Job ID = 6529559 SRX = SRX3166311 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: 00:12:52 53291036 reads; of these: 53291036 (100.00%) were unpaired; of these: 2107831 (3.96%) aligned 0 times 42259830 (79.30%) aligned exactly 1 time 8923375 (16.74%) aligned >1 times 96.04% overall alignment rate Time searching: 00:12:52 Overall time: 00:12:52 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 24 files... [bam_rmdupse_core] 7806142 / 51183205 = 0.1525 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 02:42:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3166311/SRX3166311.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3166311/SRX3166311.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3166311/SRX3166311.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3166311/SRX3166311.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 02:42:35: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:42:35: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:42:40: 1000000 INFO @ Tue, 30 Jun 2020 02:42:45: 2000000 INFO @ Tue, 30 Jun 2020 02:42:50: 3000000 INFO @ Tue, 30 Jun 2020 02:42:55: 4000000 INFO @ Tue, 30 Jun 2020 02:43:01: 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 02:43:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3166311/SRX3166311.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3166311/SRX3166311.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3166311/SRX3166311.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3166311/SRX3166311.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 02:43:05: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:43:05: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:43:06: 6000000 INFO @ Tue, 30 Jun 2020 02:43:10: 1000000 INFO @ Tue, 30 Jun 2020 02:43:11: 7000000 INFO @ Tue, 30 Jun 2020 02:43:15: 2000000 INFO @ Tue, 30 Jun 2020 02:43:16: 8000000 INFO @ Tue, 30 Jun 2020 02:43:21: 3000000 INFO @ Tue, 30 Jun 2020 02:43:22: 9000000 INFO @ Tue, 30 Jun 2020 02:43:26: 4000000 INFO @ Tue, 30 Jun 2020 02:43:27: 10000000 INFO @ Tue, 30 Jun 2020 02:43:31: 5000000 INFO @ Tue, 30 Jun 2020 02:43:32: 11000000 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 02:43:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3166311/SRX3166311.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3166311/SRX3166311.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3166311/SRX3166311.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3166311/SRX3166311.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 02:43:35: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:43:35: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:43:37: 6000000 INFO @ Tue, 30 Jun 2020 02:43:38: 12000000 INFO @ Tue, 30 Jun 2020 02:43:41: 1000000 INFO @ Tue, 30 Jun 2020 02:43:42: 7000000 INFO @ Tue, 30 Jun 2020 02:43:43: 13000000 INFO @ Tue, 30 Jun 2020 02:43:47: 2000000 INFO @ Tue, 30 Jun 2020 02:43:48: 8000000 INFO @ Tue, 30 Jun 2020 02:43:48: 14000000 INFO @ Tue, 30 Jun 2020 02:43:53: 3000000 INFO @ Tue, 30 Jun 2020 02:43:54: 15000000 INFO @ Tue, 30 Jun 2020 02:43:54: 9000000 INFO @ Tue, 30 Jun 2020 02:43:59: 16000000 INFO @ Tue, 30 Jun 2020 02:43:59: 4000000 INFO @ Tue, 30 Jun 2020 02:44:00: 10000000 INFO @ Tue, 30 Jun 2020 02:44:04: 17000000 INFO @ Tue, 30 Jun 2020 02:44:05: 5000000 INFO @ Tue, 30 Jun 2020 02:44:05: 11000000 INFO @ Tue, 30 Jun 2020 02:44:09: 18000000 INFO @ Tue, 30 Jun 2020 02:44:11: 6000000 INFO @ Tue, 30 Jun 2020 02:44:11: 12000000 INFO @ Tue, 30 Jun 2020 02:44:15: 19000000 INFO @ Tue, 30 Jun 2020 02:44:17: 7000000 INFO @ Tue, 30 Jun 2020 02:44:17: 13000000 INFO @ Tue, 30 Jun 2020 02:44:20: 20000000 INFO @ Tue, 30 Jun 2020 02:44:23: 14000000 INFO @ Tue, 30 Jun 2020 02:44:23: 8000000 INFO @ Tue, 30 Jun 2020 02:44:25: 21000000 INFO @ Tue, 30 Jun 2020 02:44:29: 15000000 INFO @ Tue, 30 Jun 2020 02:44:29: 9000000 INFO @ Tue, 30 Jun 2020 02:44:31: 22000000 INFO @ Tue, 30 Jun 2020 02:44:34: 16000000 INFO @ Tue, 30 Jun 2020 02:44:35: 10000000 INFO @ Tue, 30 Jun 2020 02:44:36: 23000000 INFO @ Tue, 30 Jun 2020 02:44:40: 17000000 INFO @ Tue, 30 Jun 2020 02:44:41: 11000000 INFO @ Tue, 30 Jun 2020 02:44:41: 24000000 INFO @ Tue, 30 Jun 2020 02:44:46: 18000000 INFO @ Tue, 30 Jun 2020 02:44:46: 25000000 INFO @ Tue, 30 Jun 2020 02:44:47: 12000000 INFO @ Tue, 30 Jun 2020 02:44:52: 26000000 INFO @ Tue, 30 Jun 2020 02:44:52: 19000000 INFO @ Tue, 30 Jun 2020 02:44:53: 13000000 INFO @ Tue, 30 Jun 2020 02:44:58: 27000000 INFO @ Tue, 30 Jun 2020 02:44:58: 20000000 INFO @ Tue, 30 Jun 2020 02:44:59: 14000000 INFO @ Tue, 30 Jun 2020 02:45:03: 21000000 INFO @ Tue, 30 Jun 2020 02:45:04: 28000000 INFO @ Tue, 30 Jun 2020 02:45:05: 15000000 INFO @ Tue, 30 Jun 2020 02:45:09: 22000000 INFO @ Tue, 30 Jun 2020 02:45:10: 29000000 INFO @ Tue, 30 Jun 2020 02:45:11: 16000000 INFO @ Tue, 30 Jun 2020 02:45:15: 23000000 INFO @ Tue, 30 Jun 2020 02:45:16: 30000000 INFO @ Tue, 30 Jun 2020 02:45:17: 17000000 INFO @ Tue, 30 Jun 2020 02:45:21: 24000000 INFO @ Tue, 30 Jun 2020 02:45:22: 31000000 INFO @ Tue, 30 Jun 2020 02:45:23: 18000000 INFO @ Tue, 30 Jun 2020 02:45:27: 25000000 INFO @ Tue, 30 Jun 2020 02:45:28: 32000000 INFO @ Tue, 30 Jun 2020 02:45:29: 19000000 INFO @ Tue, 30 Jun 2020 02:45:34: 26000000 INFO @ Tue, 30 Jun 2020 02:45:34: 33000000 INFO @ Tue, 30 Jun 2020 02:45:36: 20000000 INFO @ Tue, 30 Jun 2020 02:45:40: 27000000 INFO @ Tue, 30 Jun 2020 02:45:41: 34000000 INFO @ Tue, 30 Jun 2020 02:45:42: 21000000 INFO @ Tue, 30 Jun 2020 02:45:46: 28000000 INFO @ Tue, 30 Jun 2020 02:45:48: 35000000 INFO @ Tue, 30 Jun 2020 02:45:48: 22000000 INFO @ Tue, 30 Jun 2020 02:45:53: 29000000 INFO @ Tue, 30 Jun 2020 02:45:54: 36000000 INFO @ Tue, 30 Jun 2020 02:45:54: 23000000 INFO @ Tue, 30 Jun 2020 02:45:59: 30000000 INFO @ Tue, 30 Jun 2020 02:46:01: 24000000 INFO @ Tue, 30 Jun 2020 02:46:01: 37000000 INFO @ Tue, 30 Jun 2020 02:46:06: 31000000 INFO @ Tue, 30 Jun 2020 02:46:07: 25000000 INFO @ Tue, 30 Jun 2020 02:46:08: 38000000 INFO @ Tue, 30 Jun 2020 02:46:13: 32000000 INFO @ Tue, 30 Jun 2020 02:46:14: 26000000 INFO @ Tue, 30 Jun 2020 02:46:14: 39000000 INFO @ Tue, 30 Jun 2020 02:46:20: 33000000 INFO @ Tue, 30 Jun 2020 02:46:20: 27000000 INFO @ Tue, 30 Jun 2020 02:46:21: 40000000 INFO @ Tue, 30 Jun 2020 02:46:26: 34000000 INFO @ Tue, 30 Jun 2020 02:46:27: 28000000 INFO @ Tue, 30 Jun 2020 02:46:28: 41000000 INFO @ Tue, 30 Jun 2020 02:46:34: 29000000 INFO @ Tue, 30 Jun 2020 02:46:34: 35000000 INFO @ Tue, 30 Jun 2020 02:46:35: 42000000 INFO @ Tue, 30 Jun 2020 02:46:40: 36000000 INFO @ Tue, 30 Jun 2020 02:46:41: 30000000 INFO @ Tue, 30 Jun 2020 02:46:42: 43000000 INFO @ Tue, 30 Jun 2020 02:46:45: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 02:46:45: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 02:46:45: #1 total tags in treatment: 43377063 INFO @ Tue, 30 Jun 2020 02:46:45: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:46:45: #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 02:46:46: #1 tags after filtering in treatment: 43377013 INFO @ Tue, 30 Jun 2020 02:46:46: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:46:46: #1 finished! INFO @ Tue, 30 Jun 2020 02:46:46: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:46:46: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:46:47: 37000000 INFO @ Tue, 30 Jun 2020 02:46:47: 31000000 INFO @ Tue, 30 Jun 2020 02:46:49: #2 number of paired peaks: 109 WARNING @ Tue, 30 Jun 2020 02:46:49: Fewer paired peaks (109) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 109 pairs to build model! INFO @ Tue, 30 Jun 2020 02:46:49: start model_add_line... INFO @ Tue, 30 Jun 2020 02:46:49: start X-correlation... INFO @ Tue, 30 Jun 2020 02:46:49: end of X-cor INFO @ Tue, 30 Jun 2020 02:46:49: #2 finished! INFO @ Tue, 30 Jun 2020 02:46:49: #2 predicted fragment length is 0 bps INFO @ Tue, 30 Jun 2020 02:46:49: #2 alternative fragment length(s) may be 0,47,565 bps INFO @ Tue, 30 Jun 2020 02:46:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3166311/SRX3166311.05_model.r WARNING @ Tue, 30 Jun 2020 02:46:49: #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 02:46:49: #2 You may need to consider one of the other alternative d(s): 0,47,565 WARNING @ Tue, 30 Jun 2020 02:46:49: #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 02:46:49: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:46:49: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:46:54: 38000000 INFO @ Tue, 30 Jun 2020 02:46:54: 32000000 INFO @ Tue, 30 Jun 2020 02:47:00: 39000000 INFO @ Tue, 30 Jun 2020 02:47:01: 33000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:47:06: 40000000 INFO @ Tue, 30 Jun 2020 02:47:07: 34000000 INFO @ Tue, 30 Jun 2020 02:47:12: 41000000 INFO @ Tue, 30 Jun 2020 02:47:13: 35000000 INFO @ Tue, 30 Jun 2020 02:47:18: 42000000 INFO @ Tue, 30 Jun 2020 02:47:19: 36000000 INFO @ Tue, 30 Jun 2020 02:47:24: 43000000 INFO @ Tue, 30 Jun 2020 02:47:26: 37000000 INFO @ Tue, 30 Jun 2020 02:47:27: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 02:47:27: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 02:47:27: #1 total tags in treatment: 43377063 INFO @ Tue, 30 Jun 2020 02:47:27: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:47:27: #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 02:47:29: #1 tags after filtering in treatment: 43377013 INFO @ Tue, 30 Jun 2020 02:47:29: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:47:29: #1 finished! INFO @ Tue, 30 Jun 2020 02:47:29: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:47:29: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:47:31: 38000000 INFO @ Tue, 30 Jun 2020 02:47:31: #2 number of paired peaks: 109 WARNING @ Tue, 30 Jun 2020 02:47:31: Fewer paired peaks (109) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 109 pairs to build model! INFO @ Tue, 30 Jun 2020 02:47:31: start model_add_line... INFO @ Tue, 30 Jun 2020 02:47:31: start X-correlation... INFO @ Tue, 30 Jun 2020 02:47:31: end of X-cor INFO @ Tue, 30 Jun 2020 02:47:31: #2 finished! INFO @ Tue, 30 Jun 2020 02:47:31: #2 predicted fragment length is 0 bps INFO @ Tue, 30 Jun 2020 02:47:31: #2 alternative fragment length(s) may be 0,47,565 bps INFO @ Tue, 30 Jun 2020 02:47:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3166311/SRX3166311.10_model.r WARNING @ Tue, 30 Jun 2020 02:47:31: #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 02:47:31: #2 You may need to consider one of the other alternative d(s): 0,47,565 WARNING @ Tue, 30 Jun 2020 02:47:31: #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 02:47:31: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:47:31: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:47:36: 39000000 INFO @ Tue, 30 Jun 2020 02:47:42: 40000000 INFO @ Tue, 30 Jun 2020 02:47:47: 41000000 INFO @ Tue, 30 Jun 2020 02:47:52: 42000000 INFO @ Tue, 30 Jun 2020 02:47:58: 43000000 INFO @ Tue, 30 Jun 2020 02:48:01: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 02:48:01: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 02:48:01: #1 total tags in treatment: 43377063 INFO @ Tue, 30 Jun 2020 02:48:01: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:48:01: #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 02:48:03: #1 tags after filtering in treatment: 43377013 INFO @ Tue, 30 Jun 2020 02:48:03: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:48:03: #1 finished! INFO @ Tue, 30 Jun 2020 02:48:03: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:48:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:48:05: #2 number of paired peaks: 109 WARNING @ Tue, 30 Jun 2020 02:48:05: Fewer paired peaks (109) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 109 pairs to build model! INFO @ Tue, 30 Jun 2020 02:48:05: start model_add_line... INFO @ Tue, 30 Jun 2020 02:48:05: start X-correlation... INFO @ Tue, 30 Jun 2020 02:48:05: end of X-cor INFO @ Tue, 30 Jun 2020 02:48:05: #2 finished! INFO @ Tue, 30 Jun 2020 02:48:05: #2 predicted fragment length is 0 bps INFO @ Tue, 30 Jun 2020 02:48:05: #2 alternative fragment length(s) may be 0,47,565 bps INFO @ Tue, 30 Jun 2020 02:48:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3166311/SRX3166311.20_model.r WARNING @ Tue, 30 Jun 2020 02:48:05: #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 02:48:05: #2 You may need to consider one of the other alternative d(s): 0,47,565 WARNING @ Tue, 30 Jun 2020 02:48:05: #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 02:48:05: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:48:05: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 /var/spool/uge/it007/job_scripts/6529559: line 293: 21976 Terminated MACS $i /var/spool/uge/it007/job_scripts/6529559: line 293: 22072 Terminated MACS $i /var/spool/uge/it007/job_scripts/6529559: line 293: 22186 Terminated MACS $i ls: cannot access SRX3166311.05.bed: No such file or directory mv: cannot stat ‘SRX3166311.05.bed’: No such file or directory mv: cannot stat ‘SRX3166311.05.bb’: No such file or directory ls: cannot access SRX3166311.10.bed: No such file or directory mv: cannot stat ‘SRX3166311.10.bed’: No such file or directory mv: cannot stat ‘SRX3166311.10.bb’: No such file or directory ls: cannot access SRX3166311.20.bed: No such file or directory mv: cannot stat ‘SRX3166311.20.bed’: No such file or directory mv: cannot stat ‘SRX3166311.20.bb’: No such file or directory