Job ID = 2009919 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 11,429,365 reads read : 22,858,730 reads written : 22,858,730 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR5008413.sra.cache’: 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: 00:13:20 11429365 reads; of these: 11429365 (100.00%) were paired; of these: 2081391 (18.21%) aligned concordantly 0 times 7160498 (62.65%) aligned concordantly exactly 1 time 2187476 (19.14%) aligned concordantly >1 times ---- 2081391 pairs aligned concordantly 0 times; of these: 72810 (3.50%) aligned discordantly 1 time ---- 2008581 pairs aligned 0 times concordantly or discordantly; of these: 4017162 mates make up the pairs; of these: 3472730 (86.45%) aligned 0 times 366566 (9.12%) aligned exactly 1 time 177866 (4.43%) aligned >1 times 84.81% overall alignment rate Time searching: 00:13:20 Overall time: 00:13:20 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_sort_core] merging from 8 files... [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] 3226659 / 9395205 = 0.3434 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 @ Fri, 05 Jul 2019 21:03:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX2339854/SRX2339854.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX2339854/SRX2339854.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX2339854/SRX2339854.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX2339854/SRX2339854.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 @ Fri, 05 Jul 2019 21:03:36: #1 read tag files... INFO @ Fri, 05 Jul 2019 21:03:36: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 21:03:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX2339854/SRX2339854.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX2339854/SRX2339854.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX2339854/SRX2339854.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX2339854/SRX2339854.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 @ Fri, 05 Jul 2019 21:03:37: #1 read tag files... INFO @ Fri, 05 Jul 2019 21:03:37: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 21:03:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX2339854/SRX2339854.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX2339854/SRX2339854.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX2339854/SRX2339854.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX2339854/SRX2339854.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 @ Fri, 05 Jul 2019 21:03:38: #1 read tag files... INFO @ Fri, 05 Jul 2019 21:03:38: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 21:03:45: 1000000 INFO @ Fri, 05 Jul 2019 21:03:45: 1000000 INFO @ Fri, 05 Jul 2019 21:03:46: 1000000 INFO @ Fri, 05 Jul 2019 21:03:54: 2000000 INFO @ Fri, 05 Jul 2019 21:03:54: 2000000 INFO @ Fri, 05 Jul 2019 21:03:55: 2000000 INFO @ Fri, 05 Jul 2019 21:04:02: 3000000 INFO @ Fri, 05 Jul 2019 21:04:03: 3000000 INFO @ Fri, 05 Jul 2019 21:04:03: 3000000 INFO @ Fri, 05 Jul 2019 21:04:10: 4000000 INFO @ Fri, 05 Jul 2019 21:04:11: 4000000 INFO @ Fri, 05 Jul 2019 21:04:12: 4000000 INFO @ Fri, 05 Jul 2019 21:04:18: 5000000 INFO @ Fri, 05 Jul 2019 21:04:19: 5000000 INFO @ Fri, 05 Jul 2019 21:04:20: 5000000 INFO @ Fri, 05 Jul 2019 21:04:26: 6000000 INFO @ Fri, 05 Jul 2019 21:04:27: 6000000 INFO @ Fri, 05 Jul 2019 21:04:28: 6000000 INFO @ Fri, 05 Jul 2019 21:04:34: 7000000 INFO @ Fri, 05 Jul 2019 21:04:35: 7000000 INFO @ Fri, 05 Jul 2019 21:04:36: 7000000 INFO @ Fri, 05 Jul 2019 21:04:42: 8000000 INFO @ Fri, 05 Jul 2019 21:04:44: 8000000 INFO @ Fri, 05 Jul 2019 21:04:45: 8000000 INFO @ Fri, 05 Jul 2019 21:04:50: 9000000 INFO @ Fri, 05 Jul 2019 21:04:52: 9000000 INFO @ Fri, 05 Jul 2019 21:04:53: 9000000 INFO @ Fri, 05 Jul 2019 21:04:58: 10000000 INFO @ Fri, 05 Jul 2019 21:04:59: 10000000 INFO @ Fri, 05 Jul 2019 21:05:00: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 21:05:06: 11000000 INFO @ Fri, 05 Jul 2019 21:05:07: 11000000 INFO @ Fri, 05 Jul 2019 21:05:08: 11000000 BigWig に変換しました。 INFO @ Fri, 05 Jul 2019 21:05:14: 12000000 INFO @ Fri, 05 Jul 2019 21:05:15: 12000000 INFO @ Fri, 05 Jul 2019 21:05:16: 12000000 INFO @ Fri, 05 Jul 2019 21:05:22: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 21:05:22: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 21:05:22: #1 total tags in treatment: 6133319 INFO @ Fri, 05 Jul 2019 21:05:22: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 21:05:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 21:05:22: #1 tags after filtering in treatment: 2936353 INFO @ Fri, 05 Jul 2019 21:05:22: #1 Redundant rate of treatment: 0.52 INFO @ Fri, 05 Jul 2019 21:05:22: #1 finished! INFO @ Fri, 05 Jul 2019 21:05:22: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 21:05:22: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 21:05:22: #2 number of paired peaks: 842 WARNING @ Fri, 05 Jul 2019 21:05:22: Fewer paired peaks (842) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 842 pairs to build model! INFO @ Fri, 05 Jul 2019 21:05:22: start model_add_line... INFO @ Fri, 05 Jul 2019 21:05:22: start X-correlation... INFO @ Fri, 05 Jul 2019 21:05:22: end of X-cor INFO @ Fri, 05 Jul 2019 21:05:22: #2 finished! INFO @ Fri, 05 Jul 2019 21:05:22: #2 predicted fragment length is 294 bps INFO @ Fri, 05 Jul 2019 21:05:22: #2 alternative fragment length(s) may be 106,155,186,218,237,247,260,276,294,315,366,423,590 bps INFO @ Fri, 05 Jul 2019 21:05:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX2339854/SRX2339854.10_model.r INFO @ Fri, 05 Jul 2019 21:05:22: #3 Call peaks... INFO @ Fri, 05 Jul 2019 21:05:22: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 21:05:23: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 21:05:23: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 21:05:23: #1 total tags in treatment: 6133319 INFO @ Fri, 05 Jul 2019 21:05:23: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 21:05:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 21:05:23: #1 tags after filtering in treatment: 2936353 INFO @ Fri, 05 Jul 2019 21:05:23: #1 Redundant rate of treatment: 0.52 INFO @ Fri, 05 Jul 2019 21:05:23: #1 finished! INFO @ Fri, 05 Jul 2019 21:05:23: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 21:05:23: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 21:05:23: #2 number of paired peaks: 842 WARNING @ Fri, 05 Jul 2019 21:05:23: Fewer paired peaks (842) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 842 pairs to build model! INFO @ Fri, 05 Jul 2019 21:05:23: start model_add_line... INFO @ Fri, 05 Jul 2019 21:05:23: start X-correlation... INFO @ Fri, 05 Jul 2019 21:05:23: end of X-cor INFO @ Fri, 05 Jul 2019 21:05:23: #2 finished! INFO @ Fri, 05 Jul 2019 21:05:23: #2 predicted fragment length is 294 bps INFO @ Fri, 05 Jul 2019 21:05:23: #2 alternative fragment length(s) may be 106,155,186,218,237,247,260,276,294,315,366,423,590 bps INFO @ Fri, 05 Jul 2019 21:05:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX2339854/SRX2339854.20_model.r INFO @ Fri, 05 Jul 2019 21:05:23: #3 Call peaks... INFO @ Fri, 05 Jul 2019 21:05:23: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 21:05:24: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 21:05:24: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 21:05:24: #1 total tags in treatment: 6133319 INFO @ Fri, 05 Jul 2019 21:05:24: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 21:05:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 21:05:24: #1 tags after filtering in treatment: 2936353 INFO @ Fri, 05 Jul 2019 21:05:24: #1 Redundant rate of treatment: 0.52 INFO @ Fri, 05 Jul 2019 21:05:24: #1 finished! INFO @ Fri, 05 Jul 2019 21:05:24: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 21:05:24: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 21:05:24: #2 number of paired peaks: 842 WARNING @ Fri, 05 Jul 2019 21:05:24: Fewer paired peaks (842) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 842 pairs to build model! INFO @ Fri, 05 Jul 2019 21:05:24: start model_add_line... INFO @ Fri, 05 Jul 2019 21:05:24: start X-correlation... INFO @ Fri, 05 Jul 2019 21:05:24: end of X-cor INFO @ Fri, 05 Jul 2019 21:05:24: #2 finished! INFO @ Fri, 05 Jul 2019 21:05:24: #2 predicted fragment length is 294 bps INFO @ Fri, 05 Jul 2019 21:05:24: #2 alternative fragment length(s) may be 106,155,186,218,237,247,260,276,294,315,366,423,590 bps INFO @ Fri, 05 Jul 2019 21:05:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX2339854/SRX2339854.05_model.r INFO @ Fri, 05 Jul 2019 21:05:24: #3 Call peaks... INFO @ Fri, 05 Jul 2019 21:05:24: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 21:05:46: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 21:05:47: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 21:05:48: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 21:05:48: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX2339854/SRX2339854.10_peaks.xls INFO @ Fri, 05 Jul 2019 21:05:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX2339854/SRX2339854.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 21:05:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX2339854/SRX2339854.10_summits.bed INFO @ Fri, 05 Jul 2019 21:05:48: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (168 records, 4 fields): 3 millis INFO @ Fri, 05 Jul 2019 21:05:49: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX2339854/SRX2339854.20_peaks.xls INFO @ Fri, 05 Jul 2019 21:05:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX2339854/SRX2339854.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 21:05:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX2339854/SRX2339854.20_summits.bed INFO @ Fri, 05 Jul 2019 21:05:49: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (78 records, 4 fields): 2 millis INFO @ Fri, 05 Jul 2019 21:05:51: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX2339854/SRX2339854.05_peaks.xls INFO @ Fri, 05 Jul 2019 21:05:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX2339854/SRX2339854.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 21:05:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX2339854/SRX2339854.05_summits.bed INFO @ Fri, 05 Jul 2019 21:05:51: Done! CompletedMACS2peakCalling pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (349 records, 4 fields): 7 millis CompletedMACS2peakCalling CompletedMACS2peakCalling