Job ID = 2011926 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 3,370,092 reads read : 6,740,184 reads written : 6,740,184 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: 00:02:14 3370092 reads; of these: 3370092 (100.00%) were paired; of these: 360926 (10.71%) aligned concordantly 0 times 2592356 (76.92%) aligned concordantly exactly 1 time 416810 (12.37%) aligned concordantly >1 times ---- 360926 pairs aligned concordantly 0 times; of these: 208499 (57.77%) aligned discordantly 1 time ---- 152427 pairs aligned 0 times concordantly or discordantly; of these: 304854 mates make up the pairs; of these: 180712 (59.28%) aligned 0 times 55804 (18.31%) aligned exactly 1 time 68338 (22.42%) aligned >1 times 97.32% overall alignment rate Time searching: 00:02:14 Overall time: 00:02:14 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] 90153 / 3215847 = 0.0280 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 03:26:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5391494/SRX5391494.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5391494/SRX5391494.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5391494/SRX5391494.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5391494/SRX5391494.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 03:26:01: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:26:01: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:26:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5391494/SRX5391494.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5391494/SRX5391494.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5391494/SRX5391494.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5391494/SRX5391494.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 03:26:03: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:26:03: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:26:07: 1000000 INFO @ Sat, 06 Jul 2019 03:26:09: 1000000 INFO @ Sat, 06 Jul 2019 03:26:12: 2000000 INFO @ Sat, 06 Jul 2019 03:26:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5391494/SRX5391494.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5391494/SRX5391494.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5391494/SRX5391494.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5391494/SRX5391494.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 03:26:13: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:26:13: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:26:14: 2000000 INFO @ Sat, 06 Jul 2019 03:26:18: 3000000 INFO @ Sat, 06 Jul 2019 03:26:19: 1000000 INFO @ Sat, 06 Jul 2019 03:26:21: 3000000 INFO @ Sat, 06 Jul 2019 03:26:24: 4000000 INFO @ Sat, 06 Jul 2019 03:26:26: 2000000 INFO @ Sat, 06 Jul 2019 03:26:27: 4000000 INFO @ Sat, 06 Jul 2019 03:26:29: 5000000 INFO @ Sat, 06 Jul 2019 03:26:32: 3000000 INFO @ Sat, 06 Jul 2019 03:26:33: 5000000 INFO @ Sat, 06 Jul 2019 03:26:35: 6000000 INFO @ Sat, 06 Jul 2019 03:26:37: #1 tag size is determined as 37 bps INFO @ Sat, 06 Jul 2019 03:26:37: #1 tag size = 37 INFO @ Sat, 06 Jul 2019 03:26:37: #1 total tags in treatment: 2922974 INFO @ Sat, 06 Jul 2019 03:26:37: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:26:37: #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 03:26:37: #1 tags after filtering in treatment: 2497480 INFO @ Sat, 06 Jul 2019 03:26:37: #1 Redundant rate of treatment: 0.15 INFO @ Sat, 06 Jul 2019 03:26:37: #1 finished! INFO @ Sat, 06 Jul 2019 03:26:37: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:26:37: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:26:37: #2 number of paired peaks: 150 WARNING @ Sat, 06 Jul 2019 03:26:37: Fewer paired peaks (150) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 150 pairs to build model! INFO @ Sat, 06 Jul 2019 03:26:37: start model_add_line... INFO @ Sat, 06 Jul 2019 03:26:37: start X-correlation... INFO @ Sat, 06 Jul 2019 03:26:37: end of X-cor INFO @ Sat, 06 Jul 2019 03:26:37: #2 finished! INFO @ Sat, 06 Jul 2019 03:26:37: #2 predicted fragment length is 228 bps INFO @ Sat, 06 Jul 2019 03:26:37: #2 alternative fragment length(s) may be 1,13,45,99,135,151,180,202,205,228,252,272,296,320,361,394,461,503,508,542,582 bps INFO @ Sat, 06 Jul 2019 03:26:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5391494/SRX5391494.05_model.r INFO @ Sat, 06 Jul 2019 03:26:37: #3 Call peaks... INFO @ Sat, 06 Jul 2019 03:26:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 06 Jul 2019 03:26:37: 4000000 INFO @ Sat, 06 Jul 2019 03:26:39: 6000000 INFO @ Sat, 06 Jul 2019 03:26:41: #1 tag size is determined as 37 bps INFO @ Sat, 06 Jul 2019 03:26:41: #1 tag size = 37 INFO @ Sat, 06 Jul 2019 03:26:41: #1 total tags in treatment: 2922974 INFO @ Sat, 06 Jul 2019 03:26:41: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:26:41: #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 03:26:41: #1 tags after filtering in treatment: 2497480 INFO @ Sat, 06 Jul 2019 03:26:41: #1 Redundant rate of treatment: 0.15 INFO @ Sat, 06 Jul 2019 03:26:41: #1 finished! INFO @ Sat, 06 Jul 2019 03:26:41: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:26:41: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:26:41: #2 number of paired peaks: 150 WARNING @ Sat, 06 Jul 2019 03:26:41: Fewer paired peaks (150) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 150 pairs to build model! INFO @ Sat, 06 Jul 2019 03:26:41: start model_add_line... INFO @ Sat, 06 Jul 2019 03:26:41: start X-correlation... INFO @ Sat, 06 Jul 2019 03:26:41: end of X-cor INFO @ Sat, 06 Jul 2019 03:26:41: #2 finished! INFO @ Sat, 06 Jul 2019 03:26:41: #2 predicted fragment length is 228 bps INFO @ Sat, 06 Jul 2019 03:26:41: #2 alternative fragment length(s) may be 1,13,45,99,135,151,180,202,205,228,252,272,296,320,361,394,461,503,508,542,582 bps INFO @ Sat, 06 Jul 2019 03:26:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5391494/SRX5391494.10_model.r INFO @ Sat, 06 Jul 2019 03:26:41: #3 Call peaks... INFO @ Sat, 06 Jul 2019 03:26:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 06 Jul 2019 03:26:43: 5000000 INFO @ Sat, 06 Jul 2019 03:26:44: #3 Call peaks for each chromosome... INFO @ Sat, 06 Jul 2019 03:26:46: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5391494/SRX5391494.05_peaks.xls INFO @ Sat, 06 Jul 2019 03:26:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5391494/SRX5391494.05_peaks.narrowPeak INFO @ Sat, 06 Jul 2019 03:26:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5391494/SRX5391494.05_summits.bed INFO @ Sat, 06 Jul 2019 03:26:46: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (12 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 03:26:48: #3 Call peaks for each chromosome... INFO @ Sat, 06 Jul 2019 03:26:49: 6000000 INFO @ Sat, 06 Jul 2019 03:26:51: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5391494/SRX5391494.10_peaks.xls INFO @ Sat, 06 Jul 2019 03:26:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5391494/SRX5391494.10_peaks.narrowPeak INFO @ Sat, 06 Jul 2019 03:26:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5391494/SRX5391494.10_summits.bed INFO @ Sat, 06 Jul 2019 03:26:51: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (10 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 03:26:51: #1 tag size is determined as 37 bps INFO @ Sat, 06 Jul 2019 03:26:51: #1 tag size = 37 INFO @ Sat, 06 Jul 2019 03:26:51: #1 total tags in treatment: 2922974 INFO @ Sat, 06 Jul 2019 03:26:51: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:26:51: #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 03:26:51: #1 tags after filtering in treatment: 2497480 INFO @ Sat, 06 Jul 2019 03:26:51: #1 Redundant rate of treatment: 0.15 INFO @ Sat, 06 Jul 2019 03:26:51: #1 finished! INFO @ Sat, 06 Jul 2019 03:26:51: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:26:51: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:26:52: #2 number of paired peaks: 150 WARNING @ Sat, 06 Jul 2019 03:26:52: Fewer paired peaks (150) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 150 pairs to build model! INFO @ Sat, 06 Jul 2019 03:26:52: start model_add_line... INFO @ Sat, 06 Jul 2019 03:26:52: start X-correlation... INFO @ Sat, 06 Jul 2019 03:26:52: end of X-cor INFO @ Sat, 06 Jul 2019 03:26:52: #2 finished! INFO @ Sat, 06 Jul 2019 03:26:52: #2 predicted fragment length is 228 bps INFO @ Sat, 06 Jul 2019 03:26:52: #2 alternative fragment length(s) may be 1,13,45,99,135,151,180,202,205,228,252,272,296,320,361,394,461,503,508,542,582 bps INFO @ Sat, 06 Jul 2019 03:26:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5391494/SRX5391494.20_model.r INFO @ Sat, 06 Jul 2019 03:26:52: #3 Call peaks... INFO @ Sat, 06 Jul 2019 03:26:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 06 Jul 2019 03:26:59: #3 Call peaks for each chromosome... INFO @ Sat, 06 Jul 2019 03:27:01: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5391494/SRX5391494.20_peaks.xls INFO @ Sat, 06 Jul 2019 03:27:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5391494/SRX5391494.20_peaks.narrowPeak INFO @ Sat, 06 Jul 2019 03:27:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5391494/SRX5391494.20_summits.bed INFO @ Sat, 06 Jul 2019 03:27:01: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (6 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。