Job ID = 6497542 SRX = SRX514730 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T22:35:35 prefetch.2.10.7: 1) Downloading 'SRR1231451'... 2020-06-25T22:35:35 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:42:32 prefetch.2.10.7: HTTPS download succeed 2020-06-25T22:42:32 prefetch.2.10.7: 1) 'SRR1231451' was downloaded successfully Read 32932978 spots for SRR1231451/SRR1231451.sra Written 32932978 spots for SRR1231451/SRR1231451.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:06:33 32932978 reads; of these: 32932978 (100.00%) were unpaired; of these: 423035 (1.28%) aligned 0 times 26713006 (81.11%) aligned exactly 1 time 5796937 (17.60%) aligned >1 times 98.72% overall alignment rate Time searching: 00:06:34 Overall time: 00:06:34 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] 6593897 / 32509943 = 0.2028 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 @ Fri, 26 Jun 2020 07:57:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX514730/SRX514730.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX514730/SRX514730.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX514730/SRX514730.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX514730/SRX514730.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 @ Fri, 26 Jun 2020 07:57:36: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:57:36: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:57:42: 1000000 INFO @ Fri, 26 Jun 2020 07:57:49: 2000000 INFO @ Fri, 26 Jun 2020 07:57:55: 3000000 INFO @ Fri, 26 Jun 2020 07:58:02: 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 @ Fri, 26 Jun 2020 07:58:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX514730/SRX514730.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX514730/SRX514730.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX514730/SRX514730.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX514730/SRX514730.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 @ Fri, 26 Jun 2020 07:58:05: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:58:05: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:58:08: 5000000 INFO @ Fri, 26 Jun 2020 07:58:12: 1000000 INFO @ Fri, 26 Jun 2020 07:58:15: 6000000 INFO @ Fri, 26 Jun 2020 07:58:19: 2000000 INFO @ Fri, 26 Jun 2020 07:58:22: 7000000 INFO @ Fri, 26 Jun 2020 07:58:26: 3000000 INFO @ Fri, 26 Jun 2020 07:58:29: 8000000 INFO @ Fri, 26 Jun 2020 07:58:33: 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 @ Fri, 26 Jun 2020 07:58:36: 9000000 INFO @ Fri, 26 Jun 2020 07:58:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX514730/SRX514730.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX514730/SRX514730.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX514730/SRX514730.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX514730/SRX514730.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 @ Fri, 26 Jun 2020 07:58:36: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:58:36: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:58:39: 5000000 INFO @ Fri, 26 Jun 2020 07:58:43: 10000000 INFO @ Fri, 26 Jun 2020 07:58:43: 1000000 INFO @ Fri, 26 Jun 2020 07:58:46: 6000000 INFO @ Fri, 26 Jun 2020 07:58:50: 11000000 INFO @ Fri, 26 Jun 2020 07:58:50: 2000000 INFO @ Fri, 26 Jun 2020 07:58:53: 7000000 INFO @ Fri, 26 Jun 2020 07:58:57: 12000000 INFO @ Fri, 26 Jun 2020 07:58:57: 3000000 INFO @ Fri, 26 Jun 2020 07:59:00: 8000000 INFO @ Fri, 26 Jun 2020 07:59:04: 13000000 INFO @ Fri, 26 Jun 2020 07:59:04: 4000000 INFO @ Fri, 26 Jun 2020 07:59:07: 9000000 INFO @ Fri, 26 Jun 2020 07:59:11: 14000000 INFO @ Fri, 26 Jun 2020 07:59:11: 5000000 INFO @ Fri, 26 Jun 2020 07:59:14: 10000000 INFO @ Fri, 26 Jun 2020 07:59:18: 15000000 INFO @ Fri, 26 Jun 2020 07:59:18: 6000000 INFO @ Fri, 26 Jun 2020 07:59:21: 11000000 INFO @ Fri, 26 Jun 2020 07:59:25: 7000000 INFO @ Fri, 26 Jun 2020 07:59:25: 16000000 INFO @ Fri, 26 Jun 2020 07:59:28: 12000000 INFO @ Fri, 26 Jun 2020 07:59:32: 8000000 INFO @ Fri, 26 Jun 2020 07:59:32: 17000000 INFO @ Fri, 26 Jun 2020 07:59:35: 13000000 INFO @ Fri, 26 Jun 2020 07:59:38: 9000000 INFO @ Fri, 26 Jun 2020 07:59:39: 18000000 INFO @ Fri, 26 Jun 2020 07:59:41: 14000000 INFO @ Fri, 26 Jun 2020 07:59:45: 10000000 INFO @ Fri, 26 Jun 2020 07:59:46: 19000000 INFO @ Fri, 26 Jun 2020 07:59:48: 15000000 INFO @ Fri, 26 Jun 2020 07:59:52: 11000000 INFO @ Fri, 26 Jun 2020 07:59:53: 20000000 INFO @ Fri, 26 Jun 2020 07:59:55: 16000000 INFO @ Fri, 26 Jun 2020 07:59:59: 12000000 INFO @ Fri, 26 Jun 2020 07:59:59: 21000000 INFO @ Fri, 26 Jun 2020 08:00:02: 17000000 INFO @ Fri, 26 Jun 2020 08:00:06: 13000000 INFO @ Fri, 26 Jun 2020 08:00:06: 22000000 INFO @ Fri, 26 Jun 2020 08:00:09: 18000000 INFO @ Fri, 26 Jun 2020 08:00:13: 14000000 INFO @ Fri, 26 Jun 2020 08:00:13: 23000000 INFO @ Fri, 26 Jun 2020 08:00:16: 19000000 INFO @ Fri, 26 Jun 2020 08:00:19: 15000000 INFO @ Fri, 26 Jun 2020 08:00:20: 24000000 INFO @ Fri, 26 Jun 2020 08:00:23: 20000000 INFO @ Fri, 26 Jun 2020 08:00:26: 16000000 INFO @ Fri, 26 Jun 2020 08:00:27: 25000000 INFO @ Fri, 26 Jun 2020 08:00:29: 21000000 INFO @ Fri, 26 Jun 2020 08:00:33: 17000000 INFO @ Fri, 26 Jun 2020 08:00:33: #1 tag size is determined as 42 bps INFO @ Fri, 26 Jun 2020 08:00:33: #1 tag size = 42 INFO @ Fri, 26 Jun 2020 08:00:33: #1 total tags in treatment: 25916046 INFO @ Fri, 26 Jun 2020 08:00:33: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:00:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 08:00:34: #1 tags after filtering in treatment: 25916046 INFO @ Fri, 26 Jun 2020 08:00:34: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 08:00:34: #1 finished! INFO @ Fri, 26 Jun 2020 08:00:34: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:00:34: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:00:35: #2 number of paired peaks: 123 WARNING @ Fri, 26 Jun 2020 08:00:35: Fewer paired peaks (123) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 123 pairs to build model! INFO @ Fri, 26 Jun 2020 08:00:35: start model_add_line... INFO @ Fri, 26 Jun 2020 08:00:35: start X-correlation... INFO @ Fri, 26 Jun 2020 08:00:35: end of X-cor INFO @ Fri, 26 Jun 2020 08:00:35: #2 finished! INFO @ Fri, 26 Jun 2020 08:00:35: #2 predicted fragment length is 0 bps INFO @ Fri, 26 Jun 2020 08:00:35: #2 alternative fragment length(s) may be 0,38,132,293,306,419,482,503,593 bps INFO @ Fri, 26 Jun 2020 08:00:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX514730/SRX514730.05_model.r WARNING @ Fri, 26 Jun 2020 08:00:36: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 08:00:36: #2 You may need to consider one of the other alternative d(s): 0,38,132,293,306,419,482,503,593 WARNING @ Fri, 26 Jun 2020 08:00:36: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 08:00:36: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:00:36: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:00:36: 22000000 INFO @ Fri, 26 Jun 2020 08:00:40: 18000000 INFO @ Fri, 26 Jun 2020 08:00:43: 23000000 INFO @ Fri, 26 Jun 2020 08:00:46: 19000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 08:00:49: 24000000 INFO @ Fri, 26 Jun 2020 08:00:53: 20000000 INFO @ Fri, 26 Jun 2020 08:00:56: 25000000 INFO @ Fri, 26 Jun 2020 08:00:59: 21000000 INFO @ Fri, 26 Jun 2020 08:01:02: #1 tag size is determined as 42 bps INFO @ Fri, 26 Jun 2020 08:01:02: #1 tag size = 42 INFO @ Fri, 26 Jun 2020 08:01:02: #1 total tags in treatment: 25916046 INFO @ Fri, 26 Jun 2020 08:01:02: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:01:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 08:01:02: #1 tags after filtering in treatment: 25916046 INFO @ Fri, 26 Jun 2020 08:01:02: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 08:01:02: #1 finished! INFO @ Fri, 26 Jun 2020 08:01:02: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:01:02: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:01:04: #2 number of paired peaks: 123 WARNING @ Fri, 26 Jun 2020 08:01:04: Fewer paired peaks (123) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 123 pairs to build model! INFO @ Fri, 26 Jun 2020 08:01:04: start model_add_line... INFO @ Fri, 26 Jun 2020 08:01:04: start X-correlation... INFO @ Fri, 26 Jun 2020 08:01:04: end of X-cor INFO @ Fri, 26 Jun 2020 08:01:04: #2 finished! INFO @ Fri, 26 Jun 2020 08:01:04: #2 predicted fragment length is 0 bps INFO @ Fri, 26 Jun 2020 08:01:04: #2 alternative fragment length(s) may be 0,38,132,293,306,419,482,503,593 bps INFO @ Fri, 26 Jun 2020 08:01:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX514730/SRX514730.10_model.r WARNING @ Fri, 26 Jun 2020 08:01:04: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 08:01:04: #2 You may need to consider one of the other alternative d(s): 0,38,132,293,306,419,482,503,593 WARNING @ Fri, 26 Jun 2020 08:01:04: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 08:01:04: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:01:04: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:01:06: 22000000 INFO @ Fri, 26 Jun 2020 08:01:12: 23000000 INFO @ Fri, 26 Jun 2020 08:01:18: 24000000 INFO @ Fri, 26 Jun 2020 08:01:24: 25000000 INFO @ Fri, 26 Jun 2020 08:01:30: #1 tag size is determined as 42 bps INFO @ Fri, 26 Jun 2020 08:01:30: #1 tag size = 42 INFO @ Fri, 26 Jun 2020 08:01:30: #1 total tags in treatment: 25916046 INFO @ Fri, 26 Jun 2020 08:01:30: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:01:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 08:01:30: #1 tags after filtering in treatment: 25916046 INFO @ Fri, 26 Jun 2020 08:01:30: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 08:01:30: #1 finished! INFO @ Fri, 26 Jun 2020 08:01:30: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:01:30: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:01:32: #2 number of paired peaks: 123 WARNING @ Fri, 26 Jun 2020 08:01:32: Fewer paired peaks (123) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 123 pairs to build model! INFO @ Fri, 26 Jun 2020 08:01:32: start model_add_line... INFO @ Fri, 26 Jun 2020 08:01:32: start X-correlation... INFO @ Fri, 26 Jun 2020 08:01:32: end of X-cor INFO @ Fri, 26 Jun 2020 08:01:32: #2 finished! INFO @ Fri, 26 Jun 2020 08:01:32: #2 predicted fragment length is 0 bps INFO @ Fri, 26 Jun 2020 08:01:32: #2 alternative fragment length(s) may be 0,38,132,293,306,419,482,503,593 bps INFO @ Fri, 26 Jun 2020 08:01:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX514730/SRX514730.20_model.r WARNING @ Fri, 26 Jun 2020 08:01:32: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 08:01:32: #2 You may need to consider one of the other alternative d(s): 0,38,132,293,306,419,482,503,593 WARNING @ Fri, 26 Jun 2020 08:01:32: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 08:01:32: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:01:32: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 /var/spool/uge/at163/job_scripts/6497542: line 274: 30663 Terminated MACS $i /var/spool/uge/at163/job_scripts/6497542: line 274: 50652 Terminated MACS $i /var/spool/uge/at163/job_scripts/6497542: line 274: 70171 Terminated MACS $i ls: cannot access SRX514730.05.bed: No such file or directory mv: cannot stat ‘SRX514730.05.bed’: No such file or directory mv: cannot stat ‘SRX514730.05.bb’: No such file or directory ls: cannot access SRX514730.10.bed: No such file or directory mv: cannot stat ‘SRX514730.10.bed’: No such file or directory mv: cannot stat ‘SRX514730.10.bb’: No such file or directory ls: cannot access SRX514730.20.bed: No such file or directory mv: cannot stat ‘SRX514730.20.bed’: No such file or directory mv: cannot stat ‘SRX514730.20.bb’: No such file or directory