Job ID = 14520359 SRX = SRX11781106 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2022-01-15T10:00:07 prefetch.2.10.7: 1) Downloading 'SRR15481049'... 2022-01-15T10:00:07 prefetch.2.10.7: Downloading via HTTPS... 2022-01-15T10:01:29 prefetch.2.10.7: HTTPS download succeed 2022-01-15T10:01:29 prefetch.2.10.7: 1) 'SRR15481049' was downloaded successfully 2022-01-15T10:01:29 prefetch.2.10.7: 'SRR15481049' has 0 unresolved dependencies Read 17233642 spots for SRR15481049/SRR15481049.sra Written 17233642 spots for SRR15481049/SRR15481049.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: 00:41:46 17233642 reads; of these: 17233642 (100.00%) were paired; of these: 3591114 (20.84%) aligned concordantly 0 times 5115432 (29.68%) aligned concordantly exactly 1 time 8527096 (49.48%) aligned concordantly >1 times ---- 3591114 pairs aligned concordantly 0 times; of these: 54847 (1.53%) aligned discordantly 1 time ---- 3536267 pairs aligned 0 times concordantly or discordantly; of these: 7072534 mates make up the pairs; of these: 5212057 (73.69%) aligned 0 times 687360 (9.72%) aligned exactly 1 time 1173117 (16.59%) aligned >1 times 84.88% overall alignment rate Time searching: 00:41:46 Overall time: 00:41:46 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] 2490649 / 13696609 = 0.1818 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 19:56:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781106/SRX11781106.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781106/SRX11781106.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781106/SRX11781106.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781106/SRX11781106.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 19:56:01: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:56:01: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:56:09: 1000000 INFO @ Sat, 15 Jan 2022 19:56:16: 2000000 INFO @ Sat, 15 Jan 2022 19:56:24: 3000000 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 19:56:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781106/SRX11781106.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781106/SRX11781106.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781106/SRX11781106.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781106/SRX11781106.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 19:56:31: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:56:31: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:56:31: 4000000 INFO @ Sat, 15 Jan 2022 19:56:38: 1000000 INFO @ Sat, 15 Jan 2022 19:56:39: 5000000 INFO @ Sat, 15 Jan 2022 19:56:45: 2000000 INFO @ Sat, 15 Jan 2022 19:56:47: 6000000 INFO @ Sat, 15 Jan 2022 19:56:52: 3000000 INFO @ Sat, 15 Jan 2022 19:56:55: 7000000 INFO @ Sat, 15 Jan 2022 19:56:59: 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 19:57:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781106/SRX11781106.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781106/SRX11781106.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781106/SRX11781106.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781106/SRX11781106.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 19:57:01: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:57:01: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:57:02: 8000000 INFO @ Sat, 15 Jan 2022 19:57:06: 5000000 INFO @ Sat, 15 Jan 2022 19:57:08: 1000000 INFO @ Sat, 15 Jan 2022 19:57:10: 9000000 INFO @ Sat, 15 Jan 2022 19:57:13: 6000000 INFO @ Sat, 15 Jan 2022 19:57:16: 2000000 INFO @ Sat, 15 Jan 2022 19:57:18: 10000000 INFO @ Sat, 15 Jan 2022 19:57:20: 7000000 INFO @ Sat, 15 Jan 2022 19:57:23: 3000000 INFO @ Sat, 15 Jan 2022 19:57:26: 11000000 INFO @ Sat, 15 Jan 2022 19:57:28: 8000000 INFO @ Sat, 15 Jan 2022 19:57:30: 4000000 INFO @ Sat, 15 Jan 2022 19:57:34: 12000000 INFO @ Sat, 15 Jan 2022 19:57:35: 9000000 INFO @ Sat, 15 Jan 2022 19:57:37: 5000000 INFO @ Sat, 15 Jan 2022 19:57:42: 13000000 INFO @ Sat, 15 Jan 2022 19:57:42: 10000000 INFO @ Sat, 15 Jan 2022 19:57:45: 6000000 INFO @ Sat, 15 Jan 2022 19:57:49: 11000000 INFO @ Sat, 15 Jan 2022 19:57:50: 14000000 INFO @ Sat, 15 Jan 2022 19:57:52: 7000000 INFO @ Sat, 15 Jan 2022 19:57:57: 12000000 INFO @ Sat, 15 Jan 2022 19:57:57: 15000000 INFO @ Sat, 15 Jan 2022 19:57:59: 8000000 INFO @ Sat, 15 Jan 2022 19:58:04: 13000000 INFO @ Sat, 15 Jan 2022 19:58:05: 16000000 INFO @ Sat, 15 Jan 2022 19:58:06: 9000000 INFO @ Sat, 15 Jan 2022 19:58:11: 14000000 INFO @ Sat, 15 Jan 2022 19:58:13: 17000000 INFO @ Sat, 15 Jan 2022 19:58:14: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 19:58:18: 15000000 INFO @ Sat, 15 Jan 2022 19:58:20: 18000000 INFO @ Sat, 15 Jan 2022 19:58:21: 11000000 INFO @ Sat, 15 Jan 2022 19:58:25: 16000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 19:58:28: 12000000 INFO @ Sat, 15 Jan 2022 19:58:28: 19000000 INFO @ Sat, 15 Jan 2022 19:58:32: 17000000 INFO @ Sat, 15 Jan 2022 19:58:35: 13000000 INFO @ Sat, 15 Jan 2022 19:58:36: 20000000 INFO @ Sat, 15 Jan 2022 19:58:39: 18000000 INFO @ Sat, 15 Jan 2022 19:58:42: 14000000 INFO @ Sat, 15 Jan 2022 19:58:43: 21000000 INFO @ Sat, 15 Jan 2022 19:58:47: 19000000 INFO @ Sat, 15 Jan 2022 19:58:50: 15000000 INFO @ Sat, 15 Jan 2022 19:58:51: 22000000 INFO @ Sat, 15 Jan 2022 19:58:54: 20000000 INFO @ Sat, 15 Jan 2022 19:58:57: 16000000 INFO @ Sat, 15 Jan 2022 19:58:59: 23000000 INFO @ Sat, 15 Jan 2022 19:59:01: 21000000 INFO @ Sat, 15 Jan 2022 19:59:04: 17000000 INFO @ Sat, 15 Jan 2022 19:59:07: 24000000 INFO @ Sat, 15 Jan 2022 19:59:08: 22000000 INFO @ Sat, 15 Jan 2022 19:59:09: #1 tag size is determined as 75 bps INFO @ Sat, 15 Jan 2022 19:59:09: #1 tag size = 75 INFO @ Sat, 15 Jan 2022 19:59:09: #1 total tags in treatment: 11156016 INFO @ Sat, 15 Jan 2022 19:59:09: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:59:09: #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 19:59:09: #1 tags after filtering in treatment: 3775278 INFO @ Sat, 15 Jan 2022 19:59:09: #1 Redundant rate of treatment: 0.66 INFO @ Sat, 15 Jan 2022 19:59:09: #1 finished! INFO @ Sat, 15 Jan 2022 19:59:09: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:59:09: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:59:09: #2 number of paired peaks: 125 WARNING @ Sat, 15 Jan 2022 19:59:09: Fewer paired peaks (125) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 125 pairs to build model! INFO @ Sat, 15 Jan 2022 19:59:09: start model_add_line... INFO @ Sat, 15 Jan 2022 19:59:09: start X-correlation... INFO @ Sat, 15 Jan 2022 19:59:09: end of X-cor INFO @ Sat, 15 Jan 2022 19:59:09: #2 finished! INFO @ Sat, 15 Jan 2022 19:59:09: #2 predicted fragment length is 0 bps INFO @ Sat, 15 Jan 2022 19:59:09: #2 alternative fragment length(s) may be 0,56,80,108,125,150,181,226,233,315,339,413,438,501,559 bps INFO @ Sat, 15 Jan 2022 19:59:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781106/SRX11781106.05_model.r WARNING @ Sat, 15 Jan 2022 19:59:09: #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 19:59:09: #2 You may need to consider one of the other alternative d(s): 0,56,80,108,125,150,181,226,233,315,339,413,438,501,559 WARNING @ Sat, 15 Jan 2022 19:59:09: #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 19:59:09: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:59:09: #3 Pre-compute pvalue-qvalue table... /var/spool/uge/at164/job_scripts/14520359: line 297: 8081 Terminated MACS $i /var/spool/uge/at164/job_scripts/14520359: line 297: 9224 Terminated MACS $i /var/spool/uge/at164/job_scripts/14520359: line 297: 9330 Terminated MACS $i ls: cannot access SRX11781106.05.bed: No such file or directory mv: cannot stat ‘SRX11781106.05.bed’: No such file or directory mv: cannot stat ‘SRX11781106.05.bb’: No such file or directory ls: cannot access SRX11781106.10.bed: No such file or directory mv: cannot stat ‘SRX11781106.10.bed’: No such file or directory mv: cannot stat ‘SRX11781106.10.bb’: No such file or directory ls: cannot access SRX11781106.20.bed: No such file or directory mv: cannot stat ‘SRX11781106.20.bed’: No such file or directory mv: cannot stat ‘SRX11781106.20.bb’: No such file or directory