Job ID = 6529668 SRX = SRX3981631 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 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: 00:10:36 37320052 reads; of these: 37320052 (100.00%) were unpaired; of these: 1464910 (3.93%) aligned 0 times 26898836 (72.08%) aligned exactly 1 time 8956306 (24.00%) aligned >1 times 96.07% overall alignment rate Time searching: 00:10:36 Overall time: 00:10:36 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] 4513993 / 35855142 = 0.1259 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 @ Tue, 30 Jun 2020 02:53:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981631/SRX3981631.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981631/SRX3981631.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981631/SRX3981631.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981631/SRX3981631.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 @ Tue, 30 Jun 2020 02:53:00: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:53:00: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:53:05: 1000000 INFO @ Tue, 30 Jun 2020 02:53:11: 2000000 INFO @ Tue, 30 Jun 2020 02:53:16: 3000000 INFO @ Tue, 30 Jun 2020 02:53:21: 4000000 INFO @ Tue, 30 Jun 2020 02:53:27: 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 @ Tue, 30 Jun 2020 02:53:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981631/SRX3981631.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981631/SRX3981631.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981631/SRX3981631.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981631/SRX3981631.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 @ Tue, 30 Jun 2020 02:53:30: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:53:30: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:53:32: 6000000 INFO @ Tue, 30 Jun 2020 02:53:36: 1000000 INFO @ Tue, 30 Jun 2020 02:53:38: 7000000 INFO @ Tue, 30 Jun 2020 02:53:42: 2000000 INFO @ Tue, 30 Jun 2020 02:53:44: 8000000 INFO @ Tue, 30 Jun 2020 02:53:48: 3000000 INFO @ Tue, 30 Jun 2020 02:53:50: 9000000 INFO @ Tue, 30 Jun 2020 02:53:54: 4000000 INFO @ Tue, 30 Jun 2020 02:53:56: 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 @ Tue, 30 Jun 2020 02:54:00: 5000000 INFO @ Tue, 30 Jun 2020 02:54:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981631/SRX3981631.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981631/SRX3981631.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981631/SRX3981631.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981631/SRX3981631.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 @ Tue, 30 Jun 2020 02:54:00: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:54:00: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:54:02: 11000000 INFO @ Tue, 30 Jun 2020 02:54:06: 1000000 INFO @ Tue, 30 Jun 2020 02:54:06: 6000000 INFO @ Tue, 30 Jun 2020 02:54:08: 12000000 INFO @ Tue, 30 Jun 2020 02:54:11: 2000000 INFO @ Tue, 30 Jun 2020 02:54:12: 7000000 INFO @ Tue, 30 Jun 2020 02:54:13: 13000000 INFO @ Tue, 30 Jun 2020 02:54:16: 3000000 INFO @ Tue, 30 Jun 2020 02:54:17: 8000000 INFO @ Tue, 30 Jun 2020 02:54:19: 14000000 INFO @ Tue, 30 Jun 2020 02:54:22: 4000000 INFO @ Tue, 30 Jun 2020 02:54:22: 9000000 INFO @ Tue, 30 Jun 2020 02:54:24: 15000000 INFO @ Tue, 30 Jun 2020 02:54:27: 5000000 INFO @ Tue, 30 Jun 2020 02:54:28: 10000000 INFO @ Tue, 30 Jun 2020 02:54:29: 16000000 INFO @ Tue, 30 Jun 2020 02:54:32: 6000000 INFO @ Tue, 30 Jun 2020 02:54:33: 11000000 INFO @ Tue, 30 Jun 2020 02:54:35: 17000000 INFO @ Tue, 30 Jun 2020 02:54:37: 7000000 INFO @ Tue, 30 Jun 2020 02:54:39: 12000000 INFO @ Tue, 30 Jun 2020 02:54:40: 18000000 INFO @ Tue, 30 Jun 2020 02:54:43: 8000000 INFO @ Tue, 30 Jun 2020 02:54:44: 13000000 INFO @ Tue, 30 Jun 2020 02:54:45: 19000000 INFO @ Tue, 30 Jun 2020 02:54:48: 9000000 INFO @ Tue, 30 Jun 2020 02:54:49: 14000000 INFO @ Tue, 30 Jun 2020 02:54:51: 20000000 INFO @ Tue, 30 Jun 2020 02:54:53: 10000000 INFO @ Tue, 30 Jun 2020 02:54:55: 15000000 INFO @ Tue, 30 Jun 2020 02:54:56: 21000000 INFO @ Tue, 30 Jun 2020 02:54:58: 11000000 INFO @ Tue, 30 Jun 2020 02:55:00: 16000000 INFO @ Tue, 30 Jun 2020 02:55:01: 22000000 INFO @ Tue, 30 Jun 2020 02:55:04: 12000000 INFO @ Tue, 30 Jun 2020 02:55:05: 17000000 INFO @ Tue, 30 Jun 2020 02:55:07: 23000000 INFO @ Tue, 30 Jun 2020 02:55:09: 13000000 INFO @ Tue, 30 Jun 2020 02:55:10: 18000000 INFO @ Tue, 30 Jun 2020 02:55:12: 24000000 INFO @ Tue, 30 Jun 2020 02:55:14: 14000000 INFO @ Tue, 30 Jun 2020 02:55:16: 19000000 INFO @ Tue, 30 Jun 2020 02:55:17: 25000000 INFO @ Tue, 30 Jun 2020 02:55:19: 15000000 INFO @ Tue, 30 Jun 2020 02:55:21: 20000000 INFO @ Tue, 30 Jun 2020 02:55:22: 26000000 INFO @ Tue, 30 Jun 2020 02:55:24: 16000000 INFO @ Tue, 30 Jun 2020 02:55:27: 21000000 INFO @ Tue, 30 Jun 2020 02:55:28: 27000000 INFO @ Tue, 30 Jun 2020 02:55:29: 17000000 INFO @ Tue, 30 Jun 2020 02:55:32: 22000000 INFO @ Tue, 30 Jun 2020 02:55:34: 28000000 INFO @ Tue, 30 Jun 2020 02:55:34: 18000000 INFO @ Tue, 30 Jun 2020 02:55:37: 23000000 INFO @ Tue, 30 Jun 2020 02:55:39: 29000000 INFO @ Tue, 30 Jun 2020 02:55:40: 19000000 INFO @ Tue, 30 Jun 2020 02:55:43: 24000000 INFO @ Tue, 30 Jun 2020 02:55:44: 30000000 INFO @ Tue, 30 Jun 2020 02:55:45: 20000000 INFO @ Tue, 30 Jun 2020 02:55:48: 25000000 INFO @ Tue, 30 Jun 2020 02:55:50: 21000000 INFO @ Tue, 30 Jun 2020 02:55:50: 31000000 INFO @ Tue, 30 Jun 2020 02:55:52: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 02:55:52: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 02:55:52: #1 total tags in treatment: 31341149 INFO @ Tue, 30 Jun 2020 02:55:52: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:55:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 02:55:53: #1 tags after filtering in treatment: 31341088 INFO @ Tue, 30 Jun 2020 02:55:53: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:55:53: #1 finished! INFO @ Tue, 30 Jun 2020 02:55:53: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:55:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:55:53: 26000000 INFO @ Tue, 30 Jun 2020 02:55:55: 22000000 INFO @ Tue, 30 Jun 2020 02:55:55: #2 number of paired peaks: 188 WARNING @ Tue, 30 Jun 2020 02:55:55: Fewer paired peaks (188) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 188 pairs to build model! INFO @ Tue, 30 Jun 2020 02:55:55: start model_add_line... INFO @ Tue, 30 Jun 2020 02:55:55: start X-correlation... INFO @ Tue, 30 Jun 2020 02:55:55: end of X-cor INFO @ Tue, 30 Jun 2020 02:55:55: #2 finished! INFO @ Tue, 30 Jun 2020 02:55:55: #2 predicted fragment length is 0 bps INFO @ Tue, 30 Jun 2020 02:55:55: #2 alternative fragment length(s) may be 0,47,564 bps INFO @ Tue, 30 Jun 2020 02:55:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981631/SRX3981631.05_model.r WARNING @ Tue, 30 Jun 2020 02:55:55: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:55:55: #2 You may need to consider one of the other alternative d(s): 0,47,564 WARNING @ Tue, 30 Jun 2020 02:55:55: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 02:55:55: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:55:55: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:55:59: 27000000 INFO @ Tue, 30 Jun 2020 02:56:00: 23000000 INFO @ Tue, 30 Jun 2020 02:56:04: 28000000 INFO @ Tue, 30 Jun 2020 02:56:05: 24000000 INFO @ Tue, 30 Jun 2020 02:56:09: 29000000 INFO @ Tue, 30 Jun 2020 02:56:10: 25000000 INFO @ Tue, 30 Jun 2020 02:56:14: 30000000 INFO @ Tue, 30 Jun 2020 02:56:15: 26000000 INFO @ Tue, 30 Jun 2020 02:56:19: 31000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:56:21: 27000000 INFO @ Tue, 30 Jun 2020 02:56:21: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 02:56:21: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 02:56:21: #1 total tags in treatment: 31341149 INFO @ Tue, 30 Jun 2020 02:56:21: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:56:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 02:56:22: #1 tags after filtering in treatment: 31341088 INFO @ Tue, 30 Jun 2020 02:56:22: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:56:22: #1 finished! INFO @ Tue, 30 Jun 2020 02:56:22: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:56:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:56:24: #2 number of paired peaks: 188 WARNING @ Tue, 30 Jun 2020 02:56:24: Fewer paired peaks (188) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 188 pairs to build model! INFO @ Tue, 30 Jun 2020 02:56:24: start model_add_line... INFO @ Tue, 30 Jun 2020 02:56:24: start X-correlation... INFO @ Tue, 30 Jun 2020 02:56:24: end of X-cor INFO @ Tue, 30 Jun 2020 02:56:24: #2 finished! INFO @ Tue, 30 Jun 2020 02:56:24: #2 predicted fragment length is 0 bps INFO @ Tue, 30 Jun 2020 02:56:24: #2 alternative fragment length(s) may be 0,47,564 bps INFO @ Tue, 30 Jun 2020 02:56:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981631/SRX3981631.10_model.r WARNING @ Tue, 30 Jun 2020 02:56:24: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:56:24: #2 You may need to consider one of the other alternative d(s): 0,47,564 WARNING @ Tue, 30 Jun 2020 02:56:24: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 02:56:24: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:56:24: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:56:26: 28000000 INFO @ Tue, 30 Jun 2020 02:56:31: 29000000 INFO @ Tue, 30 Jun 2020 02:56:36: 30000000 INFO @ Tue, 30 Jun 2020 02:56:41: 31000000 INFO @ Tue, 30 Jun 2020 02:56:43: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 02:56:43: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 02:56:43: #1 total tags in treatment: 31341149 INFO @ Tue, 30 Jun 2020 02:56:43: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:56:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 02:56:44: #1 tags after filtering in treatment: 31341088 INFO @ Tue, 30 Jun 2020 02:56:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:56:44: #1 finished! INFO @ Tue, 30 Jun 2020 02:56:44: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:56:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:56:46: #2 number of paired peaks: 188 WARNING @ Tue, 30 Jun 2020 02:56:46: Fewer paired peaks (188) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 188 pairs to build model! INFO @ Tue, 30 Jun 2020 02:56:46: start model_add_line... INFO @ Tue, 30 Jun 2020 02:56:46: start X-correlation... INFO @ Tue, 30 Jun 2020 02:56:46: end of X-cor INFO @ Tue, 30 Jun 2020 02:56:46: #2 finished! INFO @ Tue, 30 Jun 2020 02:56:46: #2 predicted fragment length is 0 bps INFO @ Tue, 30 Jun 2020 02:56:46: #2 alternative fragment length(s) may be 0,47,564 bps INFO @ Tue, 30 Jun 2020 02:56:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981631/SRX3981631.20_model.r WARNING @ Tue, 30 Jun 2020 02:56:46: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:56:46: #2 You may need to consider one of the other alternative d(s): 0,47,564 WARNING @ Tue, 30 Jun 2020 02:56:46: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 02:56:46: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:56:46: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 /var/spool/uge/at157/job_scripts/6529668: line 293: 121543 Terminated MACS $i /var/spool/uge/at157/job_scripts/6529668: line 293: 33103 Terminated MACS $i /var/spool/uge/at157/job_scripts/6529668: line 293: 44762 Terminated MACS $i ls: cannot access SRX3981631.05.bed: No such file or directory mv: cannot stat ‘SRX3981631.05.bed’: No such file or directory mv: cannot stat ‘SRX3981631.05.bb’: No such file or directory ls: cannot access SRX3981631.10.bed: No such file or directory mv: cannot stat ‘SRX3981631.10.bed’: No such file or directory mv: cannot stat ‘SRX3981631.10.bb’: No such file or directory ls: cannot access SRX3981631.20.bed: No such file or directory mv: cannot stat ‘SRX3981631.20.bed’: No such file or directory mv: cannot stat ‘SRX3981631.20.bb’: No such file or directory