Job ID = 6497418 SRX = SRX494830 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T21:53:59 prefetch.2.10.7: 1) Downloading 'SRR1198362'... 2020-06-25T21:53:59 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T21:56:10 prefetch.2.10.7: HTTPS download succeed 2020-06-25T21:56:10 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: 00:04:32 28506467 reads; of these: 28506467 (100.00%) were unpaired; of these: 7645503 (26.82%) aligned 0 times 17049413 (59.81%) aligned exactly 1 time 3811551 (13.37%) aligned >1 times 73.18% overall alignment rate Time searching: 00:04:32 Overall time: 00:04:32 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] 3133497 / 20860964 = 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 07:07:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494830/SRX494830.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494830/SRX494830.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494830/SRX494830.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/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 07:07:00: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:07:00: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:07:06: 1000000 INFO @ Fri, 26 Jun 2020 07:07:11: 2000000 INFO @ Fri, 26 Jun 2020 07:07:17: 3000000 INFO @ Fri, 26 Jun 2020 07:07:22: 4000000 INFO @ Fri, 26 Jun 2020 07:07:28: 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 @ Fri, 26 Jun 2020 07:07:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494830/SRX494830.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494830/SRX494830.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494830/SRX494830.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/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 07:07:30: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:07:30: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:07:33: 6000000 INFO @ Fri, 26 Jun 2020 07:07:36: 1000000 INFO @ Fri, 26 Jun 2020 07:07:39: 7000000 INFO @ Fri, 26 Jun 2020 07:07:42: 2000000 INFO @ Fri, 26 Jun 2020 07:07:45: 8000000 INFO @ Fri, 26 Jun 2020 07:07:48: 3000000 INFO @ Fri, 26 Jun 2020 07:07:51: 9000000 INFO @ Fri, 26 Jun 2020 07:07:54: 4000000 INFO @ Fri, 26 Jun 2020 07:07:57: 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 @ Fri, 26 Jun 2020 07:08:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494830/SRX494830.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494830/SRX494830.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494830/SRX494830.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/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 07:08:00: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:08:00: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:08:00: 5000000 INFO @ Fri, 26 Jun 2020 07:08:04: 11000000 INFO @ Fri, 26 Jun 2020 07:08:07: 1000000 INFO @ Fri, 26 Jun 2020 07:08:07: 6000000 INFO @ Fri, 26 Jun 2020 07:08:10: 12000000 INFO @ Fri, 26 Jun 2020 07:08:13: 2000000 INFO @ Fri, 26 Jun 2020 07:08:13: 7000000 INFO @ Fri, 26 Jun 2020 07:08:16: 13000000 INFO @ Fri, 26 Jun 2020 07:08:19: 3000000 INFO @ Fri, 26 Jun 2020 07:08:19: 8000000 INFO @ Fri, 26 Jun 2020 07:08:22: 14000000 INFO @ Fri, 26 Jun 2020 07:08:25: 4000000 INFO @ Fri, 26 Jun 2020 07:08:26: 9000000 INFO @ Fri, 26 Jun 2020 07:08:28: 15000000 INFO @ Fri, 26 Jun 2020 07:08:32: 5000000 INFO @ Fri, 26 Jun 2020 07:08:32: 10000000 INFO @ Fri, 26 Jun 2020 07:08:34: 16000000 INFO @ Fri, 26 Jun 2020 07:08:38: 6000000 INFO @ Fri, 26 Jun 2020 07:08:38: 11000000 INFO @ Fri, 26 Jun 2020 07:08:40: 17000000 INFO @ Fri, 26 Jun 2020 07:08:44: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 07:08:44: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 07:08:44: #1 total tags in treatment: 17727467 INFO @ Fri, 26 Jun 2020 07:08:44: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:08:44: #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 07:08:44: 7000000 INFO @ Fri, 26 Jun 2020 07:08:44: 12000000 INFO @ Fri, 26 Jun 2020 07:08:44: #1 tags after filtering in treatment: 17727467 INFO @ Fri, 26 Jun 2020 07:08:44: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:08:44: #1 finished! INFO @ Fri, 26 Jun 2020 07:08:44: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:08:44: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:08:46: #2 number of paired peaks: 224 WARNING @ Fri, 26 Jun 2020 07:08:46: Fewer paired peaks (224) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 224 pairs to build model! INFO @ Fri, 26 Jun 2020 07:08:46: start model_add_line... INFO @ Fri, 26 Jun 2020 07:08:46: start X-correlation... INFO @ Fri, 26 Jun 2020 07:08:46: end of X-cor INFO @ Fri, 26 Jun 2020 07:08:46: #2 finished! INFO @ Fri, 26 Jun 2020 07:08:46: #2 predicted fragment length is 0 bps INFO @ Fri, 26 Jun 2020 07:08:46: #2 alternative fragment length(s) may be 0,32,445,548 bps INFO @ Fri, 26 Jun 2020 07:08:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494830/SRX494830.05_model.r INFO @ Fri, 26 Jun 2020 07:08:50: 13000000 INFO @ Fri, 26 Jun 2020 07:08:50: 8000000 INFO @ Fri, 26 Jun 2020 07:08:56: 14000000 INFO @ Fri, 26 Jun 2020 07:08:56: 9000000 WARNING @ Fri, 26 Jun 2020 07:08:59: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:08:59: #2 You may need to consider one of the other alternative d(s): 0,32,445,548 WARNING @ Fri, 26 Jun 2020 07:08:59: #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 07:08:59: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:08:59: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:09:02: 15000000 INFO @ Fri, 26 Jun 2020 07:09:02: 10000000 INFO @ Fri, 26 Jun 2020 07:09:08: 16000000 INFO @ Fri, 26 Jun 2020 07:09:08: 11000000 INFO @ Fri, 26 Jun 2020 07:09:14: 17000000 INFO @ Fri, 26 Jun 2020 07:09:14: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 07:09:19: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 07:09:19: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 07:09:19: #1 total tags in treatment: 17727467 INFO @ Fri, 26 Jun 2020 07:09:19: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:09:19: #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 07:09:19: #1 tags after filtering in treatment: 17727467 INFO @ Fri, 26 Jun 2020 07:09:19: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:09:19: #1 finished! INFO @ Fri, 26 Jun 2020 07:09:19: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:09:19: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:09:20: #2 number of paired peaks: 224 WARNING @ Fri, 26 Jun 2020 07:09:20: Fewer paired peaks (224) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 224 pairs to build model! INFO @ Fri, 26 Jun 2020 07:09:20: start model_add_line... INFO @ Fri, 26 Jun 2020 07:09:20: start X-correlation... INFO @ Fri, 26 Jun 2020 07:09:20: end of X-cor INFO @ Fri, 26 Jun 2020 07:09:20: #2 finished! INFO @ Fri, 26 Jun 2020 07:09:20: #2 predicted fragment length is 0 bps INFO @ Fri, 26 Jun 2020 07:09:20: #2 alternative fragment length(s) may be 0,32,445,548 bps INFO @ Fri, 26 Jun 2020 07:09:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494830/SRX494830.10_model.r INFO @ Fri, 26 Jun 2020 07:09:20: 13000000 INFO @ Fri, 26 Jun 2020 07:09:26: 14000000 INFO @ Fri, 26 Jun 2020 07:09:31: 15000000 WARNING @ Fri, 26 Jun 2020 07:09:35: #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 07:09:35: #2 You may need to consider one of the other alternative d(s): 0,32,445,548 WARNING @ Fri, 26 Jun 2020 07:09:35: #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 07:09:35: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:09:35: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:09:37: 16000000 INFO @ Fri, 26 Jun 2020 07:09:42: 17000000 INFO @ Fri, 26 Jun 2020 07:09:46: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 07:09:46: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 07:09:46: #1 total tags in treatment: 17727467 INFO @ Fri, 26 Jun 2020 07:09:46: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:09:46: #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 07:09:46: #1 tags after filtering in treatment: 17727467 INFO @ Fri, 26 Jun 2020 07:09:46: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:09:46: #1 finished! INFO @ Fri, 26 Jun 2020 07:09:46: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:09:46: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:09:48: #2 number of paired peaks: 224 WARNING @ Fri, 26 Jun 2020 07:09:48: Fewer paired peaks (224) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 224 pairs to build model! INFO @ Fri, 26 Jun 2020 07:09:48: start model_add_line... INFO @ Fri, 26 Jun 2020 07:09:48: start X-correlation... INFO @ Fri, 26 Jun 2020 07:09:48: end of X-cor INFO @ Fri, 26 Jun 2020 07:09:48: #2 finished! INFO @ Fri, 26 Jun 2020 07:09:48: #2 predicted fragment length is 0 bps INFO @ Fri, 26 Jun 2020 07:09:48: #2 alternative fragment length(s) may be 0,32,445,548 bps INFO @ Fri, 26 Jun 2020 07:09:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494830/SRX494830.20_model.r WARNING @ Fri, 26 Jun 2020 07:09:55: #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 07:09:55: #2 You may need to consider one of the other alternative d(s): 0,32,445,548 WARNING @ Fri, 26 Jun 2020 07:09:55: #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 07:09:55: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:09:55: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 /var/spool/uge/at148/job_scripts/6497418: line 274: 72839 Terminated MACS $i /var/spool/uge/at148/job_scripts/6497418: line 274: 74581 Terminated MACS $i /var/spool/uge/at148/job_scripts/6497418: line 274: 76421 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