Job ID = 7099500 SRX = SRX6911507 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 8024433 spots for SRR10191134/SRR10191134.sra Written 8024433 spots for SRR10191134/SRR10191134.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: 00:09:32 8024433 reads; of these: 8024433 (100.00%) were paired; of these: 1399517 (17.44%) aligned concordantly 0 times 5579670 (69.53%) aligned concordantly exactly 1 time 1045246 (13.03%) aligned concordantly >1 times ---- 1399517 pairs aligned concordantly 0 times; of these: 420961 (30.08%) aligned discordantly 1 time ---- 978556 pairs aligned 0 times concordantly or discordantly; of these: 1957112 mates make up the pairs; of these: 1202785 (61.46%) aligned 0 times 500309 (25.56%) aligned exactly 1 time 254018 (12.98%) aligned >1 times 92.51% overall alignment rate Time searching: 00:09:32 Overall time: 00:09:32 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] 461858 / 7040068 = 0.0656 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 12:19:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6911507/SRX6911507.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6911507/SRX6911507.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6911507/SRX6911507.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6911507/SRX6911507.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 12:19:13: #1 read tag files... INFO @ Wed, 22 Jul 2020 12:19:13: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 12:19:22: 1000000 INFO @ Wed, 22 Jul 2020 12:19:30: 2000000 INFO @ Wed, 22 Jul 2020 12:19:39: 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 12:19:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6911507/SRX6911507.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6911507/SRX6911507.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6911507/SRX6911507.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6911507/SRX6911507.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 12:19:43: #1 read tag files... INFO @ Wed, 22 Jul 2020 12:19:43: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 12:19:48: 4000000 INFO @ Wed, 22 Jul 2020 12:19:52: 1000000 INFO @ Wed, 22 Jul 2020 12:19:57: 5000000 INFO @ Wed, 22 Jul 2020 12:20:02: 2000000 INFO @ Wed, 22 Jul 2020 12:20:08: 6000000 INFO @ Wed, 22 Jul 2020 12:20:11: 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 12:20:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6911507/SRX6911507.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6911507/SRX6911507.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6911507/SRX6911507.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6911507/SRX6911507.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 12:20:13: #1 read tag files... INFO @ Wed, 22 Jul 2020 12:20:13: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 12:20:18: 7000000 INFO @ Wed, 22 Jul 2020 12:20:20: 4000000 INFO @ Wed, 22 Jul 2020 12:20:23: 1000000 INFO @ Wed, 22 Jul 2020 12:20:28: 8000000 INFO @ Wed, 22 Jul 2020 12:20:30: 5000000 INFO @ Wed, 22 Jul 2020 12:20:32: 2000000 INFO @ Wed, 22 Jul 2020 12:20:38: 9000000 INFO @ Wed, 22 Jul 2020 12:20:39: 6000000 INFO @ Wed, 22 Jul 2020 12:20:41: 3000000 INFO @ Wed, 22 Jul 2020 12:20:48: 10000000 INFO @ Wed, 22 Jul 2020 12:20:49: 7000000 INFO @ Wed, 22 Jul 2020 12:20:51: 4000000 INFO @ Wed, 22 Jul 2020 12:20:59: 11000000 INFO @ Wed, 22 Jul 2020 12:20:59: 8000000 INFO @ Wed, 22 Jul 2020 12:21:00: 5000000 INFO @ Wed, 22 Jul 2020 12:21:09: 12000000 INFO @ Wed, 22 Jul 2020 12:21:09: 9000000 INFO @ Wed, 22 Jul 2020 12:21:10: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Jul 2020 12:21:18: 10000000 INFO @ Wed, 22 Jul 2020 12:21:19: 13000000 INFO @ Wed, 22 Jul 2020 12:21:19: 7000000 BigWig に変換しました。 INFO @ Wed, 22 Jul 2020 12:21:27: #1 tag size is determined as 101 bps INFO @ Wed, 22 Jul 2020 12:21:27: #1 tag size = 101 INFO @ Wed, 22 Jul 2020 12:21:27: #1 total tags in treatment: 6180356 INFO @ Wed, 22 Jul 2020 12:21:27: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 12:21:27: #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 12:21:27: #1 tags after filtering in treatment: 3926855 INFO @ Wed, 22 Jul 2020 12:21:27: #1 Redundant rate of treatment: 0.36 INFO @ Wed, 22 Jul 2020 12:21:27: #1 finished! INFO @ Wed, 22 Jul 2020 12:21:27: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 12:21:27: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 12:21:28: #2 number of paired peaks: 163 WARNING @ Wed, 22 Jul 2020 12:21:28: Fewer paired peaks (163) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 163 pairs to build model! INFO @ Wed, 22 Jul 2020 12:21:28: start model_add_line... INFO @ Wed, 22 Jul 2020 12:21:28: start X-correlation... INFO @ Wed, 22 Jul 2020 12:21:28: end of X-cor INFO @ Wed, 22 Jul 2020 12:21:28: #2 finished! INFO @ Wed, 22 Jul 2020 12:21:28: #2 predicted fragment length is 0 bps INFO @ Wed, 22 Jul 2020 12:21:28: #2 alternative fragment length(s) may be 0,66,89,109,139,157,223,238,269,275,305,331,352,383,411,453,469,488,538,590 bps INFO @ Wed, 22 Jul 2020 12:21:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX6911507/SRX6911507.05_model.r WARNING @ Wed, 22 Jul 2020 12:21:28: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Jul 2020 12:21:28: #2 You may need to consider one of the other alternative d(s): 0,66,89,109,139,157,223,238,269,275,305,331,352,383,411,453,469,488,538,590 WARNING @ Wed, 22 Jul 2020 12:21:28: #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 12:21:28: #3 Call peaks... INFO @ Wed, 22 Jul 2020 12:21:28: #3 Pre-compute pvalue-qvalue table... /var/spool/uge/at150/job_scripts/7099500: line 297: 7768 Terminated MACS $i /var/spool/uge/at150/job_scripts/7099500: line 297: 8470 Terminated MACS $i /var/spool/uge/at150/job_scripts/7099500: line 297: 10304 Terminated MACS $i ls: cannot access SRX6911507.05.bed: No such file or directory mv: cannot stat ‘SRX6911507.05.bed’: No such file or directory mv: cannot stat ‘SRX6911507.05.bb’: No such file or directory ls: cannot access SRX6911507.10.bed: No such file or directory mv: cannot stat ‘SRX6911507.10.bed’: No such file or directory mv: cannot stat ‘SRX6911507.10.bb’: No such file or directory ls: cannot access SRX6911507.20.bed: No such file or directory mv: cannot stat ‘SRX6911507.20.bed’: No such file or directory mv: cannot stat ‘SRX6911507.20.bb’: No such file or directory