Job ID = 2010570 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 12,020,479 reads read : 24,040,958 reads written : 24,040,958 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: 00:10:46 12020479 reads; of these: 12020479 (100.00%) were paired; of these: 1650173 (13.73%) aligned concordantly 0 times 8378455 (69.70%) aligned concordantly exactly 1 time 1991851 (16.57%) aligned concordantly >1 times ---- 1650173 pairs aligned concordantly 0 times; of these: 108189 (6.56%) aligned discordantly 1 time ---- 1541984 pairs aligned 0 times concordantly or discordantly; of these: 3083968 mates make up the pairs; of these: 2647149 (85.84%) aligned 0 times 288180 (9.34%) aligned exactly 1 time 148639 (4.82%) aligned >1 times 88.99% overall alignment rate Time searching: 00:10:46 Overall time: 00:10:46 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] 1286312 / 10464792 = 0.1229 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 23:39:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381271/SRX381271.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381271/SRX381271.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381271/SRX381271.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381271/SRX381271.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 23:39:57: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:39:57: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:39:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381271/SRX381271.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381271/SRX381271.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381271/SRX381271.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381271/SRX381271.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 23:39:58: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:39:58: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:39:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381271/SRX381271.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381271/SRX381271.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381271/SRX381271.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381271/SRX381271.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 23:39:59: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:39:59: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:40:07: 1000000 INFO @ Fri, 05 Jul 2019 23:40:07: 1000000 INFO @ Fri, 05 Jul 2019 23:40:08: 1000000 INFO @ Fri, 05 Jul 2019 23:40:14: 2000000 INFO @ Fri, 05 Jul 2019 23:40:16: 2000000 INFO @ Fri, 05 Jul 2019 23:40:17: 2000000 INFO @ Fri, 05 Jul 2019 23:40:22: 3000000 INFO @ Fri, 05 Jul 2019 23:40:24: 3000000 INFO @ Fri, 05 Jul 2019 23:40:27: 3000000 INFO @ Fri, 05 Jul 2019 23:40:29: 4000000 INFO @ Fri, 05 Jul 2019 23:40:31: 4000000 INFO @ Fri, 05 Jul 2019 23:40:36: 4000000 INFO @ Fri, 05 Jul 2019 23:40:37: 5000000 INFO @ Fri, 05 Jul 2019 23:40:39: 5000000 INFO @ Fri, 05 Jul 2019 23:40:44: 6000000 INFO @ Fri, 05 Jul 2019 23:40:46: 6000000 INFO @ Fri, 05 Jul 2019 23:40:46: 5000000 INFO @ Fri, 05 Jul 2019 23:40:51: 7000000 INFO @ Fri, 05 Jul 2019 23:40:53: 7000000 INFO @ Fri, 05 Jul 2019 23:40:55: 6000000 INFO @ Fri, 05 Jul 2019 23:40:58: 8000000 INFO @ Fri, 05 Jul 2019 23:41:00: 8000000 INFO @ Fri, 05 Jul 2019 23:41:05: 7000000 INFO @ Fri, 05 Jul 2019 23:41:05: 9000000 INFO @ Fri, 05 Jul 2019 23:41:07: 9000000 INFO @ Fri, 05 Jul 2019 23:41:13: 10000000 INFO @ Fri, 05 Jul 2019 23:41:15: 10000000 INFO @ Fri, 05 Jul 2019 23:41:15: 8000000 INFO @ Fri, 05 Jul 2019 23:41:20: 11000000 INFO @ Fri, 05 Jul 2019 23:41:22: 11000000 INFO @ Fri, 05 Jul 2019 23:41:24: 9000000 INFO @ Fri, 05 Jul 2019 23:41:28: 12000000 INFO @ Fri, 05 Jul 2019 23:41:29: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 23:41:34: 10000000 INFO @ Fri, 05 Jul 2019 23:41:36: 13000000 INFO @ Fri, 05 Jul 2019 23:41:37: 13000000 BigWig に変換しました。 INFO @ Fri, 05 Jul 2019 23:41:44: 14000000 INFO @ Fri, 05 Jul 2019 23:41:44: 11000000 INFO @ Fri, 05 Jul 2019 23:41:45: 14000000 INFO @ Fri, 05 Jul 2019 23:41:53: 15000000 INFO @ Fri, 05 Jul 2019 23:41:54: 15000000 INFO @ Fri, 05 Jul 2019 23:41:54: 12000000 INFO @ Fri, 05 Jul 2019 23:42:02: 16000000 INFO @ Fri, 05 Jul 2019 23:42:03: 16000000 INFO @ Fri, 05 Jul 2019 23:42:05: 13000000 INFO @ Fri, 05 Jul 2019 23:42:11: 17000000 INFO @ Fri, 05 Jul 2019 23:42:12: 17000000 INFO @ Fri, 05 Jul 2019 23:42:15: 14000000 INFO @ Fri, 05 Jul 2019 23:42:20: 18000000 INFO @ Fri, 05 Jul 2019 23:42:21: 18000000 INFO @ Fri, 05 Jul 2019 23:42:25: 15000000 INFO @ Fri, 05 Jul 2019 23:42:28: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:42:28: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:42:28: #1 total tags in treatment: 9089607 INFO @ Fri, 05 Jul 2019 23:42:28: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:42:28: #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 23:42:28: #1 tags after filtering in treatment: 2565043 INFO @ Fri, 05 Jul 2019 23:42:28: #1 Redundant rate of treatment: 0.72 INFO @ Fri, 05 Jul 2019 23:42:28: #1 finished! INFO @ Fri, 05 Jul 2019 23:42:28: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:42:28: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:42:28: #2 number of paired peaks: 1295 INFO @ Fri, 05 Jul 2019 23:42:28: start model_add_line... INFO @ Fri, 05 Jul 2019 23:42:28: start X-correlation... INFO @ Fri, 05 Jul 2019 23:42:28: end of X-cor INFO @ Fri, 05 Jul 2019 23:42:28: #2 finished! INFO @ Fri, 05 Jul 2019 23:42:28: #2 predicted fragment length is 0 bps INFO @ Fri, 05 Jul 2019 23:42:28: #2 alternative fragment length(s) may be 0,31,58,83,116,125,132,145,167,182,216,246,271,294,325,397,434,469 bps INFO @ Fri, 05 Jul 2019 23:42:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX381271/SRX381271.20_model.r WARNING @ Fri, 05 Jul 2019 23:42:28: #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 23:42:28: #2 You may need to consider one of the other alternative d(s): 0,31,58,83,116,125,132,145,167,182,216,246,271,294,325,397,434,469 WARNING @ Fri, 05 Jul 2019 23:42:28: #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 23:42:28: #3 Call peaks... INFO @ Fri, 05 Jul 2019 23:42:28: #3 Pre-compute pvalue-qvalue table... ls: cannot access SRX381271.05.bed: No such file or directory mv: cannot stat ‘SRX381271.05.bed’: No such file or directory /var/spool/uge/at125/job_scripts/2010570: line 335: 9279 Terminated MACS $i /var/spool/uge/at125/job_scripts/2010570: line 335: 9306 Terminated MACS $i /var/spool/uge/at125/job_scripts/2010570: line 335: 9323 Terminated MACS $i mv: cannot stat ‘SRX381271.05.bb’: No such file or directory ls: cannot access SRX381271.10.bed: No such file or directory mv: cannot stat ‘SRX381271.10.bed’: No such file or directory mv: cannot stat ‘SRX381271.10.bb’: No such file or directory ls: cannot access SRX381271.20.bed: No such file or directory mv: cannot stat ‘SRX381271.20.bed’: No such file or directory mv: cannot stat ‘SRX381271.20.bb’: No such file or directory