Job ID = 6368685 SRX = SRX5402711 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:26:49 prefetch.2.10.7: 1) Downloading 'SRR8602945'... 2020-06-16T00:26:49 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:29:46 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:29:46 prefetch.2.10.7: 1) 'SRR8602945' was downloaded successfully Read 34531212 spots for SRR8602945/SRR8602945.sra Written 34531212 spots for SRR8602945/SRR8602945.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: 00:05:54 34531212 reads; of these: 34531212 (100.00%) were unpaired; of these: 7697992 (22.29%) aligned 0 times 22824472 (66.10%) aligned exactly 1 time 4008748 (11.61%) aligned >1 times 77.71% overall alignment rate Time searching: 00:05:54 Overall time: 00:05:54 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] 4771698 / 26833220 = 0.1778 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 09:43:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402711/SRX5402711.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402711/SRX5402711.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402711/SRX5402711.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402711/SRX5402711.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 09:43:10: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:43:10: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:43:17: 1000000 INFO @ Tue, 16 Jun 2020 09:43:24: 2000000 INFO @ Tue, 16 Jun 2020 09:43:31: 3000000 INFO @ Tue, 16 Jun 2020 09:43:38: 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 09:43:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402711/SRX5402711.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402711/SRX5402711.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402711/SRX5402711.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402711/SRX5402711.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 09:43:40: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:43:40: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:43:45: 5000000 INFO @ Tue, 16 Jun 2020 09:43:47: 1000000 INFO @ Tue, 16 Jun 2020 09:43:52: 6000000 INFO @ Tue, 16 Jun 2020 09:43:54: 2000000 INFO @ Tue, 16 Jun 2020 09:44:00: 7000000 INFO @ Tue, 16 Jun 2020 09:44:01: 3000000 INFO @ Tue, 16 Jun 2020 09:44:08: 8000000 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 09:44:08: 4000000 INFO @ Tue, 16 Jun 2020 09:44:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402711/SRX5402711.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402711/SRX5402711.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402711/SRX5402711.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402711/SRX5402711.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 09:44:10: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:44:10: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:44:15: 9000000 INFO @ Tue, 16 Jun 2020 09:44:16: 5000000 INFO @ Tue, 16 Jun 2020 09:44:17: 1000000 INFO @ Tue, 16 Jun 2020 09:44:23: 6000000 INFO @ Tue, 16 Jun 2020 09:44:23: 10000000 INFO @ Tue, 16 Jun 2020 09:44:24: 2000000 INFO @ Tue, 16 Jun 2020 09:44:30: 7000000 INFO @ Tue, 16 Jun 2020 09:44:30: 11000000 INFO @ Tue, 16 Jun 2020 09:44:32: 3000000 INFO @ Tue, 16 Jun 2020 09:44:37: 8000000 INFO @ Tue, 16 Jun 2020 09:44:38: 12000000 INFO @ Tue, 16 Jun 2020 09:44:38: 4000000 INFO @ Tue, 16 Jun 2020 09:44:44: 9000000 INFO @ Tue, 16 Jun 2020 09:44:45: 13000000 INFO @ Tue, 16 Jun 2020 09:44:45: 5000000 INFO @ Tue, 16 Jun 2020 09:44:50: 10000000 INFO @ Tue, 16 Jun 2020 09:44:52: 6000000 INFO @ Tue, 16 Jun 2020 09:44:53: 14000000 INFO @ Tue, 16 Jun 2020 09:44:57: 11000000 INFO @ Tue, 16 Jun 2020 09:44:59: 7000000 INFO @ Tue, 16 Jun 2020 09:45:01: 15000000 INFO @ Tue, 16 Jun 2020 09:45:04: 12000000 INFO @ Tue, 16 Jun 2020 09:45:06: 8000000 INFO @ Tue, 16 Jun 2020 09:45:09: 16000000 INFO @ Tue, 16 Jun 2020 09:45:11: 13000000 INFO @ Tue, 16 Jun 2020 09:45:13: 9000000 INFO @ Tue, 16 Jun 2020 09:45:16: 17000000 INFO @ Tue, 16 Jun 2020 09:45:18: 14000000 INFO @ Tue, 16 Jun 2020 09:45:20: 10000000 INFO @ Tue, 16 Jun 2020 09:45:24: 18000000 INFO @ Tue, 16 Jun 2020 09:45:25: 15000000 INFO @ Tue, 16 Jun 2020 09:45:27: 11000000 INFO @ Tue, 16 Jun 2020 09:45:32: 19000000 INFO @ Tue, 16 Jun 2020 09:45:32: 16000000 INFO @ Tue, 16 Jun 2020 09:45:34: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:45:39: 17000000 INFO @ Tue, 16 Jun 2020 09:45:39: 20000000 INFO @ Tue, 16 Jun 2020 09:45:41: 13000000 INFO @ Tue, 16 Jun 2020 09:45:46: 18000000 INFO @ Tue, 16 Jun 2020 09:45:46: 21000000 INFO @ Tue, 16 Jun 2020 09:45:48: 14000000 INFO @ Tue, 16 Jun 2020 09:45:53: 19000000 INFO @ Tue, 16 Jun 2020 09:45:54: 22000000 INFO @ Tue, 16 Jun 2020 09:45:54: 15000000 INFO @ Tue, 16 Jun 2020 09:45:54: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:45:54: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:45:54: #1 total tags in treatment: 22061522 INFO @ Tue, 16 Jun 2020 09:45:54: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:45:54: #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 09:45:55: #1 tags after filtering in treatment: 22061522 INFO @ Tue, 16 Jun 2020 09:45:55: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:45:55: #1 finished! INFO @ Tue, 16 Jun 2020 09:45:55: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:45:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:45:56: #2 number of paired peaks: 159 WARNING @ Tue, 16 Jun 2020 09:45:56: Fewer paired peaks (159) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 159 pairs to build model! INFO @ Tue, 16 Jun 2020 09:45:56: start model_add_line... INFO @ Tue, 16 Jun 2020 09:45:56: start X-correlation... INFO @ Tue, 16 Jun 2020 09:45:56: end of X-cor INFO @ Tue, 16 Jun 2020 09:45:56: #2 finished! INFO @ Tue, 16 Jun 2020 09:45:56: #2 predicted fragment length is 0 bps INFO @ Tue, 16 Jun 2020 09:45:56: #2 alternative fragment length(s) may be 0,44,47,534,562 bps INFO @ Tue, 16 Jun 2020 09:45:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402711/SRX5402711.05_model.r WARNING @ Tue, 16 Jun 2020 09:45:56: #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 09:45:56: #2 You may need to consider one of the other alternative d(s): 0,44,47,534,562 WARNING @ Tue, 16 Jun 2020 09:45:56: #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 09:45:56: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:45:56: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:45:59: 20000000 INFO @ Tue, 16 Jun 2020 09:46:01: 16000000 INFO @ Tue, 16 Jun 2020 09:46:06: 21000000 INFO @ Tue, 16 Jun 2020 09:46:08: 17000000 INFO @ Tue, 16 Jun 2020 09:46:13: 22000000 INFO @ Tue, 16 Jun 2020 09:46:13: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:46:13: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:46:13: #1 total tags in treatment: 22061522 INFO @ Tue, 16 Jun 2020 09:46:13: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:46:13: #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 09:46:14: #1 tags after filtering in treatment: 22061522 INFO @ Tue, 16 Jun 2020 09:46:14: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:46:14: #1 finished! INFO @ Tue, 16 Jun 2020 09:46:14: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:46:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:46:14: 18000000 INFO @ Tue, 16 Jun 2020 09:46:15: #2 number of paired peaks: 159 WARNING @ Tue, 16 Jun 2020 09:46:15: Fewer paired peaks (159) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 159 pairs to build model! INFO @ Tue, 16 Jun 2020 09:46:15: start model_add_line... INFO @ Tue, 16 Jun 2020 09:46:15: start X-correlation... INFO @ Tue, 16 Jun 2020 09:46:15: end of X-cor INFO @ Tue, 16 Jun 2020 09:46:15: #2 finished! INFO @ Tue, 16 Jun 2020 09:46:15: #2 predicted fragment length is 0 bps INFO @ Tue, 16 Jun 2020 09:46:15: #2 alternative fragment length(s) may be 0,44,47,534,562 bps INFO @ Tue, 16 Jun 2020 09:46:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402711/SRX5402711.10_model.r WARNING @ Tue, 16 Jun 2020 09:46:15: #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 09:46:15: #2 You may need to consider one of the other alternative d(s): 0,44,47,534,562 WARNING @ Tue, 16 Jun 2020 09:46:15: #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 09:46:15: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:46:15: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 /var/spool/uge/at163/job_scripts/6368685: line 271: 80465 Terminated MACS $i /var/spool/uge/at163/job_scripts/6368685: line 271: 81109 Terminated MACS $i /var/spool/uge/at163/job_scripts/6368685: line 271: 85446 Terminated MACS $i ls: cannot access SRX5402711.05.bed: No such file or directory mv: cannot stat ‘SRX5402711.05.bed’: No such file or directory mv: cannot stat ‘SRX5402711.05.bb’: No such file or directory ls: cannot access SRX5402711.10.bed: No such file or directory mv: cannot stat ‘SRX5402711.10.bed’: No such file or directory mv: cannot stat ‘SRX5402711.10.bb’: No such file or directory ls: cannot access SRX5402711.20.bed: No such file or directory mv: cannot stat ‘SRX5402711.20.bed’: No such file or directory mv: cannot stat ‘SRX5402711.20.bb’: No such file or directory