Job ID = 14520478 SRX = SRX11781042 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2022-01-15T10:12:10 prefetch.2.10.7: 1) Downloading 'SRR15480985'... 2022-01-15T10:12:10 prefetch.2.10.7: Downloading via HTTPS... 2022-01-15T10:12:44 prefetch.2.10.7: HTTPS download succeed 2022-01-15T10:12:45 prefetch.2.10.7: 'SRR15480985' is valid 2022-01-15T10:12:45 prefetch.2.10.7: 1) 'SRR15480985' was downloaded successfully 2022-01-15T10:12:45 prefetch.2.10.7: 'SRR15480985' has 0 unresolved dependencies Read 6959943 spots for SRR15480985/SRR15480985.sra Written 6959943 spots for SRR15480985/SRR15480985.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: 00:08:43 6959943 reads; of these: 6959943 (100.00%) were paired; of these: 1775055 (25.50%) aligned concordantly 0 times 3207061 (46.08%) aligned concordantly exactly 1 time 1977827 (28.42%) aligned concordantly >1 times ---- 1775055 pairs aligned concordantly 0 times; of these: 291555 (16.43%) aligned discordantly 1 time ---- 1483500 pairs aligned 0 times concordantly or discordantly; of these: 2967000 mates make up the pairs; of these: 1803781 (60.79%) aligned 0 times 597345 (20.13%) aligned exactly 1 time 565874 (19.07%) aligned >1 times 87.04% overall alignment rate Time searching: 00:08:43 Overall time: 00:08:43 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] 1065093 / 5404430 = 0.1971 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 19:27:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781042/SRX11781042.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781042/SRX11781042.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781042/SRX11781042.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781042/SRX11781042.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 19:27:20: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:27:20: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:27:26: 1000000 INFO @ Sat, 15 Jan 2022 19:27:31: 2000000 INFO @ Sat, 15 Jan 2022 19:27:36: 3000000 INFO @ Sat, 15 Jan 2022 19:27:41: 4000000 INFO @ Sat, 15 Jan 2022 19:27:47: 5000000 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 19:27:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781042/SRX11781042.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781042/SRX11781042.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781042/SRX11781042.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781042/SRX11781042.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 19:27:51: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:27:51: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:27:52: 6000000 INFO @ Sat, 15 Jan 2022 19:27:56: 1000000 INFO @ Sat, 15 Jan 2022 19:27:58: 7000000 INFO @ Sat, 15 Jan 2022 19:28:01: 2000000 INFO @ Sat, 15 Jan 2022 19:28:03: 8000000 INFO @ Sat, 15 Jan 2022 19:28:07: 3000000 INFO @ Sat, 15 Jan 2022 19:28:09: 9000000 INFO @ Sat, 15 Jan 2022 19:28:12: 4000000 INFO @ Sat, 15 Jan 2022 19:28:14: #1 tag size is determined as 80 bps INFO @ Sat, 15 Jan 2022 19:28:14: #1 tag size = 80 INFO @ Sat, 15 Jan 2022 19:28:14: #1 total tags in treatment: 4156208 INFO @ Sat, 15 Jan 2022 19:28:14: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:28:14: #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 19:28:14: #1 tags after filtering in treatment: 2202787 INFO @ Sat, 15 Jan 2022 19:28:14: #1 Redundant rate of treatment: 0.47 INFO @ Sat, 15 Jan 2022 19:28:14: #1 finished! INFO @ Sat, 15 Jan 2022 19:28:14: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:28:14: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:28:15: #2 number of paired peaks: 187 WARNING @ Sat, 15 Jan 2022 19:28:15: Fewer paired peaks (187) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 187 pairs to build model! INFO @ Sat, 15 Jan 2022 19:28:15: start model_add_line... INFO @ Sat, 15 Jan 2022 19:28:15: start X-correlation... INFO @ Sat, 15 Jan 2022 19:28:15: end of X-cor INFO @ Sat, 15 Jan 2022 19:28:15: #2 finished! INFO @ Sat, 15 Jan 2022 19:28:15: #2 predicted fragment length is 0 bps INFO @ Sat, 15 Jan 2022 19:28:15: #2 alternative fragment length(s) may be 0,27,56,78,102,132,226,306,504,543,571,584 bps INFO @ Sat, 15 Jan 2022 19:28:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781042/SRX11781042.05_model.r WARNING @ Sat, 15 Jan 2022 19:28:15: #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 19:28:15: #2 You may need to consider one of the other alternative d(s): 0,27,56,78,102,132,226,306,504,543,571,584 WARNING @ Sat, 15 Jan 2022 19:28:15: #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 19:28:15: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:28:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:28:17: 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 19:28:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781042/SRX11781042.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781042/SRX11781042.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781042/SRX11781042.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781042/SRX11781042.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 19:28:20: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:28:20: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:28:23: 6000000 INFO @ Sat, 15 Jan 2022 19:28:26: 1000000 INFO @ Sat, 15 Jan 2022 19:28:28: 7000000 INFO @ Sat, 15 Jan 2022 19:28:32: 2000000 INFO @ Sat, 15 Jan 2022 19:28:33: 8000000 INFO @ Sat, 15 Jan 2022 19:28:37: 3000000 INFO @ Sat, 15 Jan 2022 19:28:39: 9000000 INFO @ Sat, 15 Jan 2022 19:28:43: 4000000 INFO @ Sat, 15 Jan 2022 19:28:44: #1 tag size is determined as 80 bps INFO @ Sat, 15 Jan 2022 19:28:44: #1 tag size = 80 INFO @ Sat, 15 Jan 2022 19:28:44: #1 total tags in treatment: 4156208 INFO @ Sat, 15 Jan 2022 19:28:44: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:28:44: #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 19:28:44: #1 tags after filtering in treatment: 2202787 INFO @ Sat, 15 Jan 2022 19:28:44: #1 Redundant rate of treatment: 0.47 INFO @ Sat, 15 Jan 2022 19:28:44: #1 finished! INFO @ Sat, 15 Jan 2022 19:28:44: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:28:44: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:28:44: #2 number of paired peaks: 187 WARNING @ Sat, 15 Jan 2022 19:28:44: Fewer paired peaks (187) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 187 pairs to build model! INFO @ Sat, 15 Jan 2022 19:28:44: start model_add_line... INFO @ Sat, 15 Jan 2022 19:28:44: start X-correlation... INFO @ Sat, 15 Jan 2022 19:28:44: end of X-cor INFO @ Sat, 15 Jan 2022 19:28:44: #2 finished! INFO @ Sat, 15 Jan 2022 19:28:44: #2 predicted fragment length is 0 bps INFO @ Sat, 15 Jan 2022 19:28:44: #2 alternative fragment length(s) may be 0,27,56,78,102,132,226,306,504,543,571,584 bps INFO @ Sat, 15 Jan 2022 19:28:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781042/SRX11781042.10_model.r WARNING @ Sat, 15 Jan 2022 19:28:44: #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 19:28:44: #2 You may need to consider one of the other alternative d(s): 0,27,56,78,102,132,226,306,504,543,571,584 WARNING @ Sat, 15 Jan 2022 19:28:44: #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 19:28:44: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:28:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:28:48: 5000000 INFO @ Sat, 15 Jan 2022 19:28:54: 6000000 INFO @ Sat, 15 Jan 2022 19:28:59: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 19:29:05: 8000000 INFO @ Sat, 15 Jan 2022 19:29:10: 9000000 BigWig に変換しました。 /var/spool/uge/it005/job_scripts/14520478: line 297: 5782 Terminated MACS $i /var/spool/uge/it005/job_scripts/14520478: line 297: 6879 Terminated MACS $i /var/spool/uge/it005/job_scripts/14520478: line 297: 8050 Terminated MACS $i ls: cannot access SRX11781042.05.bed: No such file or directory mv: cannot stat ‘SRX11781042.05.bed’: No such file or directory mv: cannot stat ‘SRX11781042.05.bb’: No such file or directory ls: cannot access SRX11781042.10.bed: No such file or directory mv: cannot stat ‘SRX11781042.10.bed’: No such file or directory mv: cannot stat ‘SRX11781042.10.bb’: No such file or directory ls: cannot access SRX11781042.20.bed: No such file or directory mv: cannot stat ‘SRX11781042.20.bed’: No such file or directory mv: cannot stat ‘SRX11781042.20.bb’: No such file or directory