Job ID = 2010556 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 13,520,492 reads read : 27,040,984 reads written : 27,040,984 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: 00:09:18 13520492 reads; of these: 13520492 (100.00%) were paired; of these: 5227318 (38.66%) aligned concordantly 0 times 5843199 (43.22%) aligned concordantly exactly 1 time 2449975 (18.12%) aligned concordantly >1 times ---- 5227318 pairs aligned concordantly 0 times; of these: 106383 (2.04%) aligned discordantly 1 time ---- 5120935 pairs aligned 0 times concordantly or discordantly; of these: 10241870 mates make up the pairs; of these: 9928960 (96.94%) aligned 0 times 152062 (1.48%) aligned exactly 1 time 160848 (1.57%) aligned >1 times 63.28% overall alignment rate Time searching: 00:09:18 Overall time: 00:09:18 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] 1093509 / 8387124 = 0.1304 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 23:23:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381257/SRX381257.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381257/SRX381257.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381257/SRX381257.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381257/SRX381257.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 23:23:14: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:23:14: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:23:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381257/SRX381257.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381257/SRX381257.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381257/SRX381257.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381257/SRX381257.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 23:23:14: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:23:14: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:23:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381257/SRX381257.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381257/SRX381257.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381257/SRX381257.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381257/SRX381257.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 23:23:16: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:23:16: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:23:23: 1000000 INFO @ Fri, 05 Jul 2019 23:23:24: 1000000 INFO @ Fri, 05 Jul 2019 23:23:24: 1000000 INFO @ Fri, 05 Jul 2019 23:23:31: 2000000 INFO @ Fri, 05 Jul 2019 23:23:33: 2000000 INFO @ Fri, 05 Jul 2019 23:23:35: 2000000 INFO @ Fri, 05 Jul 2019 23:23:39: 3000000 INFO @ Fri, 05 Jul 2019 23:23:41: 3000000 INFO @ Fri, 05 Jul 2019 23:23:45: 3000000 INFO @ Fri, 05 Jul 2019 23:23:47: 4000000 INFO @ Fri, 05 Jul 2019 23:23:50: 4000000 INFO @ Fri, 05 Jul 2019 23:23:55: 4000000 INFO @ Fri, 05 Jul 2019 23:23:56: 5000000 INFO @ Fri, 05 Jul 2019 23:23:58: 5000000 INFO @ Fri, 05 Jul 2019 23:24:04: 6000000 INFO @ Fri, 05 Jul 2019 23:24:05: 5000000 INFO @ Fri, 05 Jul 2019 23:24:07: 6000000 INFO @ Fri, 05 Jul 2019 23:24:13: 7000000 INFO @ Fri, 05 Jul 2019 23:24:15: 6000000 INFO @ Fri, 05 Jul 2019 23:24:16: 7000000 INFO @ Fri, 05 Jul 2019 23:24:22: 8000000 INFO @ Fri, 05 Jul 2019 23:24:25: 8000000 INFO @ Fri, 05 Jul 2019 23:24:25: 7000000 INFO @ Fri, 05 Jul 2019 23:24:31: 9000000 INFO @ Fri, 05 Jul 2019 23:24:34: 9000000 INFO @ Fri, 05 Jul 2019 23:24:35: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 23:24:40: 10000000 BigWig に変換しました。 INFO @ Fri, 05 Jul 2019 23:24:43: 10000000 INFO @ Fri, 05 Jul 2019 23:24:45: 9000000 INFO @ Fri, 05 Jul 2019 23:24:49: 11000000 INFO @ Fri, 05 Jul 2019 23:24:52: 11000000 INFO @ Fri, 05 Jul 2019 23:24:55: 10000000 INFO @ Fri, 05 Jul 2019 23:24:59: 12000000 INFO @ Fri, 05 Jul 2019 23:25:02: 12000000 INFO @ Fri, 05 Jul 2019 23:25:05: 11000000 INFO @ Fri, 05 Jul 2019 23:25:08: 13000000 INFO @ Fri, 05 Jul 2019 23:25:11: 13000000 INFO @ Fri, 05 Jul 2019 23:25:15: 12000000 INFO @ Fri, 05 Jul 2019 23:25:16: 14000000 INFO @ Fri, 05 Jul 2019 23:25:20: 14000000 INFO @ Fri, 05 Jul 2019 23:25:23: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:25:23: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:25:23: #1 total tags in treatment: 7202641 INFO @ Fri, 05 Jul 2019 23:25:23: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:25:23: #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 23:25:24: #1 tags after filtering in treatment: 2582027 INFO @ Fri, 05 Jul 2019 23:25:24: #1 Redundant rate of treatment: 0.64 INFO @ Fri, 05 Jul 2019 23:25:24: #1 finished! INFO @ Fri, 05 Jul 2019 23:25:24: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:25:24: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:25:24: #2 number of paired peaks: 1442 INFO @ Fri, 05 Jul 2019 23:25:24: start model_add_line... INFO @ Fri, 05 Jul 2019 23:25:24: start X-correlation... INFO @ Fri, 05 Jul 2019 23:25:24: end of X-cor INFO @ Fri, 05 Jul 2019 23:25:24: #2 finished! INFO @ Fri, 05 Jul 2019 23:25:24: #2 predicted fragment length is 0 bps INFO @ Fri, 05 Jul 2019 23:25:24: #2 alternative fragment length(s) may be 0,11,27,50,74,87,102,117,129,146,176,204,538,564 bps INFO @ Fri, 05 Jul 2019 23:25:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX381257/SRX381257.10_model.r INFO @ Fri, 05 Jul 2019 23:25:25: 13000000 INFO @ Fri, 05 Jul 2019 23:25:28: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:25:28: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:25:28: #1 total tags in treatment: 7202641 INFO @ Fri, 05 Jul 2019 23:25:28: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:25:28: #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 23:25:28: #1 tags after filtering in treatment: 2582027 INFO @ Fri, 05 Jul 2019 23:25:28: #1 Redundant rate of treatment: 0.64 INFO @ Fri, 05 Jul 2019 23:25:28: #1 finished! INFO @ Fri, 05 Jul 2019 23:25:28: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:25:28: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:25:28: #2 number of paired peaks: 1442 INFO @ Fri, 05 Jul 2019 23:25:28: start model_add_line... INFO @ Fri, 05 Jul 2019 23:25:28: start X-correlation... INFO @ Fri, 05 Jul 2019 23:25:28: end of X-cor INFO @ Fri, 05 Jul 2019 23:25:28: #2 finished! INFO @ Fri, 05 Jul 2019 23:25:28: #2 predicted fragment length is 0 bps INFO @ Fri, 05 Jul 2019 23:25:28: #2 alternative fragment length(s) may be 0,11,27,50,74,87,102,117,129,146,176,204,538,564 bps INFO @ Fri, 05 Jul 2019 23:25:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX381257/SRX381257.20_model.r WARNING @ Fri, 05 Jul 2019 23:25:33: #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 23:25:33: #2 You may need to consider one of the other alternative d(s): 0,11,27,50,74,87,102,117,129,146,176,204,538,564 WARNING @ Fri, 05 Jul 2019 23:25:33: #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 23:25:33: #3 Call peaks... INFO @ Fri, 05 Jul 2019 23:25:33: #3 Pre-compute pvalue-qvalue table... WARNING @ Fri, 05 Jul 2019 23:25:33: #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 23:25:33: #2 You may need to consider one of the other alternative d(s): 0,11,27,50,74,87,102,117,129,146,176,204,538,564 WARNING @ Fri, 05 Jul 2019 23:25:33: #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 23:25:33: #3 Call peaks... INFO @ Fri, 05 Jul 2019 23:25:33: #3 Pre-compute pvalue-qvalue table... ls: cannot access SRX381257.05.bed: No such file or directory mv: cannot stat ‘SRX381257.05.bed’: No such file or directory /var/spool/uge/at075/job_scripts/2010556: line 335: 4898 Terminated MACS $i /var/spool/uge/at075/job_scripts/2010556: line 335: 4914 Terminated MACS $i /var/spool/uge/at075/job_scripts/2010556: line 335: 4928 Terminated MACS $i mv: cannot stat ‘SRX381257.05.bb’: No such file or directory ls: cannot access SRX381257.10.bed: No such file or directory mv: cannot stat ‘SRX381257.10.bed’: No such file or directory mv: cannot stat ‘SRX381257.10.bb’: No such file or directory ls: cannot access SRX381257.20.bed: No such file or directory mv: cannot stat ‘SRX381257.20.bed’: No such file or directory mv: cannot stat ‘SRX381257.20.bb’: No such file or directory