Job ID = 7107106 SRX = SRX6911545 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 16209584 spots for SRR10191172/SRR10191172.sra Written 16209584 spots for SRR10191172/SRR10191172.sra 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: 00:13:57 16209584 reads; of these: 16209584 (100.00%) were paired; of these: 4994784 (30.81%) aligned concordantly 0 times 10289643 (63.48%) aligned concordantly exactly 1 time 925157 (5.71%) aligned concordantly >1 times ---- 4994784 pairs aligned concordantly 0 times; of these: 738732 (14.79%) aligned discordantly 1 time ---- 4256052 pairs aligned 0 times concordantly or discordantly; of these: 8512104 mates make up the pairs; of these: 7506783 (88.19%) aligned 0 times 757141 (8.89%) aligned exactly 1 time 248180 (2.92%) aligned >1 times 76.84% overall alignment rate Time searching: 00:13:57 Overall time: 00:13:57 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] 1214845 / 11951535 = 0.1016 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 22 Jul 2020 13:24:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6911545/SRX6911545.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6911545/SRX6911545.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6911545/SRX6911545.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6911545/SRX6911545.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 @ Wed, 22 Jul 2020 13:24:15: #1 read tag files... INFO @ Wed, 22 Jul 2020 13:24:15: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 13:24:24: 1000000 INFO @ Wed, 22 Jul 2020 13:24:33: 2000000 INFO @ Wed, 22 Jul 2020 13:24:42: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 22 Jul 2020 13:24:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6911545/SRX6911545.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6911545/SRX6911545.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6911545/SRX6911545.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6911545/SRX6911545.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 @ Wed, 22 Jul 2020 13:24:45: #1 read tag files... INFO @ Wed, 22 Jul 2020 13:24:45: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 13:24:51: 4000000 INFO @ Wed, 22 Jul 2020 13:24:54: 1000000 INFO @ Wed, 22 Jul 2020 13:25:01: 5000000 INFO @ Wed, 22 Jul 2020 13:25:03: 2000000 INFO @ Wed, 22 Jul 2020 13:25:11: 6000000 INFO @ Wed, 22 Jul 2020 13:25:13: 3000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 22 Jul 2020 13:25:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6911545/SRX6911545.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6911545/SRX6911545.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6911545/SRX6911545.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6911545/SRX6911545.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 @ Wed, 22 Jul 2020 13:25:15: #1 read tag files... INFO @ Wed, 22 Jul 2020 13:25:15: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 13:25:21: 7000000 INFO @ Wed, 22 Jul 2020 13:25:22: 4000000 INFO @ Wed, 22 Jul 2020 13:25:25: 1000000 INFO @ Wed, 22 Jul 2020 13:25:31: 8000000 INFO @ Wed, 22 Jul 2020 13:25:32: 5000000 INFO @ Wed, 22 Jul 2020 13:25:35: 2000000 INFO @ Wed, 22 Jul 2020 13:25:40: 9000000 INFO @ Wed, 22 Jul 2020 13:25:42: 6000000 INFO @ Wed, 22 Jul 2020 13:25:45: 3000000 INFO @ Wed, 22 Jul 2020 13:25:50: 10000000 INFO @ Wed, 22 Jul 2020 13:25:51: 7000000 INFO @ Wed, 22 Jul 2020 13:25:55: 4000000 INFO @ Wed, 22 Jul 2020 13:26:00: 11000000 INFO @ Wed, 22 Jul 2020 13:26:01: 8000000 INFO @ Wed, 22 Jul 2020 13:26:05: 5000000 INFO @ Wed, 22 Jul 2020 13:26:10: 12000000 INFO @ Wed, 22 Jul 2020 13:26:10: 9000000 INFO @ Wed, 22 Jul 2020 13:26:15: 6000000 INFO @ Wed, 22 Jul 2020 13:26:19: 10000000 INFO @ Wed, 22 Jul 2020 13:26:20: 13000000 INFO @ Wed, 22 Jul 2020 13:26:24: 7000000 INFO @ Wed, 22 Jul 2020 13:26:29: 11000000 INFO @ Wed, 22 Jul 2020 13:26:30: 14000000 INFO @ Wed, 22 Jul 2020 13:26:34: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Jul 2020 13:26:39: 12000000 INFO @ Wed, 22 Jul 2020 13:26:40: 15000000 BigWig に変換しました。 INFO @ Wed, 22 Jul 2020 13:26:44: 9000000 INFO @ Wed, 22 Jul 2020 13:26:49: 13000000 INFO @ Wed, 22 Jul 2020 13:26:50: 16000000 INFO @ Wed, 22 Jul 2020 13:26:54: 10000000 INFO @ Wed, 22 Jul 2020 13:26:59: 14000000 INFO @ Wed, 22 Jul 2020 13:27:00: 17000000 INFO @ Wed, 22 Jul 2020 13:27:04: 11000000 INFO @ Wed, 22 Jul 2020 13:27:08: 15000000 INFO @ Wed, 22 Jul 2020 13:27:10: 18000000 INFO @ Wed, 22 Jul 2020 13:27:14: 12000000 INFO @ Wed, 22 Jul 2020 13:27:18: 16000000 INFO @ Wed, 22 Jul 2020 13:27:20: 19000000 INFO @ Wed, 22 Jul 2020 13:27:24: 13000000 INFO @ Wed, 22 Jul 2020 13:27:28: 17000000 INFO @ Wed, 22 Jul 2020 13:27:30: 20000000 INFO @ Wed, 22 Jul 2020 13:27:34: 14000000 INFO @ Wed, 22 Jul 2020 13:27:38: 18000000 INFO @ Wed, 22 Jul 2020 13:27:40: 21000000 INFO @ Wed, 22 Jul 2020 13:27:43: 15000000 INFO @ Wed, 22 Jul 2020 13:27:48: 19000000 INFO @ Wed, 22 Jul 2020 13:27:50: 22000000 INFO @ Wed, 22 Jul 2020 13:27:53: 16000000 INFO @ Wed, 22 Jul 2020 13:27:55: #1 tag size is determined as 101 bps INFO @ Wed, 22 Jul 2020 13:27:55: #1 tag size = 101 INFO @ Wed, 22 Jul 2020 13:27:55: #1 total tags in treatment: 10035482 INFO @ Wed, 22 Jul 2020 13:27:55: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 13:27:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Jul 2020 13:27:55: #1 tags after filtering in treatment: 4422317 INFO @ Wed, 22 Jul 2020 13:27:55: #1 Redundant rate of treatment: 0.56 INFO @ Wed, 22 Jul 2020 13:27:55: #1 finished! INFO @ Wed, 22 Jul 2020 13:27:55: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 13:27:55: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 13:27:55: #2 number of paired peaks: 133 WARNING @ Wed, 22 Jul 2020 13:27:55: Fewer paired peaks (133) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 133 pairs to build model! INFO @ Wed, 22 Jul 2020 13:27:55: start model_add_line... INFO @ Wed, 22 Jul 2020 13:27:55: start X-correlation... INFO @ Wed, 22 Jul 2020 13:27:55: end of X-cor INFO @ Wed, 22 Jul 2020 13:27:55: #2 finished! INFO @ Wed, 22 Jul 2020 13:27:55: #2 predicted fragment length is 0 bps INFO @ Wed, 22 Jul 2020 13:27:55: #2 alternative fragment length(s) may be 0,10,28,63,66,99,142,172,221,224,238,261,288,336,367,398,424,428,437,463,468,491,531,555,572 bps INFO @ Wed, 22 Jul 2020 13:27:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX6911545/SRX6911545.05_model.r WARNING @ Wed, 22 Jul 2020 13:27:55: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Jul 2020 13:27:55: #2 You may need to consider one of the other alternative d(s): 0,10,28,63,66,99,142,172,221,224,238,261,288,336,367,398,424,428,437,463,468,491,531,555,572 WARNING @ Wed, 22 Jul 2020 13:27:55: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 22 Jul 2020 13:27:55: #3 Call peaks... INFO @ Wed, 22 Jul 2020 13:27:55: #3 Pre-compute pvalue-qvalue table... /var/spool/uge/at158/job_scripts/7107106: line 297: 90572 Terminated MACS $i /var/spool/uge/at158/job_scripts/7107106: line 297: 92397 Terminated MACS $i /var/spool/uge/at158/job_scripts/7107106: line 297: 92767 Terminated MACS $i ls: cannot access SRX6911545.05.bed: No such file or directory mv: cannot stat ‘SRX6911545.05.bed’: No such file or directory mv: cannot stat ‘SRX6911545.05.bb’: No such file or directory ls: cannot access SRX6911545.10.bed: No such file or directory mv: cannot stat ‘SRX6911545.10.bed’: No such file or directory mv: cannot stat ‘SRX6911545.10.bb’: No such file or directory ls: cannot access SRX6911545.20.bed: No such file or directory mv: cannot stat ‘SRX6911545.20.bed’: No such file or directory mv: cannot stat ‘SRX6911545.20.bb’: No such file or directory