Job ID = 2011917 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 3,608,060 reads read : 7,216,120 reads written : 7,216,120 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: 00:02:11 3608060 reads; of these: 3608060 (100.00%) were paired; of these: 349952 (9.70%) aligned concordantly 0 times 2958053 (81.98%) aligned concordantly exactly 1 time 300055 (8.32%) aligned concordantly >1 times ---- 349952 pairs aligned concordantly 0 times; of these: 204623 (58.47%) aligned discordantly 1 time ---- 145329 pairs aligned 0 times concordantly or discordantly; of these: 290658 mates make up the pairs; of these: 179857 (61.88%) aligned 0 times 57697 (19.85%) aligned exactly 1 time 53104 (18.27%) aligned >1 times 97.51% overall alignment rate Time searching: 00:02:11 Overall time: 00:02:11 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] 708560 / 3461378 = 0.2047 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 03:21:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5383690/SRX5383690.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5383690/SRX5383690.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5383690/SRX5383690.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5383690/SRX5383690.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 03:21:38: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:21:38: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:21:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5383690/SRX5383690.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5383690/SRX5383690.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5383690/SRX5383690.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5383690/SRX5383690.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 03:21:39: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:21:39: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:21:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5383690/SRX5383690.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5383690/SRX5383690.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5383690/SRX5383690.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5383690/SRX5383690.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 03:21:39: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:21:39: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:21:43: 1000000 INFO @ Sat, 06 Jul 2019 03:21:45: 1000000 INFO @ Sat, 06 Jul 2019 03:21:46: 1000000 INFO @ Sat, 06 Jul 2019 03:21:49: 2000000 INFO @ Sat, 06 Jul 2019 03:21:51: 2000000 INFO @ Sat, 06 Jul 2019 03:21:52: 2000000 INFO @ Sat, 06 Jul 2019 03:21:54: 3000000 INFO @ Sat, 06 Jul 2019 03:21:58: 3000000 INFO @ Sat, 06 Jul 2019 03:21:59: 3000000 INFO @ Sat, 06 Jul 2019 03:22:00: 4000000 INFO @ Sat, 06 Jul 2019 03:22:05: 5000000 INFO @ Sat, 06 Jul 2019 03:22:06: 4000000 INFO @ Sat, 06 Jul 2019 03:22:06: 4000000 INFO @ Sat, 06 Jul 2019 03:22:09: #1 tag size is determined as 37 bps INFO @ Sat, 06 Jul 2019 03:22:09: #1 tag size = 37 INFO @ Sat, 06 Jul 2019 03:22:09: #1 total tags in treatment: 2557605 INFO @ Sat, 06 Jul 2019 03:22:09: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:22:09: #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 03:22:09: #1 tags after filtering in treatment: 1281484 INFO @ Sat, 06 Jul 2019 03:22:09: #1 Redundant rate of treatment: 0.50 INFO @ Sat, 06 Jul 2019 03:22:09: #1 finished! INFO @ Sat, 06 Jul 2019 03:22:09: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:22:09: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:22:09: #2 number of paired peaks: 282 WARNING @ Sat, 06 Jul 2019 03:22:09: Fewer paired peaks (282) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 282 pairs to build model! INFO @ Sat, 06 Jul 2019 03:22:09: start model_add_line... INFO @ Sat, 06 Jul 2019 03:22:09: start X-correlation... INFO @ Sat, 06 Jul 2019 03:22:09: end of X-cor INFO @ Sat, 06 Jul 2019 03:22:09: #2 finished! INFO @ Sat, 06 Jul 2019 03:22:09: #2 predicted fragment length is 274 bps INFO @ Sat, 06 Jul 2019 03:22:09: #2 alternative fragment length(s) may be 274 bps INFO @ Sat, 06 Jul 2019 03:22:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5383690/SRX5383690.05_model.r INFO @ Sat, 06 Jul 2019 03:22:09: #3 Call peaks... INFO @ Sat, 06 Jul 2019 03:22:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 06 Jul 2019 03:22:12: 5000000 INFO @ Sat, 06 Jul 2019 03:22:13: 5000000 INFO @ Sat, 06 Jul 2019 03:22:15: #3 Call peaks for each chromosome... INFO @ Sat, 06 Jul 2019 03:22:16: #1 tag size is determined as 37 bps INFO @ Sat, 06 Jul 2019 03:22:16: #1 tag size = 37 INFO @ Sat, 06 Jul 2019 03:22:16: #1 total tags in treatment: 2557605 INFO @ Sat, 06 Jul 2019 03:22:16: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:22:16: #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 03:22:16: #1 tags after filtering in treatment: 1281484 INFO @ Sat, 06 Jul 2019 03:22:16: #1 Redundant rate of treatment: 0.50 INFO @ Sat, 06 Jul 2019 03:22:16: #1 finished! INFO @ Sat, 06 Jul 2019 03:22:16: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:22:16: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:22:16: #2 number of paired peaks: 282 WARNING @ Sat, 06 Jul 2019 03:22:16: Fewer paired peaks (282) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 282 pairs to build model! INFO @ Sat, 06 Jul 2019 03:22:16: start model_add_line... INFO @ Sat, 06 Jul 2019 03:22:17: start X-correlation... INFO @ Sat, 06 Jul 2019 03:22:17: end of X-cor INFO @ Sat, 06 Jul 2019 03:22:17: #2 finished! INFO @ Sat, 06 Jul 2019 03:22:17: #2 predicted fragment length is 274 bps INFO @ Sat, 06 Jul 2019 03:22:17: #2 alternative fragment length(s) may be 274 bps INFO @ Sat, 06 Jul 2019 03:22:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5383690/SRX5383690.20_model.r INFO @ Sat, 06 Jul 2019 03:22:17: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5383690/SRX5383690.05_peaks.xls INFO @ Sat, 06 Jul 2019 03:22:18: #1 tag size is determined as 37 bps INFO @ Sat, 06 Jul 2019 03:22:18: #1 tag size = 37 INFO @ Sat, 06 Jul 2019 03:22:18: #1 total tags in treatment: 2557605 INFO @ Sat, 06 Jul 2019 03:22:18: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:22:18: #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 03:22:18: #1 tags after filtering in treatment: 1281484 INFO @ Sat, 06 Jul 2019 03:22:18: #1 Redundant rate of treatment: 0.50 INFO @ Sat, 06 Jul 2019 03:22:18: #1 finished! INFO @ Sat, 06 Jul 2019 03:22:18: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:22:18: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:22:18: #2 number of paired peaks: 282 WARNING @ Sat, 06 Jul 2019 03:22:18: Fewer paired peaks (282) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 282 pairs to build model! INFO @ Sat, 06 Jul 2019 03:22:18: start model_add_line... INFO @ Sat, 06 Jul 2019 03:22:18: start X-correlation... INFO @ Sat, 06 Jul 2019 03:22:18: end of X-cor INFO @ Sat, 06 Jul 2019 03:22:18: #2 finished! INFO @ Sat, 06 Jul 2019 03:22:18: #2 predicted fragment length is 274 bps INFO @ Sat, 06 Jul 2019 03:22:18: #2 alternative fragment length(s) may be 274 bps INFO @ Sat, 06 Jul 2019 03:22:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5383690/SRX5383690.10_model.r BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 06 Jul 2019 03:22:47: #3 Call peaks... INFO @ Sat, 06 Jul 2019 03:22:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 06 Jul 2019 03:22:47: #3 Call peaks... INFO @ Sat, 06 Jul 2019 03:22:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 06 Jul 2019 03:22:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5383690/SRX5383690.05_peaks.narrowPeak INFO @ Sat, 06 Jul 2019 03:22:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5383690/SRX5383690.05_summits.bed INFO @ Sat, 06 Jul 2019 03:22:47: Done! pass1 - making usageList (17 chroms): 2 millis pass2 - checking and writing primary data (703 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 03:22:53: #3 Call peaks for each chromosome... INFO @ Sat, 06 Jul 2019 03:22:53: #3 Call peaks for each chromosome... INFO @ Sat, 06 Jul 2019 03:22:55: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5383690/SRX5383690.20_peaks.xls BigWig に変換しました。 INFO @ Sat, 06 Jul 2019 03:22:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5383690/SRX5383690.20_peaks.narrowPeak INFO @ Sat, 06 Jul 2019 03:22:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5383690/SRX5383690.20_summits.bed INFO @ Sat, 06 Jul 2019 03:22:55: Done! INFO @ Sat, 06 Jul 2019 03:22:55: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5383690/SRX5383690.10_peaks.xls INFO @ Sat, 06 Jul 2019 03:22:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5383690/SRX5383690.10_peaks.narrowPeak INFO @ Sat, 06 Jul 2019 03:22:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5383690/SRX5383690.10_summits.bed INFO @ Sat, 06 Jul 2019 03:22:55: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (323 records, 4 fields): 2 millis pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (508 records, 4 fields): 4 millis CompletedMACS2peakCalling CompletedMACS2peakCalling