Job ID = 2010552 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 12,520,008 reads read : 25,040,016 reads written : 25,040,016 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: 00:11:46 12520008 reads; of these: 12520008 (100.00%) were paired; of these: 992851 (7.93%) aligned concordantly 0 times 9298620 (74.27%) aligned concordantly exactly 1 time 2228537 (17.80%) aligned concordantly >1 times ---- 992851 pairs aligned concordantly 0 times; of these: 123815 (12.47%) aligned discordantly 1 time ---- 869036 pairs aligned 0 times concordantly or discordantly; of these: 1738072 mates make up the pairs; of these: 1438384 (82.76%) aligned 0 times 153642 (8.84%) aligned exactly 1 time 146046 (8.40%) aligned >1 times 94.26% overall alignment rate Time searching: 00:11:46 Overall time: 00:11:46 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] 1039249 / 11637657 = 0.0893 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 23:27:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381253/SRX381253.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381253/SRX381253.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381253/SRX381253.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381253/SRX381253.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 23:27:29: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:27:29: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:27:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381253/SRX381253.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381253/SRX381253.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381253/SRX381253.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381253/SRX381253.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 23:27:30: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:27:30: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:27:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381253/SRX381253.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381253/SRX381253.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381253/SRX381253.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381253/SRX381253.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 23:27:32: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:27:32: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:27:38: 1000000 INFO @ Fri, 05 Jul 2019 23:27:40: 1000000 INFO @ Fri, 05 Jul 2019 23:27:41: 1000000 INFO @ Fri, 05 Jul 2019 23:27:46: 2000000 INFO @ Fri, 05 Jul 2019 23:27:49: 2000000 INFO @ Fri, 05 Jul 2019 23:27:50: 2000000 INFO @ Fri, 05 Jul 2019 23:27:54: 3000000 INFO @ Fri, 05 Jul 2019 23:27:59: 3000000 INFO @ Fri, 05 Jul 2019 23:28:00: 3000000 INFO @ Fri, 05 Jul 2019 23:28:03: 4000000 INFO @ Fri, 05 Jul 2019 23:28:08: 4000000 INFO @ Fri, 05 Jul 2019 23:28:09: 4000000 INFO @ Fri, 05 Jul 2019 23:28:11: 5000000 INFO @ Fri, 05 Jul 2019 23:28:17: 5000000 INFO @ Fri, 05 Jul 2019 23:28:18: 5000000 INFO @ Fri, 05 Jul 2019 23:28:19: 6000000 INFO @ Fri, 05 Jul 2019 23:28:26: 6000000 INFO @ Fri, 05 Jul 2019 23:28:27: 6000000 INFO @ Fri, 05 Jul 2019 23:28:27: 7000000 INFO @ Fri, 05 Jul 2019 23:28:35: 7000000 INFO @ Fri, 05 Jul 2019 23:28:35: 8000000 INFO @ Fri, 05 Jul 2019 23:28:36: 7000000 INFO @ Fri, 05 Jul 2019 23:28:43: 9000000 INFO @ Fri, 05 Jul 2019 23:28:44: 8000000 INFO @ Fri, 05 Jul 2019 23:28:45: 8000000 INFO @ Fri, 05 Jul 2019 23:28:52: 10000000 INFO @ Fri, 05 Jul 2019 23:28:53: 9000000 INFO @ Fri, 05 Jul 2019 23:28:54: 9000000 INFO @ Fri, 05 Jul 2019 23:29:00: 11000000 INFO @ Fri, 05 Jul 2019 23:29:02: 10000000 INFO @ Fri, 05 Jul 2019 23:29:03: 10000000 INFO @ Fri, 05 Jul 2019 23:29:08: 12000000 INFO @ Fri, 05 Jul 2019 23:29:11: 11000000 INFO @ Fri, 05 Jul 2019 23:29:12: 11000000 INFO @ Fri, 05 Jul 2019 23:29:16: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 23:29:20: 12000000 INFO @ Fri, 05 Jul 2019 23:29:22: 12000000 INFO @ Fri, 05 Jul 2019 23:29:24: 14000000 INFO @ Fri, 05 Jul 2019 23:29:30: 13000000 INFO @ Fri, 05 Jul 2019 23:29:31: 13000000 INFO @ Fri, 05 Jul 2019 23:29:33: 15000000 INFO @ Fri, 05 Jul 2019 23:29:39: 14000000 INFO @ Fri, 05 Jul 2019 23:29:40: 14000000 INFO @ Fri, 05 Jul 2019 23:29:41: 16000000 BigWig に変換しました。 INFO @ Fri, 05 Jul 2019 23:29:48: 15000000 INFO @ Fri, 05 Jul 2019 23:29:49: 17000000 INFO @ Fri, 05 Jul 2019 23:29:49: 15000000 INFO @ Fri, 05 Jul 2019 23:29:57: 16000000 INFO @ Fri, 05 Jul 2019 23:29:57: 18000000 INFO @ Fri, 05 Jul 2019 23:29:58: 16000000 INFO @ Fri, 05 Jul 2019 23:30:06: 19000000 INFO @ Fri, 05 Jul 2019 23:30:06: 17000000 INFO @ Fri, 05 Jul 2019 23:30:07: 17000000 INFO @ Fri, 05 Jul 2019 23:30:14: 20000000 INFO @ Fri, 05 Jul 2019 23:30:15: 18000000 INFO @ Fri, 05 Jul 2019 23:30:16: 18000000 INFO @ Fri, 05 Jul 2019 23:30:22: 21000000 INFO @ Fri, 05 Jul 2019 23:30:24: 19000000 INFO @ Fri, 05 Jul 2019 23:30:26: 19000000 INFO @ Fri, 05 Jul 2019 23:30:26: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:30:26: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:30:26: #1 total tags in treatment: 10490816 INFO @ Fri, 05 Jul 2019 23:30:26: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:30:26: #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 23:30:27: #1 tags after filtering in treatment: 3228757 INFO @ Fri, 05 Jul 2019 23:30:27: #1 Redundant rate of treatment: 0.69 INFO @ Fri, 05 Jul 2019 23:30:27: #1 finished! INFO @ Fri, 05 Jul 2019 23:30:27: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:30:27: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:30:27: #2 number of paired peaks: 1407 INFO @ Fri, 05 Jul 2019 23:30:27: start model_add_line... INFO @ Fri, 05 Jul 2019 23:30:27: start X-correlation... INFO @ Fri, 05 Jul 2019 23:30:27: end of X-cor INFO @ Fri, 05 Jul 2019 23:30:27: #2 finished! INFO @ Fri, 05 Jul 2019 23:30:27: #2 predicted fragment length is 0 bps INFO @ Fri, 05 Jul 2019 23:30:27: #2 alternative fragment length(s) may be 0,19,64,84,101,121,146,173,205,247,530,556 bps INFO @ Fri, 05 Jul 2019 23:30:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX381253/SRX381253.05_model.r INFO @ Fri, 05 Jul 2019 23:30:33: 20000000 INFO @ Fri, 05 Jul 2019 23:30:34: 20000000 INFO @ Fri, 05 Jul 2019 23:30:42: 21000000 INFO @ Fri, 05 Jul 2019 23:30:43: 21000000 WARNING @ Fri, 05 Jul 2019 23:30:47: #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 23:30:47: #2 You may need to consider one of the other alternative d(s): 0,19,64,84,101,121,146,173,205,247,530,556 WARNING @ Fri, 05 Jul 2019 23:30:47: #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 23:30:47: #3 Call peaks... INFO @ Fri, 05 Jul 2019 23:30:47: #3 Pre-compute pvalue-qvalue table... ls: cannot access SRX381253.05.bed: No such file or directory mv: cannot stat ‘SRX381253.05.bed’: No such file or directory /var/spool/uge/at087/job_scripts/2010552: line 335: 42186 Terminated MACS $i /var/spool/uge/at087/job_scripts/2010552: line 335: 42201 Terminated MACS $i /var/spool/uge/at087/job_scripts/2010552: line 335: 42214 Terminated MACS $i mv: cannot stat ‘SRX381253.05.bb’: No such file or directory ls: cannot access SRX381253.10.bed: No such file or directory mv: cannot stat ‘SRX381253.10.bed’: No such file or directory mv: cannot stat ‘SRX381253.10.bb’: No such file or directory ls: cannot access SRX381253.20.bed: No such file or directory mv: cannot stat ‘SRX381253.20.bed’: No such file or directory mv: cannot stat ‘SRX381253.20.bb’: No such file or directory