Job ID = 2011924 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 5,986,669 reads read : 11,973,338 reads written : 11,973,338 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: 00:03:53 5986669 reads; of these: 5986669 (100.00%) were paired; of these: 714104 (11.93%) aligned concordantly 0 times 4582493 (76.54%) aligned concordantly exactly 1 time 690072 (11.53%) aligned concordantly >1 times ---- 714104 pairs aligned concordantly 0 times; of these: 353981 (49.57%) aligned discordantly 1 time ---- 360123 pairs aligned 0 times concordantly or discordantly; of these: 720246 mates make up the pairs; of these: 490393 (68.09%) aligned 0 times 110955 (15.41%) aligned exactly 1 time 118898 (16.51%) aligned >1 times 95.90% overall alignment rate Time searching: 00:03:53 Overall time: 00:03:53 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] 179903 / 5624092 = 0.0320 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 03:30:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5383697/SRX5383697.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5383697/SRX5383697.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5383697/SRX5383697.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5383697/SRX5383697.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 03:30:31: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:30:31: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:30:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5383697/SRX5383697.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5383697/SRX5383697.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5383697/SRX5383697.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5383697/SRX5383697.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 03:30:32: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:30:32: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:30:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5383697/SRX5383697.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5383697/SRX5383697.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5383697/SRX5383697.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5383697/SRX5383697.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 03:30:35: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:30:35: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:30:37: 1000000 INFO @ Sat, 06 Jul 2019 03:30:38: 1000000 INFO @ Sat, 06 Jul 2019 03:30:42: 1000000 INFO @ Sat, 06 Jul 2019 03:30:42: 2000000 INFO @ Sat, 06 Jul 2019 03:30:44: 2000000 INFO @ Sat, 06 Jul 2019 03:30:48: 3000000 INFO @ Sat, 06 Jul 2019 03:30:48: 2000000 INFO @ Sat, 06 Jul 2019 03:30:49: 3000000 INFO @ Sat, 06 Jul 2019 03:30:53: 4000000 INFO @ Sat, 06 Jul 2019 03:30:53: 3000000 INFO @ Sat, 06 Jul 2019 03:30:55: 4000000 INFO @ Sat, 06 Jul 2019 03:30:59: 5000000 INFO @ Sat, 06 Jul 2019 03:30:59: 4000000 INFO @ Sat, 06 Jul 2019 03:31:00: 5000000 INFO @ Sat, 06 Jul 2019 03:31:05: 6000000 INFO @ Sat, 06 Jul 2019 03:31:05: 5000000 INFO @ Sat, 06 Jul 2019 03:31:05: 6000000 INFO @ Sat, 06 Jul 2019 03:31:10: 7000000 INFO @ Sat, 06 Jul 2019 03:31:11: 7000000 INFO @ Sat, 06 Jul 2019 03:31:11: 6000000 INFO @ Sat, 06 Jul 2019 03:31:16: 8000000 INFO @ Sat, 06 Jul 2019 03:31:16: 8000000 INFO @ Sat, 06 Jul 2019 03:31:17: 7000000 INFO @ Sat, 06 Jul 2019 03:31:22: 9000000 INFO @ Sat, 06 Jul 2019 03:31:22: 9000000 INFO @ Sat, 06 Jul 2019 03:31:22: 8000000 INFO @ Sat, 06 Jul 2019 03:31:27: 10000000 INFO @ Sat, 06 Jul 2019 03:31:27: 10000000 INFO @ Sat, 06 Jul 2019 03:31:28: 9000000 INFO @ Sat, 06 Jul 2019 03:31:32: 11000000 INFO @ Sat, 06 Jul 2019 03:31:33: 11000000 INFO @ Sat, 06 Jul 2019 03:31:33: #1 tag size is determined as 37 bps INFO @ Sat, 06 Jul 2019 03:31:33: #1 tag size = 37 INFO @ Sat, 06 Jul 2019 03:31:33: #1 total tags in treatment: 5100039 INFO @ Sat, 06 Jul 2019 03:31:33: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:31:33: #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 03:31:33: #1 tags after filtering in treatment: 4082259 INFO @ Sat, 06 Jul 2019 03:31:33: #1 Redundant rate of treatment: 0.20 INFO @ Sat, 06 Jul 2019 03:31:33: #1 finished! INFO @ Sat, 06 Jul 2019 03:31:33: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:31:33: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:31:34: #2 number of paired peaks: 126 WARNING @ Sat, 06 Jul 2019 03:31:34: Fewer paired peaks (126) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 126 pairs to build model! INFO @ Sat, 06 Jul 2019 03:31:34: start model_add_line... INFO @ Sat, 06 Jul 2019 03:31:34: start X-correlation... INFO @ Sat, 06 Jul 2019 03:31:34: end of X-cor INFO @ Sat, 06 Jul 2019 03:31:34: #2 finished! INFO @ Sat, 06 Jul 2019 03:31:34: #2 predicted fragment length is 0 bps INFO @ Sat, 06 Jul 2019 03:31:34: #2 alternative fragment length(s) may be 0,22,49,70,108,124,154,190,227,247,266,290,297,305,325,346,365,391,417,439,458,474,513,527,552,577 bps INFO @ Sat, 06 Jul 2019 03:31:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5383697/SRX5383697.10_model.r INFO @ Sat, 06 Jul 2019 03:31:34: #1 tag size is determined as 37 bps INFO @ Sat, 06 Jul 2019 03:31:34: #1 tag size = 37 INFO @ Sat, 06 Jul 2019 03:31:34: #1 total tags in treatment: 5100039 INFO @ Sat, 06 Jul 2019 03:31:34: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:31:34: #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 03:31:34: #1 tags after filtering in treatment: 4082259 INFO @ Sat, 06 Jul 2019 03:31:34: #1 Redundant rate of treatment: 0.20 INFO @ Sat, 06 Jul 2019 03:31:34: #1 finished! INFO @ Sat, 06 Jul 2019 03:31:34: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:31:34: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:31:34: 10000000 INFO @ Sat, 06 Jul 2019 03:31:34: #2 number of paired peaks: 126 WARNING @ Sat, 06 Jul 2019 03:31:34: Fewer paired peaks (126) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 126 pairs to build model! INFO @ Sat, 06 Jul 2019 03:31:34: start model_add_line... INFO @ Sat, 06 Jul 2019 03:31:34: start X-correlation... INFO @ Sat, 06 Jul 2019 03:31:34: end of X-cor INFO @ Sat, 06 Jul 2019 03:31:34: #2 finished! INFO @ Sat, 06 Jul 2019 03:31:34: #2 predicted fragment length is 0 bps INFO @ Sat, 06 Jul 2019 03:31:34: #2 alternative fragment length(s) may be 0,22,49,70,108,124,154,190,227,247,266,290,297,305,325,346,365,391,417,439,458,474,513,527,552,577 bps INFO @ Sat, 06 Jul 2019 03:31:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5383697/SRX5383697.05_model.r WARNING @ Sat, 06 Jul 2019 03:31:38: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 06 Jul 2019 03:31:38: #2 You may need to consider one of the other alternative d(s): 0,22,49,70,108,124,154,190,227,247,266,290,297,305,325,346,365,391,417,439,458,474,513,527,552,577 WARNING @ Sat, 06 Jul 2019 03:31:38: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 06 Jul 2019 03:31:38: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. WARNING @ Sat, 06 Jul 2019 03:31:38: #2 You may need to consider one of the other alternative d(s): 0,22,49,70,108,124,154,190,227,247,266,290,297,305,325,346,365,391,417,439,458,474,513,527,552,577 INFO @ Sat, 06 Jul 2019 03:31:38: #3 Call peaks... WARNING @ Sat, 06 Jul 2019 03:31:38: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 06 Jul 2019 03:31:38: #3 Call peaks... INFO @ Sat, 06 Jul 2019 03:31:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 06 Jul 2019 03:31:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 06 Jul 2019 03:31:40: 11000000 INFO @ Sat, 06 Jul 2019 03:31:41: #1 tag size is determined as 37 bps INFO @ Sat, 06 Jul 2019 03:31:41: #1 tag size = 37 INFO @ Sat, 06 Jul 2019 03:31:41: #1 total tags in treatment: 5100039 INFO @ Sat, 06 Jul 2019 03:31:41: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:31:41: #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 03:31:41: #1 tags after filtering in treatment: 4082259 INFO @ Sat, 06 Jul 2019 03:31:41: #1 Redundant rate of treatment: 0.20 INFO @ Sat, 06 Jul 2019 03:31:41: #1 finished! INFO @ Sat, 06 Jul 2019 03:31:41: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:31:41: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:31:41: #2 number of paired peaks: 126 WARNING @ Sat, 06 Jul 2019 03:31:41: Fewer paired peaks (126) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 126 pairs to build model! INFO @ Sat, 06 Jul 2019 03:31:41: start model_add_line... INFO @ Sat, 06 Jul 2019 03:31:41: start X-correlation... INFO @ Sat, 06 Jul 2019 03:31:41: end of X-cor INFO @ Sat, 06 Jul 2019 03:31:41: #2 finished! INFO @ Sat, 06 Jul 2019 03:31:41: #2 predicted fragment length is 0 bps INFO @ Sat, 06 Jul 2019 03:31:41: #2 alternative fragment length(s) may be 0,22,49,70,108,124,154,190,227,247,266,290,297,305,325,346,365,391,417,439,458,474,513,527,552,577 bps INFO @ Sat, 06 Jul 2019 03:31:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5383697/SRX5383697.20_model.r WARNING @ Sat, 06 Jul 2019 03:31:41: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 06 Jul 2019 03:31:41: #2 You may need to consider one of the other alternative d(s): 0,22,49,70,108,124,154,190,227,247,266,290,297,305,325,346,365,391,417,439,458,474,513,527,552,577 WARNING @ Sat, 06 Jul 2019 03:31:41: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 06 Jul 2019 03:31:41: #3 Call peaks... INFO @ Sat, 06 Jul 2019 03:31:41: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 ls: cannot access SRX5383697.05.bed: No such file or directory mv: cannot stat ‘SRX5383697.05.bed’: No such file or directory /var/spool/uge/at106/job_scripts/2011924: line 335: 9186 Terminated MACS $i /var/spool/uge/at106/job_scripts/2011924: line 335: 9202 Terminated MACS $i /var/spool/uge/at106/job_scripts/2011924: line 335: 9218 Terminated MACS $i mv: cannot stat ‘SRX5383697.05.bb’: No such file or directory ls: cannot access SRX5383697.10.bed: No such file or directory mv: cannot stat ‘SRX5383697.10.bed’: No such file or directory mv: cannot stat ‘SRX5383697.10.bb’: No such file or directory ls: cannot access SRX5383697.20.bed: No such file or directory mv: cannot stat ‘SRX5383697.20.bed’: No such file or directory mv: cannot stat ‘SRX5383697.20.bb’: No such file or directory