Job ID = 14159226 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 14159442 ("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: 00:07:14 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: 00:07:14 Overall time: 00:07:14 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 08 Dec 2021 20:31:35: # 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 @ Wed, 08 Dec 2021 20:31:35: #1 read tag files... INFO @ Wed, 08 Dec 2021 20:31:35: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 20:31:40: 1000000 INFO @ Wed, 08 Dec 2021 20:31:45: 2000000 INFO @ Wed, 08 Dec 2021 20:31:50: 3000000 INFO @ Wed, 08 Dec 2021 20:31:55: 4000000 INFO @ Wed, 08 Dec 2021 20:32:00: 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 @ Wed, 08 Dec 2021 20:32:05: # 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 @ Wed, 08 Dec 2021 20:32:05: #1 read tag files... INFO @ Wed, 08 Dec 2021 20:32:05: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 20:32:06: 6000000 INFO @ Wed, 08 Dec 2021 20:32:10: 1000000 INFO @ Wed, 08 Dec 2021 20:32:11: 7000000 INFO @ Wed, 08 Dec 2021 20:32:15: 2000000 INFO @ Wed, 08 Dec 2021 20:32:16: 8000000 INFO @ Wed, 08 Dec 2021 20:32:21: 3000000 INFO @ Wed, 08 Dec 2021 20:32:21: 9000000 INFO @ Wed, 08 Dec 2021 20:32:26: 4000000 INFO @ Wed, 08 Dec 2021 20:32:26: 10000000 INFO @ Wed, 08 Dec 2021 20:32:31: 11000000 INFO @ Wed, 08 Dec 2021 20:32:31: 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 @ Wed, 08 Dec 2021 20:32:35: # 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 @ Wed, 08 Dec 2021 20:32:35: #1 read tag files... INFO @ Wed, 08 Dec 2021 20:32:35: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 20:32:37: 12000000 INFO @ Wed, 08 Dec 2021 20:32:37: 6000000 INFO @ Wed, 08 Dec 2021 20:32:39: 1000000 INFO @ Wed, 08 Dec 2021 20:32:42: 13000000 INFO @ Wed, 08 Dec 2021 20:32:42: 7000000 INFO @ Wed, 08 Dec 2021 20:32:44: 2000000 INFO @ Wed, 08 Dec 2021 20:32:47: 14000000 INFO @ Wed, 08 Dec 2021 20:32:47: 8000000 INFO @ Wed, 08 Dec 2021 20:32:49: 3000000 INFO @ Wed, 08 Dec 2021 20:32:53: 9000000 INFO @ Wed, 08 Dec 2021 20:32:53: 15000000 INFO @ Wed, 08 Dec 2021 20:32:53: 4000000 INFO @ Wed, 08 Dec 2021 20:32:58: 5000000 INFO @ Wed, 08 Dec 2021 20:32:58: 16000000 INFO @ Wed, 08 Dec 2021 20:32:58: 10000000 INFO @ Wed, 08 Dec 2021 20:33:02: 6000000 INFO @ Wed, 08 Dec 2021 20:33:03: 17000000 INFO @ Wed, 08 Dec 2021 20:33:03: 11000000 INFO @ Wed, 08 Dec 2021 20:33:07: 7000000 INFO @ Wed, 08 Dec 2021 20:33:09: 18000000 INFO @ Wed, 08 Dec 2021 20:33:09: 12000000 INFO @ Wed, 08 Dec 2021 20:33:11: 8000000 INFO @ Wed, 08 Dec 2021 20:33:14: 19000000 INFO @ Wed, 08 Dec 2021 20:33:14: 13000000 INFO @ Wed, 08 Dec 2021 20:33:16: 9000000 INFO @ Wed, 08 Dec 2021 20:33:19: 20000000 INFO @ Wed, 08 Dec 2021 20:33:20: 14000000 INFO @ Wed, 08 Dec 2021 20:33:21: 10000000 INFO @ Wed, 08 Dec 2021 20:33:24: 21000000 INFO @ Wed, 08 Dec 2021 20:33:25: 15000000 INFO @ Wed, 08 Dec 2021 20:33:25: 11000000 INFO @ Wed, 08 Dec 2021 20:33:30: 22000000 INFO @ Wed, 08 Dec 2021 20:33:30: 12000000 INFO @ Wed, 08 Dec 2021 20:33:31: 16000000 INFO @ Wed, 08 Dec 2021 20:33:34: 13000000 INFO @ Wed, 08 Dec 2021 20:33:35: 23000000 INFO @ Wed, 08 Dec 2021 20:33:36: 17000000 INFO @ Wed, 08 Dec 2021 20:33:39: 14000000 INFO @ Wed, 08 Dec 2021 20:33:40: 24000000 INFO @ Wed, 08 Dec 2021 20:33:42: 18000000 INFO @ Wed, 08 Dec 2021 20:33:44: 15000000 INFO @ Wed, 08 Dec 2021 20:33:45: 25000000 INFO @ Wed, 08 Dec 2021 20:33:47: 19000000 INFO @ Wed, 08 Dec 2021 20:33:48: 16000000 INFO @ Wed, 08 Dec 2021 20:33:50: 26000000 INFO @ Wed, 08 Dec 2021 20:33:52: 20000000 INFO @ Wed, 08 Dec 2021 20:33:53: 17000000 INFO @ Wed, 08 Dec 2021 20:33:55: 27000000 INFO @ Wed, 08 Dec 2021 20:33:55: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 20:33:55: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 20:33:55: #1 total tags in treatment: 27062358 INFO @ Wed, 08 Dec 2021 20:33:55: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 20:33:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 20:33:56: #1 tags after filtering in treatment: 27062358 INFO @ Wed, 08 Dec 2021 20:33:56: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 20:33:56: #1 finished! INFO @ Wed, 08 Dec 2021 20:33:56: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 20:33:56: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 20:33:58: 18000000 INFO @ Wed, 08 Dec 2021 20:33:58: #2 number of paired peaks: 103 WARNING @ Wed, 08 Dec 2021 20:33:58: 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 @ Wed, 08 Dec 2021 20:33:58: start model_add_line... INFO @ Wed, 08 Dec 2021 20:33:58: 21000000 INFO @ Wed, 08 Dec 2021 20:33:58: start X-correlation... INFO @ Wed, 08 Dec 2021 20:33:58: end of X-cor INFO @ Wed, 08 Dec 2021 20:33:58: #2 finished! INFO @ Wed, 08 Dec 2021 20:33:58: #2 predicted fragment length is 0 bps INFO @ Wed, 08 Dec 2021 20:33:58: #2 alternative fragment length(s) may be 0,30,46,175,483,518,560,581 bps INFO @ Wed, 08 Dec 2021 20:33:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9120618/SRX9120618.05_model.r WARNING @ Wed, 08 Dec 2021 20:33:58: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 20:33:58: #2 You may need to consider one of the other alternative d(s): 0,30,46,175,483,518,560,581 WARNING @ Wed, 08 Dec 2021 20:33:58: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 20:33:58: #3 Call peaks... INFO @ Wed, 08 Dec 2021 20:33:58: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 20:34:02: 19000000 INFO @ Wed, 08 Dec 2021 20:34:03: 22000000 INFO @ Wed, 08 Dec 2021 20:34:07: 20000000 INFO @ Wed, 08 Dec 2021 20:34:08: 23000000 INFO @ Wed, 08 Dec 2021 20:34:11: 21000000 INFO @ Wed, 08 Dec 2021 20:34:13: 24000000 INFO @ Wed, 08 Dec 2021 20:34:16: 22000000 INFO @ Wed, 08 Dec 2021 20:34:18: 25000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 20:34:20: 23000000 INFO @ Wed, 08 Dec 2021 20:34:23: 26000000 INFO @ Wed, 08 Dec 2021 20:34:25: 24000000 INFO @ Wed, 08 Dec 2021 20:34:29: 27000000 INFO @ Wed, 08 Dec 2021 20:34:29: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 20:34:29: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 20:34:29: #1 total tags in treatment: 27062358 INFO @ Wed, 08 Dec 2021 20:34:29: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 20:34:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 20:34:29: 25000000 INFO @ Wed, 08 Dec 2021 20:34:30: #1 tags after filtering in treatment: 27062358 INFO @ Wed, 08 Dec 2021 20:34:30: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 20:34:30: #1 finished! INFO @ Wed, 08 Dec 2021 20:34:30: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 20:34:30: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 20:34:31: #2 number of paired peaks: 103 WARNING @ Wed, 08 Dec 2021 20:34:31: 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 @ Wed, 08 Dec 2021 20:34:31: start model_add_line... INFO @ Wed, 08 Dec 2021 20:34:31: start X-correlation... INFO @ Wed, 08 Dec 2021 20:34:31: end of X-cor INFO @ Wed, 08 Dec 2021 20:34:31: #2 finished! INFO @ Wed, 08 Dec 2021 20:34:31: #2 predicted fragment length is 0 bps INFO @ Wed, 08 Dec 2021 20:34:31: #2 alternative fragment length(s) may be 0,30,46,175,483,518,560,581 bps INFO @ Wed, 08 Dec 2021 20:34:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9120618/SRX9120618.10_model.r WARNING @ Wed, 08 Dec 2021 20:34:31: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 20:34:31: #2 You may need to consider one of the other alternative d(s): 0,30,46,175,483,518,560,581 WARNING @ Wed, 08 Dec 2021 20:34:31: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 20:34:31: #3 Call peaks... INFO @ Wed, 08 Dec 2021 20:34:31: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 20:34:34: 26000000 INFO @ Wed, 08 Dec 2021 20:34:38: 27000000 INFO @ Wed, 08 Dec 2021 20:34:38: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 20:34:38: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 20:34:38: #1 total tags in treatment: 27062358 INFO @ Wed, 08 Dec 2021 20:34:38: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 20:34:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 20:34:39: #1 tags after filtering in treatment: 27062358 INFO @ Wed, 08 Dec 2021 20:34:39: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 20:34:39: #1 finished! INFO @ Wed, 08 Dec 2021 20:34:39: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 20:34:39: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 20:34:40: #2 number of paired peaks: 103 WARNING @ Wed, 08 Dec 2021 20:34:40: 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 @ Wed, 08 Dec 2021 20:34:40: start model_add_line... INFO @ Wed, 08 Dec 2021 20:34:41: start X-correlation... INFO @ Wed, 08 Dec 2021 20:34:41: end of X-cor INFO @ Wed, 08 Dec 2021 20:34:41: #2 finished! INFO @ Wed, 08 Dec 2021 20:34:41: #2 predicted fragment length is 0 bps INFO @ Wed, 08 Dec 2021 20:34:41: #2 alternative fragment length(s) may be 0,30,46,175,483,518,560,581 bps INFO @ Wed, 08 Dec 2021 20:34:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9120618/SRX9120618.20_model.r WARNING @ Wed, 08 Dec 2021 20:34:41: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 20:34:41: #2 You may need to consider one of the other alternative d(s): 0,30,46,175,483,518,560,581 WARNING @ Wed, 08 Dec 2021 20:34:41: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 20:34:41: #3 Call peaks... INFO @ Wed, 08 Dec 2021 20:34:41: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 /var/spool/uge/at145/job_scripts/14159226: line 297: 33863 Terminated MACS $i /var/spool/uge/at145/job_scripts/14159226: line 297: 41450 Terminated MACS $i /var/spool/uge/at145/job_scripts/14159226: line 297: 45043 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