Job ID = 14520594 SRX = SRX11781072 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2022-01-15T10:25:04 prefetch.2.10.7: 1) Downloading 'SRR15481015'... 2022-01-15T10:25:04 prefetch.2.10.7: Downloading via HTTPS... 2022-01-15T10:25:45 prefetch.2.10.7: HTTPS download succeed 2022-01-15T10:25:45 prefetch.2.10.7: 1) 'SRR15481015' was downloaded successfully 2022-01-15T10:25:45 prefetch.2.10.7: 'SRR15481015' has 0 unresolved dependencies Read 9941163 spots for SRR15481015/SRR15481015.sra Written 9941163 spots for SRR15481015/SRR15481015.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: 00:33:48 9941163 reads; of these: 9941163 (100.00%) were paired; of these: 2380759 (23.95%) aligned concordantly 0 times 3614903 (36.36%) aligned concordantly exactly 1 time 3945501 (39.69%) aligned concordantly >1 times ---- 2380759 pairs aligned concordantly 0 times; of these: 36866 (1.55%) aligned discordantly 1 time ---- 2343893 pairs aligned 0 times concordantly or discordantly; of these: 4687786 mates make up the pairs; of these: 3934468 (83.93%) aligned 0 times 370313 (7.90%) aligned exactly 1 time 383005 (8.17%) aligned >1 times 80.21% overall alignment rate Time searching: 00:33:48 Overall time: 00:33:48 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] 1079209 / 7596644 = 0.1421 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 20:07:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781072/SRX11781072.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781072/SRX11781072.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781072/SRX11781072.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781072/SRX11781072.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 20:07:37: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:07:37: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:07:46: 1000000 INFO @ Sat, 15 Jan 2022 20:07:57: 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 20:08:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781072/SRX11781072.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781072/SRX11781072.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781072/SRX11781072.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781072/SRX11781072.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 20:08:06: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:08:06: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:08:08: 3000000 INFO @ Sat, 15 Jan 2022 20:08:16: 1000000 INFO @ Sat, 15 Jan 2022 20:08:18: 4000000 INFO @ Sat, 15 Jan 2022 20:08:27: 2000000 INFO @ Sat, 15 Jan 2022 20:08:29: 5000000 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 20:08:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781072/SRX11781072.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781072/SRX11781072.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781072/SRX11781072.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781072/SRX11781072.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 20:08:36: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:08:36: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:08:37: 3000000 INFO @ Sat, 15 Jan 2022 20:08:40: 6000000 INFO @ Sat, 15 Jan 2022 20:08:47: 1000000 INFO @ Sat, 15 Jan 2022 20:08:48: 4000000 INFO @ Sat, 15 Jan 2022 20:08:51: 7000000 INFO @ Sat, 15 Jan 2022 20:08:56: 2000000 INFO @ Sat, 15 Jan 2022 20:08:58: 5000000 INFO @ Sat, 15 Jan 2022 20:09:02: 8000000 INFO @ Sat, 15 Jan 2022 20:09:07: 3000000 INFO @ Sat, 15 Jan 2022 20:09:09: 6000000 INFO @ Sat, 15 Jan 2022 20:09:13: 9000000 INFO @ Sat, 15 Jan 2022 20:09:18: 4000000 INFO @ Sat, 15 Jan 2022 20:09:20: 7000000 INFO @ Sat, 15 Jan 2022 20:09:23: 10000000 INFO @ Sat, 15 Jan 2022 20:09:28: 5000000 INFO @ Sat, 15 Jan 2022 20:09:31: 8000000 INFO @ Sat, 15 Jan 2022 20:09:33: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 20:09:38: 6000000 INFO @ Sat, 15 Jan 2022 20:09:41: 9000000 INFO @ Sat, 15 Jan 2022 20:09:42: 12000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 20:09:47: 7000000 INFO @ Sat, 15 Jan 2022 20:09:52: 10000000 INFO @ Sat, 15 Jan 2022 20:09:53: 13000000 INFO @ Sat, 15 Jan 2022 20:09:57: 8000000 INFO @ Sat, 15 Jan 2022 20:10:01: #1 tag size is determined as 75 bps INFO @ Sat, 15 Jan 2022 20:10:01: #1 tag size = 75 INFO @ Sat, 15 Jan 2022 20:10:01: #1 total tags in treatment: 6483915 INFO @ Sat, 15 Jan 2022 20:10:01: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:10:01: #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 20:10:01: #1 tags after filtering in treatment: 2823352 INFO @ Sat, 15 Jan 2022 20:10:01: #1 Redundant rate of treatment: 0.56 INFO @ Sat, 15 Jan 2022 20:10:01: #1 finished! INFO @ Sat, 15 Jan 2022 20:10:01: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:10:01: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:10:01: #2 number of paired peaks: 186 WARNING @ Sat, 15 Jan 2022 20:10:01: Fewer paired peaks (186) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 186 pairs to build model! INFO @ Sat, 15 Jan 2022 20:10:01: start model_add_line... INFO @ Sat, 15 Jan 2022 20:10:01: start X-correlation... INFO @ Sat, 15 Jan 2022 20:10:01: end of X-cor INFO @ Sat, 15 Jan 2022 20:10:01: #2 finished! INFO @ Sat, 15 Jan 2022 20:10:01: #2 predicted fragment length is 0 bps INFO @ Sat, 15 Jan 2022 20:10:01: #2 alternative fragment length(s) may be 0,68,89,122,153,178,199,228,264,342,413,533,556 bps INFO @ Sat, 15 Jan 2022 20:10:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781072/SRX11781072.05_model.r WARNING @ Sat, 15 Jan 2022 20:10:01: #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 20:10:01: #2 You may need to consider one of the other alternative d(s): 0,68,89,122,153,178,199,228,264,342,413,533,556 WARNING @ Sat, 15 Jan 2022 20:10:01: #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 20:10:01: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:10:01: #3 Pre-compute pvalue-qvalue table... /var/spool/uge/it023/job_scripts/14520594: line 297: 23992 Terminated MACS $i /var/spool/uge/it023/job_scripts/14520594: line 297: 25105 Terminated MACS $i /var/spool/uge/it023/job_scripts/14520594: line 297: 25210 Terminated MACS $i ls: cannot access SRX11781072.05.bed: No such file or directory mv: cannot stat ‘SRX11781072.05.bed’: No such file or directory mv: cannot stat ‘SRX11781072.05.bb’: No such file or directory ls: cannot access SRX11781072.10.bed: No such file or directory mv: cannot stat ‘SRX11781072.10.bed’: No such file or directory mv: cannot stat ‘SRX11781072.10.bb’: No such file or directory ls: cannot access SRX11781072.20.bed: No such file or directory mv: cannot stat ‘SRX11781072.20.bed’: No such file or directory mv: cannot stat ‘SRX11781072.20.bb’: No such file or directory