Job ID = 2009915 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 16,373,841 reads read : 32,747,682 reads written : 32,747,682 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR5008409.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: 00:12:01 16373841 reads; of these: 16373841 (100.00%) were paired; of these: 3890567 (23.76%) aligned concordantly 0 times 10083998 (61.59%) aligned concordantly exactly 1 time 2399276 (14.65%) aligned concordantly >1 times ---- 3890567 pairs aligned concordantly 0 times; of these: 135490 (3.48%) aligned discordantly 1 time ---- 3755077 pairs aligned 0 times concordantly or discordantly; of these: 7510154 mates make up the pairs; of these: 6876519 (91.56%) aligned 0 times 434849 (5.79%) aligned exactly 1 time 198786 (2.65%) aligned >1 times 79.00% overall alignment rate Time searching: 00:12:01 Overall time: 00:12:01 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 12 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] 1406035 / 12608388 = 0.1115 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 21:03:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX2339850/SRX2339850.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX2339850/SRX2339850.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX2339850/SRX2339850.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX2339850/SRX2339850.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 21:03:26: #1 read tag files... INFO @ Fri, 05 Jul 2019 21:03:26: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 21:03:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX2339850/SRX2339850.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX2339850/SRX2339850.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX2339850/SRX2339850.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX2339850/SRX2339850.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 21:03:26: #1 read tag files... INFO @ Fri, 05 Jul 2019 21:03:26: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 21:03:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX2339850/SRX2339850.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX2339850/SRX2339850.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX2339850/SRX2339850.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX2339850/SRX2339850.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 21:03:27: #1 read tag files... INFO @ Fri, 05 Jul 2019 21:03:27: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 21:03:33: 1000000 INFO @ Fri, 05 Jul 2019 21:03:34: 1000000 INFO @ Fri, 05 Jul 2019 21:03:34: 1000000 INFO @ Fri, 05 Jul 2019 21:03:40: 2000000 INFO @ Fri, 05 Jul 2019 21:03:41: 2000000 INFO @ Fri, 05 Jul 2019 21:03:42: 2000000 INFO @ Fri, 05 Jul 2019 21:03:47: 3000000 INFO @ Fri, 05 Jul 2019 21:03:48: 3000000 INFO @ Fri, 05 Jul 2019 21:03:49: 3000000 INFO @ Fri, 05 Jul 2019 21:03:54: 4000000 INFO @ Fri, 05 Jul 2019 21:03:55: 4000000 INFO @ Fri, 05 Jul 2019 21:03:57: 4000000 INFO @ Fri, 05 Jul 2019 21:04:01: 5000000 INFO @ Fri, 05 Jul 2019 21:04:01: 5000000 INFO @ Fri, 05 Jul 2019 21:04:04: 5000000 INFO @ Fri, 05 Jul 2019 21:04:07: 6000000 INFO @ Fri, 05 Jul 2019 21:04:08: 6000000 INFO @ Fri, 05 Jul 2019 21:04:11: 6000000 INFO @ Fri, 05 Jul 2019 21:04:14: 7000000 INFO @ Fri, 05 Jul 2019 21:04:14: 7000000 INFO @ Fri, 05 Jul 2019 21:04:18: 7000000 INFO @ Fri, 05 Jul 2019 21:04:21: 8000000 INFO @ Fri, 05 Jul 2019 21:04:21: 8000000 INFO @ Fri, 05 Jul 2019 21:04:26: 8000000 INFO @ Fri, 05 Jul 2019 21:04:27: 9000000 INFO @ Fri, 05 Jul 2019 21:04:28: 9000000 INFO @ Fri, 05 Jul 2019 21:04:33: 9000000 INFO @ Fri, 05 Jul 2019 21:04:34: 10000000 INFO @ Fri, 05 Jul 2019 21:04:35: 10000000 INFO @ Fri, 05 Jul 2019 21:04:41: 10000000 INFO @ Fri, 05 Jul 2019 21:04:42: 11000000 INFO @ Fri, 05 Jul 2019 21:04:43: 11000000 INFO @ Fri, 05 Jul 2019 21:04:48: 11000000 INFO @ Fri, 05 Jul 2019 21:04:49: 12000000 INFO @ Fri, 05 Jul 2019 21:04:51: 12000000 INFO @ Fri, 05 Jul 2019 21:04:56: 12000000 INFO @ Fri, 05 Jul 2019 21:04:56: 13000000 INFO @ Fri, 05 Jul 2019 21:04:58: 13000000 INFO @ Fri, 05 Jul 2019 21:05:03: 14000000 INFO @ Fri, 05 Jul 2019 21:05:03: 13000000 INFO @ Fri, 05 Jul 2019 21:05:05: 14000000 INFO @ Fri, 05 Jul 2019 21:05:10: 15000000 INFO @ Fri, 05 Jul 2019 21:05:11: 14000000 INFO @ Fri, 05 Jul 2019 21:05:12: 15000000 INFO @ Fri, 05 Jul 2019 21:05:17: 16000000 INFO @ Fri, 05 Jul 2019 21:05:19: 15000000 INFO @ Fri, 05 Jul 2019 21:05:19: 16000000 INFO @ Fri, 05 Jul 2019 21:05:23: 17000000 INFO @ Fri, 05 Jul 2019 21:05:26: 17000000 INFO @ Fri, 05 Jul 2019 21:05:27: 16000000 INFO @ Fri, 05 Jul 2019 21:05:30: 18000000 INFO @ Fri, 05 Jul 2019 21:05:33: 18000000 INFO @ Fri, 05 Jul 2019 21:05:34: 17000000 INFO @ Fri, 05 Jul 2019 21:05:37: 19000000 INFO @ Fri, 05 Jul 2019 21:05:40: 19000000 INFO @ Fri, 05 Jul 2019 21:05:41: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 21:05:44: 20000000 INFO @ Fri, 05 Jul 2019 21:05:48: 20000000 INFO @ Fri, 05 Jul 2019 21:05:49: 19000000 INFO @ Fri, 05 Jul 2019 21:05:51: 21000000 INFO @ Fri, 05 Jul 2019 21:05:55: 21000000 INFO @ Fri, 05 Jul 2019 21:05:57: 20000000 INFO @ Fri, 05 Jul 2019 21:05:57: 22000000 INFO @ Fri, 05 Jul 2019 21:06:02: 22000000 INFO @ Fri, 05 Jul 2019 21:06:04: 23000000 INFO @ Fri, 05 Jul 2019 21:06:04: 21000000 INFO @ Fri, 05 Jul 2019 21:06:05: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 21:06:05: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 21:06:05: #1 total tags in treatment: 11082804 INFO @ Fri, 05 Jul 2019 21:06:05: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 21:06:05: #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 21:06:05: #1 tags after filtering in treatment: 4205050 INFO @ Fri, 05 Jul 2019 21:06:05: #1 Redundant rate of treatment: 0.62 INFO @ Fri, 05 Jul 2019 21:06:05: #1 finished! INFO @ Fri, 05 Jul 2019 21:06:05: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 21:06:05: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 21:06:05: #2 number of paired peaks: 266 WARNING @ Fri, 05 Jul 2019 21:06:05: Fewer paired peaks (266) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 266 pairs to build model! INFO @ Fri, 05 Jul 2019 21:06:05: start model_add_line... INFO @ Fri, 05 Jul 2019 21:06:05: start X-correlation... INFO @ Fri, 05 Jul 2019 21:06:05: end of X-cor INFO @ Fri, 05 Jul 2019 21:06:05: #2 finished! INFO @ Fri, 05 Jul 2019 21:06:05: #2 predicted fragment length is 53 bps INFO @ Fri, 05 Jul 2019 21:06:05: #2 alternative fragment length(s) may be 36,53,103,129,150,187,220,237,258,284,331,334,365,385,416,418,463,489,525,550,570,588 bps INFO @ Fri, 05 Jul 2019 21:06:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX2339850/SRX2339850.20_model.r WARNING @ Fri, 05 Jul 2019 21:06:05: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 21:06:05: #2 You may need to consider one of the other alternative d(s): 36,53,103,129,150,187,220,237,258,284,331,334,365,385,416,418,463,489,525,550,570,588 WARNING @ Fri, 05 Jul 2019 21:06:05: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 05 Jul 2019 21:06:05: #3 Call peaks... INFO @ Fri, 05 Jul 2019 21:06:05: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 05 Jul 2019 21:06:09: 23000000 INFO @ Fri, 05 Jul 2019 21:06:10: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 21:06:10: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 21:06:10: #1 total tags in treatment: 11082804 INFO @ Fri, 05 Jul 2019 21:06:10: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 21:06:10: #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 21:06:10: #1 tags after filtering in treatment: 4205050 INFO @ Fri, 05 Jul 2019 21:06:10: #1 Redundant rate of treatment: 0.62 INFO @ Fri, 05 Jul 2019 21:06:10: #1 finished! INFO @ Fri, 05 Jul 2019 21:06:10: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 21:06:10: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 21:06:11: #2 number of paired peaks: 266 WARNING @ Fri, 05 Jul 2019 21:06:11: Fewer paired peaks (266) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 266 pairs to build model! INFO @ Fri, 05 Jul 2019 21:06:11: start model_add_line... INFO @ Fri, 05 Jul 2019 21:06:11: start X-correlation... INFO @ Fri, 05 Jul 2019 21:06:11: end of X-cor INFO @ Fri, 05 Jul 2019 21:06:11: #2 finished! INFO @ Fri, 05 Jul 2019 21:06:11: #2 predicted fragment length is 53 bps INFO @ Fri, 05 Jul 2019 21:06:11: #2 alternative fragment length(s) may be 36,53,103,129,150,187,220,237,258,284,331,334,365,385,416,418,463,489,525,550,570,588 bps INFO @ Fri, 05 Jul 2019 21:06:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX2339850/SRX2339850.05_model.r WARNING @ Fri, 05 Jul 2019 21:06:11: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 21:06:11: #2 You may need to consider one of the other alternative d(s): 36,53,103,129,150,187,220,237,258,284,331,334,365,385,416,418,463,489,525,550,570,588 WARNING @ Fri, 05 Jul 2019 21:06:11: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 05 Jul 2019 21:06:11: #3 Call peaks... INFO @ Fri, 05 Jul 2019 21:06:11: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 21:06:12: 22000000 INFO @ Fri, 05 Jul 2019 21:06:15: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 21:06:18: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX2339850/SRX2339850.20_peaks.xls INFO @ Fri, 05 Jul 2019 21:06:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX2339850/SRX2339850.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 21:06:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX2339850/SRX2339850.20_summits.bed INFO @ Fri, 05 Jul 2019 21:06:18: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (9 records, 4 fields): 2 millis INFO @ Fri, 05 Jul 2019 21:06:20: 23000000 INFO @ Fri, 05 Jul 2019 21:06:21: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 21:06:21: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 21:06:21: #1 total tags in treatment: 11082804 INFO @ Fri, 05 Jul 2019 21:06:21: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 21:06:21: #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 21:06:21: #1 tags after filtering in treatment: 4205050 INFO @ Fri, 05 Jul 2019 21:06:21: #1 Redundant rate of treatment: 0.62 INFO @ Fri, 05 Jul 2019 21:06:21: #1 finished! INFO @ Fri, 05 Jul 2019 21:06:21: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 21:06:21: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 21:06:21: #2 number of paired peaks: 266 WARNING @ Fri, 05 Jul 2019 21:06:21: Fewer paired peaks (266) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 266 pairs to build model! INFO @ Fri, 05 Jul 2019 21:06:21: start model_add_line... INFO @ Fri, 05 Jul 2019 21:06:21: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 21:06:21: start X-correlation... INFO @ Fri, 05 Jul 2019 21:06:21: end of X-cor INFO @ Fri, 05 Jul 2019 21:06:21: #2 finished! INFO @ Fri, 05 Jul 2019 21:06:21: #2 predicted fragment length is 53 bps INFO @ Fri, 05 Jul 2019 21:06:21: #2 alternative fragment length(s) may be 36,53,103,129,150,187,220,237,258,284,331,334,365,385,416,418,463,489,525,550,570,588 bps INFO @ Fri, 05 Jul 2019 21:06:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX2339850/SRX2339850.10_model.r WARNING @ Fri, 05 Jul 2019 21:06:21: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 21:06:21: #2 You may need to consider one of the other alternative d(s): 36,53,103,129,150,187,220,237,258,284,331,334,365,385,416,418,463,489,525,550,570,588 WARNING @ Fri, 05 Jul 2019 21:06:21: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 05 Jul 2019 21:06:21: #3 Call peaks... INFO @ Fri, 05 Jul 2019 21:06:21: #3 Pre-compute pvalue-qvalue table... CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 21:06:25: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX2339850/SRX2339850.05_peaks.xls INFO @ Fri, 05 Jul 2019 21:06:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX2339850/SRX2339850.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 21:06:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX2339850/SRX2339850.05_summits.bed INFO @ Fri, 05 Jul 2019 21:06:25: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (186 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 21:06:31: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 21:06:34: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX2339850/SRX2339850.10_peaks.xls INFO @ Fri, 05 Jul 2019 21:06:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX2339850/SRX2339850.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 21:06:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX2339850/SRX2339850.10_summits.bed INFO @ Fri, 05 Jul 2019 21:06:34: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (36 records, 4 fields): 2 millis CompletedMACS2peakCalling