Job ID = 6458891 SRX = SRX5736591 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T13:01:19 prefetch.2.10.7: 1) Downloading 'SRR8957001'... 2020-06-21T13:01:19 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:03:19 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:03:20 prefetch.2.10.7: 'SRR8957001' is valid 2020-06-21T13:03:20 prefetch.2.10.7: 1) 'SRR8957001' was downloaded successfully Read 17421633 spots for SRR8957001/SRR8957001.sra Written 17421633 spots for SRR8957001/SRR8957001.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: 00:04:14 17421633 reads; of these: 17421633 (100.00%) were unpaired; of these: 278377 (1.60%) aligned 0 times 14183285 (81.41%) aligned exactly 1 time 2959971 (16.99%) aligned >1 times 98.40% overall alignment rate Time searching: 00:04:14 Overall time: 00:04:14 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 5791418 / 17143256 = 0.3378 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 @ Sun, 21 Jun 2020 22:12:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5736591/SRX5736591.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5736591/SRX5736591.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5736591/SRX5736591.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5736591/SRX5736591.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Sun, 21 Jun 2020 22:12:11: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:12:11: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:12:16: 1000000 INFO @ Sun, 21 Jun 2020 22:12:21: 2000000 INFO @ Sun, 21 Jun 2020 22:12:26: 3000000 INFO @ Sun, 21 Jun 2020 22:12:31: 4000000 INFO @ Sun, 21 Jun 2020 22:12:35: 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 @ Sun, 21 Jun 2020 22:12:40: 6000000 INFO @ Sun, 21 Jun 2020 22:12:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5736591/SRX5736591.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5736591/SRX5736591.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5736591/SRX5736591.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5736591/SRX5736591.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Sun, 21 Jun 2020 22:12:41: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:12:41: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:12:46: 7000000 INFO @ Sun, 21 Jun 2020 22:12:46: 1000000 INFO @ Sun, 21 Jun 2020 22:12:51: 8000000 INFO @ Sun, 21 Jun 2020 22:12:52: 2000000 INFO @ Sun, 21 Jun 2020 22:12:56: 9000000 INFO @ Sun, 21 Jun 2020 22:12:57: 3000000 INFO @ Sun, 21 Jun 2020 22:13:01: 10000000 INFO @ Sun, 21 Jun 2020 22:13:02: 4000000 INFO @ Sun, 21 Jun 2020 22:13:07: 11000000 INFO @ Sun, 21 Jun 2020 22:13:07: 5000000 INFO @ Sun, 21 Jun 2020 22:13:09: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:13:09: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:13:09: #1 total tags in treatment: 11351838 INFO @ Sun, 21 Jun 2020 22:13:09: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:13:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 22:13:09: #1 tags after filtering in treatment: 11351688 INFO @ Sun, 21 Jun 2020 22:13:09: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:13:09: #1 finished! INFO @ Sun, 21 Jun 2020 22:13:09: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:13:09: #2 looking for paired plus/minus strand peaks... 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 @ Sun, 21 Jun 2020 22:13:10: #2 number of paired peaks: 970 WARNING @ Sun, 21 Jun 2020 22:13:10: Fewer paired peaks (970) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 970 pairs to build model! INFO @ Sun, 21 Jun 2020 22:13:10: start model_add_line... INFO @ Sun, 21 Jun 2020 22:13:10: start X-correlation... INFO @ Sun, 21 Jun 2020 22:13:10: end of X-cor INFO @ Sun, 21 Jun 2020 22:13:10: #2 finished! INFO @ Sun, 21 Jun 2020 22:13:10: #2 predicted fragment length is 0 bps INFO @ Sun, 21 Jun 2020 22:13:10: #2 alternative fragment length(s) may be 0,23,83,133,503 bps INFO @ Sun, 21 Jun 2020 22:13:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5736591/SRX5736591.05_model.r WARNING @ Sun, 21 Jun 2020 22:13:10: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:13:10: #2 You may need to consider one of the other alternative d(s): 0,23,83,133,503 WARNING @ Sun, 21 Jun 2020 22:13:10: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 22:13:10: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:13:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:13:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5736591/SRX5736591.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5736591/SRX5736591.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5736591/SRX5736591.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5736591/SRX5736591.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Sun, 21 Jun 2020 22:13:11: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:13:11: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:13:12: 6000000 INFO @ Sun, 21 Jun 2020 22:13:16: 1000000 INFO @ Sun, 21 Jun 2020 22:13:17: 7000000 INFO @ Sun, 21 Jun 2020 22:13:22: 2000000 INFO @ Sun, 21 Jun 2020 22:13:23: 8000000 INFO @ Sun, 21 Jun 2020 22:13:27: 3000000 INFO @ Sun, 21 Jun 2020 22:13:28: 9000000 INFO @ Sun, 21 Jun 2020 22:13:32: 4000000 INFO @ Sun, 21 Jun 2020 22:13:33: 10000000 INFO @ Sun, 21 Jun 2020 22:13:37: 5000000 INFO @ Sun, 21 Jun 2020 22:13:38: 11000000 INFO @ Sun, 21 Jun 2020 22:13:40: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:13:40: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:13:40: #1 total tags in treatment: 11351838 INFO @ Sun, 21 Jun 2020 22:13:40: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:13:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 22:13:41: #1 tags after filtering in treatment: 11351688 INFO @ Sun, 21 Jun 2020 22:13:41: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:13:41: #1 finished! INFO @ Sun, 21 Jun 2020 22:13:41: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:13:41: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:13:42: #2 number of paired peaks: 970 WARNING @ Sun, 21 Jun 2020 22:13:42: Fewer paired peaks (970) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 970 pairs to build model! INFO @ Sun, 21 Jun 2020 22:13:42: start model_add_line... INFO @ Sun, 21 Jun 2020 22:13:42: start X-correlation... INFO @ Sun, 21 Jun 2020 22:13:42: end of X-cor INFO @ Sun, 21 Jun 2020 22:13:42: #2 finished! INFO @ Sun, 21 Jun 2020 22:13:42: #2 predicted fragment length is 0 bps INFO @ Sun, 21 Jun 2020 22:13:42: #2 alternative fragment length(s) may be 0,23,83,133,503 bps INFO @ Sun, 21 Jun 2020 22:13:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5736591/SRX5736591.10_model.r WARNING @ Sun, 21 Jun 2020 22:13:42: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:13:42: #2 You may need to consider one of the other alternative d(s): 0,23,83,133,503 WARNING @ Sun, 21 Jun 2020 22:13:42: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 22:13:42: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:13:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:13:42: 6000000 INFO @ Sun, 21 Jun 2020 22:13:47: 7000000 INFO @ Sun, 21 Jun 2020 22:13:52: 8000000 INFO @ Sun, 21 Jun 2020 22:13:57: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:14:02: 10000000 INFO @ Sun, 21 Jun 2020 22:14:07: 11000000 INFO @ Sun, 21 Jun 2020 22:14:09: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:14:09: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:14:09: #1 total tags in treatment: 11351838 INFO @ Sun, 21 Jun 2020 22:14:09: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:14:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 22:14:09: #1 tags after filtering in treatment: 11351688 INFO @ Sun, 21 Jun 2020 22:14:09: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:14:09: #1 finished! INFO @ Sun, 21 Jun 2020 22:14:09: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:14:09: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:14:10: #2 number of paired peaks: 970 WARNING @ Sun, 21 Jun 2020 22:14:10: Fewer paired peaks (970) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 970 pairs to build model! INFO @ Sun, 21 Jun 2020 22:14:10: start model_add_line... INFO @ Sun, 21 Jun 2020 22:14:10: start X-correlation... INFO @ Sun, 21 Jun 2020 22:14:10: end of X-cor INFO @ Sun, 21 Jun 2020 22:14:10: #2 finished! INFO @ Sun, 21 Jun 2020 22:14:10: #2 predicted fragment length is 0 bps INFO @ Sun, 21 Jun 2020 22:14:10: #2 alternative fragment length(s) may be 0,23,83,133,503 bps INFO @ Sun, 21 Jun 2020 22:14:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5736591/SRX5736591.20_model.r WARNING @ Sun, 21 Jun 2020 22:14:10: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:14:10: #2 You may need to consider one of the other alternative d(s): 0,23,83,133,503 WARNING @ Sun, 21 Jun 2020 22:14:10: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 22:14:10: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:14:10: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 /var/spool/uge/at151/job_scripts/6458891: line 273: 93319 Terminated MACS $i /var/spool/uge/at151/job_scripts/6458891: line 273: 93472 Terminated MACS $i /var/spool/uge/at151/job_scripts/6458891: line 273: 93613 Terminated MACS $i ls: cannot access SRX5736591.05.bed: No such file or directory mv: cannot stat ‘SRX5736591.05.bed’: No such file or directory mv: cannot stat ‘SRX5736591.05.bb’: No such file or directory ls: cannot access SRX5736591.10.bed: No such file or directory mv: cannot stat ‘SRX5736591.10.bed’: No such file or directory mv: cannot stat ‘SRX5736591.10.bb’: No such file or directory ls: cannot access SRX5736591.20.bed: No such file or directory mv: cannot stat ‘SRX5736591.20.bed’: No such file or directory mv: cannot stat ‘SRX5736591.20.bb’: No such file or directory