Job ID = 6368060 SRX = SRX466523 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:46:59 prefetch.2.10.7: 1) Downloading 'SRR1163589'... 2020-06-15T23:46:59 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:49:40 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:49:40 prefetch.2.10.7: 1) 'SRR1163589' was downloaded successfully Read 30788149 spots for SRR1163589/SRR1163589.sra Written 30788149 spots for SRR1163589/SRR1163589.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: 00:05:12 30788149 reads; of these: 30788149 (100.00%) were unpaired; of these: 169795 (0.55%) aligned 0 times 25275459 (82.09%) aligned exactly 1 time 5342895 (17.35%) aligned >1 times 99.45% overall alignment rate Time searching: 00:05:12 Overall time: 00:05:12 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] 4711970 / 30618354 = 0.1539 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 09:02:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466523/SRX466523.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466523/SRX466523.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466523/SRX466523.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466523/SRX466523.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 09:02:30: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:02:30: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:02:36: 1000000 INFO @ Tue, 16 Jun 2020 09:02:42: 2000000 INFO @ Tue, 16 Jun 2020 09:02:48: 3000000 INFO @ Tue, 16 Jun 2020 09:02:54: 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 @ Tue, 16 Jun 2020 09:02:59: 5000000 INFO @ Tue, 16 Jun 2020 09:03:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466523/SRX466523.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466523/SRX466523.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466523/SRX466523.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466523/SRX466523.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 09:03:00: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:03:00: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:03:05: 6000000 INFO @ Tue, 16 Jun 2020 09:03:06: 1000000 INFO @ Tue, 16 Jun 2020 09:03:11: 2000000 INFO @ Tue, 16 Jun 2020 09:03:12: 7000000 INFO @ Tue, 16 Jun 2020 09:03:17: 3000000 INFO @ Tue, 16 Jun 2020 09:03:18: 8000000 INFO @ Tue, 16 Jun 2020 09:03:23: 4000000 INFO @ Tue, 16 Jun 2020 09:03:24: 9000000 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 09:03:28: 5000000 INFO @ Tue, 16 Jun 2020 09:03:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466523/SRX466523.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466523/SRX466523.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466523/SRX466523.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466523/SRX466523.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 09:03:30: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:03:30: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:03:30: 10000000 INFO @ Tue, 16 Jun 2020 09:03:34: 6000000 INFO @ Tue, 16 Jun 2020 09:03:36: 1000000 INFO @ Tue, 16 Jun 2020 09:03:37: 11000000 INFO @ Tue, 16 Jun 2020 09:03:40: 7000000 INFO @ Tue, 16 Jun 2020 09:03:42: 2000000 INFO @ Tue, 16 Jun 2020 09:03:43: 12000000 INFO @ Tue, 16 Jun 2020 09:03:46: 8000000 INFO @ Tue, 16 Jun 2020 09:03:47: 3000000 INFO @ Tue, 16 Jun 2020 09:03:49: 13000000 INFO @ Tue, 16 Jun 2020 09:03:52: 9000000 INFO @ Tue, 16 Jun 2020 09:03:53: 4000000 INFO @ Tue, 16 Jun 2020 09:03:56: 14000000 INFO @ Tue, 16 Jun 2020 09:03:57: 10000000 INFO @ Tue, 16 Jun 2020 09:03:59: 5000000 INFO @ Tue, 16 Jun 2020 09:04:02: 15000000 INFO @ Tue, 16 Jun 2020 09:04:03: 11000000 INFO @ Tue, 16 Jun 2020 09:04:05: 6000000 INFO @ Tue, 16 Jun 2020 09:04:09: 16000000 INFO @ Tue, 16 Jun 2020 09:04:09: 12000000 INFO @ Tue, 16 Jun 2020 09:04:11: 7000000 INFO @ Tue, 16 Jun 2020 09:04:15: 13000000 INFO @ Tue, 16 Jun 2020 09:04:15: 17000000 INFO @ Tue, 16 Jun 2020 09:04:16: 8000000 INFO @ Tue, 16 Jun 2020 09:04:20: 14000000 INFO @ Tue, 16 Jun 2020 09:04:21: 18000000 INFO @ Tue, 16 Jun 2020 09:04:22: 9000000 INFO @ Tue, 16 Jun 2020 09:04:26: 15000000 INFO @ Tue, 16 Jun 2020 09:04:27: 19000000 INFO @ Tue, 16 Jun 2020 09:04:28: 10000000 INFO @ Tue, 16 Jun 2020 09:04:32: 16000000 INFO @ Tue, 16 Jun 2020 09:04:33: 20000000 INFO @ Tue, 16 Jun 2020 09:04:34: 11000000 INFO @ Tue, 16 Jun 2020 09:04:38: 17000000 INFO @ Tue, 16 Jun 2020 09:04:39: 21000000 INFO @ Tue, 16 Jun 2020 09:04:39: 12000000 INFO @ Tue, 16 Jun 2020 09:04:44: 18000000 INFO @ Tue, 16 Jun 2020 09:04:45: 13000000 INFO @ Tue, 16 Jun 2020 09:04:46: 22000000 INFO @ Tue, 16 Jun 2020 09:04:50: 19000000 INFO @ Tue, 16 Jun 2020 09:04:51: 14000000 INFO @ Tue, 16 Jun 2020 09:04:52: 23000000 INFO @ Tue, 16 Jun 2020 09:04:55: 20000000 INFO @ Tue, 16 Jun 2020 09:04:57: 15000000 INFO @ Tue, 16 Jun 2020 09:04:58: 24000000 INFO @ Tue, 16 Jun 2020 09:05:01: 21000000 INFO @ Tue, 16 Jun 2020 09:05:03: 16000000 INFO @ Tue, 16 Jun 2020 09:05:04: 25000000 INFO @ Tue, 16 Jun 2020 09:05:07: 22000000 INFO @ Tue, 16 Jun 2020 09:05:08: 17000000 INFO @ Tue, 16 Jun 2020 09:05:10: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 09:05:10: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 09:05:10: #1 total tags in treatment: 25906384 INFO @ Tue, 16 Jun 2020 09:05:10: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:05:10: #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 09:05:10: #1 tags after filtering in treatment: 25906384 INFO @ Tue, 16 Jun 2020 09:05:10: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:05:10: #1 finished! INFO @ Tue, 16 Jun 2020 09:05:10: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:05:10: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:05:12: #2 number of paired peaks: 151 WARNING @ Tue, 16 Jun 2020 09:05:12: Fewer paired peaks (151) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 151 pairs to build model! INFO @ Tue, 16 Jun 2020 09:05:12: start model_add_line... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:05:12: start X-correlation... INFO @ Tue, 16 Jun 2020 09:05:12: end of X-cor INFO @ Tue, 16 Jun 2020 09:05:12: #2 finished! INFO @ Tue, 16 Jun 2020 09:05:12: #2 predicted fragment length is 0 bps INFO @ Tue, 16 Jun 2020 09:05:12: #2 alternative fragment length(s) may be 0,12,30,412,472,497 bps INFO @ Tue, 16 Jun 2020 09:05:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466523/SRX466523.05_model.r WARNING @ Tue, 16 Jun 2020 09:05:12: #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 09:05:12: #2 You may need to consider one of the other alternative d(s): 0,12,30,412,472,497 WARNING @ Tue, 16 Jun 2020 09:05:12: #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 09:05:12: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:05:12: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:05:12: 23000000 INFO @ Tue, 16 Jun 2020 09:05:14: 18000000 INFO @ Tue, 16 Jun 2020 09:05:18: 24000000 INFO @ Tue, 16 Jun 2020 09:05:19: 19000000 INFO @ Tue, 16 Jun 2020 09:05:23: 25000000 INFO @ Tue, 16 Jun 2020 09:05:25: 20000000 INFO @ Tue, 16 Jun 2020 09:05:28: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 09:05:28: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 09:05:28: #1 total tags in treatment: 25906384 INFO @ Tue, 16 Jun 2020 09:05:28: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:05:28: #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 09:05:29: #1 tags after filtering in treatment: 25906384 INFO @ Tue, 16 Jun 2020 09:05:29: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:05:29: #1 finished! INFO @ Tue, 16 Jun 2020 09:05:29: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:05:29: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:05:30: 21000000 INFO @ Tue, 16 Jun 2020 09:05:30: #2 number of paired peaks: 151 WARNING @ Tue, 16 Jun 2020 09:05:30: Fewer paired peaks (151) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 151 pairs to build model! INFO @ Tue, 16 Jun 2020 09:05:30: start model_add_line... INFO @ Tue, 16 Jun 2020 09:05:30: start X-correlation... INFO @ Tue, 16 Jun 2020 09:05:30: end of X-cor INFO @ Tue, 16 Jun 2020 09:05:30: #2 finished! INFO @ Tue, 16 Jun 2020 09:05:30: #2 predicted fragment length is 0 bps INFO @ Tue, 16 Jun 2020 09:05:30: #2 alternative fragment length(s) may be 0,12,30,412,472,497 bps INFO @ Tue, 16 Jun 2020 09:05:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466523/SRX466523.10_model.r WARNING @ Tue, 16 Jun 2020 09:05:30: #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 09:05:30: #2 You may need to consider one of the other alternative d(s): 0,12,30,412,472,497 WARNING @ Tue, 16 Jun 2020 09:05:30: #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 09:05:30: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:05:30: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:05:35: 22000000 INFO @ Tue, 16 Jun 2020 09:05:40: 23000000 INFO @ Tue, 16 Jun 2020 09:05:45: 24000000 INFO @ Tue, 16 Jun 2020 09:05:50: 25000000 INFO @ Tue, 16 Jun 2020 09:05:55: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 09:05:55: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 09:05:55: #1 total tags in treatment: 25906384 INFO @ Tue, 16 Jun 2020 09:05:55: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:05:55: #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 09:05:55: #1 tags after filtering in treatment: 25906384 INFO @ Tue, 16 Jun 2020 09:05:55: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:05:55: #1 finished! INFO @ Tue, 16 Jun 2020 09:05:55: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:05:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:05:57: #2 number of paired peaks: 151 WARNING @ Tue, 16 Jun 2020 09:05:57: Fewer paired peaks (151) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 151 pairs to build model! INFO @ Tue, 16 Jun 2020 09:05:57: start model_add_line... INFO @ Tue, 16 Jun 2020 09:05:57: start X-correlation... INFO @ Tue, 16 Jun 2020 09:05:57: end of X-cor INFO @ Tue, 16 Jun 2020 09:05:57: #2 finished! INFO @ Tue, 16 Jun 2020 09:05:57: #2 predicted fragment length is 0 bps INFO @ Tue, 16 Jun 2020 09:05:57: #2 alternative fragment length(s) may be 0,12,30,412,472,497 bps INFO @ Tue, 16 Jun 2020 09:05:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466523/SRX466523.20_model.r WARNING @ Tue, 16 Jun 2020 09:05:57: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:05:57: #2 You may need to consider one of the other alternative d(s): 0,12,30,412,472,497 WARNING @ Tue, 16 Jun 2020 09:05:57: #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 09:05:57: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:05:57: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 /var/spool/uge/at151/job_scripts/6368060: line 271: 24193 Terminated MACS $i /var/spool/uge/at151/job_scripts/6368060: line 271: 24925 Terminated MACS $i /var/spool/uge/at151/job_scripts/6368060: line 271: 25738 Terminated MACS $i ls: cannot access SRX466523.05.bed: No such file or directory mv: cannot stat ‘SRX466523.05.bed’: No such file or directory mv: cannot stat ‘SRX466523.05.bb’: No such file or directory ls: cannot access SRX466523.10.bed: No such file or directory mv: cannot stat ‘SRX466523.10.bed’: No such file or directory mv: cannot stat ‘SRX466523.10.bb’: No such file or directory ls: cannot access SRX466523.20.bed: No such file or directory mv: cannot stat ‘SRX466523.20.bed’: No such file or directory mv: cannot stat ‘SRX466523.20.bb’: No such file or directory