Job ID = 10165939 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:10:08 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: 00:10:09 Overall time: 00:10:09 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 08 Oct 2020 20:30:30: # 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 @ Thu, 08 Oct 2020 20:30:30: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:30:30: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:30:37: 1000000 INFO @ Thu, 08 Oct 2020 20:30:44: 2000000 INFO @ Thu, 08 Oct 2020 20:30:50: 3000000 INFO @ Thu, 08 Oct 2020 20:30:57: 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 @ Thu, 08 Oct 2020 20:31:00: # 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 @ Thu, 08 Oct 2020 20:31:00: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:31:00: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:31:04: 5000000 INFO @ Thu, 08 Oct 2020 20:31:07: 1000000 INFO @ Thu, 08 Oct 2020 20:31:11: 6000000 INFO @ Thu, 08 Oct 2020 20:31:14: 2000000 INFO @ Thu, 08 Oct 2020 20:31:18: 7000000 INFO @ Thu, 08 Oct 2020 20:31:20: 3000000 INFO @ Thu, 08 Oct 2020 20:31:25: 8000000 INFO @ Thu, 08 Oct 2020 20:31:27: 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 @ Thu, 08 Oct 2020 20:31:30: # 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 @ Thu, 08 Oct 2020 20:31:30: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:31:30: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:31:33: 9000000 INFO @ Thu, 08 Oct 2020 20:31:34: 5000000 INFO @ Thu, 08 Oct 2020 20:31:37: 1000000 INFO @ Thu, 08 Oct 2020 20:31:40: 10000000 INFO @ Thu, 08 Oct 2020 20:31:41: 6000000 INFO @ Thu, 08 Oct 2020 20:31:44: 2000000 INFO @ Thu, 08 Oct 2020 20:31:47: 11000000 INFO @ Thu, 08 Oct 2020 20:31:48: 7000000 INFO @ Thu, 08 Oct 2020 20:31:52: 3000000 INFO @ Thu, 08 Oct 2020 20:31:55: 12000000 INFO @ Thu, 08 Oct 2020 20:31:55: 8000000 INFO @ Thu, 08 Oct 2020 20:31:59: 4000000 INFO @ Thu, 08 Oct 2020 20:32:02: 13000000 INFO @ Thu, 08 Oct 2020 20:32:02: 9000000 INFO @ Thu, 08 Oct 2020 20:32:06: 5000000 INFO @ Thu, 08 Oct 2020 20:32:09: 14000000 INFO @ Thu, 08 Oct 2020 20:32:09: 10000000 INFO @ Thu, 08 Oct 2020 20:32:13: 6000000 INFO @ Thu, 08 Oct 2020 20:32:16: 11000000 INFO @ Thu, 08 Oct 2020 20:32:16: 15000000 INFO @ Thu, 08 Oct 2020 20:32:20: 7000000 INFO @ Thu, 08 Oct 2020 20:32:23: 12000000 INFO @ Thu, 08 Oct 2020 20:32:24: 16000000 INFO @ Thu, 08 Oct 2020 20:32:27: 8000000 INFO @ Thu, 08 Oct 2020 20:32:30: 13000000 INFO @ Thu, 08 Oct 2020 20:32:31: 17000000 INFO @ Thu, 08 Oct 2020 20:32:34: 9000000 INFO @ Thu, 08 Oct 2020 20:32:37: 14000000 INFO @ Thu, 08 Oct 2020 20:32:38: 18000000 INFO @ Thu, 08 Oct 2020 20:32:41: 10000000 INFO @ Thu, 08 Oct 2020 20:32:44: 15000000 INFO @ Thu, 08 Oct 2020 20:32:45: 19000000 INFO @ Thu, 08 Oct 2020 20:32:48: 11000000 INFO @ Thu, 08 Oct 2020 20:32:51: 16000000 INFO @ Thu, 08 Oct 2020 20:32:53: 20000000 INFO @ Thu, 08 Oct 2020 20:32:54: 12000000 INFO @ Thu, 08 Oct 2020 20:32:58: 17000000 INFO @ Thu, 08 Oct 2020 20:33:00: 21000000 INFO @ Thu, 08 Oct 2020 20:33:01: 13000000 INFO @ Thu, 08 Oct 2020 20:33:05: 18000000 INFO @ Thu, 08 Oct 2020 20:33:07: 22000000 INFO @ Thu, 08 Oct 2020 20:33:08: 14000000 INFO @ Thu, 08 Oct 2020 20:33:12: 19000000 INFO @ Thu, 08 Oct 2020 20:33:14: 23000000 INFO @ Thu, 08 Oct 2020 20:33:15: 15000000 INFO @ Thu, 08 Oct 2020 20:33:19: 20000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 08 Oct 2020 20:33:22: 24000000 INFO @ Thu, 08 Oct 2020 20:33:22: 16000000 INFO @ Thu, 08 Oct 2020 20:33:26: 21000000 INFO @ Thu, 08 Oct 2020 20:33:29: 25000000 INFO @ Thu, 08 Oct 2020 20:33:29: 17000000 INFO @ Thu, 08 Oct 2020 20:33:33: 22000000 INFO @ Thu, 08 Oct 2020 20:33:36: 26000000 INFO @ Thu, 08 Oct 2020 20:33:36: 18000000 INFO @ Thu, 08 Oct 2020 20:33:38: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 20:33:38: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 20:33:38: #1 total tags in treatment: 26240834 INFO @ Thu, 08 Oct 2020 20:33:38: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:33:38: #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 20:33:38: #1 tags after filtering in treatment: 26240834 INFO @ Thu, 08 Oct 2020 20:33:38: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:33:38: #1 finished! INFO @ Thu, 08 Oct 2020 20:33:38: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:33:38: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:33:40: 23000000 INFO @ Thu, 08 Oct 2020 20:33:40: #2 number of paired peaks: 300 WARNING @ Thu, 08 Oct 2020 20:33:40: 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 @ Thu, 08 Oct 2020 20:33:40: start model_add_line... INFO @ Thu, 08 Oct 2020 20:33:40: start X-correlation... INFO @ Thu, 08 Oct 2020 20:33:40: end of X-cor INFO @ Thu, 08 Oct 2020 20:33:40: #2 finished! INFO @ Thu, 08 Oct 2020 20:33:40: #2 predicted fragment length is 0 bps INFO @ Thu, 08 Oct 2020 20:33:40: #2 alternative fragment length(s) may be 0,13,50,484,563,591 bps INFO @ Thu, 08 Oct 2020 20:33:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX6799189/SRX6799189.05_model.r WARNING @ Thu, 08 Oct 2020 20:33:40: #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 20:33:40: #2 You may need to consider one of the other alternative d(s): 0,13,50,484,563,591 WARNING @ Thu, 08 Oct 2020 20:33:40: #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 20:33:40: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:33:40: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:33:43: 19000000 INFO @ Thu, 08 Oct 2020 20:33:46: 24000000 INFO @ Thu, 08 Oct 2020 20:33:49: 20000000 INFO @ Thu, 08 Oct 2020 20:33:53: 25000000 INFO @ Thu, 08 Oct 2020 20:33:56: 21000000 INFO @ Thu, 08 Oct 2020 20:33:59: 26000000 INFO @ Thu, 08 Oct 2020 20:34:01: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 20:34:01: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 20:34:01: #1 total tags in treatment: 26240834 INFO @ Thu, 08 Oct 2020 20:34:01: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:34:01: #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 20:34:01: #1 tags after filtering in treatment: 26240834 INFO @ Thu, 08 Oct 2020 20:34:01: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:34:01: #1 finished! INFO @ Thu, 08 Oct 2020 20:34:01: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:34:01: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:34:02: 22000000 INFO @ Thu, 08 Oct 2020 20:34:03: #2 number of paired peaks: 300 WARNING @ Thu, 08 Oct 2020 20:34:03: 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 @ Thu, 08 Oct 2020 20:34:03: start model_add_line... INFO @ Thu, 08 Oct 2020 20:34:03: start X-correlation... INFO @ Thu, 08 Oct 2020 20:34:03: end of X-cor INFO @ Thu, 08 Oct 2020 20:34:03: #2 finished! INFO @ Thu, 08 Oct 2020 20:34:03: #2 predicted fragment length is 0 bps INFO @ Thu, 08 Oct 2020 20:34:03: #2 alternative fragment length(s) may be 0,13,50,484,563,591 bps INFO @ Thu, 08 Oct 2020 20:34:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX6799189/SRX6799189.10_model.r WARNING @ Thu, 08 Oct 2020 20:34:03: #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 20:34:03: #2 You may need to consider one of the other alternative d(s): 0,13,50,484,563,591 WARNING @ Thu, 08 Oct 2020 20:34:03: #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 20:34:03: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:34:03: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:34:08: 23000000 BigWig に変換しました。 /var/spool/uge/at160/job_scripts/10165939: line 297: 84091 Terminated MACS $i /var/spool/uge/at160/job_scripts/10165939: line 297: 5644 Terminated MACS $i /var/spool/uge/at160/job_scripts/10165939: line 297: 60471 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