Job ID = 6368793 SRX = SRX5709759 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:24:36 prefetch.2.10.7: 1) Downloading 'SRR8928709'... 2020-06-16T00:24:36 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:26:17 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:26:17 prefetch.2.10.7: 1) 'SRR8928709' was downloaded successfully 2020-06-16T00:26:17 prefetch.2.10.7: 'SRR8928709' has 0 unresolved dependencies Read 27890199 spots for SRR8928709/SRR8928709.sra Written 27890199 spots for SRR8928709/SRR8928709.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: 00:06:43 27890199 reads; of these: 27890199 (100.00%) were unpaired; of these: 819338 (2.94%) aligned 0 times 22568627 (80.92%) aligned exactly 1 time 4502234 (16.14%) aligned >1 times 97.06% overall alignment rate Time searching: 00:06:43 Overall time: 00:06:43 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 12 files... [bam_rmdupse_core] 5424198 / 27070861 = 0.2004 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 09:40:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5709759/SRX5709759.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5709759/SRX5709759.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5709759/SRX5709759.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5709759/SRX5709759.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 09:40:57: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:40:57: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:41:03: 1000000 INFO @ Tue, 16 Jun 2020 09:41:08: 2000000 INFO @ Tue, 16 Jun 2020 09:41:14: 3000000 INFO @ Tue, 16 Jun 2020 09:41:20: 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 09:41:26: 5000000 INFO @ Tue, 16 Jun 2020 09:41:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5709759/SRX5709759.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5709759/SRX5709759.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5709759/SRX5709759.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5709759/SRX5709759.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 09:41:26: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:41:26: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:41:32: 6000000 INFO @ Tue, 16 Jun 2020 09:41:32: 1000000 INFO @ Tue, 16 Jun 2020 09:41:38: 7000000 INFO @ Tue, 16 Jun 2020 09:41:38: 2000000 INFO @ Tue, 16 Jun 2020 09:41:44: 8000000 INFO @ Tue, 16 Jun 2020 09:41:44: 3000000 INFO @ Tue, 16 Jun 2020 09:41:50: 9000000 INFO @ Tue, 16 Jun 2020 09:41:50: 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 @ Tue, 16 Jun 2020 09:41:56: 10000000 INFO @ Tue, 16 Jun 2020 09:41:56: 5000000 INFO @ Tue, 16 Jun 2020 09:41:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5709759/SRX5709759.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5709759/SRX5709759.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5709759/SRX5709759.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5709759/SRX5709759.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 09:41:57: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:41:57: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:42:02: 11000000 INFO @ Tue, 16 Jun 2020 09:42:02: 6000000 INFO @ Tue, 16 Jun 2020 09:42:03: 1000000 INFO @ Tue, 16 Jun 2020 09:42:08: 12000000 INFO @ Tue, 16 Jun 2020 09:42:08: 7000000 INFO @ Tue, 16 Jun 2020 09:42:09: 2000000 INFO @ Tue, 16 Jun 2020 09:42:14: 13000000 INFO @ Tue, 16 Jun 2020 09:42:15: 8000000 INFO @ Tue, 16 Jun 2020 09:42:15: 3000000 INFO @ Tue, 16 Jun 2020 09:42:20: 14000000 INFO @ Tue, 16 Jun 2020 09:42:21: 9000000 INFO @ Tue, 16 Jun 2020 09:42:21: 4000000 INFO @ Tue, 16 Jun 2020 09:42:26: 15000000 INFO @ Tue, 16 Jun 2020 09:42:27: 10000000 INFO @ Tue, 16 Jun 2020 09:42:27: 5000000 INFO @ Tue, 16 Jun 2020 09:42:32: 16000000 INFO @ Tue, 16 Jun 2020 09:42:33: 11000000 INFO @ Tue, 16 Jun 2020 09:42:33: 6000000 INFO @ Tue, 16 Jun 2020 09:42:37: 17000000 INFO @ Tue, 16 Jun 2020 09:42:39: 12000000 INFO @ Tue, 16 Jun 2020 09:42:39: 7000000 INFO @ Tue, 16 Jun 2020 09:42:43: 18000000 INFO @ Tue, 16 Jun 2020 09:42:45: 13000000 INFO @ Tue, 16 Jun 2020 09:42:45: 8000000 INFO @ Tue, 16 Jun 2020 09:42:49: 19000000 INFO @ Tue, 16 Jun 2020 09:42:51: 14000000 INFO @ Tue, 16 Jun 2020 09:42:51: 9000000 INFO @ Tue, 16 Jun 2020 09:42:55: 20000000 INFO @ Tue, 16 Jun 2020 09:42:57: 15000000 INFO @ Tue, 16 Jun 2020 09:42:57: 10000000 INFO @ Tue, 16 Jun 2020 09:43:01: 21000000 INFO @ Tue, 16 Jun 2020 09:43:03: 16000000 INFO @ Tue, 16 Jun 2020 09:43:03: 11000000 INFO @ Tue, 16 Jun 2020 09:43:06: #1 tag size is determined as 49 bps INFO @ Tue, 16 Jun 2020 09:43:06: #1 tag size = 49 INFO @ Tue, 16 Jun 2020 09:43:06: #1 total tags in treatment: 21646663 INFO @ Tue, 16 Jun 2020 09:43:06: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:43:06: #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 09:43:06: #1 tags after filtering in treatment: 21646663 INFO @ Tue, 16 Jun 2020 09:43:06: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:43:06: #1 finished! INFO @ Tue, 16 Jun 2020 09:43:06: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:43:06: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:43:07: #2 number of paired peaks: 222 WARNING @ Tue, 16 Jun 2020 09:43:07: Fewer paired peaks (222) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 222 pairs to build model! INFO @ Tue, 16 Jun 2020 09:43:07: start model_add_line... INFO @ Tue, 16 Jun 2020 09:43:08: start X-correlation... INFO @ Tue, 16 Jun 2020 09:43:08: end of X-cor INFO @ Tue, 16 Jun 2020 09:43:08: #2 finished! INFO @ Tue, 16 Jun 2020 09:43:08: #2 predicted fragment length is 0 bps INFO @ Tue, 16 Jun 2020 09:43:08: #2 alternative fragment length(s) may be 0,15,20,23,42 bps INFO @ Tue, 16 Jun 2020 09:43:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5709759/SRX5709759.05_model.r WARNING @ Tue, 16 Jun 2020 09:43:08: #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 09:43:08: #2 You may need to consider one of the other alternative d(s): 0,15,20,23,42 WARNING @ Tue, 16 Jun 2020 09:43:08: #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 09:43:08: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:43:08: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:43:09: 17000000 INFO @ Tue, 16 Jun 2020 09:43:09: 12000000 INFO @ Tue, 16 Jun 2020 09:43:15: 18000000 INFO @ Tue, 16 Jun 2020 09:43:15: 13000000 INFO @ Tue, 16 Jun 2020 09:43:20: 19000000 INFO @ Tue, 16 Jun 2020 09:43:21: 14000000 INFO @ Tue, 16 Jun 2020 09:43:26: 20000000 INFO @ Tue, 16 Jun 2020 09:43:27: 15000000 INFO @ Tue, 16 Jun 2020 09:43:32: 21000000 INFO @ Tue, 16 Jun 2020 09:43:32: 16000000 INFO @ Tue, 16 Jun 2020 09:43:36: #1 tag size is determined as 49 bps INFO @ Tue, 16 Jun 2020 09:43:36: #1 tag size = 49 INFO @ Tue, 16 Jun 2020 09:43:36: #1 total tags in treatment: 21646663 INFO @ Tue, 16 Jun 2020 09:43:36: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:43:36: #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 09:43:36: #1 tags after filtering in treatment: 21646663 INFO @ Tue, 16 Jun 2020 09:43:36: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:43:36: #1 finished! INFO @ Tue, 16 Jun 2020 09:43:36: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:43:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:43:37: #2 number of paired peaks: 222 WARNING @ Tue, 16 Jun 2020 09:43:37: Fewer paired peaks (222) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 222 pairs to build model! INFO @ Tue, 16 Jun 2020 09:43:37: start model_add_line... INFO @ Tue, 16 Jun 2020 09:43:38: start X-correlation... INFO @ Tue, 16 Jun 2020 09:43:38: end of X-cor INFO @ Tue, 16 Jun 2020 09:43:38: #2 finished! INFO @ Tue, 16 Jun 2020 09:43:38: #2 predicted fragment length is 0 bps INFO @ Tue, 16 Jun 2020 09:43:38: #2 alternative fragment length(s) may be 0,15,20,23,42 bps INFO @ Tue, 16 Jun 2020 09:43:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5709759/SRX5709759.10_model.r WARNING @ Tue, 16 Jun 2020 09:43:38: #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 09:43:38: #2 You may need to consider one of the other alternative d(s): 0,15,20,23,42 WARNING @ Tue, 16 Jun 2020 09:43:38: #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 09:43:38: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:43:38: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:43:38: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:43:44: 18000000 INFO @ Tue, 16 Jun 2020 09:43:49: 19000000 INFO @ Tue, 16 Jun 2020 09:43:55: 20000000 INFO @ Tue, 16 Jun 2020 09:44:00: 21000000 INFO @ Tue, 16 Jun 2020 09:44:04: #1 tag size is determined as 49 bps INFO @ Tue, 16 Jun 2020 09:44:04: #1 tag size = 49 INFO @ Tue, 16 Jun 2020 09:44:04: #1 total tags in treatment: 21646663 INFO @ Tue, 16 Jun 2020 09:44:04: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:44:04: #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 09:44:05: #1 tags after filtering in treatment: 21646663 INFO @ Tue, 16 Jun 2020 09:44:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:44:05: #1 finished! INFO @ Tue, 16 Jun 2020 09:44:05: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:44:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:44:06: #2 number of paired peaks: 222 WARNING @ Tue, 16 Jun 2020 09:44:06: Fewer paired peaks (222) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 222 pairs to build model! INFO @ Tue, 16 Jun 2020 09:44:06: start model_add_line... INFO @ Tue, 16 Jun 2020 09:44:06: start X-correlation... INFO @ Tue, 16 Jun 2020 09:44:06: end of X-cor INFO @ Tue, 16 Jun 2020 09:44:06: #2 finished! INFO @ Tue, 16 Jun 2020 09:44:06: #2 predicted fragment length is 0 bps INFO @ Tue, 16 Jun 2020 09:44:06: #2 alternative fragment length(s) may be 0,15,20,23,42 bps INFO @ Tue, 16 Jun 2020 09:44:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5709759/SRX5709759.20_model.r WARNING @ Tue, 16 Jun 2020 09:44:06: #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 09:44:06: #2 You may need to consider one of the other alternative d(s): 0,15,20,23,42 WARNING @ Tue, 16 Jun 2020 09:44:06: #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 09:44:06: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:44:06: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 /var/spool/uge/at154/job_scripts/6368793: line 271: 92571 Terminated MACS $i /var/spool/uge/at154/job_scripts/6368793: line 271: 93165 Terminated MACS $i /var/spool/uge/at154/job_scripts/6368793: line 271: 99839 Terminated MACS $i ls: cannot access SRX5709759.05.bed: No such file or directory mv: cannot stat ‘SRX5709759.05.bed’: No such file or directory mv: cannot stat ‘SRX5709759.05.bb’: No such file or directory ls: cannot access SRX5709759.10.bed: No such file or directory mv: cannot stat ‘SRX5709759.10.bed’: No such file or directory mv: cannot stat ‘SRX5709759.10.bb’: No such file or directory ls: cannot access SRX5709759.20.bed: No such file or directory mv: cannot stat ‘SRX5709759.20.bed’: No such file or directory mv: cannot stat ‘SRX5709759.20.bb’: No such file or directory