Job ID = 6368658 SRX = SRX529218 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:22:48 prefetch.2.10.7: 1) Downloading 'SRR1265822'... 2020-06-16T00:22:48 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:26:10 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:26:10 prefetch.2.10.7: 1) 'SRR1265822' was downloaded successfully Read 29706298 spots for SRR1265822/SRR1265822.sra Written 29706298 spots for SRR1265822/SRR1265822.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: 00:00:00 Multiseed full-index search: 00:04:41 29706298 reads; of these: 29706298 (100.00%) were unpaired; of these: 7082791 (23.84%) aligned 0 times 18665027 (62.83%) aligned exactly 1 time 3958480 (13.33%) aligned >1 times 76.16% overall alignment rate Time searching: 00:04:41 Overall time: 00:04:41 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 8 files... [bam_rmdupse_core] 2636270 / 22623507 = 0.1165 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 09:36:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX529218/SRX529218.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX529218/SRX529218.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX529218/SRX529218.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX529218/SRX529218.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 09:36:55: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:36:55: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:37:00: 1000000 INFO @ Tue, 16 Jun 2020 09:37:05: 2000000 INFO @ Tue, 16 Jun 2020 09:37:10: 3000000 INFO @ Tue, 16 Jun 2020 09:37:15: 4000000 INFO @ Tue, 16 Jun 2020 09:37:20: 5000000 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 09:37:25: 6000000 INFO @ Tue, 16 Jun 2020 09:37:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX529218/SRX529218.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX529218/SRX529218.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX529218/SRX529218.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX529218/SRX529218.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 09:37:25: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:37:25: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:37:30: 7000000 INFO @ Tue, 16 Jun 2020 09:37:31: 1000000 INFO @ Tue, 16 Jun 2020 09:37:36: 8000000 INFO @ Tue, 16 Jun 2020 09:37:36: 2000000 INFO @ Tue, 16 Jun 2020 09:37:41: 9000000 INFO @ Tue, 16 Jun 2020 09:37:41: 3000000 INFO @ Tue, 16 Jun 2020 09:37:46: 10000000 INFO @ Tue, 16 Jun 2020 09:37:47: 4000000 INFO @ Tue, 16 Jun 2020 09:37:52: 11000000 INFO @ Tue, 16 Jun 2020 09:37:52: 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 @ Tue, 16 Jun 2020 09:37:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX529218/SRX529218.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX529218/SRX529218.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX529218/SRX529218.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX529218/SRX529218.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 09:37:55: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:37:55: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:37:57: 12000000 INFO @ Tue, 16 Jun 2020 09:37:58: 6000000 INFO @ Tue, 16 Jun 2020 09:38:01: 1000000 INFO @ Tue, 16 Jun 2020 09:38:03: 13000000 INFO @ Tue, 16 Jun 2020 09:38:03: 7000000 INFO @ Tue, 16 Jun 2020 09:38:06: 2000000 INFO @ Tue, 16 Jun 2020 09:38:08: 14000000 INFO @ Tue, 16 Jun 2020 09:38:08: 8000000 INFO @ Tue, 16 Jun 2020 09:38:12: 3000000 INFO @ Tue, 16 Jun 2020 09:38:13: 15000000 INFO @ Tue, 16 Jun 2020 09:38:14: 9000000 INFO @ Tue, 16 Jun 2020 09:38:17: 4000000 INFO @ Tue, 16 Jun 2020 09:38:19: 16000000 INFO @ Tue, 16 Jun 2020 09:38:19: 10000000 INFO @ Tue, 16 Jun 2020 09:38:23: 5000000 INFO @ Tue, 16 Jun 2020 09:38:24: 17000000 INFO @ Tue, 16 Jun 2020 09:38:25: 11000000 INFO @ Tue, 16 Jun 2020 09:38:28: 6000000 INFO @ Tue, 16 Jun 2020 09:38:30: 18000000 INFO @ Tue, 16 Jun 2020 09:38:30: 12000000 INFO @ Tue, 16 Jun 2020 09:38:33: 7000000 INFO @ Tue, 16 Jun 2020 09:38:35: 19000000 INFO @ Tue, 16 Jun 2020 09:38:36: 13000000 INFO @ Tue, 16 Jun 2020 09:38:39: 8000000 INFO @ Tue, 16 Jun 2020 09:38:41: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 09:38:41: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 09:38:41: #1 total tags in treatment: 19987237 INFO @ Tue, 16 Jun 2020 09:38:41: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:38:41: #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 09:38:41: #1 tags after filtering in treatment: 19987237 INFO @ Tue, 16 Jun 2020 09:38:41: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:38:41: #1 finished! INFO @ Tue, 16 Jun 2020 09:38:41: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:38:41: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:38:41: 14000000 INFO @ Tue, 16 Jun 2020 09:38:42: #2 number of paired peaks: 174 WARNING @ Tue, 16 Jun 2020 09:38:42: Fewer paired peaks (174) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 174 pairs to build model! INFO @ Tue, 16 Jun 2020 09:38:42: start model_add_line... INFO @ Tue, 16 Jun 2020 09:38:42: start X-correlation... INFO @ Tue, 16 Jun 2020 09:38:42: end of X-cor INFO @ Tue, 16 Jun 2020 09:38:42: #2 finished! INFO @ Tue, 16 Jun 2020 09:38:42: #2 predicted fragment length is 0 bps INFO @ Tue, 16 Jun 2020 09:38:42: #2 alternative fragment length(s) may be 0,32,178,183,417,432,462,566 bps INFO @ Tue, 16 Jun 2020 09:38:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX529218/SRX529218.05_model.r WARNING @ Tue, 16 Jun 2020 09:38:42: #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 09:38:42: #2 You may need to consider one of the other alternative d(s): 0,32,178,183,417,432,462,566 WARNING @ Tue, 16 Jun 2020 09:38:42: #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 09:38:42: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:38:42: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:38:44: 9000000 INFO @ Tue, 16 Jun 2020 09:38:46: 15000000 INFO @ Tue, 16 Jun 2020 09:38:50: 10000000 INFO @ Tue, 16 Jun 2020 09:38:52: 16000000 INFO @ Tue, 16 Jun 2020 09:38:55: 11000000 INFO @ Tue, 16 Jun 2020 09:38:57: 17000000 INFO @ Tue, 16 Jun 2020 09:39:00: 12000000 INFO @ Tue, 16 Jun 2020 09:39:03: 18000000 INFO @ Tue, 16 Jun 2020 09:39:06: 13000000 INFO @ Tue, 16 Jun 2020 09:39:08: 19000000 INFO @ Tue, 16 Jun 2020 09:39:11: 14000000 INFO @ Tue, 16 Jun 2020 09:39:13: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 09:39:13: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 09:39:13: #1 total tags in treatment: 19987237 INFO @ Tue, 16 Jun 2020 09:39:13: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:39:13: #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 09:39:14: #1 tags after filtering in treatment: 19987237 INFO @ Tue, 16 Jun 2020 09:39:14: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:39:14: #1 finished! INFO @ Tue, 16 Jun 2020 09:39:14: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:39:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:39:15: #2 number of paired peaks: 174 WARNING @ Tue, 16 Jun 2020 09:39:15: Fewer paired peaks (174) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 174 pairs to build model! INFO @ Tue, 16 Jun 2020 09:39:15: start model_add_line... INFO @ Tue, 16 Jun 2020 09:39:15: start X-correlation... INFO @ Tue, 16 Jun 2020 09:39:15: end of X-cor INFO @ Tue, 16 Jun 2020 09:39:15: #2 finished! INFO @ Tue, 16 Jun 2020 09:39:15: #2 predicted fragment length is 0 bps INFO @ Tue, 16 Jun 2020 09:39:15: #2 alternative fragment length(s) may be 0,32,178,183,417,432,462,566 bps INFO @ Tue, 16 Jun 2020 09:39:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX529218/SRX529218.10_model.r WARNING @ Tue, 16 Jun 2020 09:39:15: #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 09:39:15: #2 You may need to consider one of the other alternative d(s): 0,32,178,183,417,432,462,566 WARNING @ Tue, 16 Jun 2020 09:39:15: #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 09:39:15: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:39:15: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:39:16: 15000000 INFO @ Tue, 16 Jun 2020 09:39:21: 16000000 INFO @ Tue, 16 Jun 2020 09:39:26: 17000000 INFO @ Tue, 16 Jun 2020 09:39:31: 18000000 INFO @ Tue, 16 Jun 2020 09:39:36: 19000000 INFO @ Tue, 16 Jun 2020 09:39:41: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 09:39:41: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 09:39:41: #1 total tags in treatment: 19987237 INFO @ Tue, 16 Jun 2020 09:39:41: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:39:41: #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 09:39:42: #1 tags after filtering in treatment: 19987237 INFO @ Tue, 16 Jun 2020 09:39:42: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:39:42: #1 finished! INFO @ Tue, 16 Jun 2020 09:39:42: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:39:42: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:39:43: #2 number of paired peaks: 174 WARNING @ Tue, 16 Jun 2020 09:39:43: Fewer paired peaks (174) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 174 pairs to build model! INFO @ Tue, 16 Jun 2020 09:39:43: start model_add_line... INFO @ Tue, 16 Jun 2020 09:39:43: start X-correlation... INFO @ Tue, 16 Jun 2020 09:39:43: end of X-cor INFO @ Tue, 16 Jun 2020 09:39:43: #2 finished! INFO @ Tue, 16 Jun 2020 09:39:43: #2 predicted fragment length is 0 bps INFO @ Tue, 16 Jun 2020 09:39:43: #2 alternative fragment length(s) may be 0,32,178,183,417,432,462,566 bps INFO @ Tue, 16 Jun 2020 09:39:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX529218/SRX529218.20_model.r WARNING @ Tue, 16 Jun 2020 09:39:43: #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 09:39:43: #2 You may need to consider one of the other alternative d(s): 0,32,178,183,417,432,462,566 WARNING @ Tue, 16 Jun 2020 09:39:43: #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 09:39:43: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:39:43: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 /var/spool/uge/at160/job_scripts/6368658: line 271: 2221 Terminated MACS $i /var/spool/uge/at160/job_scripts/6368658: line 271: 32446 Terminated MACS $i /var/spool/uge/at160/job_scripts/6368658: line 271: 71203 Terminated MACS $i ls: cannot access SRX529218.05.bed: No such file or directory mv: cannot stat ‘SRX529218.05.bed’: No such file or directory mv: cannot stat ‘SRX529218.05.bb’: No such file or directory ls: cannot access SRX529218.10.bed: No such file or directory mv: cannot stat ‘SRX529218.10.bed’: No such file or directory mv: cannot stat ‘SRX529218.10.bb’: No such file or directory ls: cannot access SRX529218.20.bed: No such file or directory mv: cannot stat ‘SRX529218.20.bed’: No such file or directory mv: cannot stat ‘SRX529218.20.bb’: No such file or directory