Job ID = 10165788 SRX = SRX9120618 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 33805134 spots for SRR12638561/SRR12638561.sra Written 33805134 spots for SRR12638561/SRR12638561.sra fastq に変換しました。 bowtie でマッピング中... Your job 10166121 ("srTce11") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:07:08 33805134 reads; of these: 33805134 (100.00%) were unpaired; of these: 848643 (2.51%) aligned 0 times 27552992 (81.51%) aligned exactly 1 time 5403499 (15.98%) aligned >1 times 97.49% overall alignment rate Time searching: 00:07:08 Overall time: 00:07:08 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] 5894133 / 32956491 = 0.1788 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 @ Thu, 08 Oct 2020 20:06:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9120618/SRX9120618.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9120618/SRX9120618.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9120618/SRX9120618.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9120618/SRX9120618.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 @ Thu, 08 Oct 2020 20:06:57: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:06:57: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:07:02: 1000000 INFO @ Thu, 08 Oct 2020 20:07:07: 2000000 INFO @ Thu, 08 Oct 2020 20:07:11: 3000000 INFO @ Thu, 08 Oct 2020 20:07:16: 4000000 INFO @ Thu, 08 Oct 2020 20:07:20: 5000000 INFO @ Thu, 08 Oct 2020 20:07:25: 6000000 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 @ Thu, 08 Oct 2020 20:07:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9120618/SRX9120618.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9120618/SRX9120618.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9120618/SRX9120618.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9120618/SRX9120618.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 @ Thu, 08 Oct 2020 20:07:27: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:07:27: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:07:29: 7000000 INFO @ Thu, 08 Oct 2020 20:07:33: 1000000 INFO @ Thu, 08 Oct 2020 20:07:34: 8000000 INFO @ Thu, 08 Oct 2020 20:07:38: 2000000 INFO @ Thu, 08 Oct 2020 20:07:38: 9000000 INFO @ Thu, 08 Oct 2020 20:07:43: 10000000 INFO @ Thu, 08 Oct 2020 20:07:44: 3000000 INFO @ Thu, 08 Oct 2020 20:07:48: 11000000 INFO @ Thu, 08 Oct 2020 20:07:49: 4000000 INFO @ Thu, 08 Oct 2020 20:07:52: 12000000 INFO @ Thu, 08 Oct 2020 20:07:54: 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 @ Thu, 08 Oct 2020 20:07:57: 13000000 INFO @ Thu, 08 Oct 2020 20:07:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9120618/SRX9120618.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9120618/SRX9120618.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9120618/SRX9120618.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9120618/SRX9120618.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 @ Thu, 08 Oct 2020 20:07:57: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:07:57: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:08:00: 6000000 INFO @ Thu, 08 Oct 2020 20:08:02: 14000000 INFO @ Thu, 08 Oct 2020 20:08:03: 1000000 INFO @ Thu, 08 Oct 2020 20:08:05: 7000000 INFO @ Thu, 08 Oct 2020 20:08:06: 15000000 INFO @ Thu, 08 Oct 2020 20:08:08: 2000000 INFO @ Thu, 08 Oct 2020 20:08:10: 8000000 INFO @ Thu, 08 Oct 2020 20:08:11: 16000000 INFO @ Thu, 08 Oct 2020 20:08:13: 3000000 INFO @ Thu, 08 Oct 2020 20:08:15: 9000000 INFO @ Thu, 08 Oct 2020 20:08:16: 17000000 INFO @ Thu, 08 Oct 2020 20:08:18: 4000000 INFO @ Thu, 08 Oct 2020 20:08:20: 18000000 INFO @ Thu, 08 Oct 2020 20:08:21: 10000000 INFO @ Thu, 08 Oct 2020 20:08:24: 5000000 INFO @ Thu, 08 Oct 2020 20:08:25: 19000000 INFO @ Thu, 08 Oct 2020 20:08:26: 11000000 INFO @ Thu, 08 Oct 2020 20:08:29: 6000000 INFO @ Thu, 08 Oct 2020 20:08:30: 20000000 INFO @ Thu, 08 Oct 2020 20:08:32: 12000000 INFO @ Thu, 08 Oct 2020 20:08:34: 21000000 INFO @ Thu, 08 Oct 2020 20:08:35: 7000000 INFO @ Thu, 08 Oct 2020 20:08:37: 13000000 INFO @ Thu, 08 Oct 2020 20:08:39: 22000000 INFO @ Thu, 08 Oct 2020 20:08:40: 8000000 INFO @ Thu, 08 Oct 2020 20:08:43: 14000000 INFO @ Thu, 08 Oct 2020 20:08:44: 23000000 INFO @ Thu, 08 Oct 2020 20:08:46: 9000000 INFO @ Thu, 08 Oct 2020 20:08:49: 24000000 INFO @ Thu, 08 Oct 2020 20:08:49: 15000000 INFO @ Thu, 08 Oct 2020 20:08:51: 10000000 INFO @ Thu, 08 Oct 2020 20:08:53: 25000000 INFO @ Thu, 08 Oct 2020 20:08:54: 16000000 INFO @ Thu, 08 Oct 2020 20:08:56: 11000000 INFO @ Thu, 08 Oct 2020 20:08:58: 26000000 INFO @ Thu, 08 Oct 2020 20:09:00: 17000000 INFO @ Thu, 08 Oct 2020 20:09:01: 12000000 INFO @ Thu, 08 Oct 2020 20:09:03: 27000000 INFO @ Thu, 08 Oct 2020 20:09:03: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 20:09:03: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 20:09:03: #1 total tags in treatment: 27062358 INFO @ Thu, 08 Oct 2020 20:09:03: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:09:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 20:09:03: #1 tags after filtering in treatment: 27062358 INFO @ Thu, 08 Oct 2020 20:09:03: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:09:03: #1 finished! INFO @ Thu, 08 Oct 2020 20:09:03: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:09:03: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:09:05: #2 number of paired peaks: 103 WARNING @ Thu, 08 Oct 2020 20:09:05: Fewer paired peaks (103) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 103 pairs to build model! INFO @ Thu, 08 Oct 2020 20:09:05: start model_add_line... INFO @ Thu, 08 Oct 2020 20:09:05: start X-correlation... INFO @ Thu, 08 Oct 2020 20:09:05: end of X-cor INFO @ Thu, 08 Oct 2020 20:09:05: #2 finished! INFO @ Thu, 08 Oct 2020 20:09:05: #2 predicted fragment length is 0 bps INFO @ Thu, 08 Oct 2020 20:09:05: #2 alternative fragment length(s) may be 0,30,46,175,483,518,560,581 bps INFO @ Thu, 08 Oct 2020 20:09:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9120618/SRX9120618.05_model.r WARNING @ Thu, 08 Oct 2020 20:09:05: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:09:05: #2 You may need to consider one of the other alternative d(s): 0,30,46,175,483,518,560,581 WARNING @ Thu, 08 Oct 2020 20:09:05: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 20:09:05: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:09:05: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:09:05: 18000000 INFO @ Thu, 08 Oct 2020 20:09:07: 13000000 INFO @ Thu, 08 Oct 2020 20:09:11: 19000000 INFO @ Thu, 08 Oct 2020 20:09:12: 14000000 INFO @ Thu, 08 Oct 2020 20:09:17: 20000000 INFO @ Thu, 08 Oct 2020 20:09:17: 15000000 INFO @ Thu, 08 Oct 2020 20:09:22: 21000000 INFO @ Thu, 08 Oct 2020 20:09:22: 16000000 INFO @ Thu, 08 Oct 2020 20:09:28: 22000000 INFO @ Thu, 08 Oct 2020 20:09:28: 17000000 INFO @ Thu, 08 Oct 2020 20:09:33: 18000000 INFO @ Thu, 08 Oct 2020 20:09:33: 23000000 INFO @ Thu, 08 Oct 2020 20:09:38: 19000000 INFO @ Thu, 08 Oct 2020 20:09:39: 24000000 INFO @ Thu, 08 Oct 2020 20:09:43: 20000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 08 Oct 2020 20:09:44: 25000000 INFO @ Thu, 08 Oct 2020 20:09:48: 21000000 INFO @ Thu, 08 Oct 2020 20:09:49: 26000000 INFO @ Thu, 08 Oct 2020 20:09:54: 22000000 INFO @ Thu, 08 Oct 2020 20:09:54: 27000000 INFO @ Thu, 08 Oct 2020 20:09:55: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 20:09:55: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 20:09:55: #1 total tags in treatment: 27062358 INFO @ Thu, 08 Oct 2020 20:09:55: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:09:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 20:09:55: #1 tags after filtering in treatment: 27062358 INFO @ Thu, 08 Oct 2020 20:09:55: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:09:55: #1 finished! INFO @ Thu, 08 Oct 2020 20:09:55: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:09:55: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:09:57: #2 number of paired peaks: 103 WARNING @ Thu, 08 Oct 2020 20:09:57: Fewer paired peaks (103) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 103 pairs to build model! INFO @ Thu, 08 Oct 2020 20:09:57: start model_add_line... INFO @ Thu, 08 Oct 2020 20:09:57: start X-correlation... INFO @ Thu, 08 Oct 2020 20:09:57: end of X-cor INFO @ Thu, 08 Oct 2020 20:09:57: #2 finished! INFO @ Thu, 08 Oct 2020 20:09:57: #2 predicted fragment length is 0 bps INFO @ Thu, 08 Oct 2020 20:09:57: #2 alternative fragment length(s) may be 0,30,46,175,483,518,560,581 bps INFO @ Thu, 08 Oct 2020 20:09:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9120618/SRX9120618.10_model.r WARNING @ Thu, 08 Oct 2020 20:09:57: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:09:57: #2 You may need to consider one of the other alternative d(s): 0,30,46,175,483,518,560,581 WARNING @ Thu, 08 Oct 2020 20:09:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 20:09:57: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:09:57: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:09:59: 23000000 INFO @ Thu, 08 Oct 2020 20:10:04: 24000000 INFO @ Thu, 08 Oct 2020 20:10:09: 25000000 INFO @ Thu, 08 Oct 2020 20:10:14: 26000000 INFO @ Thu, 08 Oct 2020 20:10:19: 27000000 INFO @ Thu, 08 Oct 2020 20:10:20: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 20:10:20: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 20:10:20: #1 total tags in treatment: 27062358 INFO @ Thu, 08 Oct 2020 20:10:20: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:10:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 20:10:20: #1 tags after filtering in treatment: 27062358 INFO @ Thu, 08 Oct 2020 20:10:20: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:10:20: #1 finished! INFO @ Thu, 08 Oct 2020 20:10:20: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:10:20: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:10:22: #2 number of paired peaks: 103 WARNING @ Thu, 08 Oct 2020 20:10:22: Fewer paired peaks (103) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 103 pairs to build model! INFO @ Thu, 08 Oct 2020 20:10:22: start model_add_line... INFO @ Thu, 08 Oct 2020 20:10:22: start X-correlation... INFO @ Thu, 08 Oct 2020 20:10:22: end of X-cor INFO @ Thu, 08 Oct 2020 20:10:22: #2 finished! INFO @ Thu, 08 Oct 2020 20:10:22: #2 predicted fragment length is 0 bps INFO @ Thu, 08 Oct 2020 20:10:22: #2 alternative fragment length(s) may be 0,30,46,175,483,518,560,581 bps INFO @ Thu, 08 Oct 2020 20:10:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9120618/SRX9120618.20_model.r WARNING @ Thu, 08 Oct 2020 20:10:22: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:10:22: #2 You may need to consider one of the other alternative d(s): 0,30,46,175,483,518,560,581 WARNING @ Thu, 08 Oct 2020 20:10:22: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 20:10:22: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:10:22: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 /var/spool/uge/at158/job_scripts/10165788: line 297: 119440 Terminated MACS $i /var/spool/uge/at158/job_scripts/10165788: line 297: 124064 Terminated MACS $i /var/spool/uge/at158/job_scripts/10165788: line 297: 10888 Terminated MACS $i ls: cannot access SRX9120618.05.bed: No such file or directory mv: cannot stat ‘SRX9120618.05.bed’: No such file or directory mv: cannot stat ‘SRX9120618.05.bb’: No such file or directory ls: cannot access SRX9120618.10.bed: No such file or directory mv: cannot stat ‘SRX9120618.10.bed’: No such file or directory mv: cannot stat ‘SRX9120618.10.bb’: No such file or directory ls: cannot access SRX9120618.20.bed: No such file or directory mv: cannot stat ‘SRX9120618.20.bed’: No such file or directory mv: cannot stat ‘SRX9120618.20.bb’: No such file or directory