Job ID = 6368891 SRX = SRX6619593 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:48:43 prefetch.2.10.7: 1) Downloading 'SRR9866016'... 2020-06-16T00:48:43 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:52:16 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:52:16 prefetch.2.10.7: 1) 'SRR9866016' was downloaded successfully 2020-06-16T00:52:16 prefetch.2.10.7: 'SRR9866016' has 0 unresolved dependencies Read 48056231 spots for SRR9866016/SRR9866016.sra Written 48056231 spots for SRR9866016/SRR9866016.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: 00:09:58 48056231 reads; of these: 48056231 (100.00%) were unpaired; of these: 2562888 (5.33%) aligned 0 times 38467275 (80.05%) aligned exactly 1 time 7026068 (14.62%) aligned >1 times 94.67% overall alignment rate Time searching: 00:09:58 Overall time: 00:09:58 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 20 files... [bam_rmdupse_core] 11182244 / 45493343 = 0.2458 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, 16 Jun 2020 10:17:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX6619593/SRX6619593.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX6619593/SRX6619593.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX6619593/SRX6619593.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX6619593/SRX6619593.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 @ Tue, 16 Jun 2020 10:17:51: #1 read tag files... INFO @ Tue, 16 Jun 2020 10:17:51: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 10:17:57: 1000000 INFO @ Tue, 16 Jun 2020 10:18:03: 2000000 INFO @ Tue, 16 Jun 2020 10:18:09: 3000000 INFO @ Tue, 16 Jun 2020 10:18:15: 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 @ Tue, 16 Jun 2020 10:18:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX6619593/SRX6619593.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX6619593/SRX6619593.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX6619593/SRX6619593.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX6619593/SRX6619593.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 @ Tue, 16 Jun 2020 10:18:21: #1 read tag files... INFO @ Tue, 16 Jun 2020 10:18:21: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 10:18:22: 5000000 INFO @ Tue, 16 Jun 2020 10:18:28: 6000000 INFO @ Tue, 16 Jun 2020 10:18:28: 1000000 INFO @ Tue, 16 Jun 2020 10:18:34: 7000000 INFO @ Tue, 16 Jun 2020 10:18:35: 2000000 INFO @ Tue, 16 Jun 2020 10:18:40: 8000000 INFO @ Tue, 16 Jun 2020 10:18:42: 3000000 INFO @ Tue, 16 Jun 2020 10:18:47: 9000000 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, 16 Jun 2020 10:18:50: 4000000 INFO @ Tue, 16 Jun 2020 10:18:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX6619593/SRX6619593.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX6619593/SRX6619593.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX6619593/SRX6619593.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX6619593/SRX6619593.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 @ Tue, 16 Jun 2020 10:18:51: #1 read tag files... INFO @ Tue, 16 Jun 2020 10:18:51: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 10:18:53: 10000000 INFO @ Tue, 16 Jun 2020 10:18:57: 5000000 INFO @ Tue, 16 Jun 2020 10:18:58: 1000000 INFO @ Tue, 16 Jun 2020 10:18:59: 11000000 INFO @ Tue, 16 Jun 2020 10:19:05: 6000000 INFO @ Tue, 16 Jun 2020 10:19:05: 12000000 INFO @ Tue, 16 Jun 2020 10:19:06: 2000000 INFO @ Tue, 16 Jun 2020 10:19:12: 13000000 INFO @ Tue, 16 Jun 2020 10:19:12: 7000000 INFO @ Tue, 16 Jun 2020 10:19:13: 3000000 INFO @ Tue, 16 Jun 2020 10:19:18: 14000000 INFO @ Tue, 16 Jun 2020 10:19:20: 8000000 INFO @ Tue, 16 Jun 2020 10:19:21: 4000000 INFO @ Tue, 16 Jun 2020 10:19:24: 15000000 INFO @ Tue, 16 Jun 2020 10:19:27: 9000000 INFO @ Tue, 16 Jun 2020 10:19:28: 5000000 INFO @ Tue, 16 Jun 2020 10:19:30: 16000000 INFO @ Tue, 16 Jun 2020 10:19:34: 10000000 INFO @ Tue, 16 Jun 2020 10:19:36: 6000000 INFO @ Tue, 16 Jun 2020 10:19:36: 17000000 INFO @ Tue, 16 Jun 2020 10:19:41: 11000000 INFO @ Tue, 16 Jun 2020 10:19:43: 18000000 INFO @ Tue, 16 Jun 2020 10:19:43: 7000000 INFO @ Tue, 16 Jun 2020 10:19:48: 19000000 INFO @ Tue, 16 Jun 2020 10:19:48: 12000000 INFO @ Tue, 16 Jun 2020 10:19:50: 8000000 INFO @ Tue, 16 Jun 2020 10:19:53: 20000000 INFO @ Tue, 16 Jun 2020 10:19:55: 13000000 INFO @ Tue, 16 Jun 2020 10:19:57: 9000000 INFO @ Tue, 16 Jun 2020 10:19:59: 21000000 INFO @ Tue, 16 Jun 2020 10:20:02: 14000000 INFO @ Tue, 16 Jun 2020 10:20:04: 22000000 INFO @ Tue, 16 Jun 2020 10:20:04: 10000000 INFO @ Tue, 16 Jun 2020 10:20:10: 23000000 INFO @ Tue, 16 Jun 2020 10:20:10: 15000000 INFO @ Tue, 16 Jun 2020 10:20:11: 11000000 INFO @ Tue, 16 Jun 2020 10:20:15: 24000000 INFO @ Tue, 16 Jun 2020 10:20:17: 16000000 INFO @ Tue, 16 Jun 2020 10:20:18: 12000000 INFO @ Tue, 16 Jun 2020 10:20:20: 25000000 INFO @ Tue, 16 Jun 2020 10:20:23: 17000000 INFO @ Tue, 16 Jun 2020 10:20:25: 13000000 INFO @ Tue, 16 Jun 2020 10:20:26: 26000000 INFO @ Tue, 16 Jun 2020 10:20:30: 18000000 INFO @ Tue, 16 Jun 2020 10:20:31: 27000000 INFO @ Tue, 16 Jun 2020 10:20:32: 14000000 INFO @ Tue, 16 Jun 2020 10:20:36: 28000000 INFO @ Tue, 16 Jun 2020 10:20:36: 19000000 INFO @ Tue, 16 Jun 2020 10:20:38: 15000000 INFO @ Tue, 16 Jun 2020 10:20:41: 29000000 INFO @ Tue, 16 Jun 2020 10:20:43: 20000000 INFO @ Tue, 16 Jun 2020 10:20:45: 16000000 INFO @ Tue, 16 Jun 2020 10:20:47: 30000000 INFO @ Tue, 16 Jun 2020 10:20:50: 21000000 INFO @ Tue, 16 Jun 2020 10:20:52: 17000000 INFO @ Tue, 16 Jun 2020 10:20:52: 31000000 INFO @ Tue, 16 Jun 2020 10:20:57: 22000000 INFO @ Tue, 16 Jun 2020 10:20:57: 32000000 INFO @ Tue, 16 Jun 2020 10:20:59: 18000000 INFO @ Tue, 16 Jun 2020 10:21:03: 33000000 INFO @ Tue, 16 Jun 2020 10:21:04: 23000000 INFO @ Tue, 16 Jun 2020 10:21:05: 19000000 INFO @ Tue, 16 Jun 2020 10:21:08: 34000000 INFO @ Tue, 16 Jun 2020 10:21:10: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 10:21:10: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 10:21:10: #1 total tags in treatment: 34311099 INFO @ Tue, 16 Jun 2020 10:21:10: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:21:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 10:21:10: 24000000 INFO @ Tue, 16 Jun 2020 10:21:11: #1 tags after filtering in treatment: 34311099 INFO @ Tue, 16 Jun 2020 10:21:11: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 10:21:11: #1 finished! INFO @ Tue, 16 Jun 2020 10:21:11: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:21:11: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:21:12: 20000000 INFO @ Tue, 16 Jun 2020 10:21:13: #2 number of paired peaks: 100 WARNING @ Tue, 16 Jun 2020 10:21:13: Fewer paired peaks (100) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 100 pairs to build model! INFO @ Tue, 16 Jun 2020 10:21:13: start model_add_line... INFO @ Tue, 16 Jun 2020 10:21:13: start X-correlation... INFO @ Tue, 16 Jun 2020 10:21:13: end of X-cor INFO @ Tue, 16 Jun 2020 10:21:13: #2 finished! INFO @ Tue, 16 Jun 2020 10:21:13: #2 predicted fragment length is 0 bps INFO @ Tue, 16 Jun 2020 10:21:13: #2 alternative fragment length(s) may be 0,13,24,49,87,113,132,148,182,208,243,255,257,279,302,326,361,396,408,431,455,507,521,528,582 bps INFO @ Tue, 16 Jun 2020 10:21:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX6619593/SRX6619593.05_model.r WARNING @ Tue, 16 Jun 2020 10:21:13: #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, 16 Jun 2020 10:21:13: #2 You may need to consider one of the other alternative d(s): 0,13,24,49,87,113,132,148,182,208,243,255,257,279,302,326,361,396,408,431,455,507,521,528,582 WARNING @ Tue, 16 Jun 2020 10:21:13: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 10:21:13: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:21:13: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 10:21:17: 25000000 INFO @ Tue, 16 Jun 2020 10:21:19: 21000000 INFO @ Tue, 16 Jun 2020 10:21:24: 26000000 INFO @ Tue, 16 Jun 2020 10:21:26: 22000000 INFO @ Tue, 16 Jun 2020 10:21:31: 27000000 INFO @ Tue, 16 Jun 2020 10:21:32: 23000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 10:21:37: 28000000 INFO @ Tue, 16 Jun 2020 10:21:39: 24000000 INFO @ Tue, 16 Jun 2020 10:21:44: 29000000 INFO @ Tue, 16 Jun 2020 10:21:46: 25000000 INFO @ Tue, 16 Jun 2020 10:21:50: 30000000 INFO @ Tue, 16 Jun 2020 10:21:53: 26000000 INFO @ Tue, 16 Jun 2020 10:21:57: 31000000 INFO @ Tue, 16 Jun 2020 10:21:59: 27000000 INFO @ Tue, 16 Jun 2020 10:22:03: 32000000 INFO @ Tue, 16 Jun 2020 10:22:06: 28000000 INFO @ Tue, 16 Jun 2020 10:22:10: 33000000 INFO @ Tue, 16 Jun 2020 10:22:12: 29000000 INFO @ Tue, 16 Jun 2020 10:22:16: 34000000 INFO @ Tue, 16 Jun 2020 10:22:19: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 10:22:19: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 10:22:19: #1 total tags in treatment: 34311099 INFO @ Tue, 16 Jun 2020 10:22:19: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:22:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 10:22:19: 30000000 INFO @ Tue, 16 Jun 2020 10:22:19: #1 tags after filtering in treatment: 34311099 INFO @ Tue, 16 Jun 2020 10:22:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 10:22:19: #1 finished! INFO @ Tue, 16 Jun 2020 10:22:19: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:22:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:22:21: #2 number of paired peaks: 100 WARNING @ Tue, 16 Jun 2020 10:22:21: Fewer paired peaks (100) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 100 pairs to build model! INFO @ Tue, 16 Jun 2020 10:22:21: start model_add_line... INFO @ Tue, 16 Jun 2020 10:22:22: start X-correlation... INFO @ Tue, 16 Jun 2020 10:22:22: end of X-cor INFO @ Tue, 16 Jun 2020 10:22:22: #2 finished! INFO @ Tue, 16 Jun 2020 10:22:22: #2 predicted fragment length is 0 bps INFO @ Tue, 16 Jun 2020 10:22:22: #2 alternative fragment length(s) may be 0,13,24,49,87,113,132,148,182,208,243,255,257,279,302,326,361,396,408,431,455,507,521,528,582 bps INFO @ Tue, 16 Jun 2020 10:22:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX6619593/SRX6619593.10_model.r WARNING @ Tue, 16 Jun 2020 10:22:22: #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, 16 Jun 2020 10:22:22: #2 You may need to consider one of the other alternative d(s): 0,13,24,49,87,113,132,148,182,208,243,255,257,279,302,326,361,396,408,431,455,507,521,528,582 WARNING @ Tue, 16 Jun 2020 10:22:22: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 10:22:22: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:22:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 10:22:25: 31000000 INFO @ Tue, 16 Jun 2020 10:22:31: 32000000 INFO @ Tue, 16 Jun 2020 10:22:37: 33000000 INFO @ Tue, 16 Jun 2020 10:22:43: 34000000 INFO @ Tue, 16 Jun 2020 10:22:45: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 10:22:45: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 10:22:45: #1 total tags in treatment: 34311099 INFO @ Tue, 16 Jun 2020 10:22:45: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:22:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 10:22:46: #1 tags after filtering in treatment: 34311099 INFO @ Tue, 16 Jun 2020 10:22:46: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 10:22:46: #1 finished! INFO @ Tue, 16 Jun 2020 10:22:46: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:22:46: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:22:48: #2 number of paired peaks: 100 WARNING @ Tue, 16 Jun 2020 10:22:48: Fewer paired peaks (100) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 100 pairs to build model! INFO @ Tue, 16 Jun 2020 10:22:48: start model_add_line... INFO @ Tue, 16 Jun 2020 10:22:48: start X-correlation... INFO @ Tue, 16 Jun 2020 10:22:48: end of X-cor INFO @ Tue, 16 Jun 2020 10:22:48: #2 finished! INFO @ Tue, 16 Jun 2020 10:22:48: #2 predicted fragment length is 0 bps INFO @ Tue, 16 Jun 2020 10:22:48: #2 alternative fragment length(s) may be 0,13,24,49,87,113,132,148,182,208,243,255,257,279,302,326,361,396,408,431,455,507,521,528,582 bps INFO @ Tue, 16 Jun 2020 10:22:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX6619593/SRX6619593.20_model.r WARNING @ Tue, 16 Jun 2020 10:22:48: #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, 16 Jun 2020 10:22:48: #2 You may need to consider one of the other alternative d(s): 0,13,24,49,87,113,132,148,182,208,243,255,257,279,302,326,361,396,408,431,455,507,521,528,582 WARNING @ Tue, 16 Jun 2020 10:22:48: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 10:22:48: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:22:48: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 /var/spool/uge/it034/job_scripts/6368891: line 271: 498 Terminated MACS $i /var/spool/uge/it034/job_scripts/6368891: line 271: 764 Terminated MACS $i /var/spool/uge/it034/job_scripts/6368891: line 271: 867 Terminated MACS $i ls: cannot access SRX6619593.05.bed: No such file or directory mv: cannot stat ‘SRX6619593.05.bed’: No such file or directory mv: cannot stat ‘SRX6619593.05.bb’: No such file or directory ls: cannot access SRX6619593.10.bed: No such file or directory mv: cannot stat ‘SRX6619593.10.bed’: No such file or directory mv: cannot stat ‘SRX6619593.10.bb’: No such file or directory ls: cannot access SRX6619593.20.bed: No such file or directory mv: cannot stat ‘SRX6619593.20.bed’: No such file or directory mv: cannot stat ‘SRX6619593.20.bb’: No such file or directory