Job ID = 6368794 SRX = SRX5709760 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:34:40 prefetch.2.10.7: 1) Downloading 'SRR8928710'... 2020-06-16T00:34:40 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:38:03 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:38:03 prefetch.2.10.7: 1) 'SRR8928710' was downloaded successfully 2020-06-16T00:38:03 prefetch.2.10.7: 'SRR8928710' has 0 unresolved dependencies Read 30155426 spots for SRR8928710/SRR8928710.sra Written 30155426 spots for SRR8928710/SRR8928710.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: 00:00:01 Multiseed full-index search: 00:07:03 30155426 reads; of these: 30155426 (100.00%) were unpaired; of these: 905498 (3.00%) aligned 0 times 24402991 (80.92%) aligned exactly 1 time 4846937 (16.07%) aligned >1 times 97.00% overall alignment rate Time searching: 00:07:04 Overall time: 00:07:04 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 12 files... [bam_rmdupse_core] 6011794 / 29249928 = 0.2055 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 09:53:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5709760/SRX5709760.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5709760/SRX5709760.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5709760/SRX5709760.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5709760/SRX5709760.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 09:53:37: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:53:37: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:53:43: 1000000 INFO @ Tue, 16 Jun 2020 09:53:49: 2000000 INFO @ Tue, 16 Jun 2020 09:53:55: 3000000 INFO @ Tue, 16 Jun 2020 09:54:01: 4000000 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 09:54:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5709760/SRX5709760.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5709760/SRX5709760.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5709760/SRX5709760.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5709760/SRX5709760.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 09:54:06: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:54:06: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:54:08: 5000000 INFO @ Tue, 16 Jun 2020 09:54:13: 1000000 INFO @ Tue, 16 Jun 2020 09:54:15: 6000000 INFO @ Tue, 16 Jun 2020 09:54:19: 2000000 INFO @ Tue, 16 Jun 2020 09:54:22: 7000000 INFO @ Tue, 16 Jun 2020 09:54:27: 3000000 INFO @ Tue, 16 Jun 2020 09:54:29: 8000000 INFO @ Tue, 16 Jun 2020 09:54:33: 4000000 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 09:54:36: 9000000 INFO @ Tue, 16 Jun 2020 09:54:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5709760/SRX5709760.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5709760/SRX5709760.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5709760/SRX5709760.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5709760/SRX5709760.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 09:54:36: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:54:36: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:54:40: 5000000 INFO @ Tue, 16 Jun 2020 09:54:43: 10000000 INFO @ Tue, 16 Jun 2020 09:54:43: 1000000 INFO @ Tue, 16 Jun 2020 09:54:47: 6000000 INFO @ Tue, 16 Jun 2020 09:54:50: 11000000 INFO @ Tue, 16 Jun 2020 09:54:50: 2000000 INFO @ Tue, 16 Jun 2020 09:54:54: 7000000 INFO @ Tue, 16 Jun 2020 09:54:57: 12000000 INFO @ Tue, 16 Jun 2020 09:54:57: 3000000 INFO @ Tue, 16 Jun 2020 09:55:00: 8000000 INFO @ Tue, 16 Jun 2020 09:55:04: 13000000 INFO @ Tue, 16 Jun 2020 09:55:04: 4000000 INFO @ Tue, 16 Jun 2020 09:55:07: 9000000 INFO @ Tue, 16 Jun 2020 09:55:10: 14000000 INFO @ Tue, 16 Jun 2020 09:55:10: 5000000 INFO @ Tue, 16 Jun 2020 09:55:14: 10000000 INFO @ Tue, 16 Jun 2020 09:55:17: 15000000 INFO @ Tue, 16 Jun 2020 09:55:17: 6000000 INFO @ Tue, 16 Jun 2020 09:55:21: 11000000 INFO @ Tue, 16 Jun 2020 09:55:24: 16000000 INFO @ Tue, 16 Jun 2020 09:55:24: 7000000 INFO @ Tue, 16 Jun 2020 09:55:28: 12000000 INFO @ Tue, 16 Jun 2020 09:55:31: 17000000 INFO @ Tue, 16 Jun 2020 09:55:31: 8000000 INFO @ Tue, 16 Jun 2020 09:55:35: 13000000 INFO @ Tue, 16 Jun 2020 09:55:38: 18000000 INFO @ Tue, 16 Jun 2020 09:55:38: 9000000 INFO @ Tue, 16 Jun 2020 09:55:42: 14000000 INFO @ Tue, 16 Jun 2020 09:55:45: 19000000 INFO @ Tue, 16 Jun 2020 09:55:45: 10000000 INFO @ Tue, 16 Jun 2020 09:55:49: 15000000 INFO @ Tue, 16 Jun 2020 09:55:52: 20000000 INFO @ Tue, 16 Jun 2020 09:55:52: 11000000 INFO @ Tue, 16 Jun 2020 09:55:56: 16000000 INFO @ Tue, 16 Jun 2020 09:55:59: 21000000 INFO @ Tue, 16 Jun 2020 09:55:59: 12000000 INFO @ Tue, 16 Jun 2020 09:56:03: 17000000 INFO @ Tue, 16 Jun 2020 09:56:06: 22000000 INFO @ Tue, 16 Jun 2020 09:56:06: 13000000 INFO @ Tue, 16 Jun 2020 09:56:10: 18000000 INFO @ Tue, 16 Jun 2020 09:56:12: 23000000 INFO @ Tue, 16 Jun 2020 09:56:13: 14000000 INFO @ Tue, 16 Jun 2020 09:56:14: #1 tag size is determined as 49 bps INFO @ Tue, 16 Jun 2020 09:56:14: #1 tag size = 49 INFO @ Tue, 16 Jun 2020 09:56:14: #1 total tags in treatment: 23238134 INFO @ Tue, 16 Jun 2020 09:56:14: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:56:14: #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 09:56:15: #1 tags after filtering in treatment: 23238134 INFO @ Tue, 16 Jun 2020 09:56:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:56:15: #1 finished! INFO @ Tue, 16 Jun 2020 09:56:15: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:56:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:56:16: #2 number of paired peaks: 192 WARNING @ Tue, 16 Jun 2020 09:56:16: Fewer paired peaks (192) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 192 pairs to build model! INFO @ Tue, 16 Jun 2020 09:56:16: start model_add_line... INFO @ Tue, 16 Jun 2020 09:56:16: start X-correlation... INFO @ Tue, 16 Jun 2020 09:56:16: end of X-cor INFO @ Tue, 16 Jun 2020 09:56:16: #2 finished! INFO @ Tue, 16 Jun 2020 09:56:16: #2 predicted fragment length is 0 bps INFO @ Tue, 16 Jun 2020 09:56:16: #2 alternative fragment length(s) may be 0,45,529,559,575,582 bps INFO @ Tue, 16 Jun 2020 09:56:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5709760/SRX5709760.05_model.r WARNING @ Tue, 16 Jun 2020 09:56:16: #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 09:56:16: #2 You may need to consider one of the other alternative d(s): 0,45,529,559,575,582 WARNING @ Tue, 16 Jun 2020 09:56:16: #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 09:56:16: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:56:16: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:56:17: 19000000 INFO @ Tue, 16 Jun 2020 09:56:20: 15000000 INFO @ Tue, 16 Jun 2020 09:56:24: 20000000 INFO @ Tue, 16 Jun 2020 09:56:27: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:56:30: 21000000 INFO @ Tue, 16 Jun 2020 09:56:33: 17000000 INFO @ Tue, 16 Jun 2020 09:56:37: 22000000 INFO @ Tue, 16 Jun 2020 09:56:40: 18000000 INFO @ Tue, 16 Jun 2020 09:56:44: 23000000 INFO @ Tue, 16 Jun 2020 09:56:45: #1 tag size is determined as 49 bps INFO @ Tue, 16 Jun 2020 09:56:45: #1 tag size = 49 INFO @ Tue, 16 Jun 2020 09:56:45: #1 total tags in treatment: 23238134 INFO @ Tue, 16 Jun 2020 09:56:45: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:56:45: #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 09:56:46: #1 tags after filtering in treatment: 23238134 INFO @ Tue, 16 Jun 2020 09:56:46: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:56:46: #1 finished! INFO @ Tue, 16 Jun 2020 09:56:46: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:56:46: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:56:47: 19000000 INFO @ Tue, 16 Jun 2020 09:56:47: #2 number of paired peaks: 192 WARNING @ Tue, 16 Jun 2020 09:56:47: Fewer paired peaks (192) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 192 pairs to build model! INFO @ Tue, 16 Jun 2020 09:56:47: start model_add_line... INFO @ Tue, 16 Jun 2020 09:56:48: start X-correlation... INFO @ Tue, 16 Jun 2020 09:56:48: end of X-cor INFO @ Tue, 16 Jun 2020 09:56:48: #2 finished! INFO @ Tue, 16 Jun 2020 09:56:48: #2 predicted fragment length is 0 bps INFO @ Tue, 16 Jun 2020 09:56:48: #2 alternative fragment length(s) may be 0,45,529,559,575,582 bps INFO @ Tue, 16 Jun 2020 09:56:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5709760/SRX5709760.10_model.r WARNING @ Tue, 16 Jun 2020 09:56:48: #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 09:56:48: #2 You may need to consider one of the other alternative d(s): 0,45,529,559,575,582 WARNING @ Tue, 16 Jun 2020 09:56:48: #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 09:56:48: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:56:48: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:56:53: 20000000 INFO @ Tue, 16 Jun 2020 09:56:59: 21000000 INFO @ Tue, 16 Jun 2020 09:57:05: 22000000 INFO @ Tue, 16 Jun 2020 09:57:11: 23000000 INFO @ Tue, 16 Jun 2020 09:57:13: #1 tag size is determined as 49 bps INFO @ Tue, 16 Jun 2020 09:57:13: #1 tag size = 49 INFO @ Tue, 16 Jun 2020 09:57:13: #1 total tags in treatment: 23238134 INFO @ Tue, 16 Jun 2020 09:57:13: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:57:13: #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 09:57:13: #1 tags after filtering in treatment: 23238134 INFO @ Tue, 16 Jun 2020 09:57:13: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:57:13: #1 finished! INFO @ Tue, 16 Jun 2020 09:57:13: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:57:13: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:57:15: #2 number of paired peaks: 192 WARNING @ Tue, 16 Jun 2020 09:57:15: Fewer paired peaks (192) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 192 pairs to build model! INFO @ Tue, 16 Jun 2020 09:57:15: start model_add_line... INFO @ Tue, 16 Jun 2020 09:57:15: start X-correlation... INFO @ Tue, 16 Jun 2020 09:57:15: end of X-cor INFO @ Tue, 16 Jun 2020 09:57:15: #2 finished! INFO @ Tue, 16 Jun 2020 09:57:15: #2 predicted fragment length is 0 bps INFO @ Tue, 16 Jun 2020 09:57:15: #2 alternative fragment length(s) may be 0,45,529,559,575,582 bps INFO @ Tue, 16 Jun 2020 09:57:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5709760/SRX5709760.20_model.r WARNING @ Tue, 16 Jun 2020 09:57:15: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:57:15: #2 You may need to consider one of the other alternative d(s): 0,45,529,559,575,582 WARNING @ Tue, 16 Jun 2020 09:57:15: #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 09:57:15: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:57:15: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 /var/spool/uge/at161/job_scripts/6368794: line 271: 27440 Terminated MACS $i /var/spool/uge/at161/job_scripts/6368794: line 271: 42861 Terminated MACS $i /var/spool/uge/at161/job_scripts/6368794: line 271: 43532 Terminated MACS $i ls: cannot access SRX5709760.05.bed: No such file or directory mv: cannot stat ‘SRX5709760.05.bed’: No such file or directory mv: cannot stat ‘SRX5709760.05.bb’: No such file or directory ls: cannot access SRX5709760.10.bed: No such file or directory mv: cannot stat ‘SRX5709760.10.bed’: No such file or directory mv: cannot stat ‘SRX5709760.10.bb’: No such file or directory ls: cannot access SRX5709760.20.bed: No such file or directory mv: cannot stat ‘SRX5709760.20.bed’: No such file or directory mv: cannot stat ‘SRX5709760.20.bb’: No such file or directory