Job ID = 14520514 SRX = SRX11781053 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2022-01-15T10:16:11 prefetch.2.10.7: 1) Downloading 'SRR15480996'... 2022-01-15T10:16:11 prefetch.2.10.7: Downloading via HTTPS... 2022-01-15T10:16:44 prefetch.2.10.7: HTTPS download succeed 2022-01-15T10:16:45 prefetch.2.10.7: 'SRR15480996' is valid 2022-01-15T10:16:45 prefetch.2.10.7: 1) 'SRR15480996' was downloaded successfully 2022-01-15T10:16:45 prefetch.2.10.7: 'SRR15480996' has 0 unresolved dependencies Read 6924356 spots for SRR15480996/SRR15480996.sra Written 6924356 spots for SRR15480996/SRR15480996.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: 00:08:05 6924356 reads; of these: 6924356 (100.00%) were paired; of these: 1794563 (25.92%) aligned concordantly 0 times 3906777 (56.42%) aligned concordantly exactly 1 time 1223016 (17.66%) aligned concordantly >1 times ---- 1794563 pairs aligned concordantly 0 times; of these: 395517 (22.04%) aligned discordantly 1 time ---- 1399046 pairs aligned 0 times concordantly or discordantly; of these: 2798092 mates make up the pairs; of these: 2078368 (74.28%) aligned 0 times 370514 (13.24%) aligned exactly 1 time 349210 (12.48%) aligned >1 times 84.99% overall alignment rate Time searching: 00:08:05 Overall time: 00:08:05 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] 392581 / 5473145 = 0.0717 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 19:31:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781053/SRX11781053.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781053/SRX11781053.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781053/SRX11781053.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781053/SRX11781053.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 19:31:37: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:31:37: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:31:50: 1000000 INFO @ Sat, 15 Jan 2022 19:32:04: 2000000 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 19:32:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781053/SRX11781053.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781053/SRX11781053.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781053/SRX11781053.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781053/SRX11781053.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 19:32:07: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:32:07: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:32:18: 3000000 INFO @ Sat, 15 Jan 2022 19:32:18: 1000000 INFO @ Sat, 15 Jan 2022 19:32:28: 2000000 INFO @ Sat, 15 Jan 2022 19:32:32: 4000000 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 19:32:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781053/SRX11781053.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781053/SRX11781053.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781053/SRX11781053.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781053/SRX11781053.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 19:32:37: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:32:37: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:32:38: 3000000 INFO @ Sat, 15 Jan 2022 19:32:47: 5000000 INFO @ Sat, 15 Jan 2022 19:32:48: 4000000 INFO @ Sat, 15 Jan 2022 19:32:50: 1000000 INFO @ Sat, 15 Jan 2022 19:32:58: 5000000 INFO @ Sat, 15 Jan 2022 19:33:02: 6000000 INFO @ Sat, 15 Jan 2022 19:33:04: 2000000 INFO @ Sat, 15 Jan 2022 19:33:08: 6000000 INFO @ Sat, 15 Jan 2022 19:33:16: 3000000 INFO @ Sat, 15 Jan 2022 19:33:17: 7000000 INFO @ Sat, 15 Jan 2022 19:33:18: 7000000 INFO @ Sat, 15 Jan 2022 19:33:26: 4000000 INFO @ Sat, 15 Jan 2022 19:33:28: 8000000 INFO @ Sat, 15 Jan 2022 19:33:32: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 19:33:36: 5000000 INFO @ Sat, 15 Jan 2022 19:33:39: 9000000 INFO @ Sat, 15 Jan 2022 19:33:46: 9000000 INFO @ Sat, 15 Jan 2022 19:33:46: 6000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 19:33:49: 10000000 INFO @ Sat, 15 Jan 2022 19:33:57: 7000000 INFO @ Sat, 15 Jan 2022 19:33:59: #1 tag size is determined as 80 bps INFO @ Sat, 15 Jan 2022 19:33:59: #1 tag size = 80 INFO @ Sat, 15 Jan 2022 19:33:59: #1 total tags in treatment: 4761201 INFO @ Sat, 15 Jan 2022 19:33:59: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:33:59: #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 19:33:59: #1 tags after filtering in treatment: 3407690 INFO @ Sat, 15 Jan 2022 19:33:59: #1 Redundant rate of treatment: 0.28 INFO @ Sat, 15 Jan 2022 19:33:59: #1 finished! INFO @ Sat, 15 Jan 2022 19:33:59: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:33:59: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:33:59: #2 number of paired peaks: 161 WARNING @ Sat, 15 Jan 2022 19:33:59: Fewer paired peaks (161) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 161 pairs to build model! INFO @ Sat, 15 Jan 2022 19:33:59: start model_add_line... INFO @ Sat, 15 Jan 2022 19:33:59: start X-correlation... INFO @ Sat, 15 Jan 2022 19:33:59: end of X-cor INFO @ Sat, 15 Jan 2022 19:33:59: #2 finished! INFO @ Sat, 15 Jan 2022 19:33:59: #2 predicted fragment length is 0 bps INFO @ Sat, 15 Jan 2022 19:33:59: #2 alternative fragment length(s) may be 0,65,91,131,173,219,421,456,483,512,535,558 bps INFO @ Sat, 15 Jan 2022 19:33:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781053/SRX11781053.10_model.r WARNING @ Sat, 15 Jan 2022 19:33:59: #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 19:33:59: #2 You may need to consider one of the other alternative d(s): 0,65,91,131,173,219,421,456,483,512,535,558 WARNING @ Sat, 15 Jan 2022 19:33:59: #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 19:33:59: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:33:59: #3 Pre-compute pvalue-qvalue table... /var/spool/uge/at074/job_scripts/14520514: line 297: 43792 Terminated MACS $i /var/spool/uge/at074/job_scripts/14520514: line 297: 44907 Terminated MACS $i /var/spool/uge/at074/job_scripts/14520514: line 297: 45006 Terminated MACS $i ls: cannot access SRX11781053.05.bed: No such file or directory mv: cannot stat ‘SRX11781053.05.bed’: No such file or directory mv: cannot stat ‘SRX11781053.05.bb’: No such file or directory ls: cannot access SRX11781053.10.bed: No such file or directory mv: cannot stat ‘SRX11781053.10.bed’: No such file or directory mv: cannot stat ‘SRX11781053.10.bb’: No such file or directory ls: cannot access SRX11781053.20.bed: No such file or directory mv: cannot stat ‘SRX11781053.20.bed’: No such file or directory mv: cannot stat ‘SRX11781053.20.bb’: No such file or directory