Job ID = 6527416 SRX = SRX5402765 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T12:12:30 prefetch.2.10.7: 1) Downloading 'SRR8602999'... 2020-06-29T12:12:30 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T12:15:17 prefetch.2.10.7: HTTPS download succeed 2020-06-29T12:15:17 prefetch.2.10.7: 1) 'SRR8602999' was downloaded successfully Read 28004945 spots for SRR8602999/SRR8602999.sra Written 28004945 spots for SRR8602999/SRR8602999.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: 00:06:09 28004945 reads; of these: 28004945 (100.00%) were unpaired; of these: 1172153 (4.19%) aligned 0 times 22114145 (78.97%) aligned exactly 1 time 4718647 (16.85%) aligned >1 times 95.81% overall alignment rate Time searching: 00:06:09 Overall time: 00:06:10 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] 7441993 / 26832792 = 0.2773 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 21:39:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402765/SRX5402765.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402765/SRX5402765.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402765/SRX5402765.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402765/SRX5402765.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 21:39:04: #1 read tag files... INFO @ Mon, 29 Jun 2020 21:39:04: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 21:39:10: 1000000 INFO @ Mon, 29 Jun 2020 21:39:15: 2000000 INFO @ Mon, 29 Jun 2020 21:39:20: 3000000 INFO @ Mon, 29 Jun 2020 21:39:26: 4000000 INFO @ Mon, 29 Jun 2020 21:39:31: 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 @ Mon, 29 Jun 2020 21:39:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402765/SRX5402765.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402765/SRX5402765.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402765/SRX5402765.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402765/SRX5402765.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 21:39:34: #1 read tag files... INFO @ Mon, 29 Jun 2020 21:39:34: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 21:39:36: 6000000 INFO @ Mon, 29 Jun 2020 21:39:41: 1000000 INFO @ Mon, 29 Jun 2020 21:39:42: 7000000 INFO @ Mon, 29 Jun 2020 21:39:47: 2000000 INFO @ Mon, 29 Jun 2020 21:39:47: 8000000 INFO @ Mon, 29 Jun 2020 21:39:52: 9000000 INFO @ Mon, 29 Jun 2020 21:39:53: 3000000 INFO @ Mon, 29 Jun 2020 21:39:58: 10000000 INFO @ Mon, 29 Jun 2020 21:39:59: 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 @ Mon, 29 Jun 2020 21:40:03: 11000000 INFO @ Mon, 29 Jun 2020 21:40:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402765/SRX5402765.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402765/SRX5402765.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402765/SRX5402765.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402765/SRX5402765.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 21:40:04: #1 read tag files... INFO @ Mon, 29 Jun 2020 21:40:04: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 21:40:05: 5000000 INFO @ Mon, 29 Jun 2020 21:40:09: 12000000 INFO @ Mon, 29 Jun 2020 21:40:10: 1000000 INFO @ Mon, 29 Jun 2020 21:40:11: 6000000 INFO @ Mon, 29 Jun 2020 21:40:15: 13000000 INFO @ Mon, 29 Jun 2020 21:40:16: 2000000 INFO @ Mon, 29 Jun 2020 21:40:17: 7000000 INFO @ Mon, 29 Jun 2020 21:40:20: 14000000 INFO @ Mon, 29 Jun 2020 21:40:22: 3000000 INFO @ Mon, 29 Jun 2020 21:40:23: 8000000 INFO @ Mon, 29 Jun 2020 21:40:26: 15000000 INFO @ Mon, 29 Jun 2020 21:40:27: 4000000 INFO @ Mon, 29 Jun 2020 21:40:29: 9000000 INFO @ Mon, 29 Jun 2020 21:40:32: 16000000 INFO @ Mon, 29 Jun 2020 21:40:33: 5000000 INFO @ Mon, 29 Jun 2020 21:40:35: 10000000 INFO @ Mon, 29 Jun 2020 21:40:38: 17000000 INFO @ Mon, 29 Jun 2020 21:40:39: 6000000 INFO @ Mon, 29 Jun 2020 21:40:41: 11000000 INFO @ Mon, 29 Jun 2020 21:40:43: 18000000 INFO @ Mon, 29 Jun 2020 21:40:45: 7000000 INFO @ Mon, 29 Jun 2020 21:40:47: 12000000 INFO @ Mon, 29 Jun 2020 21:40:49: 19000000 INFO @ Mon, 29 Jun 2020 21:40:50: 8000000 INFO @ Mon, 29 Jun 2020 21:40:52: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 21:40:52: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 21:40:52: #1 total tags in treatment: 19390799 INFO @ Mon, 29 Jun 2020 21:40:52: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 21:40:52: #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 21:40:52: #1 tags after filtering in treatment: 19390799 INFO @ Mon, 29 Jun 2020 21:40:52: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 21:40:52: #1 finished! INFO @ Mon, 29 Jun 2020 21:40:52: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 21:40:52: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 21:40:53: #2 number of paired peaks: 294 WARNING @ Mon, 29 Jun 2020 21:40:53: Fewer paired peaks (294) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 294 pairs to build model! INFO @ Mon, 29 Jun 2020 21:40:53: start model_add_line... INFO @ Mon, 29 Jun 2020 21:40:53: 13000000 INFO @ Mon, 29 Jun 2020 21:40:53: start X-correlation... INFO @ Mon, 29 Jun 2020 21:40:53: end of X-cor INFO @ Mon, 29 Jun 2020 21:40:53: #2 finished! INFO @ Mon, 29 Jun 2020 21:40:53: #2 predicted fragment length is 0 bps INFO @ Mon, 29 Jun 2020 21:40:53: #2 alternative fragment length(s) may be 0,538,588 bps INFO @ Mon, 29 Jun 2020 21:40:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402765/SRX5402765.05_model.r WARNING @ Mon, 29 Jun 2020 21:40:53: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 21:40:53: #2 You may need to consider one of the other alternative d(s): 0,538,588 WARNING @ Mon, 29 Jun 2020 21:40:53: #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 21:40:53: #3 Call peaks... INFO @ Mon, 29 Jun 2020 21:40:53: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 21:40:56: 9000000 INFO @ Mon, 29 Jun 2020 21:40:59: 14000000 INFO @ Mon, 29 Jun 2020 21:41:01: 10000000 INFO @ Mon, 29 Jun 2020 21:41:05: 15000000 INFO @ Mon, 29 Jun 2020 21:41:06: 11000000 INFO @ Mon, 29 Jun 2020 21:41:11: 12000000 INFO @ Mon, 29 Jun 2020 21:41:11: 16000000 INFO @ Mon, 29 Jun 2020 21:41:16: 13000000 INFO @ Mon, 29 Jun 2020 21:41:17: 17000000 INFO @ Mon, 29 Jun 2020 21:41:21: 14000000 INFO @ Mon, 29 Jun 2020 21:41:23: 18000000 INFO @ Mon, 29 Jun 2020 21:41:26: 15000000 INFO @ Mon, 29 Jun 2020 21:41:29: 19000000 INFO @ Mon, 29 Jun 2020 21:41:31: 16000000 INFO @ Mon, 29 Jun 2020 21:41:32: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 21:41:32: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 21:41:32: #1 total tags in treatment: 19390799 INFO @ Mon, 29 Jun 2020 21:41:32: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 21:41:32: #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 21:41:32: #1 tags after filtering in treatment: 19390799 INFO @ Mon, 29 Jun 2020 21:41:32: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 21:41:32: #1 finished! INFO @ Mon, 29 Jun 2020 21:41:32: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 21:41:32: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 21:41:33: #2 number of paired peaks: 294 WARNING @ Mon, 29 Jun 2020 21:41:33: Fewer paired peaks (294) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 294 pairs to build model! INFO @ Mon, 29 Jun 2020 21:41:33: start model_add_line... INFO @ Mon, 29 Jun 2020 21:41:34: start X-correlation... INFO @ Mon, 29 Jun 2020 21:41:34: end of X-cor INFO @ Mon, 29 Jun 2020 21:41:34: #2 finished! INFO @ Mon, 29 Jun 2020 21:41:34: #2 predicted fragment length is 0 bps INFO @ Mon, 29 Jun 2020 21:41:34: #2 alternative fragment length(s) may be 0,538,588 bps INFO @ Mon, 29 Jun 2020 21:41:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402765/SRX5402765.10_model.r WARNING @ Mon, 29 Jun 2020 21:41:34: #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 21:41:34: #2 You may need to consider one of the other alternative d(s): 0,538,588 WARNING @ Mon, 29 Jun 2020 21:41:34: #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 21:41:34: #3 Call peaks... INFO @ Mon, 29 Jun 2020 21:41:34: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 21:41:36: 17000000 INFO @ Mon, 29 Jun 2020 21:41:41: 18000000 INFO @ Mon, 29 Jun 2020 21:41:46: 19000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 29 Jun 2020 21:41:48: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 21:41:48: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 21:41:48: #1 total tags in treatment: 19390799 INFO @ Mon, 29 Jun 2020 21:41:48: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 21:41:48: #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 21:41:49: #1 tags after filtering in treatment: 19390799 INFO @ Mon, 29 Jun 2020 21:41:49: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 21:41:49: #1 finished! INFO @ Mon, 29 Jun 2020 21:41:49: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 21:41:49: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 21:41:50: #2 number of paired peaks: 294 WARNING @ Mon, 29 Jun 2020 21:41:50: Fewer paired peaks (294) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 294 pairs to build model! INFO @ Mon, 29 Jun 2020 21:41:50: start model_add_line... INFO @ Mon, 29 Jun 2020 21:41:50: start X-correlation... INFO @ Mon, 29 Jun 2020 21:41:50: end of X-cor INFO @ Mon, 29 Jun 2020 21:41:50: #2 finished! INFO @ Mon, 29 Jun 2020 21:41:50: #2 predicted fragment length is 0 bps INFO @ Mon, 29 Jun 2020 21:41:50: #2 alternative fragment length(s) may be 0,538,588 bps INFO @ Mon, 29 Jun 2020 21:41:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402765/SRX5402765.20_model.r WARNING @ Mon, 29 Jun 2020 21:41:50: #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 21:41:50: #2 You may need to consider one of the other alternative d(s): 0,538,588 WARNING @ Mon, 29 Jun 2020 21:41:50: #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 21:41:50: #3 Call peaks... INFO @ Mon, 29 Jun 2020 21:41:50: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 /var/spool/uge/it034/job_scripts/6527416: line 293: 19654 Terminated MACS $i /var/spool/uge/it034/job_scripts/6527416: line 293: 19765 Terminated MACS $i /var/spool/uge/it034/job_scripts/6527416: line 293: 20018 Terminated MACS $i ls: cannot access SRX5402765.05.bed: No such file or directory mv: cannot stat ‘SRX5402765.05.bed’: No such file or directory mv: cannot stat ‘SRX5402765.05.bb’: No such file or directory ls: cannot access SRX5402765.10.bed: No such file or directory mv: cannot stat ‘SRX5402765.10.bed’: No such file or directory mv: cannot stat ‘SRX5402765.10.bb’: No such file or directory ls: cannot access SRX5402765.20.bed: No such file or directory mv: cannot stat ‘SRX5402765.20.bed’: No such file or directory mv: cannot stat ‘SRX5402765.20.bb’: No such file or directory