Job ID = 6366277 SRX = SRX105311 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:25:59 prefetch.2.10.7: 1) Downloading 'SRR363998'... 2020-06-15T22:25:59 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:28:21 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:28:21 prefetch.2.10.7: 1) 'SRR363998' was downloaded successfully Read 29706298 spots for SRR363998/SRR363998.sra Written 29706298 spots for SRR363998/SRR363998.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: 00:05:04 29706298 reads; of these: 29706298 (100.00%) were unpaired; of these: 7082800 (23.84%) aligned 0 times 18665047 (62.83%) aligned exactly 1 time 3958451 (13.33%) aligned >1 times 76.16% overall alignment rate Time searching: 00:05:04 Overall time: 00:05:04 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 8 files... [bam_rmdupse_core] 2635644 / 22623498 = 0.1165 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 07:39:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX105311/SRX105311.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX105311/SRX105311.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX105311/SRX105311.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX105311/SRX105311.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 07:39:38: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:39:38: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:39:43: 1000000 INFO @ Tue, 16 Jun 2020 07:39:49: 2000000 INFO @ Tue, 16 Jun 2020 07:39:54: 3000000 INFO @ Tue, 16 Jun 2020 07:39:59: 4000000 INFO @ Tue, 16 Jun 2020 07:40:04: 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 07:40:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX105311/SRX105311.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX105311/SRX105311.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX105311/SRX105311.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX105311/SRX105311.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 07:40:08: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:40:08: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:40:09: 6000000 INFO @ Tue, 16 Jun 2020 07:40:13: 1000000 INFO @ Tue, 16 Jun 2020 07:40:15: 7000000 INFO @ Tue, 16 Jun 2020 07:40:19: 2000000 INFO @ Tue, 16 Jun 2020 07:40:20: 8000000 INFO @ Tue, 16 Jun 2020 07:40:24: 3000000 INFO @ Tue, 16 Jun 2020 07:40:26: 9000000 INFO @ Tue, 16 Jun 2020 07:40:29: 4000000 INFO @ Tue, 16 Jun 2020 07:40:31: 10000000 INFO @ Tue, 16 Jun 2020 07:40:35: 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 07:40:36: 11000000 INFO @ Tue, 16 Jun 2020 07:40:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX105311/SRX105311.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX105311/SRX105311.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX105311/SRX105311.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX105311/SRX105311.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 07:40:38: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:40:38: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:40:40: 6000000 INFO @ Tue, 16 Jun 2020 07:40:42: 12000000 INFO @ Tue, 16 Jun 2020 07:40:43: 1000000 INFO @ Tue, 16 Jun 2020 07:40:46: 7000000 INFO @ Tue, 16 Jun 2020 07:40:48: 13000000 INFO @ Tue, 16 Jun 2020 07:40:49: 2000000 INFO @ Tue, 16 Jun 2020 07:40:51: 8000000 INFO @ Tue, 16 Jun 2020 07:40:54: 14000000 INFO @ Tue, 16 Jun 2020 07:40:55: 3000000 INFO @ Tue, 16 Jun 2020 07:40:57: 9000000 INFO @ Tue, 16 Jun 2020 07:41:00: 15000000 INFO @ Tue, 16 Jun 2020 07:41:01: 4000000 INFO @ Tue, 16 Jun 2020 07:41:03: 10000000 INFO @ Tue, 16 Jun 2020 07:41:06: 16000000 INFO @ Tue, 16 Jun 2020 07:41:06: 5000000 INFO @ Tue, 16 Jun 2020 07:41:09: 11000000 INFO @ Tue, 16 Jun 2020 07:41:12: 17000000 INFO @ Tue, 16 Jun 2020 07:41:12: 6000000 INFO @ Tue, 16 Jun 2020 07:41:14: 12000000 INFO @ Tue, 16 Jun 2020 07:41:18: 18000000 INFO @ Tue, 16 Jun 2020 07:41:18: 7000000 INFO @ Tue, 16 Jun 2020 07:41:20: 13000000 INFO @ Tue, 16 Jun 2020 07:41:23: 19000000 INFO @ Tue, 16 Jun 2020 07:41:23: 8000000 INFO @ Tue, 16 Jun 2020 07:41:25: 14000000 INFO @ Tue, 16 Jun 2020 07:41:29: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 07:41:29: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 07:41:29: #1 total tags in treatment: 19987854 INFO @ Tue, 16 Jun 2020 07:41:29: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:41:29: #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 07:41:29: 9000000 INFO @ Tue, 16 Jun 2020 07:41:29: #1 tags after filtering in treatment: 19987854 INFO @ Tue, 16 Jun 2020 07:41:29: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:41:29: #1 finished! INFO @ Tue, 16 Jun 2020 07:41:29: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:41:29: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:41:31: #2 number of paired peaks: 178 WARNING @ Tue, 16 Jun 2020 07:41:31: Fewer paired peaks (178) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 178 pairs to build model! INFO @ Tue, 16 Jun 2020 07:41:31: start model_add_line... INFO @ Tue, 16 Jun 2020 07:41:31: 15000000 INFO @ Tue, 16 Jun 2020 07:41:31: start X-correlation... INFO @ Tue, 16 Jun 2020 07:41:31: end of X-cor INFO @ Tue, 16 Jun 2020 07:41:31: #2 finished! INFO @ Tue, 16 Jun 2020 07:41:31: #2 predicted fragment length is 0 bps INFO @ Tue, 16 Jun 2020 07:41:31: #2 alternative fragment length(s) may be 0,33,423,445 bps INFO @ Tue, 16 Jun 2020 07:41:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX105311/SRX105311.05_model.r WARNING @ Tue, 16 Jun 2020 07:41:31: #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 07:41:31: #2 You may need to consider one of the other alternative d(s): 0,33,423,445 WARNING @ Tue, 16 Jun 2020 07:41:31: #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 07:41:31: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:41:31: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:41:35: 10000000 INFO @ Tue, 16 Jun 2020 07:41:36: 16000000 INFO @ Tue, 16 Jun 2020 07:41:40: 11000000 INFO @ Tue, 16 Jun 2020 07:41:42: 17000000 INFO @ Tue, 16 Jun 2020 07:41:45: 12000000 INFO @ Tue, 16 Jun 2020 07:41:47: 18000000 INFO @ Tue, 16 Jun 2020 07:41:51: 13000000 INFO @ Tue, 16 Jun 2020 07:41:53: 19000000 INFO @ Tue, 16 Jun 2020 07:41:56: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:41:58: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 07:41:58: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 07:41:58: #1 total tags in treatment: 19987854 INFO @ Tue, 16 Jun 2020 07:41:58: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:41:58: #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 07:41:58: #1 tags after filtering in treatment: 19987854 INFO @ Tue, 16 Jun 2020 07:41:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:41:58: #1 finished! INFO @ Tue, 16 Jun 2020 07:41:58: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:41:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:42:00: #2 number of paired peaks: 178 WARNING @ Tue, 16 Jun 2020 07:42:00: Fewer paired peaks (178) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 178 pairs to build model! INFO @ Tue, 16 Jun 2020 07:42:00: start model_add_line... INFO @ Tue, 16 Jun 2020 07:42:00: start X-correlation... INFO @ Tue, 16 Jun 2020 07:42:00: end of X-cor INFO @ Tue, 16 Jun 2020 07:42:00: #2 finished! INFO @ Tue, 16 Jun 2020 07:42:00: #2 predicted fragment length is 0 bps INFO @ Tue, 16 Jun 2020 07:42:00: #2 alternative fragment length(s) may be 0,33,423,445 bps INFO @ Tue, 16 Jun 2020 07:42:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX105311/SRX105311.10_model.r WARNING @ Tue, 16 Jun 2020 07:42:00: #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 07:42:00: #2 You may need to consider one of the other alternative d(s): 0,33,423,445 WARNING @ Tue, 16 Jun 2020 07:42:00: #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 07:42:00: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:42:00: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:42:02: 15000000 INFO @ Tue, 16 Jun 2020 07:42:07: 16000000 INFO @ Tue, 16 Jun 2020 07:42:12: 17000000 INFO @ Tue, 16 Jun 2020 07:42:17: 18000000 INFO @ Tue, 16 Jun 2020 07:42:23: 19000000 INFO @ Tue, 16 Jun 2020 07:42:28: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 07:42:28: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 07:42:28: #1 total tags in treatment: 19987854 INFO @ Tue, 16 Jun 2020 07:42:28: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:42:28: #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 07:42:28: #1 tags after filtering in treatment: 19987854 INFO @ Tue, 16 Jun 2020 07:42:28: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:42:28: #1 finished! INFO @ Tue, 16 Jun 2020 07:42:28: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:42:28: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:42:29: #2 number of paired peaks: 178 WARNING @ Tue, 16 Jun 2020 07:42:29: Fewer paired peaks (178) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 178 pairs to build model! INFO @ Tue, 16 Jun 2020 07:42:29: start model_add_line... INFO @ Tue, 16 Jun 2020 07:42:29: start X-correlation... INFO @ Tue, 16 Jun 2020 07:42:29: end of X-cor INFO @ Tue, 16 Jun 2020 07:42:29: #2 finished! INFO @ Tue, 16 Jun 2020 07:42:29: #2 predicted fragment length is 0 bps INFO @ Tue, 16 Jun 2020 07:42:29: #2 alternative fragment length(s) may be 0,33,423,445 bps INFO @ Tue, 16 Jun 2020 07:42:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX105311/SRX105311.20_model.r WARNING @ Tue, 16 Jun 2020 07:42:29: #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 07:42:29: #2 You may need to consider one of the other alternative d(s): 0,33,423,445 WARNING @ Tue, 16 Jun 2020 07:42:29: #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 07:42:29: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:42:29: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 /var/spool/uge/at153/job_scripts/6366277: line 271: 2533 Terminated MACS $i /var/spool/uge/at153/job_scripts/6366277: line 271: 3044 Terminated MACS $i /var/spool/uge/at153/job_scripts/6366277: line 271: 10326 Terminated MACS $i ls: cannot access SRX105311.05.bed: No such file or directory mv: cannot stat ‘SRX105311.05.bed’: No such file or directory mv: cannot stat ‘SRX105311.05.bb’: No such file or directory ls: cannot access SRX105311.10.bed: No such file or directory mv: cannot stat ‘SRX105311.10.bed’: No such file or directory mv: cannot stat ‘SRX105311.10.bb’: No such file or directory ls: cannot access SRX105311.20.bed: No such file or directory mv: cannot stat ‘SRX105311.20.bed’: No such file or directory mv: cannot stat ‘SRX105311.20.bb’: No such file or directory