Job ID = 6507826 SRX = SRX494830 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T13:15:19 prefetch.2.10.7: 1) Downloading 'SRR1198362'... 2020-06-26T13:15:19 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T13:17:14 prefetch.2.10.7: HTTPS download succeed 2020-06-26T13:17:14 prefetch.2.10.7: 1) 'SRR1198362' was downloaded successfully Read 28506467 spots for SRR1198362/SRR1198362.sra Written 28506467 spots for SRR1198362/SRR1198362.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: 00:04:04 28506467 reads; of these: 28506467 (100.00%) were unpaired; of these: 7643121 (26.81%) aligned 0 times 17051544 (59.82%) aligned exactly 1 time 3811802 (13.37%) aligned >1 times 73.19% overall alignment rate Time searching: 00:04:04 Overall time: 00:04:04 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] 3134005 / 20863346 = 0.1502 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 22:28:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494830/SRX494830.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494830/SRX494830.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494830/SRX494830.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494830/SRX494830.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 22:28:33: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:28:33: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:28:39: 1000000 INFO @ Fri, 26 Jun 2020 22:28:44: 2000000 INFO @ Fri, 26 Jun 2020 22:28:50: 3000000 INFO @ Fri, 26 Jun 2020 22:28:56: 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 22:29:02: 5000000 INFO @ Fri, 26 Jun 2020 22:29:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494830/SRX494830.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494830/SRX494830.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494830/SRX494830.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494830/SRX494830.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 22:29:03: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:29:03: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:29:07: 6000000 INFO @ Fri, 26 Jun 2020 22:29:10: 1000000 INFO @ Fri, 26 Jun 2020 22:29:13: 7000000 INFO @ Fri, 26 Jun 2020 22:29:17: 2000000 INFO @ Fri, 26 Jun 2020 22:29:19: 8000000 INFO @ Fri, 26 Jun 2020 22:29:24: 3000000 INFO @ Fri, 26 Jun 2020 22:29:25: 9000000 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 22:29:31: 10000000 INFO @ Fri, 26 Jun 2020 22:29:31: 4000000 INFO @ Fri, 26 Jun 2020 22:29:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494830/SRX494830.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494830/SRX494830.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494830/SRX494830.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494830/SRX494830.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 22:29:33: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:29:33: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:29:37: 11000000 INFO @ Fri, 26 Jun 2020 22:29:39: 5000000 INFO @ Fri, 26 Jun 2020 22:29:41: 1000000 INFO @ Fri, 26 Jun 2020 22:29:43: 12000000 INFO @ Fri, 26 Jun 2020 22:29:47: 6000000 INFO @ Fri, 26 Jun 2020 22:29:49: 2000000 INFO @ Fri, 26 Jun 2020 22:29:49: 13000000 INFO @ Fri, 26 Jun 2020 22:29:54: 7000000 INFO @ Fri, 26 Jun 2020 22:29:56: 14000000 INFO @ Fri, 26 Jun 2020 22:29:57: 3000000 INFO @ Fri, 26 Jun 2020 22:30:02: 15000000 INFO @ Fri, 26 Jun 2020 22:30:02: 8000000 INFO @ Fri, 26 Jun 2020 22:30:04: 4000000 INFO @ Fri, 26 Jun 2020 22:30:08: 16000000 INFO @ Fri, 26 Jun 2020 22:30:09: 9000000 INFO @ Fri, 26 Jun 2020 22:30:12: 5000000 INFO @ Fri, 26 Jun 2020 22:30:14: 17000000 INFO @ Fri, 26 Jun 2020 22:30:16: 10000000 INFO @ Fri, 26 Jun 2020 22:30:18: 6000000 INFO @ Fri, 26 Jun 2020 22:30:19: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 22:30:19: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 22:30:19: #1 total tags in treatment: 17729341 INFO @ Fri, 26 Jun 2020 22:30:19: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:30:19: #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 22:30:19: #1 tags after filtering in treatment: 17729341 INFO @ Fri, 26 Jun 2020 22:30:19: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:30:19: #1 finished! INFO @ Fri, 26 Jun 2020 22:30:19: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:30:19: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:30:20: #2 number of paired peaks: 222 WARNING @ Fri, 26 Jun 2020 22:30:20: Fewer paired peaks (222) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 222 pairs to build model! INFO @ Fri, 26 Jun 2020 22:30:20: start model_add_line... INFO @ Fri, 26 Jun 2020 22:30:20: start X-correlation... INFO @ Fri, 26 Jun 2020 22:30:20: end of X-cor INFO @ Fri, 26 Jun 2020 22:30:20: #2 finished! INFO @ Fri, 26 Jun 2020 22:30:20: #2 predicted fragment length is 0 bps INFO @ Fri, 26 Jun 2020 22:30:20: #2 alternative fragment length(s) may be 0,32,549 bps INFO @ Fri, 26 Jun 2020 22:30:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494830/SRX494830.05_model.r WARNING @ Fri, 26 Jun 2020 22:30:20: #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 22:30:20: #2 You may need to consider one of the other alternative d(s): 0,32,549 WARNING @ Fri, 26 Jun 2020 22:30:20: #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 22:30:20: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:30:20: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:30:23: 11000000 INFO @ Fri, 26 Jun 2020 22:30:25: 7000000 INFO @ Fri, 26 Jun 2020 22:30:29: 12000000 INFO @ Fri, 26 Jun 2020 22:30:31: 8000000 INFO @ Fri, 26 Jun 2020 22:30:36: 13000000 INFO @ Fri, 26 Jun 2020 22:30:37: 9000000 INFO @ Fri, 26 Jun 2020 22:30:43: 10000000 INFO @ Fri, 26 Jun 2020 22:30:43: 14000000 INFO @ Fri, 26 Jun 2020 22:30:50: 11000000 INFO @ Fri, 26 Jun 2020 22:30:50: 15000000 INFO @ Fri, 26 Jun 2020 22:30:57: 16000000 INFO @ Fri, 26 Jun 2020 22:30:57: 12000000 INFO @ Fri, 26 Jun 2020 22:31:03: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 22:31:03: 17000000 INFO @ Fri, 26 Jun 2020 22:31:08: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 22:31:08: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 22:31:08: #1 total tags in treatment: 17729341 INFO @ Fri, 26 Jun 2020 22:31:08: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:31:08: #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 22:31:09: #1 tags after filtering in treatment: 17729341 INFO @ Fri, 26 Jun 2020 22:31:09: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:31:09: #1 finished! INFO @ Fri, 26 Jun 2020 22:31:09: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:31:09: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:31:09: 14000000 INFO @ Fri, 26 Jun 2020 22:31:10: #2 number of paired peaks: 222 WARNING @ Fri, 26 Jun 2020 22:31:10: Fewer paired peaks (222) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 222 pairs to build model! INFO @ Fri, 26 Jun 2020 22:31:10: start model_add_line... INFO @ Fri, 26 Jun 2020 22:31:10: start X-correlation... INFO @ Fri, 26 Jun 2020 22:31:10: end of X-cor INFO @ Fri, 26 Jun 2020 22:31:10: #2 finished! INFO @ Fri, 26 Jun 2020 22:31:10: #2 predicted fragment length is 0 bps INFO @ Fri, 26 Jun 2020 22:31:10: #2 alternative fragment length(s) may be 0,32,549 bps INFO @ Fri, 26 Jun 2020 22:31:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494830/SRX494830.10_model.r WARNING @ Fri, 26 Jun 2020 22:31:10: #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 22:31:10: #2 You may need to consider one of the other alternative d(s): 0,32,549 WARNING @ Fri, 26 Jun 2020 22:31:10: #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 22:31:10: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:31:10: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:31:15: 15000000 INFO @ Fri, 26 Jun 2020 22:31:21: 16000000 INFO @ Fri, 26 Jun 2020 22:31:27: 17000000 INFO @ Fri, 26 Jun 2020 22:31:31: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 22:31:31: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 22:31:31: #1 total tags in treatment: 17729341 INFO @ Fri, 26 Jun 2020 22:31:31: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:31:31: #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 22:31:31: #1 tags after filtering in treatment: 17729341 INFO @ Fri, 26 Jun 2020 22:31:31: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:31:31: #1 finished! INFO @ Fri, 26 Jun 2020 22:31:31: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:31:31: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:31:33: #2 number of paired peaks: 222 WARNING @ Fri, 26 Jun 2020 22:31:33: Fewer paired peaks (222) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 222 pairs to build model! INFO @ Fri, 26 Jun 2020 22:31:33: start model_add_line... INFO @ Fri, 26 Jun 2020 22:31:33: start X-correlation... INFO @ Fri, 26 Jun 2020 22:31:33: end of X-cor INFO @ Fri, 26 Jun 2020 22:31:33: #2 finished! INFO @ Fri, 26 Jun 2020 22:31:33: #2 predicted fragment length is 0 bps INFO @ Fri, 26 Jun 2020 22:31:33: #2 alternative fragment length(s) may be 0,32,549 bps INFO @ Fri, 26 Jun 2020 22:31:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494830/SRX494830.20_model.r WARNING @ Fri, 26 Jun 2020 22:31:33: #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 22:31:33: #2 You may need to consider one of the other alternative d(s): 0,32,549 WARNING @ Fri, 26 Jun 2020 22:31:33: #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 22:31:33: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:31:33: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 /var/spool/uge/it018/job_scripts/6507826: line 274: 8054 Terminated MACS $i /var/spool/uge/it018/job_scripts/6507826: line 274: 8148 Terminated MACS $i /var/spool/uge/it018/job_scripts/6507826: line 274: 8298 Terminated MACS $i ls: cannot access SRX494830.05.bed: No such file or directory mv: cannot stat ‘SRX494830.05.bed’: No such file or directory mv: cannot stat ‘SRX494830.05.bb’: No such file or directory ls: cannot access SRX494830.10.bed: No such file or directory mv: cannot stat ‘SRX494830.10.bed’: No such file or directory mv: cannot stat ‘SRX494830.10.bb’: No such file or directory ls: cannot access SRX494830.20.bed: No such file or directory mv: cannot stat ‘SRX494830.20.bed’: No such file or directory mv: cannot stat ‘SRX494830.20.bb’: No such file or directory