Job ID = 2009996 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 7,281,221 reads read : 14,562,442 reads written : 14,562,442 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR5008419.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: 00:05:28 7281221 reads; of these: 7281221 (100.00%) were paired; of these: 946394 (13.00%) aligned concordantly 0 times 5408245 (74.28%) aligned concordantly exactly 1 time 926582 (12.73%) aligned concordantly >1 times ---- 946394 pairs aligned concordantly 0 times; of these: 194285 (20.53%) aligned discordantly 1 time ---- 752109 pairs aligned 0 times concordantly or discordantly; of these: 1504218 mates make up the pairs; of these: 1256528 (83.53%) aligned 0 times 147218 (9.79%) aligned exactly 1 time 100472 (6.68%) aligned >1 times 91.37% overall alignment rate Time searching: 00:05:30 Overall time: 00:05:30 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] 226667 / 6495724 = 0.0349 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 20:55:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX2339860/SRX2339860.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX2339860/SRX2339860.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX2339860/SRX2339860.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX2339860/SRX2339860.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 20:55:12: #1 read tag files... INFO @ Fri, 05 Jul 2019 20:55:12: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 20:55:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX2339860/SRX2339860.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX2339860/SRX2339860.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX2339860/SRX2339860.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX2339860/SRX2339860.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 20:55:13: #1 read tag files... INFO @ Fri, 05 Jul 2019 20:55:13: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 20:55:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX2339860/SRX2339860.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX2339860/SRX2339860.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX2339860/SRX2339860.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX2339860/SRX2339860.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 20:55:14: #1 read tag files... INFO @ Fri, 05 Jul 2019 20:55:14: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 20:55:19: 1000000 INFO @ Fri, 05 Jul 2019 20:55:19: 1000000 INFO @ Fri, 05 Jul 2019 20:55:21: 1000000 INFO @ Fri, 05 Jul 2019 20:55:26: 2000000 INFO @ Fri, 05 Jul 2019 20:55:26: 2000000 INFO @ Fri, 05 Jul 2019 20:55:28: 2000000 INFO @ Fri, 05 Jul 2019 20:55:32: 3000000 INFO @ Fri, 05 Jul 2019 20:55:33: 3000000 INFO @ Fri, 05 Jul 2019 20:55:34: 3000000 INFO @ Fri, 05 Jul 2019 20:55:38: 4000000 INFO @ Fri, 05 Jul 2019 20:55:40: 4000000 INFO @ Fri, 05 Jul 2019 20:55:41: 4000000 INFO @ Fri, 05 Jul 2019 20:55:44: 5000000 INFO @ Fri, 05 Jul 2019 20:55:46: 5000000 INFO @ Fri, 05 Jul 2019 20:55:47: 5000000 INFO @ Fri, 05 Jul 2019 20:55:50: 6000000 INFO @ Fri, 05 Jul 2019 20:55:53: 6000000 INFO @ Fri, 05 Jul 2019 20:55:54: 6000000 INFO @ Fri, 05 Jul 2019 20:55:57: 7000000 INFO @ Fri, 05 Jul 2019 20:55:59: 7000000 INFO @ Fri, 05 Jul 2019 20:56:01: 7000000 INFO @ Fri, 05 Jul 2019 20:56:03: 8000000 INFO @ Fri, 05 Jul 2019 20:56:06: 8000000 INFO @ Fri, 05 Jul 2019 20:56:07: 8000000 INFO @ Fri, 05 Jul 2019 20:56:09: 9000000 INFO @ Fri, 05 Jul 2019 20:56:13: 9000000 INFO @ Fri, 05 Jul 2019 20:56:14: 9000000 INFO @ Fri, 05 Jul 2019 20:56:15: 10000000 INFO @ Fri, 05 Jul 2019 20:56:19: 10000000 INFO @ Fri, 05 Jul 2019 20:56:21: 10000000 INFO @ Fri, 05 Jul 2019 20:56:21: 11000000 INFO @ Fri, 05 Jul 2019 20:56:26: 11000000 INFO @ Fri, 05 Jul 2019 20:56:27: 11000000 INFO @ Fri, 05 Jul 2019 20:56:27: 12000000 INFO @ Fri, 05 Jul 2019 20:56:33: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 20:56:33: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 20:56:33: #1 total tags in treatment: 6112839 INFO @ Fri, 05 Jul 2019 20:56:33: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 20:56:33: #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 20:56:33: 12000000 INFO @ Fri, 05 Jul 2019 20:56:33: #1 tags after filtering in treatment: 3947920 INFO @ Fri, 05 Jul 2019 20:56:33: #1 Redundant rate of treatment: 0.35 INFO @ Fri, 05 Jul 2019 20:56:33: #1 finished! INFO @ Fri, 05 Jul 2019 20:56:33: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 20:56:33: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 20:56:33: #2 number of paired peaks: 165 WARNING @ Fri, 05 Jul 2019 20:56:33: Fewer paired peaks (165) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 165 pairs to build model! INFO @ Fri, 05 Jul 2019 20:56:33: start model_add_line... INFO @ Fri, 05 Jul 2019 20:56:33: start X-correlation... INFO @ Fri, 05 Jul 2019 20:56:33: end of X-cor INFO @ Fri, 05 Jul 2019 20:56:33: #2 finished! INFO @ Fri, 05 Jul 2019 20:56:33: #2 predicted fragment length is 0 bps INFO @ Fri, 05 Jul 2019 20:56:33: #2 alternative fragment length(s) may be 0,36,47,73,103,121,220,247,266,288,311,326,363,383,406,420,455,495,546,580 bps INFO @ Fri, 05 Jul 2019 20:56:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX2339860/SRX2339860.10_model.r WARNING @ Fri, 05 Jul 2019 20:56:33: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 20:56:33: #2 You may need to consider one of the other alternative d(s): 0,36,47,73,103,121,220,247,266,288,311,326,363,383,406,420,455,495,546,580 WARNING @ Fri, 05 Jul 2019 20:56:33: #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 20:56:33: #3 Call peaks... INFO @ Fri, 05 Jul 2019 20:56:33: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 20:56:34: 12000000 INFO @ Fri, 05 Jul 2019 20:56:39: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 20:56:39: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 20:56:39: #1 total tags in treatment: 6112839 INFO @ Fri, 05 Jul 2019 20:56:39: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 20:56:39: #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 20:56:39: #1 tags after filtering in treatment: 3947920 INFO @ Fri, 05 Jul 2019 20:56:39: #1 Redundant rate of treatment: 0.35 INFO @ Fri, 05 Jul 2019 20:56:39: #1 finished! INFO @ Fri, 05 Jul 2019 20:56:39: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 20:56:39: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 20:56:39: #2 number of paired peaks: 165 WARNING @ Fri, 05 Jul 2019 20:56:39: Fewer paired peaks (165) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 165 pairs to build model! INFO @ Fri, 05 Jul 2019 20:56:39: start model_add_line... INFO @ Fri, 05 Jul 2019 20:56:39: start X-correlation... INFO @ Fri, 05 Jul 2019 20:56:39: end of X-cor INFO @ Fri, 05 Jul 2019 20:56:39: #2 finished! INFO @ Fri, 05 Jul 2019 20:56:39: #2 predicted fragment length is 0 bps INFO @ Fri, 05 Jul 2019 20:56:39: #2 alternative fragment length(s) may be 0,36,47,73,103,121,220,247,266,288,311,326,363,383,406,420,455,495,546,580 bps INFO @ Fri, 05 Jul 2019 20:56:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX2339860/SRX2339860.05_model.r WARNING @ Fri, 05 Jul 2019 20:56:39: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 20:56:39: #2 You may need to consider one of the other alternative d(s): 0,36,47,73,103,121,220,247,266,288,311,326,363,383,406,420,455,495,546,580 WARNING @ Fri, 05 Jul 2019 20:56:39: #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 20:56:39: #3 Call peaks... INFO @ Fri, 05 Jul 2019 20:56:39: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 20:56:40: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 20:56:40: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 20:56:40: #1 total tags in treatment: 6112839 INFO @ Fri, 05 Jul 2019 20:56:40: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 20:56:40: #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 20:56:40: #1 tags after filtering in treatment: 3947920 INFO @ Fri, 05 Jul 2019 20:56:40: #1 Redundant rate of treatment: 0.35 INFO @ Fri, 05 Jul 2019 20:56:40: #1 finished! INFO @ Fri, 05 Jul 2019 20:56:40: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 20:56:40: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 20:56:40: #2 number of paired peaks: 165 WARNING @ Fri, 05 Jul 2019 20:56:40: Fewer paired peaks (165) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 165 pairs to build model! INFO @ Fri, 05 Jul 2019 20:56:40: start model_add_line... INFO @ Fri, 05 Jul 2019 20:56:40: start X-correlation... INFO @ Fri, 05 Jul 2019 20:56:40: end of X-cor INFO @ Fri, 05 Jul 2019 20:56:40: #2 finished! INFO @ Fri, 05 Jul 2019 20:56:40: #2 predicted fragment length is 0 bps INFO @ Fri, 05 Jul 2019 20:56:40: #2 alternative fragment length(s) may be 0,36,47,73,103,121,220,247,266,288,311,326,363,383,406,420,455,495,546,580 bps INFO @ Fri, 05 Jul 2019 20:56:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX2339860/SRX2339860.20_model.r WARNING @ Fri, 05 Jul 2019 20:56:40: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 20:56:40: #2 You may need to consider one of the other alternative d(s): 0,36,47,73,103,121,220,247,266,288,311,326,363,383,406,420,455,495,546,580 WARNING @ Fri, 05 Jul 2019 20:56:40: #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 20:56:40: #3 Call peaks... INFO @ Fri, 05 Jul 2019 20:56:40: #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 SRX2339860.05.bed: No such file or directory mv: cannot stat ‘SRX2339860.05.bed’: No such file or directory /var/spool/uge/at081/job_scripts/2009996: line 335: 46483 Terminated MACS $i /var/spool/uge/at081/job_scripts/2009996: line 335: 46505 Terminated MACS $i /var/spool/uge/at081/job_scripts/2009996: line 335: 46519 Terminated MACS $i mv: cannot stat ‘SRX2339860.05.bb’: No such file or directory ls: cannot access SRX2339860.10.bed: No such file or directory mv: cannot stat ‘SRX2339860.10.bed’: No such file or directory mv: cannot stat ‘SRX2339860.10.bb’: No such file or directory ls: cannot access SRX2339860.20.bed: No such file or directory mv: cannot stat ‘SRX2339860.20.bed’: No such file or directory mv: cannot stat ‘SRX2339860.20.bb’: No such file or directory