Job ID = 6367933 SRX = SRX4200542 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:03:45 prefetch.2.10.7: 1) Downloading 'SRR7298008'... 2020-06-16T00:03:45 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:06:25 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:06:25 prefetch.2.10.7: 1) 'SRR7298008' was downloaded successfully Read 30788149 spots for SRR7298008/SRR7298008.sra Written 30788149 spots for SRR7298008/SRR7298008.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: 00:05:49 30788149 reads; of these: 30788149 (100.00%) were unpaired; of these: 169819 (0.55%) aligned 0 times 25275364 (82.09%) aligned exactly 1 time 5342966 (17.35%) aligned >1 times 99.45% overall alignment rate Time searching: 00:05:49 Overall time: 00:05:49 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] 4711776 / 30618330 = 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 09:20:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4200542/SRX4200542.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4200542/SRX4200542.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4200542/SRX4200542.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4200542/SRX4200542.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 09:20:11: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:20:11: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:20:16: 1000000 INFO @ Tue, 16 Jun 2020 09:20:21: 2000000 INFO @ Tue, 16 Jun 2020 09:20:26: 3000000 INFO @ Tue, 16 Jun 2020 09:20:31: 4000000 INFO @ Tue, 16 Jun 2020 09:20:36: 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 09:20:41: 6000000 INFO @ Tue, 16 Jun 2020 09:20:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4200542/SRX4200542.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4200542/SRX4200542.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4200542/SRX4200542.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4200542/SRX4200542.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 09:20:42: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:20:42: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:20:46: 7000000 INFO @ Tue, 16 Jun 2020 09:20:47: 1000000 INFO @ Tue, 16 Jun 2020 09:20:51: 8000000 INFO @ Tue, 16 Jun 2020 09:20:52: 2000000 INFO @ Tue, 16 Jun 2020 09:20:57: 9000000 INFO @ Tue, 16 Jun 2020 09:20:58: 3000000 INFO @ Tue, 16 Jun 2020 09:21:02: 10000000 INFO @ Tue, 16 Jun 2020 09:21:03: 4000000 INFO @ Tue, 16 Jun 2020 09:21:07: 11000000 INFO @ Tue, 16 Jun 2020 09:21:08: 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 09:21:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4200542/SRX4200542.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4200542/SRX4200542.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4200542/SRX4200542.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4200542/SRX4200542.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 09:21:10: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:21:10: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:21:13: 12000000 INFO @ Tue, 16 Jun 2020 09:21:13: 6000000 INFO @ Tue, 16 Jun 2020 09:21:16: 1000000 INFO @ Tue, 16 Jun 2020 09:21:18: 13000000 INFO @ Tue, 16 Jun 2020 09:21:19: 7000000 INFO @ Tue, 16 Jun 2020 09:21:21: 2000000 INFO @ Tue, 16 Jun 2020 09:21:24: 14000000 INFO @ Tue, 16 Jun 2020 09:21:24: 8000000 INFO @ Tue, 16 Jun 2020 09:21:27: 3000000 INFO @ Tue, 16 Jun 2020 09:21:29: 15000000 INFO @ Tue, 16 Jun 2020 09:21:30: 9000000 INFO @ Tue, 16 Jun 2020 09:21:32: 4000000 INFO @ Tue, 16 Jun 2020 09:21:35: 10000000 INFO @ Tue, 16 Jun 2020 09:21:35: 16000000 INFO @ Tue, 16 Jun 2020 09:21:38: 5000000 INFO @ Tue, 16 Jun 2020 09:21:40: 11000000 INFO @ Tue, 16 Jun 2020 09:21:41: 17000000 INFO @ Tue, 16 Jun 2020 09:21:43: 6000000 INFO @ Tue, 16 Jun 2020 09:21:46: 12000000 INFO @ Tue, 16 Jun 2020 09:21:46: 18000000 INFO @ Tue, 16 Jun 2020 09:21:49: 7000000 INFO @ Tue, 16 Jun 2020 09:21:52: 13000000 INFO @ Tue, 16 Jun 2020 09:21:52: 19000000 INFO @ Tue, 16 Jun 2020 09:21:54: 8000000 INFO @ Tue, 16 Jun 2020 09:21:57: 14000000 INFO @ Tue, 16 Jun 2020 09:21:58: 20000000 INFO @ Tue, 16 Jun 2020 09:22:00: 9000000 INFO @ Tue, 16 Jun 2020 09:22:03: 15000000 INFO @ Tue, 16 Jun 2020 09:22:03: 21000000 INFO @ Tue, 16 Jun 2020 09:22:05: 10000000 INFO @ Tue, 16 Jun 2020 09:22:09: 16000000 INFO @ Tue, 16 Jun 2020 09:22:09: 22000000 INFO @ Tue, 16 Jun 2020 09:22:11: 11000000 INFO @ Tue, 16 Jun 2020 09:22:14: 17000000 INFO @ Tue, 16 Jun 2020 09:22:15: 23000000 INFO @ Tue, 16 Jun 2020 09:22:17: 12000000 INFO @ Tue, 16 Jun 2020 09:22:20: 18000000 INFO @ Tue, 16 Jun 2020 09:22:21: 24000000 INFO @ Tue, 16 Jun 2020 09:22:23: 13000000 INFO @ Tue, 16 Jun 2020 09:22:26: 19000000 INFO @ Tue, 16 Jun 2020 09:22:26: 25000000 INFO @ Tue, 16 Jun 2020 09:22:28: 14000000 INFO @ Tue, 16 Jun 2020 09:22:31: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 09:22:31: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 09:22:31: #1 total tags in treatment: 25906554 INFO @ Tue, 16 Jun 2020 09:22:31: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:22:31: #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 09:22:31: 20000000 INFO @ Tue, 16 Jun 2020 09:22:32: #1 tags after filtering in treatment: 25906554 INFO @ Tue, 16 Jun 2020 09:22:32: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:22:32: #1 finished! INFO @ Tue, 16 Jun 2020 09:22:32: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:22:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:22:34: #2 number of paired peaks: 138 WARNING @ Tue, 16 Jun 2020 09:22:34: Fewer paired peaks (138) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 138 pairs to build model! INFO @ Tue, 16 Jun 2020 09:22:34: start model_add_line... INFO @ Tue, 16 Jun 2020 09:22:34: start X-correlation... INFO @ Tue, 16 Jun 2020 09:22:34: end of X-cor INFO @ Tue, 16 Jun 2020 09:22:34: #2 finished! INFO @ Tue, 16 Jun 2020 09:22:34: #2 predicted fragment length is 0 bps INFO @ Tue, 16 Jun 2020 09:22:34: #2 alternative fragment length(s) may be 0,30,306,321,419,526,529,553,575,598 bps INFO @ Tue, 16 Jun 2020 09:22:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4200542/SRX4200542.05_model.r WARNING @ Tue, 16 Jun 2020 09:22:34: #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 09:22:34: #2 You may need to consider one of the other alternative d(s): 0,30,306,321,419,526,529,553,575,598 WARNING @ Tue, 16 Jun 2020 09:22:34: #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 09:22:34: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:22:34: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:22:34: 15000000 INFO @ Tue, 16 Jun 2020 09:22:37: 21000000 INFO @ Tue, 16 Jun 2020 09:22:40: 16000000 INFO @ Tue, 16 Jun 2020 09:22:43: 22000000 INFO @ Tue, 16 Jun 2020 09:22:45: 17000000 INFO @ Tue, 16 Jun 2020 09:22:48: 23000000 INFO @ Tue, 16 Jun 2020 09:22:51: 18000000 INFO @ Tue, 16 Jun 2020 09:22:54: 24000000 INFO @ Tue, 16 Jun 2020 09:22:56: 19000000 INFO @ Tue, 16 Jun 2020 09:22:59: 25000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:23:02: 20000000 INFO @ Tue, 16 Jun 2020 09:23:04: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 09:23:04: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 09:23:04: #1 total tags in treatment: 25906554 INFO @ Tue, 16 Jun 2020 09:23:04: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:23:04: #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 09:23:05: #1 tags after filtering in treatment: 25906554 INFO @ Tue, 16 Jun 2020 09:23:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:23:05: #1 finished! INFO @ Tue, 16 Jun 2020 09:23:05: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:23:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:23:07: #2 number of paired peaks: 138 WARNING @ Tue, 16 Jun 2020 09:23:07: Fewer paired peaks (138) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 138 pairs to build model! INFO @ Tue, 16 Jun 2020 09:23:07: start model_add_line... INFO @ Tue, 16 Jun 2020 09:23:07: start X-correlation... INFO @ Tue, 16 Jun 2020 09:23:07: end of X-cor INFO @ Tue, 16 Jun 2020 09:23:07: #2 finished! INFO @ Tue, 16 Jun 2020 09:23:07: #2 predicted fragment length is 0 bps INFO @ Tue, 16 Jun 2020 09:23:07: #2 alternative fragment length(s) may be 0,30,306,321,419,526,529,553,575,598 bps INFO @ Tue, 16 Jun 2020 09:23:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4200542/SRX4200542.10_model.r WARNING @ Tue, 16 Jun 2020 09:23:07: #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 09:23:07: #2 You may need to consider one of the other alternative d(s): 0,30,306,321,419,526,529,553,575,598 WARNING @ Tue, 16 Jun 2020 09:23:07: #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 09:23:07: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:23:07: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:23:07: 21000000 INFO @ Tue, 16 Jun 2020 09:23:13: 22000000 INFO @ Tue, 16 Jun 2020 09:23:18: 23000000 INFO @ Tue, 16 Jun 2020 09:23:24: 24000000 INFO @ Tue, 16 Jun 2020 09:23:29: 25000000 INFO @ Tue, 16 Jun 2020 09:23:34: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 09:23:34: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 09:23:34: #1 total tags in treatment: 25906554 INFO @ Tue, 16 Jun 2020 09:23:34: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:23:34: #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 09:23:34: #1 tags after filtering in treatment: 25906554 INFO @ Tue, 16 Jun 2020 09:23:34: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:23:34: #1 finished! INFO @ Tue, 16 Jun 2020 09:23:34: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:23:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:23:36: #2 number of paired peaks: 138 WARNING @ Tue, 16 Jun 2020 09:23:36: Fewer paired peaks (138) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 138 pairs to build model! INFO @ Tue, 16 Jun 2020 09:23:36: start model_add_line... INFO @ Tue, 16 Jun 2020 09:23:36: start X-correlation... INFO @ Tue, 16 Jun 2020 09:23:36: end of X-cor INFO @ Tue, 16 Jun 2020 09:23:36: #2 finished! INFO @ Tue, 16 Jun 2020 09:23:36: #2 predicted fragment length is 0 bps INFO @ Tue, 16 Jun 2020 09:23:36: #2 alternative fragment length(s) may be 0,30,306,321,419,526,529,553,575,598 bps INFO @ Tue, 16 Jun 2020 09:23:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4200542/SRX4200542.20_model.r WARNING @ Tue, 16 Jun 2020 09:23:36: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:23:36: #2 You may need to consider one of the other alternative d(s): 0,30,306,321,419,526,529,553,575,598 WARNING @ Tue, 16 Jun 2020 09:23:36: #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 09:23:36: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:23:36: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 /var/spool/uge/at149/job_scripts/6367933: line 271: 58637 Terminated MACS $i /var/spool/uge/at149/job_scripts/6367933: line 271: 58902 Terminated MACS $i /var/spool/uge/at149/job_scripts/6367933: line 271: 59146 Terminated MACS $i ls: cannot access SRX4200542.05.bed: No such file or directory mv: cannot stat ‘SRX4200542.05.bed’: No such file or directory mv: cannot stat ‘SRX4200542.05.bb’: No such file or directory ls: cannot access SRX4200542.10.bed: No such file or directory mv: cannot stat ‘SRX4200542.10.bed’: No such file or directory mv: cannot stat ‘SRX4200542.10.bb’: No such file or directory ls: cannot access SRX4200542.20.bed: No such file or directory mv: cannot stat ‘SRX4200542.20.bed’: No such file or directory mv: cannot stat ‘SRX4200542.20.bb’: No such file or directory