Job ID = 6458808 SRX = SRX5535380 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:48:10 prefetch.2.10.7: 1) Downloading 'SRR8743308'... 2020-06-21T12:48:10 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:53:00 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:53:00 prefetch.2.10.7: 1) 'SRR8743308' was downloaded successfully Read 31035337 spots for SRR8743308/SRR8743308.sra Written 31035337 spots for SRR8743308/SRR8743308.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: 00:00:01 Multiseed full-index search: 00:07:49 31035337 reads; of these: 31035337 (100.00%) were unpaired; of these: 578424 (1.86%) aligned 0 times 24376536 (78.54%) aligned exactly 1 time 6080377 (19.59%) aligned >1 times 98.14% overall alignment rate Time searching: 00:07:50 Overall time: 00:07:50 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 16 files... [bam_rmdupse_core] 14749890 / 30456913 = 0.4843 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 22:08:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5535380/SRX5535380.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5535380/SRX5535380.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5535380/SRX5535380.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5535380/SRX5535380.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 22:08:06: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:08:06: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:08:11: 1000000 INFO @ Sun, 21 Jun 2020 22:08:17: 2000000 INFO @ Sun, 21 Jun 2020 22:08:23: 3000000 INFO @ Sun, 21 Jun 2020 22:08:29: 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 @ Sun, 21 Jun 2020 22:08:34: 5000000 INFO @ Sun, 21 Jun 2020 22:08:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5535380/SRX5535380.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5535380/SRX5535380.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5535380/SRX5535380.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5535380/SRX5535380.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 22:08:36: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:08:36: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:08:40: 6000000 INFO @ Sun, 21 Jun 2020 22:08:42: 1000000 INFO @ Sun, 21 Jun 2020 22:08:46: 7000000 INFO @ Sun, 21 Jun 2020 22:08:48: 2000000 INFO @ Sun, 21 Jun 2020 22:08:52: 8000000 INFO @ Sun, 21 Jun 2020 22:08:54: 3000000 INFO @ Sun, 21 Jun 2020 22:08:58: 9000000 INFO @ Sun, 21 Jun 2020 22:09:00: 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 @ Sun, 21 Jun 2020 22:09:05: 10000000 INFO @ Sun, 21 Jun 2020 22:09:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5535380/SRX5535380.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5535380/SRX5535380.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5535380/SRX5535380.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5535380/SRX5535380.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 22:09:06: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:09:06: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:09:06: 5000000 INFO @ Sun, 21 Jun 2020 22:09:11: 11000000 INFO @ Sun, 21 Jun 2020 22:09:12: 1000000 INFO @ Sun, 21 Jun 2020 22:09:13: 6000000 INFO @ Sun, 21 Jun 2020 22:09:17: 12000000 INFO @ Sun, 21 Jun 2020 22:09:18: 2000000 INFO @ Sun, 21 Jun 2020 22:09:19: 7000000 INFO @ Sun, 21 Jun 2020 22:09:23: 13000000 INFO @ Sun, 21 Jun 2020 22:09:24: 3000000 INFO @ Sun, 21 Jun 2020 22:09:25: 8000000 INFO @ Sun, 21 Jun 2020 22:09:30: 14000000 INFO @ Sun, 21 Jun 2020 22:09:30: 4000000 INFO @ Sun, 21 Jun 2020 22:09:31: 9000000 INFO @ Sun, 21 Jun 2020 22:09:36: 15000000 INFO @ Sun, 21 Jun 2020 22:09:37: 5000000 INFO @ Sun, 21 Jun 2020 22:09:38: 10000000 INFO @ Sun, 21 Jun 2020 22:09:40: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:09:40: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:09:40: #1 total tags in treatment: 15707023 INFO @ Sun, 21 Jun 2020 22:09:40: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:09:40: #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 22:09:41: #1 tags after filtering in treatment: 15706944 INFO @ Sun, 21 Jun 2020 22:09:41: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:09:41: #1 finished! INFO @ Sun, 21 Jun 2020 22:09:41: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:09:41: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:09:42: #2 number of paired peaks: 798 WARNING @ Sun, 21 Jun 2020 22:09:42: Fewer paired peaks (798) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 798 pairs to build model! INFO @ Sun, 21 Jun 2020 22:09:42: start model_add_line... INFO @ Sun, 21 Jun 2020 22:09:42: start X-correlation... INFO @ Sun, 21 Jun 2020 22:09:42: end of X-cor INFO @ Sun, 21 Jun 2020 22:09:42: #2 finished! INFO @ Sun, 21 Jun 2020 22:09:42: #2 predicted fragment length is 0 bps INFO @ Sun, 21 Jun 2020 22:09:42: #2 alternative fragment length(s) may be 0,19,30,52,80,103,128,144,307,468,511,590 bps INFO @ Sun, 21 Jun 2020 22:09:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5535380/SRX5535380.05_model.r WARNING @ Sun, 21 Jun 2020 22:09:42: #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 22:09:42: #2 You may need to consider one of the other alternative d(s): 0,19,30,52,80,103,128,144,307,468,511,590 WARNING @ Sun, 21 Jun 2020 22:09:42: #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 22:09:42: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:09:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:09:43: 6000000 INFO @ Sun, 21 Jun 2020 22:09:44: 11000000 INFO @ Sun, 21 Jun 2020 22:09:49: 7000000 INFO @ Sun, 21 Jun 2020 22:09:50: 12000000 INFO @ Sun, 21 Jun 2020 22:09:55: 8000000 INFO @ Sun, 21 Jun 2020 22:09:56: 13000000 INFO @ Sun, 21 Jun 2020 22:10:01: 9000000 INFO @ Sun, 21 Jun 2020 22:10:03: 14000000 INFO @ Sun, 21 Jun 2020 22:10:07: 10000000 INFO @ Sun, 21 Jun 2020 22:10:09: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:10:13: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:10:13: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:10:13: #1 total tags in treatment: 15707023 INFO @ Sun, 21 Jun 2020 22:10:13: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:10:13: #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 22:10:14: 11000000 INFO @ Sun, 21 Jun 2020 22:10:14: #1 tags after filtering in treatment: 15706944 INFO @ Sun, 21 Jun 2020 22:10:14: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:10:14: #1 finished! INFO @ Sun, 21 Jun 2020 22:10:14: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:10:14: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:10:15: #2 number of paired peaks: 798 WARNING @ Sun, 21 Jun 2020 22:10:15: Fewer paired peaks (798) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 798 pairs to build model! INFO @ Sun, 21 Jun 2020 22:10:15: start model_add_line... INFO @ Sun, 21 Jun 2020 22:10:15: start X-correlation... INFO @ Sun, 21 Jun 2020 22:10:15: end of X-cor INFO @ Sun, 21 Jun 2020 22:10:15: #2 finished! INFO @ Sun, 21 Jun 2020 22:10:15: #2 predicted fragment length is 0 bps INFO @ Sun, 21 Jun 2020 22:10:15: #2 alternative fragment length(s) may be 0,19,30,52,80,103,128,144,307,468,511,590 bps INFO @ Sun, 21 Jun 2020 22:10:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5535380/SRX5535380.10_model.r WARNING @ Sun, 21 Jun 2020 22:10:15: #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 22:10:15: #2 You may need to consider one of the other alternative d(s): 0,19,30,52,80,103,128,144,307,468,511,590 WARNING @ Sun, 21 Jun 2020 22:10:15: #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 22:10:15: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:10:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:10:20: 12000000 INFO @ Sun, 21 Jun 2020 22:10:26: 13000000 INFO @ Sun, 21 Jun 2020 22:10:33: 14000000 INFO @ Sun, 21 Jun 2020 22:10:39: 15000000 INFO @ Sun, 21 Jun 2020 22:10:43: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:10:43: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:10:43: #1 total tags in treatment: 15707023 INFO @ Sun, 21 Jun 2020 22:10:43: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:10:43: #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 22:10:44: #1 tags after filtering in treatment: 15706944 INFO @ Sun, 21 Jun 2020 22:10:44: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:10:44: #1 finished! INFO @ Sun, 21 Jun 2020 22:10:44: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:10:44: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:10:45: #2 number of paired peaks: 798 WARNING @ Sun, 21 Jun 2020 22:10:45: Fewer paired peaks (798) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 798 pairs to build model! INFO @ Sun, 21 Jun 2020 22:10:45: start model_add_line... INFO @ Sun, 21 Jun 2020 22:10:45: start X-correlation... INFO @ Sun, 21 Jun 2020 22:10:45: end of X-cor INFO @ Sun, 21 Jun 2020 22:10:45: #2 finished! INFO @ Sun, 21 Jun 2020 22:10:45: #2 predicted fragment length is 0 bps INFO @ Sun, 21 Jun 2020 22:10:45: #2 alternative fragment length(s) may be 0,19,30,52,80,103,128,144,307,468,511,590 bps INFO @ Sun, 21 Jun 2020 22:10:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5535380/SRX5535380.20_model.r WARNING @ Sun, 21 Jun 2020 22:10:45: #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 22:10:45: #2 You may need to consider one of the other alternative d(s): 0,19,30,52,80,103,128,144,307,468,511,590 WARNING @ Sun, 21 Jun 2020 22:10:45: #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 22:10:45: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:10:45: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 /var/spool/uge/at162/job_scripts/6458808: line 273: 3563 Terminated MACS $i /var/spool/uge/at162/job_scripts/6458808: line 273: 16307 Terminated MACS $i /var/spool/uge/at162/job_scripts/6458808: line 273: 16596 Terminated MACS $i ls: cannot access SRX5535380.05.bed: No such file or directory mv: cannot stat ‘SRX5535380.05.bed’: No such file or directory mv: cannot stat ‘SRX5535380.05.bb’: No such file or directory ls: cannot access SRX5535380.10.bed: No such file or directory mv: cannot stat ‘SRX5535380.10.bed’: No such file or directory mv: cannot stat ‘SRX5535380.10.bb’: No such file or directory ls: cannot access SRX5535380.20.bed: No such file or directory mv: cannot stat ‘SRX5535380.20.bed’: No such file or directory mv: cannot stat ‘SRX5535380.20.bb’: No such file or directory