Job ID = 6497428 SRX = SRX494840 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T22:26:11 prefetch.2.10.7: 1) Downloading 'SRR1198372'... 2020-06-25T22:26:11 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:28:43 prefetch.2.10.7: HTTPS download succeed 2020-06-25T22:28:43 prefetch.2.10.7: 1) 'SRR1198372' was downloaded successfully Read 30788149 spots for SRR1198372/SRR1198372.sra Written 30788149 spots for SRR1198372/SRR1198372.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: 00:05:35 30788149 reads; of these: 30788149 (100.00%) were unpaired; of these: 171804 (0.56%) aligned 0 times 25273661 (82.09%) aligned exactly 1 time 5342684 (17.35%) aligned >1 times 99.44% overall alignment rate Time searching: 00:05:36 Overall time: 00:05:36 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] 4711030 / 30616345 = 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 @ Fri, 26 Jun 2020 07:42:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494840/SRX494840.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494840/SRX494840.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494840/SRX494840.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494840/SRX494840.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 07:42:25: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:42:25: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:42:30: 1000000 INFO @ Fri, 26 Jun 2020 07:42:36: 2000000 INFO @ Fri, 26 Jun 2020 07:42:42: 3000000 INFO @ Fri, 26 Jun 2020 07:42:47: 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 07:42:52: 5000000 INFO @ Fri, 26 Jun 2020 07:42:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494840/SRX494840.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494840/SRX494840.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494840/SRX494840.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494840/SRX494840.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 07:42:53: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:42:53: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:42:57: 6000000 INFO @ Fri, 26 Jun 2020 07:42:59: 1000000 INFO @ Fri, 26 Jun 2020 07:43:03: 7000000 INFO @ Fri, 26 Jun 2020 07:43:05: 2000000 INFO @ Fri, 26 Jun 2020 07:43:08: 8000000 INFO @ Fri, 26 Jun 2020 07:43:11: 3000000 INFO @ Fri, 26 Jun 2020 07:43:14: 9000000 INFO @ Fri, 26 Jun 2020 07:43:16: 4000000 INFO @ Fri, 26 Jun 2020 07:43:19: 10000000 INFO @ Fri, 26 Jun 2020 07:43:21: 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 @ Fri, 26 Jun 2020 07:43:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494840/SRX494840.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494840/SRX494840.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494840/SRX494840.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494840/SRX494840.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 07:43:23: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:43:23: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:43:25: 11000000 INFO @ Fri, 26 Jun 2020 07:43:27: 6000000 INFO @ Fri, 26 Jun 2020 07:43:29: 1000000 INFO @ Fri, 26 Jun 2020 07:43:31: 12000000 INFO @ Fri, 26 Jun 2020 07:43:32: 7000000 INFO @ Fri, 26 Jun 2020 07:43:36: 2000000 INFO @ Fri, 26 Jun 2020 07:43:36: 13000000 INFO @ Fri, 26 Jun 2020 07:43:38: 8000000 INFO @ Fri, 26 Jun 2020 07:43:42: 3000000 INFO @ Fri, 26 Jun 2020 07:43:42: 14000000 INFO @ Fri, 26 Jun 2020 07:43:44: 9000000 INFO @ Fri, 26 Jun 2020 07:43:47: 4000000 INFO @ Fri, 26 Jun 2020 07:43:48: 15000000 INFO @ Fri, 26 Jun 2020 07:43:49: 10000000 INFO @ Fri, 26 Jun 2020 07:43:53: 5000000 INFO @ Fri, 26 Jun 2020 07:43:54: 16000000 INFO @ Fri, 26 Jun 2020 07:43:55: 11000000 INFO @ Fri, 26 Jun 2020 07:43:59: 6000000 INFO @ Fri, 26 Jun 2020 07:43:59: 17000000 INFO @ Fri, 26 Jun 2020 07:44:01: 12000000 INFO @ Fri, 26 Jun 2020 07:44:04: 7000000 INFO @ Fri, 26 Jun 2020 07:44:05: 18000000 INFO @ Fri, 26 Jun 2020 07:44:06: 13000000 INFO @ Fri, 26 Jun 2020 07:44:10: 8000000 INFO @ Fri, 26 Jun 2020 07:44:11: 19000000 INFO @ Fri, 26 Jun 2020 07:44:12: 14000000 INFO @ Fri, 26 Jun 2020 07:44:16: 9000000 INFO @ Fri, 26 Jun 2020 07:44:16: 20000000 INFO @ Fri, 26 Jun 2020 07:44:18: 15000000 INFO @ Fri, 26 Jun 2020 07:44:21: 10000000 INFO @ Fri, 26 Jun 2020 07:44:22: 21000000 INFO @ Fri, 26 Jun 2020 07:44:23: 16000000 INFO @ Fri, 26 Jun 2020 07:44:27: 11000000 INFO @ Fri, 26 Jun 2020 07:44:28: 22000000 INFO @ Fri, 26 Jun 2020 07:44:29: 17000000 INFO @ Fri, 26 Jun 2020 07:44:33: 12000000 INFO @ Fri, 26 Jun 2020 07:44:33: 23000000 INFO @ Fri, 26 Jun 2020 07:44:34: 18000000 INFO @ Fri, 26 Jun 2020 07:44:38: 13000000 INFO @ Fri, 26 Jun 2020 07:44:39: 24000000 INFO @ Fri, 26 Jun 2020 07:44:40: 19000000 INFO @ Fri, 26 Jun 2020 07:44:44: 14000000 INFO @ Fri, 26 Jun 2020 07:44:45: 25000000 INFO @ Fri, 26 Jun 2020 07:44:46: 20000000 INFO @ Fri, 26 Jun 2020 07:44:50: 15000000 INFO @ Fri, 26 Jun 2020 07:44:50: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 07:44:50: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 07:44:50: #1 total tags in treatment: 25905315 INFO @ Fri, 26 Jun 2020 07:44:50: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:44:50: #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 07:44:51: #1 tags after filtering in treatment: 25905315 INFO @ Fri, 26 Jun 2020 07:44:51: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:44:51: #1 finished! INFO @ Fri, 26 Jun 2020 07:44:51: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:44:51: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:44:51: 21000000 INFO @ Fri, 26 Jun 2020 07:44:53: #2 number of paired peaks: 137 WARNING @ Fri, 26 Jun 2020 07:44:53: 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 @ Fri, 26 Jun 2020 07:44:53: start model_add_line... INFO @ Fri, 26 Jun 2020 07:44:53: start X-correlation... INFO @ Fri, 26 Jun 2020 07:44:53: end of X-cor INFO @ Fri, 26 Jun 2020 07:44:53: #2 finished! INFO @ Fri, 26 Jun 2020 07:44:53: #2 predicted fragment length is 0 bps INFO @ Fri, 26 Jun 2020 07:44:53: #2 alternative fragment length(s) may be 0,32,296,380,411,501,567,583 bps INFO @ Fri, 26 Jun 2020 07:44:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494840/SRX494840.05_model.r WARNING @ Fri, 26 Jun 2020 07:44:53: #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 07:44:53: #2 You may need to consider one of the other alternative d(s): 0,32,296,380,411,501,567,583 WARNING @ Fri, 26 Jun 2020 07:44:53: #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 07:44:53: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:44:53: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:44:56: 16000000 INFO @ Fri, 26 Jun 2020 07:44:57: 22000000 INFO @ Fri, 26 Jun 2020 07:45:01: 17000000 INFO @ Fri, 26 Jun 2020 07:45:03: 23000000 INFO @ Fri, 26 Jun 2020 07:45:07: 18000000 INFO @ Fri, 26 Jun 2020 07:45:08: 24000000 INFO @ Fri, 26 Jun 2020 07:45:13: 19000000 INFO @ Fri, 26 Jun 2020 07:45:14: 25000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 07:45:18: 20000000 INFO @ Fri, 26 Jun 2020 07:45:19: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 07:45:19: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 07:45:19: #1 total tags in treatment: 25905315 INFO @ Fri, 26 Jun 2020 07:45:19: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:45:19: #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 07:45:20: #1 tags after filtering in treatment: 25905315 INFO @ Fri, 26 Jun 2020 07:45:20: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:45:20: #1 finished! INFO @ Fri, 26 Jun 2020 07:45:20: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:45:20: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:45:21: #2 number of paired peaks: 137 WARNING @ Fri, 26 Jun 2020 07:45:21: 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 @ Fri, 26 Jun 2020 07:45:21: start model_add_line... INFO @ Fri, 26 Jun 2020 07:45:22: start X-correlation... INFO @ Fri, 26 Jun 2020 07:45:22: end of X-cor INFO @ Fri, 26 Jun 2020 07:45:22: #2 finished! INFO @ Fri, 26 Jun 2020 07:45:22: #2 predicted fragment length is 0 bps INFO @ Fri, 26 Jun 2020 07:45:22: #2 alternative fragment length(s) may be 0,32,296,380,411,501,567,583 bps INFO @ Fri, 26 Jun 2020 07:45:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494840/SRX494840.10_model.r WARNING @ Fri, 26 Jun 2020 07:45:22: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:45:22: #2 You may need to consider one of the other alternative d(s): 0,32,296,380,411,501,567,583 WARNING @ Fri, 26 Jun 2020 07:45:22: #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 07:45:22: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:45:22: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:45:24: 21000000 INFO @ Fri, 26 Jun 2020 07:45:29: 22000000 INFO @ Fri, 26 Jun 2020 07:45:34: 23000000 INFO @ Fri, 26 Jun 2020 07:45:40: 24000000 INFO @ Fri, 26 Jun 2020 07:45:45: 25000000 INFO @ Fri, 26 Jun 2020 07:45:50: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 07:45:50: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 07:45:50: #1 total tags in treatment: 25905315 INFO @ Fri, 26 Jun 2020 07:45:50: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:45:50: #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 07:45:51: #1 tags after filtering in treatment: 25905315 INFO @ Fri, 26 Jun 2020 07:45:51: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:45:51: #1 finished! INFO @ Fri, 26 Jun 2020 07:45:51: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:45:51: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:45:53: #2 number of paired peaks: 137 WARNING @ Fri, 26 Jun 2020 07:45:53: 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 @ Fri, 26 Jun 2020 07:45:53: start model_add_line... INFO @ Fri, 26 Jun 2020 07:45:53: start X-correlation... INFO @ Fri, 26 Jun 2020 07:45:53: end of X-cor INFO @ Fri, 26 Jun 2020 07:45:53: #2 finished! INFO @ Fri, 26 Jun 2020 07:45:53: #2 predicted fragment length is 0 bps INFO @ Fri, 26 Jun 2020 07:45:53: #2 alternative fragment length(s) may be 0,32,296,380,411,501,567,583 bps INFO @ Fri, 26 Jun 2020 07:45:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494840/SRX494840.20_model.r WARNING @ Fri, 26 Jun 2020 07:45:53: #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 07:45:53: #2 You may need to consider one of the other alternative d(s): 0,32,296,380,411,501,567,583 WARNING @ Fri, 26 Jun 2020 07:45:53: #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 07:45:53: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:45:53: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 /var/spool/uge/at159/job_scripts/6497428: line 274: 103115 Terminated MACS $i /var/spool/uge/at159/job_scripts/6497428: line 274: 103294 Terminated MACS $i /var/spool/uge/at159/job_scripts/6497428: line 274: 103629 Terminated MACS $i ls: cannot access SRX494840.05.bed: No such file or directory mv: cannot stat ‘SRX494840.05.bed’: No such file or directory mv: cannot stat ‘SRX494840.05.bb’: No such file or directory ls: cannot access SRX494840.10.bed: No such file or directory mv: cannot stat ‘SRX494840.10.bed’: No such file or directory mv: cannot stat ‘SRX494840.10.bb’: No such file or directory ls: cannot access SRX494840.20.bed: No such file or directory mv: cannot stat ‘SRX494840.20.bed’: No such file or directory mv: cannot stat ‘SRX494840.20.bb’: No such file or directory