Job ID = 6368077 SRX = SRX466540 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:04:45 prefetch.2.10.7: 1) Downloading 'SRR1163606'... 2020-06-16T00:04:45 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:07:00 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:07:00 prefetch.2.10.7: 1) 'SRR1163606' was downloaded successfully Read 30788149 spots for SRR1163606/SRR1163606.sra Written 30788149 spots for SRR1163606/SRR1163606.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: 00:05:34 30788149 reads; of these: 30788149 (100.00%) were unpaired; of these: 169819 (0.55%) aligned 0 times 25275438 (82.09%) aligned exactly 1 time 5342892 (17.35%) aligned >1 times 99.45% overall alignment rate Time searching: 00:05:34 Overall time: 00:05:34 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 8 files... [bam_rmdupse_core] 4711616 / 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 09:20:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466540/SRX466540.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466540/SRX466540.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466540/SRX466540.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466540/SRX466540.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 09:20:25: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:20:25: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:20:32: 1000000 INFO @ Tue, 16 Jun 2020 09:20:38: 2000000 INFO @ Tue, 16 Jun 2020 09:20:45: 3000000 INFO @ Tue, 16 Jun 2020 09:20:51: 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 09:20:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466540/SRX466540.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466540/SRX466540.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466540/SRX466540.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466540/SRX466540.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 09:20:55: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:20:55: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:20:57: 5000000 INFO @ Tue, 16 Jun 2020 09:21:01: 1000000 INFO @ Tue, 16 Jun 2020 09:21:04: 6000000 INFO @ Tue, 16 Jun 2020 09:21:07: 2000000 INFO @ Tue, 16 Jun 2020 09:21:11: 7000000 INFO @ Tue, 16 Jun 2020 09:21:13: 3000000 INFO @ Tue, 16 Jun 2020 09:21:18: 8000000 INFO @ Tue, 16 Jun 2020 09:21:19: 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 09:21:25: 9000000 INFO @ Tue, 16 Jun 2020 09:21:25: 5000000 INFO @ Tue, 16 Jun 2020 09:21:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466540/SRX466540.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466540/SRX466540.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466540/SRX466540.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466540/SRX466540.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 09:21:27: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:21:27: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:21:31: 6000000 INFO @ Tue, 16 Jun 2020 09:21:32: 10000000 INFO @ Tue, 16 Jun 2020 09:21:33: 1000000 INFO @ Tue, 16 Jun 2020 09:21:37: 7000000 INFO @ Tue, 16 Jun 2020 09:21:39: 11000000 INFO @ Tue, 16 Jun 2020 09:21:39: 2000000 INFO @ Tue, 16 Jun 2020 09:21:43: 8000000 INFO @ Tue, 16 Jun 2020 09:21:45: 3000000 INFO @ Tue, 16 Jun 2020 09:21:45: 12000000 INFO @ Tue, 16 Jun 2020 09:21:49: 9000000 INFO @ Tue, 16 Jun 2020 09:21:51: 4000000 INFO @ Tue, 16 Jun 2020 09:21:52: 13000000 INFO @ Tue, 16 Jun 2020 09:21:55: 10000000 INFO @ Tue, 16 Jun 2020 09:21:57: 5000000 INFO @ Tue, 16 Jun 2020 09:21:59: 14000000 INFO @ Tue, 16 Jun 2020 09:22:01: 11000000 INFO @ Tue, 16 Jun 2020 09:22:04: 6000000 INFO @ Tue, 16 Jun 2020 09:22:06: 15000000 INFO @ Tue, 16 Jun 2020 09:22:08: 12000000 INFO @ Tue, 16 Jun 2020 09:22:10: 7000000 INFO @ Tue, 16 Jun 2020 09:22:13: 16000000 INFO @ Tue, 16 Jun 2020 09:22:14: 13000000 INFO @ Tue, 16 Jun 2020 09:22:16: 8000000 INFO @ Tue, 16 Jun 2020 09:22:20: 14000000 INFO @ Tue, 16 Jun 2020 09:22:20: 17000000 INFO @ Tue, 16 Jun 2020 09:22:22: 9000000 INFO @ Tue, 16 Jun 2020 09:22:26: 15000000 INFO @ Tue, 16 Jun 2020 09:22:27: 18000000 INFO @ Tue, 16 Jun 2020 09:22:28: 10000000 INFO @ Tue, 16 Jun 2020 09:22:32: 16000000 INFO @ Tue, 16 Jun 2020 09:22:33: 19000000 INFO @ Tue, 16 Jun 2020 09:22:34: 11000000 INFO @ Tue, 16 Jun 2020 09:22:37: 17000000 INFO @ Tue, 16 Jun 2020 09:22:40: 12000000 INFO @ Tue, 16 Jun 2020 09:22:40: 20000000 INFO @ Tue, 16 Jun 2020 09:22:43: 18000000 INFO @ Tue, 16 Jun 2020 09:22:46: 13000000 INFO @ Tue, 16 Jun 2020 09:22:47: 21000000 INFO @ Tue, 16 Jun 2020 09:22:49: 19000000 INFO @ Tue, 16 Jun 2020 09:22:52: 14000000 INFO @ Tue, 16 Jun 2020 09:22:54: 22000000 INFO @ Tue, 16 Jun 2020 09:22:55: 20000000 INFO @ Tue, 16 Jun 2020 09:22:57: 15000000 INFO @ Tue, 16 Jun 2020 09:23:00: 23000000 INFO @ Tue, 16 Jun 2020 09:23:01: 21000000 INFO @ Tue, 16 Jun 2020 09:23:03: 16000000 INFO @ Tue, 16 Jun 2020 09:23:06: 22000000 INFO @ Tue, 16 Jun 2020 09:23:07: 24000000 INFO @ Tue, 16 Jun 2020 09:23:09: 17000000 INFO @ Tue, 16 Jun 2020 09:23:12: 23000000 INFO @ Tue, 16 Jun 2020 09:23:13: 25000000 INFO @ Tue, 16 Jun 2020 09:23:14: 18000000 INFO @ Tue, 16 Jun 2020 09:23:18: 24000000 INFO @ Tue, 16 Jun 2020 09:23:19: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 09:23:19: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 09:23:19: #1 total tags in treatment: 25906714 INFO @ Tue, 16 Jun 2020 09:23:19: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:23:19: #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 09:23:20: #1 tags after filtering in treatment: 25906714 INFO @ Tue, 16 Jun 2020 09:23:20: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:23:20: #1 finished! INFO @ Tue, 16 Jun 2020 09:23:20: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:23:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:23:20: 19000000 INFO @ Tue, 16 Jun 2020 09:23:21: #2 number of paired peaks: 137 WARNING @ Tue, 16 Jun 2020 09:23:21: Fewer paired peaks (137) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 137 pairs to build model! INFO @ Tue, 16 Jun 2020 09:23:21: start model_add_line... INFO @ Tue, 16 Jun 2020 09:23:22: start X-correlation... INFO @ Tue, 16 Jun 2020 09:23:22: end of X-cor INFO @ Tue, 16 Jun 2020 09:23:22: #2 finished! INFO @ Tue, 16 Jun 2020 09:23:22: #2 predicted fragment length is 0 bps INFO @ Tue, 16 Jun 2020 09:23:22: #2 alternative fragment length(s) may be 0,31,308,474,545,598 bps INFO @ Tue, 16 Jun 2020 09:23:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466540/SRX466540.05_model.r WARNING @ Tue, 16 Jun 2020 09:23:22: #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 09:23:22: #2 You may need to consider one of the other alternative d(s): 0,31,308,474,545,598 WARNING @ Tue, 16 Jun 2020 09:23:22: #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 09:23:22: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:23:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:23:23: 25000000 INFO @ Tue, 16 Jun 2020 09:23:26: 20000000 INFO @ Tue, 16 Jun 2020 09:23:28: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 09:23:28: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 09:23:28: #1 total tags in treatment: 25906714 INFO @ Tue, 16 Jun 2020 09:23:28: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:23:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:23:29: #1 tags after filtering in treatment: 25906714 INFO @ Tue, 16 Jun 2020 09:23:29: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:23:29: #1 finished! INFO @ Tue, 16 Jun 2020 09:23:29: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:23:29: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:23:31: #2 number of paired peaks: 137 WARNING @ Tue, 16 Jun 2020 09:23:31: Fewer paired peaks (137) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 137 pairs to build model! INFO @ Tue, 16 Jun 2020 09:23:31: start model_add_line... INFO @ Tue, 16 Jun 2020 09:23:31: start X-correlation... INFO @ Tue, 16 Jun 2020 09:23:31: end of X-cor INFO @ Tue, 16 Jun 2020 09:23:31: #2 finished! INFO @ Tue, 16 Jun 2020 09:23:31: #2 predicted fragment length is 0 bps INFO @ Tue, 16 Jun 2020 09:23:31: #2 alternative fragment length(s) may be 0,31,308,474,545,598 bps INFO @ Tue, 16 Jun 2020 09:23:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466540/SRX466540.10_model.r WARNING @ Tue, 16 Jun 2020 09:23:31: #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 09:23:31: #2 You may need to consider one of the other alternative d(s): 0,31,308,474,545,598 WARNING @ Tue, 16 Jun 2020 09:23:31: #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 09:23:31: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:23:31: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:23:31: 21000000 INFO @ Tue, 16 Jun 2020 09:23:37: 22000000 INFO @ Tue, 16 Jun 2020 09:23:42: 23000000 INFO @ Tue, 16 Jun 2020 09:23:47: 24000000 INFO @ Tue, 16 Jun 2020 09:23:52: 25000000 INFO @ Tue, 16 Jun 2020 09:23:57: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 09:23:57: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 09:23:57: #1 total tags in treatment: 25906714 INFO @ Tue, 16 Jun 2020 09:23:57: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:23:57: #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 09:23:57: #1 tags after filtering in treatment: 25906714 INFO @ Tue, 16 Jun 2020 09:23:57: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:23:57: #1 finished! INFO @ Tue, 16 Jun 2020 09:23:57: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:23:57: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:23:59: #2 number of paired peaks: 137 WARNING @ Tue, 16 Jun 2020 09:23:59: Fewer paired peaks (137) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 137 pairs to build model! INFO @ Tue, 16 Jun 2020 09:23:59: start model_add_line... INFO @ Tue, 16 Jun 2020 09:23:59: start X-correlation... INFO @ Tue, 16 Jun 2020 09:23:59: end of X-cor INFO @ Tue, 16 Jun 2020 09:23:59: #2 finished! INFO @ Tue, 16 Jun 2020 09:23:59: #2 predicted fragment length is 0 bps INFO @ Tue, 16 Jun 2020 09:23:59: #2 alternative fragment length(s) may be 0,31,308,474,545,598 bps INFO @ Tue, 16 Jun 2020 09:23:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466540/SRX466540.20_model.r WARNING @ Tue, 16 Jun 2020 09:23:59: #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 09:23:59: #2 You may need to consider one of the other alternative d(s): 0,31,308,474,545,598 WARNING @ Tue, 16 Jun 2020 09:23:59: #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 09:23:59: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:23:59: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 /var/spool/uge/at140/job_scripts/6368077: line 271: 3034 Terminated MACS $i /var/spool/uge/at140/job_scripts/6368077: line 271: 17972 Terminated MACS $i /var/spool/uge/at140/job_scripts/6368077: line 271: 26221 Terminated MACS $i ls: cannot access SRX466540.05.bed: No such file or directory mv: cannot stat ‘SRX466540.05.bed’: No such file or directory mv: cannot stat ‘SRX466540.05.bb’: No such file or directory ls: cannot access SRX466540.10.bed: No such file or directory mv: cannot stat ‘SRX466540.10.bed’: No such file or directory mv: cannot stat ‘SRX466540.10.bb’: No such file or directory ls: cannot access SRX466540.20.bed: No such file or directory mv: cannot stat ‘SRX466540.20.bed’: No such file or directory mv: cannot stat ‘SRX466540.20.bb’: No such file or directory