Job ID = 2010007 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 7,342,121 reads read : 14,684,242 reads written : 14,684,242 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: 00:05:34 7342121 reads; of these: 7342121 (100.00%) were paired; of these: 1310538 (17.85%) aligned concordantly 0 times 4119433 (56.11%) aligned concordantly exactly 1 time 1912150 (26.04%) aligned concordantly >1 times ---- 1310538 pairs aligned concordantly 0 times; of these: 61271 (4.68%) aligned discordantly 1 time ---- 1249267 pairs aligned 0 times concordantly or discordantly; of these: 2498534 mates make up the pairs; of these: 2255147 (90.26%) aligned 0 times 122976 (4.92%) aligned exactly 1 time 120411 (4.82%) aligned >1 times 84.64% overall alignment rate Time searching: 00:05:34 Overall time: 00:05:34 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] 2038430 / 6089575 = 0.3347 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 21:07:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX2339869/SRX2339869.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX2339869/SRX2339869.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX2339869/SRX2339869.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX2339869/SRX2339869.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 21:07:18: #1 read tag files... INFO @ Fri, 05 Jul 2019 21:07:18: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 21:07:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX2339869/SRX2339869.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX2339869/SRX2339869.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX2339869/SRX2339869.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX2339869/SRX2339869.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 21:07:19: #1 read tag files... INFO @ Fri, 05 Jul 2019 21:07:19: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 21:07:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX2339869/SRX2339869.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX2339869/SRX2339869.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX2339869/SRX2339869.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX2339869/SRX2339869.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 21:07:20: #1 read tag files... INFO @ Fri, 05 Jul 2019 21:07:20: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 21:07:27: 1000000 INFO @ Fri, 05 Jul 2019 21:07:28: 1000000 INFO @ Fri, 05 Jul 2019 21:07:28: 1000000 INFO @ Fri, 05 Jul 2019 21:07:36: 2000000 INFO @ Fri, 05 Jul 2019 21:07:37: 2000000 INFO @ Fri, 05 Jul 2019 21:07:37: 2000000 INFO @ Fri, 05 Jul 2019 21:07:45: 3000000 INFO @ Fri, 05 Jul 2019 21:07:46: 3000000 INFO @ Fri, 05 Jul 2019 21:07:47: 3000000 INFO @ Fri, 05 Jul 2019 21:07:54: 4000000 INFO @ Fri, 05 Jul 2019 21:07:55: 4000000 INFO @ Fri, 05 Jul 2019 21:07:56: 4000000 INFO @ Fri, 05 Jul 2019 21:08:02: 5000000 INFO @ Fri, 05 Jul 2019 21:08:04: 5000000 INFO @ Fri, 05 Jul 2019 21:08:05: 5000000 INFO @ Fri, 05 Jul 2019 21:08:10: 6000000 INFO @ Fri, 05 Jul 2019 21:08:13: 6000000 INFO @ Fri, 05 Jul 2019 21:08:14: 6000000 INFO @ Fri, 05 Jul 2019 21:08:18: 7000000 INFO @ Fri, 05 Jul 2019 21:08:22: 7000000 INFO @ Fri, 05 Jul 2019 21:08:23: 7000000 INFO @ Fri, 05 Jul 2019 21:08:26: 8000000 INFO @ Fri, 05 Jul 2019 21:08:29: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 21:08:29: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 21:08:29: #1 total tags in treatment: 4008282 INFO @ Fri, 05 Jul 2019 21:08:29: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 21:08:29: #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 21:08:29: #1 tags after filtering in treatment: 2513572 INFO @ Fri, 05 Jul 2019 21:08:29: #1 Redundant rate of treatment: 0.37 INFO @ Fri, 05 Jul 2019 21:08:29: #1 finished! INFO @ Fri, 05 Jul 2019 21:08:29: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 21:08:29: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 21:08:30: #2 number of paired peaks: 168 WARNING @ Fri, 05 Jul 2019 21:08:30: Fewer paired peaks (168) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 168 pairs to build model! INFO @ Fri, 05 Jul 2019 21:08:30: start model_add_line... INFO @ Fri, 05 Jul 2019 21:08:30: start X-correlation... INFO @ Fri, 05 Jul 2019 21:08:30: end of X-cor INFO @ Fri, 05 Jul 2019 21:08:30: #2 finished! INFO @ Fri, 05 Jul 2019 21:08:30: #2 predicted fragment length is 199 bps INFO @ Fri, 05 Jul 2019 21:08:30: #2 alternative fragment length(s) may be 2,151,175,199,225,248 bps INFO @ Fri, 05 Jul 2019 21:08:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX2339869/SRX2339869.20_model.r INFO @ Fri, 05 Jul 2019 21:08:30: #3 Call peaks... INFO @ Fri, 05 Jul 2019 21:08:30: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 21:08:31: 8000000 INFO @ Fri, 05 Jul 2019 21:08:32: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 21:08:34: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 21:08:34: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 21:08:34: #1 total tags in treatment: 4008282 INFO @ Fri, 05 Jul 2019 21:08:34: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 21:08:34: #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 21:08:34: #1 tags after filtering in treatment: 2513572 INFO @ Fri, 05 Jul 2019 21:08:34: #1 Redundant rate of treatment: 0.37 INFO @ Fri, 05 Jul 2019 21:08:34: #1 finished! INFO @ Fri, 05 Jul 2019 21:08:34: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 21:08:34: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 21:08:34: #2 number of paired peaks: 168 WARNING @ Fri, 05 Jul 2019 21:08:34: Fewer paired peaks (168) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 168 pairs to build model! INFO @ Fri, 05 Jul 2019 21:08:34: start model_add_line... INFO @ Fri, 05 Jul 2019 21:08:34: start X-correlation... INFO @ Fri, 05 Jul 2019 21:08:34: end of X-cor INFO @ Fri, 05 Jul 2019 21:08:34: #2 finished! INFO @ Fri, 05 Jul 2019 21:08:34: #2 predicted fragment length is 199 bps INFO @ Fri, 05 Jul 2019 21:08:34: #2 alternative fragment length(s) may be 2,151,175,199,225,248 bps INFO @ Fri, 05 Jul 2019 21:08:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX2339869/SRX2339869.05_model.r INFO @ Fri, 05 Jul 2019 21:08:34: #3 Call peaks... INFO @ Fri, 05 Jul 2019 21:08:34: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 21:08:35: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 21:08:35: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 21:08:35: #1 total tags in treatment: 4008282 INFO @ Fri, 05 Jul 2019 21:08:35: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 21:08:35: #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 21:08:35: #1 tags after filtering in treatment: 2513572 INFO @ Fri, 05 Jul 2019 21:08:35: #1 Redundant rate of treatment: 0.37 INFO @ Fri, 05 Jul 2019 21:08:35: #1 finished! INFO @ Fri, 05 Jul 2019 21:08:35: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 21:08:35: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 21:08:35: #2 number of paired peaks: 168 WARNING @ Fri, 05 Jul 2019 21:08:35: Fewer paired peaks (168) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 168 pairs to build model! INFO @ Fri, 05 Jul 2019 21:08:35: start model_add_line... INFO @ Fri, 05 Jul 2019 21:08:35: start X-correlation... INFO @ Fri, 05 Jul 2019 21:08:35: end of X-cor INFO @ Fri, 05 Jul 2019 21:08:35: #2 finished! INFO @ Fri, 05 Jul 2019 21:08:35: #2 predicted fragment length is 199 bps INFO @ Fri, 05 Jul 2019 21:08:35: #2 alternative fragment length(s) may be 2,151,175,199,225,248 bps INFO @ Fri, 05 Jul 2019 21:08:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX2339869/SRX2339869.10_model.r INFO @ Fri, 05 Jul 2019 21:08:35: #3 Call peaks... INFO @ Fri, 05 Jul 2019 21:08:35: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 21:08:41: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 05 Jul 2019 21:08:43: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX2339869/SRX2339869.20_peaks.xls INFO @ Fri, 05 Jul 2019 21:08:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX2339869/SRX2339869.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 21:08:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX2339869/SRX2339869.20_summits.bed INFO @ Fri, 05 Jul 2019 21:08:43: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (284 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 21:08:46: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 21:08:46: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 21:08:48: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX2339869/SRX2339869.05_peaks.xls INFO @ Fri, 05 Jul 2019 21:08:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX2339869/SRX2339869.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 21:08:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX2339869/SRX2339869.05_summits.bed INFO @ Fri, 05 Jul 2019 21:08:48: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (782 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 21:08:49: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX2339869/SRX2339869.10_peaks.xls INFO @ Fri, 05 Jul 2019 21:08:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX2339869/SRX2339869.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 21:08:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX2339869/SRX2339869.10_summits.bed INFO @ Fri, 05 Jul 2019 21:08:49: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (510 records, 4 fields): 3 millis CompletedMACS2peakCalling