Job ID = 14520570 SRX = SRX11781065 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2022-01-15T10:22:31 prefetch.2.10.7: 1) Downloading 'SRR15481008'... 2022-01-15T10:22:32 prefetch.2.10.7: Downloading via HTTPS... 2022-01-15T10:23:17 prefetch.2.10.7: HTTPS download succeed 2022-01-15T10:23:17 prefetch.2.10.7: 1) 'SRR15481008' was downloaded successfully 2022-01-15T10:23:17 prefetch.2.10.7: 'SRR15481008' has 0 unresolved dependencies Read 11243930 spots for SRR15481008/SRR15481008.sra Written 11243930 spots for SRR15481008/SRR15481008.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: 00:08:52 11243930 reads; of these: 11243930 (100.00%) were paired; of these: 1621960 (14.43%) aligned concordantly 0 times 8723489 (77.58%) aligned concordantly exactly 1 time 898481 (7.99%) aligned concordantly >1 times ---- 1621960 pairs aligned concordantly 0 times; of these: 111633 (6.88%) aligned discordantly 1 time ---- 1510327 pairs aligned 0 times concordantly or discordantly; of these: 3020654 mates make up the pairs; of these: 2090291 (69.20%) aligned 0 times 808135 (26.75%) aligned exactly 1 time 122228 (4.05%) aligned >1 times 90.70% overall alignment rate Time searching: 00:08:52 Overall time: 00:08:52 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] 1846052 / 9732829 = 0.1897 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 15 Jan 2022 19:41:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781065/SRX11781065.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781065/SRX11781065.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781065/SRX11781065.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781065/SRX11781065.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 @ Sat, 15 Jan 2022 19:41:32: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:41:32: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:41:39: 1000000 INFO @ Sat, 15 Jan 2022 19:41:45: 2000000 INFO @ Sat, 15 Jan 2022 19:41:52: 3000000 INFO @ Sat, 15 Jan 2022 19:41:59: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 15 Jan 2022 19:42:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781065/SRX11781065.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781065/SRX11781065.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781065/SRX11781065.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781065/SRX11781065.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 @ Sat, 15 Jan 2022 19:42:02: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:42:02: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:42:06: 5000000 INFO @ Sat, 15 Jan 2022 19:42:08: 1000000 INFO @ Sat, 15 Jan 2022 19:42:13: 6000000 INFO @ Sat, 15 Jan 2022 19:42:14: 2000000 INFO @ Sat, 15 Jan 2022 19:42:20: 7000000 INFO @ Sat, 15 Jan 2022 19:42:20: 3000000 INFO @ Sat, 15 Jan 2022 19:42:26: 4000000 INFO @ Sat, 15 Jan 2022 19:42:27: 8000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 15 Jan 2022 19:42:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781065/SRX11781065.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781065/SRX11781065.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781065/SRX11781065.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781065/SRX11781065.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 @ Sat, 15 Jan 2022 19:42:32: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:42:32: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:42:32: 5000000 INFO @ Sat, 15 Jan 2022 19:42:35: 9000000 INFO @ Sat, 15 Jan 2022 19:42:38: 6000000 INFO @ Sat, 15 Jan 2022 19:42:39: 1000000 INFO @ Sat, 15 Jan 2022 19:42:42: 10000000 INFO @ Sat, 15 Jan 2022 19:42:44: 7000000 INFO @ Sat, 15 Jan 2022 19:42:46: 2000000 INFO @ Sat, 15 Jan 2022 19:42:49: 11000000 INFO @ Sat, 15 Jan 2022 19:42:50: 8000000 INFO @ Sat, 15 Jan 2022 19:42:53: 3000000 INFO @ Sat, 15 Jan 2022 19:42:57: 9000000 INFO @ Sat, 15 Jan 2022 19:42:57: 12000000 INFO @ Sat, 15 Jan 2022 19:43:00: 4000000 INFO @ Sat, 15 Jan 2022 19:43:03: 10000000 INFO @ Sat, 15 Jan 2022 19:43:04: 13000000 INFO @ Sat, 15 Jan 2022 19:43:07: 5000000 INFO @ Sat, 15 Jan 2022 19:43:10: 11000000 INFO @ Sat, 15 Jan 2022 19:43:11: 14000000 INFO @ Sat, 15 Jan 2022 19:43:14: 6000000 INFO @ Sat, 15 Jan 2022 19:43:16: 12000000 INFO @ Sat, 15 Jan 2022 19:43:18: 15000000 INFO @ Sat, 15 Jan 2022 19:43:21: 7000000 INFO @ Sat, 15 Jan 2022 19:43:23: 13000000 INFO @ Sat, 15 Jan 2022 19:43:25: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 19:43:28: 8000000 INFO @ Sat, 15 Jan 2022 19:43:29: 14000000 INFO @ Sat, 15 Jan 2022 19:43:30: #1 tag size is determined as 75 bps INFO @ Sat, 15 Jan 2022 19:43:30: #1 tag size = 75 INFO @ Sat, 15 Jan 2022 19:43:30: #1 total tags in treatment: 7785628 INFO @ Sat, 15 Jan 2022 19:43:30: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:43:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Jan 2022 19:43:30: #1 tags after filtering in treatment: 4638056 INFO @ Sat, 15 Jan 2022 19:43:30: #1 Redundant rate of treatment: 0.40 INFO @ Sat, 15 Jan 2022 19:43:30: #1 finished! INFO @ Sat, 15 Jan 2022 19:43:30: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:43:30: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:43:30: #2 number of paired peaks: 136 WARNING @ Sat, 15 Jan 2022 19:43:30: Fewer paired peaks (136) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 136 pairs to build model! INFO @ Sat, 15 Jan 2022 19:43:30: start model_add_line... INFO @ Sat, 15 Jan 2022 19:43:30: start X-correlation... INFO @ Sat, 15 Jan 2022 19:43:30: end of X-cor INFO @ Sat, 15 Jan 2022 19:43:30: #2 finished! INFO @ Sat, 15 Jan 2022 19:43:30: #2 predicted fragment length is 0 bps INFO @ Sat, 15 Jan 2022 19:43:30: #2 alternative fragment length(s) may be 0,20,68,131,142,160,213,253,288,329,341,371,387,405,430,471,486,491,506,525,544,570,585 bps INFO @ Sat, 15 Jan 2022 19:43:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781065/SRX11781065.05_model.r WARNING @ Sat, 15 Jan 2022 19:43:30: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 19:43:30: #2 You may need to consider one of the other alternative d(s): 0,20,68,131,142,160,213,253,288,329,341,371,387,405,430,471,486,491,506,525,544,570,585 WARNING @ Sat, 15 Jan 2022 19:43:30: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 15 Jan 2022 19:43:30: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:43:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:43:35: 15000000 INFO @ Sat, 15 Jan 2022 19:43:36: 9000000 BigWig に変換しました。 /var/spool/uge/at156/job_scripts/14520570: line 297: 106452 Terminated MACS $i /var/spool/uge/at156/job_scripts/14520570: line 297: 106650 Terminated MACS $i /var/spool/uge/at156/job_scripts/14520570: line 297: 107765 Terminated MACS $i ls: cannot access SRX11781065.05.bed: No such file or directory mv: cannot stat ‘SRX11781065.05.bed’: No such file or directory mv: cannot stat ‘SRX11781065.05.bb’: No such file or directory ls: cannot access SRX11781065.10.bed: No such file or directory mv: cannot stat ‘SRX11781065.10.bed’: No such file or directory mv: cannot stat ‘SRX11781065.10.bb’: No such file or directory ls: cannot access SRX11781065.20.bed: No such file or directory mv: cannot stat ‘SRX11781065.20.bed’: No such file or directory mv: cannot stat ‘SRX11781065.20.bb’: No such file or directory