 06 Jul 2019 03:06:53: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:06:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 03:06:53: #1 tags after filtering in treatment: 1999933 INFO @ Sat, 06 Jul 2019 03:06:53: #1 Redundant rate of treatment: 0.16 INFO @ Sat, 06 Jul 2019 03:06:53: #1 finished! INFO @ Sat, 06 Jul 2019 03:06:53: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:06:53: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:06:54: #2 number of paired peaks: 177 WARNING @ Sat, 06 Jul 2019 03:06:54: Fewer paired peaks (177) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 177 pairs to build model! INFO @ Sat, 06 Jul 2019 03:06:54: start model_add_line... INFO @ Sat, 06 Jul 2019 03:06:54: start X-correlation... INFO @ Sat, 06 Jul 2019 03:06:54: end of X-cor INFO @ Sat, 06 Jul 2019 03:06:54: #2 finished! INFO @ Sat, 06 Jul 2019 03:06:54: #2 predicted fragment length is 233 bps INFO @ Sat, 06 Jul 2019 03:06:54: #2 alternative fragment length(s) may be 0,39,72,105,159,196,233,273,279,306,333,376,424,450,486,528,541,561,591 bps INFO @ Sat, 06 Jul 2019 03:06:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5383668/SRX5383668.10_model.r INFO @ Sat, 06 Jul 2019 03:06:54: #3 Call peaks... INFO @ Sat, 06 Jul 2019 03:06:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 06 Jul 2019 03:06:59: #3 Call peaks for each chromosome... INFO @ Sat, 06 Jul 2019 03:07:00: 5000000 INFO @ Sat, 06 Jul 2019 03:07:00: #3 Call peaks for each chromosome... INFO @ Sat, 06 Jul 2019 03:07:01: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5383668/SRX5383668.05_peaks.xls INFO @ Sat, 06 Jul 2019 03:07:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5383668/SRX5383668.05_peaks.narrowPeak INFO @ Sat, 06 Jul 2019 03:07:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5383668/SRX5383668.05_summits.bed INFO @ Sat, 06 Jul 2019 03:07:01: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (22 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 03:07:02: #1 tag size is determined as 37 bps INFO @ Sat, 06 Jul 2019 03:07:02: #1 tag size = 37 INFO @ Sat, 06 Jul 2019 03:07:02: #1 total tags in treatment: 2376020 INFO @ Sat, 06 Jul 2019 03:07:02: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:07:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 03:07:02: #1 tags after filtering in treatment: 1999933 INFO @ Sat, 06 Jul 2019 03:07:02: #1 Redundant rate of treatment: 0.16 INFO @ Sat, 06 Jul 2019 03:07:02: #1 finished! INFO @ Sat, 06 Jul 2019 03:07:02: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:07:02: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:07:02: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5383668/SRX5383668.10_peaks.xls INFO @ Sat, 06 Jul 2019 03:07:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5383668/SRX5383668.10_peaks.narrowPeak INFO @ Sat, 06 Jul 2019 03:07:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5383668/SRX5383668.10_summits.bed INFO @ Sat, 06 Jul 2019 03:07:02: #2 number of paired peaks: 177 WARNING @ Sat, 06 Jul 2019 03:07:02: Fewer paired peaks (177) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 177 pairs to build model! INFO @ Sat, 06 Jul 2019 03:07:02: start model_add_line... INFO @ Sat, 06 Jul 2019 03:07:02: start X-correlation... INFO @ Sat, 06 Jul 2019 03:07:02: end of X-cor INFO @ Sat, 06 Jul 2019 03:07:02: #2 finished! INFO @ Sat, 06 Jul 2019 03:07:02: #2 predicted fragment length is 233 bps INFO @ Sat, 06 Jul 2019 03:07:02: #2 alternative fragment length(s) may be 0,39,72,105,159,196,233,273,279,306,333,376,424,450,486,528,541,561,591 bps INFO @ Sat, 06 Jul 2019 03:07:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5383668/SRX5383668.20_model.r INFO @ Sat, 06 Jul 2019 03:07:02: #3 Call peaks... INFO @ Sat, 06 Jul 2019 03:07:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 06 Jul 2019 03:07:03: Done! pass1 - making usageList (5 chroms): 1 millis pass2 - checking and writing primary data (11 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 03:07:08: #3 Call peaks for each chromosome... INFO @ Sat, 06 Jul 2019 03:07:10: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5383668/SRX5383668.20_peaks.xls INFO @ Sat, 06 Jul 2019 03:07:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5383668/SRX5383668.20_peaks.narrowPeak INFO @ Sat, 06 Jul 2019 03:07:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5383668/SRX5383668.20_summits.bed INFO @ Sat, 06 Jul 2019 03:07:10: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (8 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。