Job ID = 14158052 SRX = SRX6799189 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 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: 00:10:38 42139643 reads; of these: 42139643 (100.00%) were unpaired; of these: 1694178 (4.02%) aligned 0 times 27802584 (65.98%) aligned exactly 1 time 12642881 (30.00%) aligned >1 times 95.98% overall alignment rate Time searching: 00:10:38 Overall time: 00:10:38 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 20 files... [bam_rmdupse_core] 14204631 / 40445465 = 0.3512 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 14:22:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX6799189/SRX6799189.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX6799189/SRX6799189.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX6799189/SRX6799189.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX6799189/SRX6799189.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 14:22:09: #1 read tag files... INFO @ Wed, 08 Dec 2021 14:22:09: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 14:22:14: 1000000 INFO @ Wed, 08 Dec 2021 14:22:19: 2000000 INFO @ Wed, 08 Dec 2021 14:22:24: 3000000 INFO @ Wed, 08 Dec 2021 14:22:29: 4000000 INFO @ Wed, 08 Dec 2021 14:22:35: 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 14:22:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX6799189/SRX6799189.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX6799189/SRX6799189.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX6799189/SRX6799189.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX6799189/SRX6799189.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 14:22:38: #1 read tag files... INFO @ Wed, 08 Dec 2021 14:22:38: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 14:22:40: 6000000 INFO @ Wed, 08 Dec 2021 14:22:44: 1000000 INFO @ Wed, 08 Dec 2021 14:22:46: 7000000 INFO @ Wed, 08 Dec 2021 14:22:50: 2000000 INFO @ Wed, 08 Dec 2021 14:22:52: 8000000 INFO @ Wed, 08 Dec 2021 14:22:56: 3000000 INFO @ Wed, 08 Dec 2021 14:22:58: 9000000 INFO @ Wed, 08 Dec 2021 14:23:01: 4000000 INFO @ Wed, 08 Dec 2021 14:23:04: 10000000 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 14:23:07: 5000000 INFO @ Wed, 08 Dec 2021 14:23:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX6799189/SRX6799189.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX6799189/SRX6799189.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX6799189/SRX6799189.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX6799189/SRX6799189.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 14:23:09: #1 read tag files... INFO @ Wed, 08 Dec 2021 14:23:09: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 14:23:10: 11000000 INFO @ Wed, 08 Dec 2021 14:23:13: 6000000 INFO @ Wed, 08 Dec 2021 14:23:15: 1000000 INFO @ Wed, 08 Dec 2021 14:23:17: 12000000 INFO @ Wed, 08 Dec 2021 14:23:20: 7000000 INFO @ Wed, 08 Dec 2021 14:23:22: 2000000 INFO @ Wed, 08 Dec 2021 14:23:23: 13000000 INFO @ Wed, 08 Dec 2021 14:23:26: 8000000 INFO @ Wed, 08 Dec 2021 14:23:29: 3000000 INFO @ Wed, 08 Dec 2021 14:23:30: 14000000 INFO @ Wed, 08 Dec 2021 14:23:32: 9000000 INFO @ Wed, 08 Dec 2021 14:23:36: 4000000 INFO @ Wed, 08 Dec 2021 14:23:36: 15000000 INFO @ Wed, 08 Dec 2021 14:23:38: 10000000 INFO @ Wed, 08 Dec 2021 14:23:42: 16000000 INFO @ Wed, 08 Dec 2021 14:23:43: 5000000 INFO @ Wed, 08 Dec 2021 14:23:45: 11000000 INFO @ Wed, 08 Dec 2021 14:23:49: 17000000 INFO @ Wed, 08 Dec 2021 14:23:51: 6000000 INFO @ Wed, 08 Dec 2021 14:23:51: 12000000 INFO @ Wed, 08 Dec 2021 14:23:55: 18000000 INFO @ Wed, 08 Dec 2021 14:23:57: 13000000 INFO @ Wed, 08 Dec 2021 14:23:58: 7000000 INFO @ Wed, 08 Dec 2021 14:24:01: 19000000 INFO @ Wed, 08 Dec 2021 14:24:04: 14000000 INFO @ Wed, 08 Dec 2021 14:24:05: 8000000 INFO @ Wed, 08 Dec 2021 14:24:08: 20000000 INFO @ Wed, 08 Dec 2021 14:24:10: 15000000 INFO @ Wed, 08 Dec 2021 14:24:12: 9000000 INFO @ Wed, 08 Dec 2021 14:24:14: 21000000 INFO @ Wed, 08 Dec 2021 14:24:16: 16000000 INFO @ Wed, 08 Dec 2021 14:24:19: 10000000 INFO @ Wed, 08 Dec 2021 14:24:20: 22000000 INFO @ Wed, 08 Dec 2021 14:24:23: 17000000 INFO @ Wed, 08 Dec 2021 14:24:25: 11000000 INFO @ Wed, 08 Dec 2021 14:24:26: 23000000 INFO @ Wed, 08 Dec 2021 14:24:29: 18000000 INFO @ Wed, 08 Dec 2021 14:24:32: 12000000 INFO @ Wed, 08 Dec 2021 14:24:32: 24000000 INFO @ Wed, 08 Dec 2021 14:24:35: 19000000 INFO @ Wed, 08 Dec 2021 14:24:39: 25000000 INFO @ Wed, 08 Dec 2021 14:24:39: 13000000 INFO @ Wed, 08 Dec 2021 14:24:41: 20000000 INFO @ Wed, 08 Dec 2021 14:24:45: 26000000 INFO @ Wed, 08 Dec 2021 14:24:46: 14000000 INFO @ Wed, 08 Dec 2021 14:24:46: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 14:24:46: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 14:24:46: #1 total tags in treatment: 26240834 INFO @ Wed, 08 Dec 2021 14:24:46: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 14:24:46: #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 14:24:47: #1 tags after filtering in treatment: 26240834 INFO @ Wed, 08 Dec 2021 14:24:47: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 14:24:47: #1 finished! INFO @ Wed, 08 Dec 2021 14:24:47: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 14:24:47: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 14:24:48: 21000000 INFO @ Wed, 08 Dec 2021 14:24:48: #2 number of paired peaks: 300 WARNING @ Wed, 08 Dec 2021 14:24:48: Fewer paired peaks (300) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 300 pairs to build model! INFO @ Wed, 08 Dec 2021 14:24:48: start model_add_line... INFO @ Wed, 08 Dec 2021 14:24:49: start X-correlation... INFO @ Wed, 08 Dec 2021 14:24:49: end of X-cor INFO @ Wed, 08 Dec 2021 14:24:49: #2 finished! INFO @ Wed, 08 Dec 2021 14:24:49: #2 predicted fragment length is 0 bps INFO @ Wed, 08 Dec 2021 14:24:49: #2 alternative fragment length(s) may be 0,13,50,484,563,591 bps INFO @ Wed, 08 Dec 2021 14:24:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX6799189/SRX6799189.05_model.r WARNING @ Wed, 08 Dec 2021 14:24:49: #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 14:24:49: #2 You may need to consider one of the other alternative d(s): 0,13,50,484,563,591 WARNING @ Wed, 08 Dec 2021 14:24:49: #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 14:24:49: #3 Call peaks... INFO @ Wed, 08 Dec 2021 14:24:49: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 14:24:52: 15000000 INFO @ Wed, 08 Dec 2021 14:24:54: 22000000 INFO @ Wed, 08 Dec 2021 14:24:59: 16000000 INFO @ Wed, 08 Dec 2021 14:25:00: 23000000 INFO @ Wed, 08 Dec 2021 14:25:06: 24000000 INFO @ Wed, 08 Dec 2021 14:25:06: 17000000 INFO @ Wed, 08 Dec 2021 14:25:12: 25000000 INFO @ Wed, 08 Dec 2021 14:25:13: 18000000 INFO @ Wed, 08 Dec 2021 14:25:18: 26000000 INFO @ Wed, 08 Dec 2021 14:25:19: 19000000 INFO @ Wed, 08 Dec 2021 14:25:19: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 14:25:19: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 14:25:19: #1 total tags in treatment: 26240834 INFO @ Wed, 08 Dec 2021 14:25:19: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 14:25:19: #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 14:25:20: #1 tags after filtering in treatment: 26240834 INFO @ Wed, 08 Dec 2021 14:25:20: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 14:25:20: #1 finished! INFO @ Wed, 08 Dec 2021 14:25:20: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 14:25:20: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 14:25:21: #2 number of paired peaks: 300 WARNING @ Wed, 08 Dec 2021 14:25:21: Fewer paired peaks (300) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 300 pairs to build model! INFO @ Wed, 08 Dec 2021 14:25:21: start model_add_line... INFO @ Wed, 08 Dec 2021 14:25:22: start X-correlation... INFO @ Wed, 08 Dec 2021 14:25:22: end of X-cor INFO @ Wed, 08 Dec 2021 14:25:22: #2 finished! INFO @ Wed, 08 Dec 2021 14:25:22: #2 predicted fragment length is 0 bps INFO @ Wed, 08 Dec 2021 14:25:22: #2 alternative fragment length(s) may be 0,13,50,484,563,591 bps INFO @ Wed, 08 Dec 2021 14:25:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX6799189/SRX6799189.10_model.r WARNING @ Wed, 08 Dec 2021 14:25:22: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 14:25:22: #2 You may need to consider one of the other alternative d(s): 0,13,50,484,563,591 WARNING @ Wed, 08 Dec 2021 14:25:22: #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 14:25:22: #3 Call peaks... INFO @ Wed, 08 Dec 2021 14:25:22: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 14:25:26: 20000000 INFO @ Wed, 08 Dec 2021 14:25:32: 21000000 INFO @ Wed, 08 Dec 2021 14:25:38: 22000000 BigWig に変換しました。 /var/spool/uge/at157/job_scripts/14158052: line 297: 84404 Terminated MACS $i /var/spool/uge/at157/job_scripts/14158052: line 297: 84545 Terminated MACS $i /var/spool/uge/at157/job_scripts/14158052: line 297: 84644 Terminated MACS $i ls: cannot access SRX6799189.05.bed: No such file or directory mv: cannot stat ‘SRX6799189.05.bed’: No such file or directory mv: cannot stat ‘SRX6799189.05.bb’: No such file or directory ls: cannot access SRX6799189.10.bed: No such file or directory mv: cannot stat ‘SRX6799189.10.bed’: No such file or directory mv: cannot stat ‘SRX6799189.10.bb’: No such file or directory ls: cannot access SRX6799189.20.bed: No such file or directory mv: cannot stat ‘SRX6799189.20.bed’: No such file or directory mv: cannot stat ‘SRX6799189.20.bb’: No such file or directory