Job ID = 6527401 SRX = SRX1078722 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T12:24:06 prefetch.2.10.7: 1) Downloading 'SRR2084329'... 2020-06-29T12:24:06 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T12:28:58 prefetch.2.10.7: HTTPS download succeed 2020-06-29T12:28:58 prefetch.2.10.7: 1) 'SRR2084329' was downloaded successfully Read 27945127 spots for SRR2084329/SRR2084329.sra Written 27945127 spots for SRR2084329/SRR2084329.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: 00:06:26 27945127 reads; of these: 27945127 (100.00%) were unpaired; of these: 371686 (1.33%) aligned 0 times 23235989 (83.15%) aligned exactly 1 time 4337452 (15.52%) aligned >1 times 98.67% overall alignment rate Time searching: 00:06:27 Overall time: 00:06:27 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 12 files... [bam_rmdupse_core] 4042182 / 27573441 = 0.1466 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 @ Mon, 29 Jun 2020 21:54:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX1078722/SRX1078722.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX1078722/SRX1078722.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX1078722/SRX1078722.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX1078722/SRX1078722.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 @ Mon, 29 Jun 2020 21:54:18: #1 read tag files... INFO @ Mon, 29 Jun 2020 21:54:18: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 21:54:25: 1000000 INFO @ Mon, 29 Jun 2020 21:54:31: 2000000 INFO @ Mon, 29 Jun 2020 21:54:38: 3000000 INFO @ Mon, 29 Jun 2020 21:54:45: 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 @ Mon, 29 Jun 2020 21:54:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX1078722/SRX1078722.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX1078722/SRX1078722.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX1078722/SRX1078722.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX1078722/SRX1078722.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 @ Mon, 29 Jun 2020 21:54:48: #1 read tag files... INFO @ Mon, 29 Jun 2020 21:54:48: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 21:54:52: 5000000 INFO @ Mon, 29 Jun 2020 21:54:54: 1000000 INFO @ Mon, 29 Jun 2020 21:54:59: 6000000 INFO @ Mon, 29 Jun 2020 21:55:00: 2000000 INFO @ Mon, 29 Jun 2020 21:55:05: 3000000 INFO @ Mon, 29 Jun 2020 21:55:05: 7000000 INFO @ Mon, 29 Jun 2020 21:55:11: 4000000 INFO @ Mon, 29 Jun 2020 21:55:12: 8000000 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 @ Mon, 29 Jun 2020 21:55:16: 5000000 INFO @ Mon, 29 Jun 2020 21:55:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX1078722/SRX1078722.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX1078722/SRX1078722.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX1078722/SRX1078722.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX1078722/SRX1078722.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 @ Mon, 29 Jun 2020 21:55:18: #1 read tag files... INFO @ Mon, 29 Jun 2020 21:55:18: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 21:55:19: 9000000 INFO @ Mon, 29 Jun 2020 21:55:22: 6000000 INFO @ Mon, 29 Jun 2020 21:55:25: 1000000 INFO @ Mon, 29 Jun 2020 21:55:26: 10000000 INFO @ Mon, 29 Jun 2020 21:55:27: 7000000 INFO @ Mon, 29 Jun 2020 21:55:32: 2000000 INFO @ Mon, 29 Jun 2020 21:55:32: 11000000 INFO @ Mon, 29 Jun 2020 21:55:33: 8000000 INFO @ Mon, 29 Jun 2020 21:55:38: 9000000 INFO @ Mon, 29 Jun 2020 21:55:39: 3000000 INFO @ Mon, 29 Jun 2020 21:55:40: 12000000 INFO @ Mon, 29 Jun 2020 21:55:44: 10000000 INFO @ Mon, 29 Jun 2020 21:55:46: 4000000 INFO @ Mon, 29 Jun 2020 21:55:46: 13000000 INFO @ Mon, 29 Jun 2020 21:55:49: 11000000 INFO @ Mon, 29 Jun 2020 21:55:53: 14000000 INFO @ Mon, 29 Jun 2020 21:55:53: 5000000 INFO @ Mon, 29 Jun 2020 21:55:55: 12000000 INFO @ Mon, 29 Jun 2020 21:56:00: 15000000 INFO @ Mon, 29 Jun 2020 21:56:00: 6000000 INFO @ Mon, 29 Jun 2020 21:56:00: 13000000 INFO @ Mon, 29 Jun 2020 21:56:05: 14000000 INFO @ Mon, 29 Jun 2020 21:56:07: 7000000 INFO @ Mon, 29 Jun 2020 21:56:07: 16000000 INFO @ Mon, 29 Jun 2020 21:56:11: 15000000 INFO @ Mon, 29 Jun 2020 21:56:14: 8000000 INFO @ Mon, 29 Jun 2020 21:56:14: 17000000 INFO @ Mon, 29 Jun 2020 21:56:16: 16000000 INFO @ Mon, 29 Jun 2020 21:56:21: 9000000 INFO @ Mon, 29 Jun 2020 21:56:21: 18000000 INFO @ Mon, 29 Jun 2020 21:56:22: 17000000 INFO @ Mon, 29 Jun 2020 21:56:27: 18000000 INFO @ Mon, 29 Jun 2020 21:56:28: 10000000 INFO @ Mon, 29 Jun 2020 21:56:28: 19000000 INFO @ Mon, 29 Jun 2020 21:56:33: 19000000 INFO @ Mon, 29 Jun 2020 21:56:35: 20000000 INFO @ Mon, 29 Jun 2020 21:56:35: 11000000 INFO @ Mon, 29 Jun 2020 21:56:38: 20000000 INFO @ Mon, 29 Jun 2020 21:56:42: 12000000 INFO @ Mon, 29 Jun 2020 21:56:42: 21000000 INFO @ Mon, 29 Jun 2020 21:56:44: 21000000 INFO @ Mon, 29 Jun 2020 21:56:49: 13000000 INFO @ Mon, 29 Jun 2020 21:56:49: 22000000 INFO @ Mon, 29 Jun 2020 21:56:49: 22000000 INFO @ Mon, 29 Jun 2020 21:56:55: 23000000 INFO @ Mon, 29 Jun 2020 21:56:55: 14000000 INFO @ Mon, 29 Jun 2020 21:56:56: 23000000 INFO @ Mon, 29 Jun 2020 21:56:58: #1 tag size is determined as 51 bps INFO @ Mon, 29 Jun 2020 21:56:58: #1 tag size = 51 INFO @ Mon, 29 Jun 2020 21:56:58: #1 total tags in treatment: 23531259 INFO @ Mon, 29 Jun 2020 21:56:58: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 21:56:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 21:56:58: #1 tags after filtering in treatment: 23531259 INFO @ Mon, 29 Jun 2020 21:56:58: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 21:56:58: #1 finished! INFO @ Mon, 29 Jun 2020 21:56:58: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 21:56:58: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 21:57:00: #1 tag size is determined as 51 bps INFO @ Mon, 29 Jun 2020 21:57:00: #1 tag size = 51 INFO @ Mon, 29 Jun 2020 21:57:00: #1 total tags in treatment: 23531259 INFO @ Mon, 29 Jun 2020 21:57:00: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 21:57:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 21:57:00: #2 number of paired peaks: 160 WARNING @ Mon, 29 Jun 2020 21:57:00: Fewer paired peaks (160) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 160 pairs to build model! INFO @ Mon, 29 Jun 2020 21:57:00: start model_add_line... INFO @ Mon, 29 Jun 2020 21:57:00: start X-correlation... INFO @ Mon, 29 Jun 2020 21:57:00: end of X-cor INFO @ Mon, 29 Jun 2020 21:57:00: #2 finished! INFO @ Mon, 29 Jun 2020 21:57:00: #2 predicted fragment length is 0 bps INFO @ Mon, 29 Jun 2020 21:57:00: #2 alternative fragment length(s) may be 0,32,567 bps INFO @ Mon, 29 Jun 2020 21:57:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX1078722/SRX1078722.10_model.r WARNING @ Mon, 29 Jun 2020 21:57:00: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 21:57:00: #2 You may need to consider one of the other alternative d(s): 0,32,567 WARNING @ Mon, 29 Jun 2020 21:57:00: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 21:57:00: #3 Call peaks... INFO @ Mon, 29 Jun 2020 21:57:00: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 21:57:00: #1 tags after filtering in treatment: 23531259 INFO @ Mon, 29 Jun 2020 21:57:00: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 21:57:00: #1 finished! INFO @ Mon, 29 Jun 2020 21:57:00: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 21:57:00: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 21:57:02: #2 number of paired peaks: 160 WARNING @ Mon, 29 Jun 2020 21:57:02: Fewer paired peaks (160) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 160 pairs to build model! INFO @ Mon, 29 Jun 2020 21:57:02: start model_add_line... INFO @ Mon, 29 Jun 2020 21:57:02: start X-correlation... INFO @ Mon, 29 Jun 2020 21:57:02: end of X-cor INFO @ Mon, 29 Jun 2020 21:57:02: #2 finished! INFO @ Mon, 29 Jun 2020 21:57:02: #2 predicted fragment length is 0 bps INFO @ Mon, 29 Jun 2020 21:57:02: #2 alternative fragment length(s) may be 0,32,567 bps INFO @ Mon, 29 Jun 2020 21:57:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX1078722/SRX1078722.05_model.r WARNING @ Mon, 29 Jun 2020 21:57:02: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 21:57:02: #2 You may need to consider one of the other alternative d(s): 0,32,567 WARNING @ Mon, 29 Jun 2020 21:57:02: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 21:57:02: #3 Call peaks... INFO @ Mon, 29 Jun 2020 21:57:02: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 21:57:02: 15000000 INFO @ Mon, 29 Jun 2020 21:57:08: 16000000 INFO @ Mon, 29 Jun 2020 21:57:15: 17000000 INFO @ Mon, 29 Jun 2020 21:57:21: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 29 Jun 2020 21:57:28: 19000000 INFO @ Mon, 29 Jun 2020 21:57:34: 20000000 INFO @ Mon, 29 Jun 2020 21:57:40: 21000000 INFO @ Mon, 29 Jun 2020 21:57:45: 22000000 INFO @ Mon, 29 Jun 2020 21:57:51: 23000000 INFO @ Mon, 29 Jun 2020 21:57:54: #1 tag size is determined as 51 bps INFO @ Mon, 29 Jun 2020 21:57:54: #1 tag size = 51 INFO @ Mon, 29 Jun 2020 21:57:54: #1 total tags in treatment: 23531259 INFO @ Mon, 29 Jun 2020 21:57:54: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 21:57:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 21:57:55: #1 tags after filtering in treatment: 23531259 INFO @ Mon, 29 Jun 2020 21:57:55: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 21:57:55: #1 finished! INFO @ Mon, 29 Jun 2020 21:57:55: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 21:57:55: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 21:57:56: #2 number of paired peaks: 160 WARNING @ Mon, 29 Jun 2020 21:57:56: Fewer paired peaks (160) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 160 pairs to build model! INFO @ Mon, 29 Jun 2020 21:57:56: start model_add_line... INFO @ Mon, 29 Jun 2020 21:57:56: start X-correlation... INFO @ Mon, 29 Jun 2020 21:57:56: end of X-cor INFO @ Mon, 29 Jun 2020 21:57:56: #2 finished! INFO @ Mon, 29 Jun 2020 21:57:56: #2 predicted fragment length is 0 bps INFO @ Mon, 29 Jun 2020 21:57:56: #2 alternative fragment length(s) may be 0,32,567 bps INFO @ Mon, 29 Jun 2020 21:57:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX1078722/SRX1078722.20_model.r WARNING @ Mon, 29 Jun 2020 21:57:56: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 21:57:56: #2 You may need to consider one of the other alternative d(s): 0,32,567 WARNING @ Mon, 29 Jun 2020 21:57:56: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 21:57:56: #3 Call peaks... INFO @ Mon, 29 Jun 2020 21:57:56: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 /var/spool/uge/it007/job_scripts/6527401: line 293: 32675 Terminated MACS $i /var/spool/uge/it007/job_scripts/6527401: line 293: 324 Terminated MACS $i /var/spool/uge/it007/job_scripts/6527401: line 293: 419 Terminated MACS $i ls: cannot access SRX1078722.05.bed: No such file or directory mv: cannot stat ‘SRX1078722.05.bed’: No such file or directory mv: cannot stat ‘SRX1078722.05.bb’: No such file or directory ls: cannot access SRX1078722.10.bed: No such file or directory mv: cannot stat ‘SRX1078722.10.bed’: No such file or directory mv: cannot stat ‘SRX1078722.10.bb’: No such file or directory ls: cannot access SRX1078722.20.bed: No such file or directory mv: cannot stat ‘SRX1078722.20.bed’: No such file or directory mv: cannot stat ‘SRX1078722.20.bb’: No such file or directory