Job ID = 6367248 SRX = SRX3104611 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:22:16 prefetch.2.10.7: 1) Downloading 'SRR5946216'... 2020-06-15T23:22:16 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:23:45 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:23:46 prefetch.2.10.7: 'SRR5946216' is valid 2020-06-15T23:23:46 prefetch.2.10.7: 1) 'SRR5946216' was downloaded successfully 2020-06-15T23:23:46 prefetch.2.10.7: 'SRR5946216' has 0 unresolved dependencies Read 30720049 spots for SRR5946216/SRR5946216.sra Written 30720049 spots for SRR5946216/SRR5946216.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: 00:07:07 30720049 reads; of these: 30720049 (100.00%) were unpaired; of these: 702456 (2.29%) aligned 0 times 25055248 (81.56%) aligned exactly 1 time 4962345 (16.15%) aligned >1 times 97.71% overall alignment rate Time searching: 00:07:07 Overall time: 00:07:07 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 16 files... [bam_rmdupse_core] 3577736 / 30017593 = 0.1192 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 16 Jun 2020 08:37:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3104611/SRX3104611.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3104611/SRX3104611.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3104611/SRX3104611.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3104611/SRX3104611.bam'] # control file = None # effective genome size = 9.00e+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 @ Tue, 16 Jun 2020 08:37:42: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:37:42: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:37:47: 1000000 INFO @ Tue, 16 Jun 2020 08:37:52: 2000000 INFO @ Tue, 16 Jun 2020 08:37:57: 3000000 INFO @ Tue, 16 Jun 2020 08:38:01: 4000000 INFO @ Tue, 16 Jun 2020 08:38:06: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 16 Jun 2020 08:38:11: 6000000 INFO @ Tue, 16 Jun 2020 08:38:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3104611/SRX3104611.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3104611/SRX3104611.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3104611/SRX3104611.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3104611/SRX3104611.bam'] # control file = None # effective genome size = 9.00e+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 @ Tue, 16 Jun 2020 08:38:12: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:38:12: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:38:16: 7000000 INFO @ Tue, 16 Jun 2020 08:38:17: 1000000 INFO @ Tue, 16 Jun 2020 08:38:21: 8000000 INFO @ Tue, 16 Jun 2020 08:38:22: 2000000 INFO @ Tue, 16 Jun 2020 08:38:26: 9000000 INFO @ Tue, 16 Jun 2020 08:38:27: 3000000 INFO @ Tue, 16 Jun 2020 08:38:31: 10000000 INFO @ Tue, 16 Jun 2020 08:38:31: 4000000 INFO @ Tue, 16 Jun 2020 08:38:36: 11000000 INFO @ Tue, 16 Jun 2020 08:38:36: 5000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 16 Jun 2020 08:38:41: 12000000 INFO @ Tue, 16 Jun 2020 08:38:41: 6000000 INFO @ Tue, 16 Jun 2020 08:38:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3104611/SRX3104611.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3104611/SRX3104611.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3104611/SRX3104611.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3104611/SRX3104611.bam'] # control file = None # effective genome size = 9.00e+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 @ Tue, 16 Jun 2020 08:38:42: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:38:42: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:38:46: 13000000 INFO @ Tue, 16 Jun 2020 08:38:46: 7000000 INFO @ Tue, 16 Jun 2020 08:38:47: 1000000 INFO @ Tue, 16 Jun 2020 08:38:51: 8000000 INFO @ Tue, 16 Jun 2020 08:38:51: 14000000 INFO @ Tue, 16 Jun 2020 08:38:52: 2000000 INFO @ Tue, 16 Jun 2020 08:38:56: 9000000 INFO @ Tue, 16 Jun 2020 08:38:56: 15000000 INFO @ Tue, 16 Jun 2020 08:38:57: 3000000 INFO @ Tue, 16 Jun 2020 08:39:01: 10000000 INFO @ Tue, 16 Jun 2020 08:39:01: 16000000 INFO @ Tue, 16 Jun 2020 08:39:02: 4000000 INFO @ Tue, 16 Jun 2020 08:39:06: 11000000 INFO @ Tue, 16 Jun 2020 08:39:06: 17000000 INFO @ Tue, 16 Jun 2020 08:39:07: 5000000 INFO @ Tue, 16 Jun 2020 08:39:11: 12000000 INFO @ Tue, 16 Jun 2020 08:39:12: 18000000 INFO @ Tue, 16 Jun 2020 08:39:12: 6000000 INFO @ Tue, 16 Jun 2020 08:39:16: 13000000 INFO @ Tue, 16 Jun 2020 08:39:17: 19000000 INFO @ Tue, 16 Jun 2020 08:39:17: 7000000 INFO @ Tue, 16 Jun 2020 08:39:21: 14000000 INFO @ Tue, 16 Jun 2020 08:39:22: 20000000 INFO @ Tue, 16 Jun 2020 08:39:22: 8000000 INFO @ Tue, 16 Jun 2020 08:39:27: 15000000 INFO @ Tue, 16 Jun 2020 08:39:27: 21000000 INFO @ Tue, 16 Jun 2020 08:39:27: 9000000 INFO @ Tue, 16 Jun 2020 08:39:32: 16000000 INFO @ Tue, 16 Jun 2020 08:39:32: 22000000 INFO @ Tue, 16 Jun 2020 08:39:32: 10000000 INFO @ Tue, 16 Jun 2020 08:39:37: 17000000 INFO @ Tue, 16 Jun 2020 08:39:37: 23000000 INFO @ Tue, 16 Jun 2020 08:39:37: 11000000 INFO @ Tue, 16 Jun 2020 08:39:42: 18000000 INFO @ Tue, 16 Jun 2020 08:39:42: 24000000 INFO @ Tue, 16 Jun 2020 08:39:43: 12000000 INFO @ Tue, 16 Jun 2020 08:39:47: 19000000 INFO @ Tue, 16 Jun 2020 08:39:47: 25000000 INFO @ Tue, 16 Jun 2020 08:39:48: 13000000 INFO @ Tue, 16 Jun 2020 08:39:52: 20000000 INFO @ Tue, 16 Jun 2020 08:39:52: 26000000 INFO @ Tue, 16 Jun 2020 08:39:53: 14000000 INFO @ Tue, 16 Jun 2020 08:39:55: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:39:55: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:39:55: #1 total tags in treatment: 26439857 INFO @ Tue, 16 Jun 2020 08:39:55: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:39:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 08:39:55: #1 tags after filtering in treatment: 26439857 INFO @ Tue, 16 Jun 2020 08:39:55: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:39:55: #1 finished! INFO @ Tue, 16 Jun 2020 08:39:55: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:39:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:39:57: #2 number of paired peaks: 113 WARNING @ Tue, 16 Jun 2020 08:39:57: Fewer paired peaks (113) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 113 pairs to build model! INFO @ Tue, 16 Jun 2020 08:39:57: start model_add_line... INFO @ Tue, 16 Jun 2020 08:39:57: start X-correlation... INFO @ Tue, 16 Jun 2020 08:39:57: end of X-cor INFO @ Tue, 16 Jun 2020 08:39:57: #2 finished! INFO @ Tue, 16 Jun 2020 08:39:57: #2 predicted fragment length is 0 bps INFO @ Tue, 16 Jun 2020 08:39:57: #2 alternative fragment length(s) may be 0,47,433,488,561,584 bps INFO @ Tue, 16 Jun 2020 08:39:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3104611/SRX3104611.05_model.r WARNING @ Tue, 16 Jun 2020 08:39:57: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:39:57: #2 You may need to consider one of the other alternative d(s): 0,47,433,488,561,584 WARNING @ Tue, 16 Jun 2020 08:39:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 08:39:57: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:39:57: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:39:57: 21000000 INFO @ Tue, 16 Jun 2020 08:39:58: 15000000 INFO @ Tue, 16 Jun 2020 08:40:02: 22000000 INFO @ Tue, 16 Jun 2020 08:40:03: 16000000 INFO @ Tue, 16 Jun 2020 08:40:07: 23000000 INFO @ Tue, 16 Jun 2020 08:40:08: 17000000 INFO @ Tue, 16 Jun 2020 08:40:12: 24000000 INFO @ Tue, 16 Jun 2020 08:40:13: 18000000 INFO @ Tue, 16 Jun 2020 08:40:17: 25000000 INFO @ Tue, 16 Jun 2020 08:40:18: 19000000 INFO @ Tue, 16 Jun 2020 08:40:22: 26000000 INFO @ Tue, 16 Jun 2020 08:40:23: 20000000 INFO @ Tue, 16 Jun 2020 08:40:25: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:40:25: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:40:25: #1 total tags in treatment: 26439857 INFO @ Tue, 16 Jun 2020 08:40:25: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:40:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 08:40:25: #1 tags after filtering in treatment: 26439857 INFO @ Tue, 16 Jun 2020 08:40:25: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:40:25: #1 finished! INFO @ Tue, 16 Jun 2020 08:40:25: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:40:25: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:40:27: #2 number of paired peaks: 113 WARNING @ Tue, 16 Jun 2020 08:40:27: Fewer paired peaks (113) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 113 pairs to build model! INFO @ Tue, 16 Jun 2020 08:40:27: start model_add_line... INFO @ Tue, 16 Jun 2020 08:40:27: start X-correlation... INFO @ Tue, 16 Jun 2020 08:40:27: end of X-cor INFO @ Tue, 16 Jun 2020 08:40:27: #2 finished! INFO @ Tue, 16 Jun 2020 08:40:27: #2 predicted fragment length is 0 bps INFO @ Tue, 16 Jun 2020 08:40:27: #2 alternative fragment length(s) may be 0,47,433,488,561,584 bps INFO @ Tue, 16 Jun 2020 08:40:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3104611/SRX3104611.10_model.r WARNING @ Tue, 16 Jun 2020 08:40:27: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:40:27: #2 You may need to consider one of the other alternative d(s): 0,47,433,488,561,584 WARNING @ Tue, 16 Jun 2020 08:40:27: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 08:40:27: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:40:27: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:40:28: 21000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:40:33: 22000000 INFO @ Tue, 16 Jun 2020 08:40:38: 23000000 INFO @ Tue, 16 Jun 2020 08:40:43: 24000000 INFO @ Tue, 16 Jun 2020 08:40:47: 25000000 INFO @ Tue, 16 Jun 2020 08:40:52: 26000000 INFO @ Tue, 16 Jun 2020 08:40:54: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:40:54: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:40:54: #1 total tags in treatment: 26439857 INFO @ Tue, 16 Jun 2020 08:40:54: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:40:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 08:40:55: #1 tags after filtering in treatment: 26439857 INFO @ Tue, 16 Jun 2020 08:40:55: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:40:55: #1 finished! INFO @ Tue, 16 Jun 2020 08:40:55: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:40:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:40:56: #2 number of paired peaks: 113 WARNING @ Tue, 16 Jun 2020 08:40:56: Fewer paired peaks (113) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 113 pairs to build model! INFO @ Tue, 16 Jun 2020 08:40:56: start model_add_line... INFO @ Tue, 16 Jun 2020 08:40:57: start X-correlation... INFO @ Tue, 16 Jun 2020 08:40:57: end of X-cor INFO @ Tue, 16 Jun 2020 08:40:57: #2 finished! INFO @ Tue, 16 Jun 2020 08:40:57: #2 predicted fragment length is 0 bps INFO @ Tue, 16 Jun 2020 08:40:57: #2 alternative fragment length(s) may be 0,47,433,488,561,584 bps INFO @ Tue, 16 Jun 2020 08:40:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3104611/SRX3104611.20_model.r WARNING @ Tue, 16 Jun 2020 08:40:57: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:40:57: #2 You may need to consider one of the other alternative d(s): 0,47,433,488,561,584 WARNING @ Tue, 16 Jun 2020 08:40:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 08:40:57: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:40:57: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 /var/spool/uge/at148/job_scripts/6367248: line 271: 77556 Terminated MACS $i /var/spool/uge/at148/job_scripts/6367248: line 271: 79685 Terminated MACS $i /var/spool/uge/at148/job_scripts/6367248: line 271: 81670 Terminated MACS $i ls: cannot access SRX3104611.05.bed: No such file or directory mv: cannot stat ‘SRX3104611.05.bed’: No such file or directory mv: cannot stat ‘SRX3104611.05.bb’: No such file or directory ls: cannot access SRX3104611.10.bed: No such file or directory mv: cannot stat ‘SRX3104611.10.bed’: No such file or directory mv: cannot stat ‘SRX3104611.10.bb’: No such file or directory ls: cannot access SRX3104611.20.bed: No such file or directory mv: cannot stat ‘SRX3104611.20.bed’: No such file or directory mv: cannot stat ‘SRX3104611.20.bb’: No such file or directory