Job ID = 2010563 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 13,730,680 reads read : 27,461,360 reads written : 27,461,360 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: 00:09:48 13730680 reads; of these: 13730680 (100.00%) were paired; of these: 4562145 (33.23%) aligned concordantly 0 times 7422860 (54.06%) aligned concordantly exactly 1 time 1745675 (12.71%) aligned concordantly >1 times ---- 4562145 pairs aligned concordantly 0 times; of these: 110697 (2.43%) aligned discordantly 1 time ---- 4451448 pairs aligned 0 times concordantly or discordantly; of these: 8902896 mates make up the pairs; of these: 8467638 (95.11%) aligned 0 times 283730 (3.19%) aligned exactly 1 time 151528 (1.70%) aligned >1 times 69.17% overall alignment rate Time searching: 00:09:48 Overall time: 00:09:48 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] 1425416 / 9269822 = 0.1538 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 23:36:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381264/SRX381264.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381264/SRX381264.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381264/SRX381264.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381264/SRX381264.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 23:36:33: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:36:33: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:36:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381264/SRX381264.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381264/SRX381264.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381264/SRX381264.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381264/SRX381264.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 23:36:33: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:36:33: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:36:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381264/SRX381264.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381264/SRX381264.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381264/SRX381264.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381264/SRX381264.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 23:36:34: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:36:34: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:36:40: 1000000 INFO @ Fri, 05 Jul 2019 23:36:41: 1000000 INFO @ Fri, 05 Jul 2019 23:36:43: 1000000 INFO @ Fri, 05 Jul 2019 23:36:47: 2000000 INFO @ Fri, 05 Jul 2019 23:36:48: 2000000 INFO @ Fri, 05 Jul 2019 23:36:52: 2000000 INFO @ Fri, 05 Jul 2019 23:36:55: 3000000 INFO @ Fri, 05 Jul 2019 23:36:55: 3000000 INFO @ Fri, 05 Jul 2019 23:37:01: 3000000 INFO @ Fri, 05 Jul 2019 23:37:01: 4000000 INFO @ Fri, 05 Jul 2019 23:37:02: 4000000 INFO @ Fri, 05 Jul 2019 23:37:08: 5000000 INFO @ Fri, 05 Jul 2019 23:37:09: 5000000 INFO @ Fri, 05 Jul 2019 23:37:10: 4000000 INFO @ Fri, 05 Jul 2019 23:37:15: 6000000 INFO @ Fri, 05 Jul 2019 23:37:16: 6000000 INFO @ Fri, 05 Jul 2019 23:37:18: 5000000 INFO @ Fri, 05 Jul 2019 23:37:22: 7000000 INFO @ Fri, 05 Jul 2019 23:37:23: 7000000 INFO @ Fri, 05 Jul 2019 23:37:26: 6000000 INFO @ Fri, 05 Jul 2019 23:37:30: 8000000 INFO @ Fri, 05 Jul 2019 23:37:30: 8000000 INFO @ Fri, 05 Jul 2019 23:37:34: 7000000 INFO @ Fri, 05 Jul 2019 23:37:37: 9000000 INFO @ Fri, 05 Jul 2019 23:37:37: 9000000 INFO @ Fri, 05 Jul 2019 23:37:43: 8000000 INFO @ Fri, 05 Jul 2019 23:37:44: 10000000 INFO @ Fri, 05 Jul 2019 23:37:44: 10000000 INFO @ Fri, 05 Jul 2019 23:37:51: 11000000 INFO @ Fri, 05 Jul 2019 23:37:51: 11000000 INFO @ Fri, 05 Jul 2019 23:37:52: 9000000 INFO @ Fri, 05 Jul 2019 23:37:58: 12000000 INFO @ Fri, 05 Jul 2019 23:37:58: 12000000 INFO @ Fri, 05 Jul 2019 23:38:00: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 23:38:04: 13000000 INFO @ Fri, 05 Jul 2019 23:38:05: 13000000 INFO @ Fri, 05 Jul 2019 23:38:09: 11000000 INFO @ Fri, 05 Jul 2019 23:38:11: 14000000 INFO @ Fri, 05 Jul 2019 23:38:11: 14000000 INFO @ Fri, 05 Jul 2019 23:38:17: 12000000 INFO @ Fri, 05 Jul 2019 23:38:17: 15000000 INFO @ Fri, 05 Jul 2019 23:38:18: 15000000 BigWig に変換しました。 INFO @ Fri, 05 Jul 2019 23:38:24: 16000000 INFO @ Fri, 05 Jul 2019 23:38:24: 16000000 INFO @ Fri, 05 Jul 2019 23:38:25: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:38:25: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:38:25: #1 total tags in treatment: 7754350 INFO @ Fri, 05 Jul 2019 23:38:25: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:38:25: #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 23:38:25: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:38:25: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:38:25: #1 total tags in treatment: 7754350 INFO @ Fri, 05 Jul 2019 23:38:25: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:38:25: #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 23:38:25: #1 tags after filtering in treatment: 2528816 INFO @ Fri, 05 Jul 2019 23:38:25: #1 Redundant rate of treatment: 0.67 INFO @ Fri, 05 Jul 2019 23:38:25: #1 finished! INFO @ Fri, 05 Jul 2019 23:38:25: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:38:25: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:38:25: #1 tags after filtering in treatment: 2528816 INFO @ Fri, 05 Jul 2019 23:38:25: #1 Redundant rate of treatment: 0.67 INFO @ Fri, 05 Jul 2019 23:38:25: #1 finished! INFO @ Fri, 05 Jul 2019 23:38:25: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:38:25: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:38:25: 13000000 INFO @ Fri, 05 Jul 2019 23:38:25: #2 number of paired peaks: 1248 INFO @ Fri, 05 Jul 2019 23:38:25: start model_add_line... INFO @ Fri, 05 Jul 2019 23:38:26: start X-correlation... INFO @ Fri, 05 Jul 2019 23:38:26: end of X-cor INFO @ Fri, 05 Jul 2019 23:38:26: #2 finished! INFO @ Fri, 05 Jul 2019 23:38:26: #2 predicted fragment length is 0 bps INFO @ Fri, 05 Jul 2019 23:38:26: #2 alternative fragment length(s) may be 0,42,45,89,110,148,160,200,211,218,224,250,281 bps INFO @ Fri, 05 Jul 2019 23:38:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX381264/SRX381264.05_model.r INFO @ Fri, 05 Jul 2019 23:38:26: #2 number of paired peaks: 1248 INFO @ Fri, 05 Jul 2019 23:38:26: start model_add_line... WARNING @ Fri, 05 Jul 2019 23:38:26: #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 23:38:26: #2 You may need to consider one of the other alternative d(s): 0,42,45,89,110,148,160,200,211,218,224,250,281 WARNING @ Fri, 05 Jul 2019 23:38:26: #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 23:38:26: #3 Call peaks... INFO @ Fri, 05 Jul 2019 23:38:26: #3 Pre-compute pvalue-qvalue table... ls: cannot access SRX381264.05.bedINFO @ Fri, 05 Jul 2019 23:38:26: start X-correlation... : No such file or directory mv: cannot stat ‘SRX381264.05.bed’: No such file or directory /var/spool/uge/at077/job_scripts/2010563: line 335: 46472 Terminated MACS $i /var/spool/uge/at077/job_scripts/2010563: line 335: 46487 Terminated MACS $i /var/spool/uge/at077/job_scripts/2010563: line 335: 46501 Terminated MACS $i mv: cannot stat ‘SRX381264.05.bb’: No such file or directory INFO @ Fri, 05 Jul 2019 23:38:26: end of X-cor INFO @ Fri, 05 Jul 2019 23:38:26: #2 finished! INFO @ Fri, 05 Jul 2019 23:38:26: #2 predicted fragment length is 0 bps INFO @ Fri, 05 Jul 2019 23:38:26: #2 alternative fragment length(s) may be 0,42,45,89,110,148,160,200,211,218,224,250,281 bps INFO @ Fri, 05 Jul 2019 23:38:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX381264/SRX381264.10_model.r ls: cannot access SRX381264.10.bed: No such file or directory mv: cannot stat ‘SRX381264.10.bed’: No such file or directory mv: cannot stat ‘SRX381264.10.bb’: No such file or directory ls: cannot access SRX381264.20.bed: No such file or directory WARNING @ Fri, 05 Jul 2019 23:38:26: #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 23:38:26: #2 You may need to consider one of the other alternative d(s): 0,42,45,89,110,148,160,200,211,218,224,250,281 WARNING @ Fri, 05 Jul 2019 23:38:26: #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 23:38:26: #3 Call peaks... INFO @ Fri, 05 Jul 2019 23:38:26: #3 Pre-compute pvalue-qvalue table... mv: cannot stat ‘SRX381264.20.bed’: No such file or directory mv: cannot stat ‘SRX381264.20.bb’: No such file or directory