Job ID = 6368239 SRX = SRX494922 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:06:16 prefetch.2.10.7: 1) Downloading 'SRR1198454'... 2020-06-16T00:06:16 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:11:35 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:11:35 prefetch.2.10.7: 1) 'SRR1198454' was downloaded successfully Read 32570721 spots for SRR1198454/SRR1198454.sra Written 32570721 spots for SRR1198454/SRR1198454.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: 00:07:29 32570721 reads; of these: 32570721 (100.00%) were unpaired; of these: 778986 (2.39%) aligned 0 times 25992533 (79.80%) aligned exactly 1 time 5799202 (17.80%) aligned >1 times 97.61% overall alignment rate Time searching: 00:07:29 Overall time: 00:07:29 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 16 files... [bam_rmdupse_core] 5126141 / 31791735 = 0.1612 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 09:27:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494922/SRX494922.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494922/SRX494922.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494922/SRX494922.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494922/SRX494922.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 09:27:53: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:27:53: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:27:59: 1000000 INFO @ Tue, 16 Jun 2020 09:28:04: 2000000 INFO @ Tue, 16 Jun 2020 09:28:10: 3000000 INFO @ Tue, 16 Jun 2020 09:28:15: 4000000 INFO @ Tue, 16 Jun 2020 09:28:21: 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 09:28:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494922/SRX494922.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494922/SRX494922.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494922/SRX494922.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494922/SRX494922.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 09:28:23: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:28:23: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:28:27: 6000000 INFO @ Tue, 16 Jun 2020 09:28:29: 1000000 INFO @ Tue, 16 Jun 2020 09:28:32: 7000000 INFO @ Tue, 16 Jun 2020 09:28:35: 2000000 INFO @ Tue, 16 Jun 2020 09:28:38: 8000000 INFO @ Tue, 16 Jun 2020 09:28:41: 3000000 INFO @ Tue, 16 Jun 2020 09:28:44: 9000000 INFO @ Tue, 16 Jun 2020 09:28:46: 4000000 INFO @ Tue, 16 Jun 2020 09:28:50: 10000000 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 09:28:52: 5000000 INFO @ Tue, 16 Jun 2020 09:28:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494922/SRX494922.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494922/SRX494922.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494922/SRX494922.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494922/SRX494922.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 09:28:54: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:28:54: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:28:55: 11000000 INFO @ Tue, 16 Jun 2020 09:28:57: 6000000 INFO @ Tue, 16 Jun 2020 09:28:59: 1000000 INFO @ Tue, 16 Jun 2020 09:29:01: 12000000 INFO @ Tue, 16 Jun 2020 09:29:03: 7000000 INFO @ Tue, 16 Jun 2020 09:29:04: 2000000 INFO @ Tue, 16 Jun 2020 09:29:07: 13000000 INFO @ Tue, 16 Jun 2020 09:29:08: 3000000 INFO @ Tue, 16 Jun 2020 09:29:09: 8000000 INFO @ Tue, 16 Jun 2020 09:29:13: 14000000 INFO @ Tue, 16 Jun 2020 09:29:13: 4000000 INFO @ Tue, 16 Jun 2020 09:29:15: 9000000 INFO @ Tue, 16 Jun 2020 09:29:18: 5000000 INFO @ Tue, 16 Jun 2020 09:29:18: 15000000 INFO @ Tue, 16 Jun 2020 09:29:20: 10000000 INFO @ Tue, 16 Jun 2020 09:29:23: 6000000 INFO @ Tue, 16 Jun 2020 09:29:24: 16000000 INFO @ Tue, 16 Jun 2020 09:29:26: 11000000 INFO @ Tue, 16 Jun 2020 09:29:28: 7000000 INFO @ Tue, 16 Jun 2020 09:29:30: 17000000 INFO @ Tue, 16 Jun 2020 09:29:32: 12000000 INFO @ Tue, 16 Jun 2020 09:29:33: 8000000 INFO @ Tue, 16 Jun 2020 09:29:36: 18000000 INFO @ Tue, 16 Jun 2020 09:29:38: 9000000 INFO @ Tue, 16 Jun 2020 09:29:38: 13000000 INFO @ Tue, 16 Jun 2020 09:29:41: 19000000 INFO @ Tue, 16 Jun 2020 09:29:43: 10000000 INFO @ Tue, 16 Jun 2020 09:29:44: 14000000 INFO @ Tue, 16 Jun 2020 09:29:47: 20000000 INFO @ Tue, 16 Jun 2020 09:29:47: 11000000 INFO @ Tue, 16 Jun 2020 09:29:50: 15000000 INFO @ Tue, 16 Jun 2020 09:29:52: 12000000 INFO @ Tue, 16 Jun 2020 09:29:53: 21000000 INFO @ Tue, 16 Jun 2020 09:29:56: 16000000 INFO @ Tue, 16 Jun 2020 09:29:57: 13000000 INFO @ Tue, 16 Jun 2020 09:29:58: 22000000 INFO @ Tue, 16 Jun 2020 09:30:02: 17000000 INFO @ Tue, 16 Jun 2020 09:30:02: 14000000 INFO @ Tue, 16 Jun 2020 09:30:04: 23000000 INFO @ Tue, 16 Jun 2020 09:30:07: 15000000 INFO @ Tue, 16 Jun 2020 09:30:08: 18000000 INFO @ Tue, 16 Jun 2020 09:30:10: 24000000 INFO @ Tue, 16 Jun 2020 09:30:12: 16000000 INFO @ Tue, 16 Jun 2020 09:30:14: 19000000 INFO @ Tue, 16 Jun 2020 09:30:16: 25000000 INFO @ Tue, 16 Jun 2020 09:30:17: 17000000 INFO @ Tue, 16 Jun 2020 09:30:20: 20000000 INFO @ Tue, 16 Jun 2020 09:30:21: 26000000 INFO @ Tue, 16 Jun 2020 09:30:22: 18000000 INFO @ Tue, 16 Jun 2020 09:30:25: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:30:25: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:30:25: #1 total tags in treatment: 26665594 INFO @ Tue, 16 Jun 2020 09:30:25: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:30:25: #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 09:30:26: 21000000 INFO @ Tue, 16 Jun 2020 09:30:26: #1 tags after filtering in treatment: 26665594 INFO @ Tue, 16 Jun 2020 09:30:26: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:30:26: #1 finished! INFO @ Tue, 16 Jun 2020 09:30:26: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:30:26: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:30:27: 19000000 INFO @ Tue, 16 Jun 2020 09:30:28: #2 number of paired peaks: 145 WARNING @ Tue, 16 Jun 2020 09:30:28: Fewer paired peaks (145) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 145 pairs to build model! INFO @ Tue, 16 Jun 2020 09:30:28: start model_add_line... INFO @ Tue, 16 Jun 2020 09:30:28: start X-correlation... INFO @ Tue, 16 Jun 2020 09:30:28: end of X-cor INFO @ Tue, 16 Jun 2020 09:30:28: #2 finished! INFO @ Tue, 16 Jun 2020 09:30:28: #2 predicted fragment length is 0 bps INFO @ Tue, 16 Jun 2020 09:30:28: #2 alternative fragment length(s) may be 0,10,13,47,529,553,567 bps INFO @ Tue, 16 Jun 2020 09:30:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494922/SRX494922.05_model.r WARNING @ Tue, 16 Jun 2020 09:30:28: #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 09:30:28: #2 You may need to consider one of the other alternative d(s): 0,10,13,47,529,553,567 WARNING @ Tue, 16 Jun 2020 09:30:28: #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 09:30:28: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:30:28: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:30:31: 20000000 INFO @ Tue, 16 Jun 2020 09:30:32: 22000000 INFO @ Tue, 16 Jun 2020 09:30:36: 21000000 INFO @ Tue, 16 Jun 2020 09:30:38: 23000000 INFO @ Tue, 16 Jun 2020 09:30:41: 22000000 INFO @ Tue, 16 Jun 2020 09:30:43: 24000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:30:46: 23000000 INFO @ Tue, 16 Jun 2020 09:30:49: 25000000 INFO @ Tue, 16 Jun 2020 09:30:51: 24000000 INFO @ Tue, 16 Jun 2020 09:30:55: 26000000 INFO @ Tue, 16 Jun 2020 09:30:56: 25000000 INFO @ Tue, 16 Jun 2020 09:30:59: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:30:59: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:30:59: #1 total tags in treatment: 26665594 INFO @ Tue, 16 Jun 2020 09:30:59: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:30:59: #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 09:31:00: #1 tags after filtering in treatment: 26665594 INFO @ Tue, 16 Jun 2020 09:31:00: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:31:00: #1 finished! INFO @ Tue, 16 Jun 2020 09:31:00: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:31:00: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:31:00: 26000000 INFO @ Tue, 16 Jun 2020 09:31:01: #2 number of paired peaks: 145 WARNING @ Tue, 16 Jun 2020 09:31:01: Fewer paired peaks (145) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 145 pairs to build model! INFO @ Tue, 16 Jun 2020 09:31:01: start model_add_line... INFO @ Tue, 16 Jun 2020 09:31:02: start X-correlation... INFO @ Tue, 16 Jun 2020 09:31:02: end of X-cor INFO @ Tue, 16 Jun 2020 09:31:02: #2 finished! INFO @ Tue, 16 Jun 2020 09:31:02: #2 predicted fragment length is 0 bps INFO @ Tue, 16 Jun 2020 09:31:02: #2 alternative fragment length(s) may be 0,10,13,47,529,553,567 bps INFO @ Tue, 16 Jun 2020 09:31:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494922/SRX494922.10_model.r WARNING @ Tue, 16 Jun 2020 09:31:02: #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 09:31:02: #2 You may need to consider one of the other alternative d(s): 0,10,13,47,529,553,567 WARNING @ Tue, 16 Jun 2020 09:31:02: #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 09:31:02: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:31:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:31:04: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:31:04: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:31:04: #1 total tags in treatment: 26665594 INFO @ Tue, 16 Jun 2020 09:31:04: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:31:04: #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 09:31:04: #1 tags after filtering in treatment: 26665594 INFO @ Tue, 16 Jun 2020 09:31:04: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:31:04: #1 finished! INFO @ Tue, 16 Jun 2020 09:31:04: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:31:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:31:06: #2 number of paired peaks: 145 WARNING @ Tue, 16 Jun 2020 09:31:06: Fewer paired peaks (145) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 145 pairs to build model! INFO @ Tue, 16 Jun 2020 09:31:06: start model_add_line... INFO @ Tue, 16 Jun 2020 09:31:06: start X-correlation... INFO @ Tue, 16 Jun 2020 09:31:06: end of X-cor INFO @ Tue, 16 Jun 2020 09:31:06: #2 finished! INFO @ Tue, 16 Jun 2020 09:31:06: #2 predicted fragment length is 0 bps INFO @ Tue, 16 Jun 2020 09:31:06: #2 alternative fragment length(s) may be 0,10,13,47,529,553,567 bps INFO @ Tue, 16 Jun 2020 09:31:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494922/SRX494922.20_model.r WARNING @ Tue, 16 Jun 2020 09:31:06: #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 09:31:06: #2 You may need to consider one of the other alternative d(s): 0,10,13,47,529,553,567 WARNING @ Tue, 16 Jun 2020 09:31:06: #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 09:31:06: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:31:06: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 /var/spool/uge/at163/job_scripts/6368239: line 271: 70356 Terminated MACS $i /var/spool/uge/at163/job_scripts/6368239: line 271: 71299 Terminated MACS $i /var/spool/uge/at163/job_scripts/6368239: line 271: 71831 Terminated MACS $i ls: cannot access SRX494922.05.bed: No such file or directory mv: cannot stat ‘SRX494922.05.bed’: No such file or directory mv: cannot stat ‘SRX494922.05.bb’: No such file or directory ls: cannot access SRX494922.10.bed: No such file or directory mv: cannot stat ‘SRX494922.10.bed’: No such file or directory mv: cannot stat ‘SRX494922.10.bb’: No such file or directory ls: cannot access SRX494922.20.bed: No such file or directory mv: cannot stat ‘SRX494922.20.bed’: No such file or directory mv: cannot stat ‘SRX494922.20.bb’: No such file or directory