Job ID = 14159523 SRX = SRX8845634 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 110063960 spots for SRR12345941/SRR12345941.sra Written 110063960 spots for SRR12345941/SRR12345941.sra fastq に変換しました。 bowtie でマッピング中... Your job 14159782 ("srTce11") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:15:26 110063960 reads; of these: 110063960 (100.00%) were unpaired; of these: 73179197 (66.49%) aligned 0 times 30364137 (27.59%) aligned exactly 1 time 6520626 (5.92%) aligned >1 times 33.51% overall alignment rate Time searching: 00:15:26 Overall time: 00:15:26 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 16 files... [bam_rmdupse_core] 6618993 / 36884763 = 0.1795 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 08 Dec 2021 22:51:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8845634/SRX8845634.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8845634/SRX8845634.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8845634/SRX8845634.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8845634/SRX8845634.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 @ Wed, 08 Dec 2021 22:51:00: #1 read tag files... INFO @ Wed, 08 Dec 2021 22:51:00: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 22:51:10: 1000000 INFO @ Wed, 08 Dec 2021 22:51:19: 2000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 08 Dec 2021 22:51:28: 3000000 INFO @ Wed, 08 Dec 2021 22:51:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8845634/SRX8845634.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8845634/SRX8845634.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8845634/SRX8845634.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8845634/SRX8845634.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 @ Wed, 08 Dec 2021 22:51:30: #1 read tag files... INFO @ Wed, 08 Dec 2021 22:51:30: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 22:51:38: 4000000 INFO @ Wed, 08 Dec 2021 22:51:41: 1000000 INFO @ Wed, 08 Dec 2021 22:51:47: 5000000 INFO @ Wed, 08 Dec 2021 22:51:51: 2000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 08 Dec 2021 22:51:57: 6000000 INFO @ Wed, 08 Dec 2021 22:52:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8845634/SRX8845634.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8845634/SRX8845634.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8845634/SRX8845634.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8845634/SRX8845634.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 @ Wed, 08 Dec 2021 22:52:00: #1 read tag files... INFO @ Wed, 08 Dec 2021 22:52:00: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 22:52:01: 3000000 INFO @ Wed, 08 Dec 2021 22:52:07: 7000000 INFO @ Wed, 08 Dec 2021 22:52:07: 1000000 INFO @ Wed, 08 Dec 2021 22:52:12: 4000000 INFO @ Wed, 08 Dec 2021 22:52:15: 2000000 INFO @ Wed, 08 Dec 2021 22:52:18: 8000000 INFO @ Wed, 08 Dec 2021 22:52:22: 3000000 INFO @ Wed, 08 Dec 2021 22:52:22: 5000000 INFO @ Wed, 08 Dec 2021 22:52:28: 9000000 INFO @ Wed, 08 Dec 2021 22:52:29: 4000000 INFO @ Wed, 08 Dec 2021 22:52:32: 6000000 INFO @ Wed, 08 Dec 2021 22:52:36: 5000000 INFO @ Wed, 08 Dec 2021 22:52:38: 10000000 INFO @ Wed, 08 Dec 2021 22:52:42: 7000000 INFO @ Wed, 08 Dec 2021 22:52:44: 6000000 INFO @ Wed, 08 Dec 2021 22:52:47: 11000000 INFO @ Wed, 08 Dec 2021 22:52:51: 7000000 INFO @ Wed, 08 Dec 2021 22:52:52: 8000000 INFO @ Wed, 08 Dec 2021 22:52:57: 12000000 INFO @ Wed, 08 Dec 2021 22:52:58: 8000000 INFO @ Wed, 08 Dec 2021 22:53:02: 9000000 INFO @ Wed, 08 Dec 2021 22:53:05: 9000000 INFO @ Wed, 08 Dec 2021 22:53:07: 13000000 INFO @ Wed, 08 Dec 2021 22:53:12: 10000000 INFO @ Wed, 08 Dec 2021 22:53:13: 10000000 INFO @ Wed, 08 Dec 2021 22:53:18: 14000000 INFO @ Wed, 08 Dec 2021 22:53:20: 11000000 INFO @ Wed, 08 Dec 2021 22:53:23: 11000000 INFO @ Wed, 08 Dec 2021 22:53:27: 12000000 INFO @ Wed, 08 Dec 2021 22:53:28: 15000000 INFO @ Wed, 08 Dec 2021 22:53:33: 12000000 INFO @ Wed, 08 Dec 2021 22:53:34: 13000000 INFO @ Wed, 08 Dec 2021 22:53:38: 16000000 INFO @ Wed, 08 Dec 2021 22:53:42: 14000000 INFO @ Wed, 08 Dec 2021 22:53:44: 13000000 INFO @ Wed, 08 Dec 2021 22:53:49: 17000000 INFO @ Wed, 08 Dec 2021 22:53:49: 15000000 INFO @ Wed, 08 Dec 2021 22:53:54: 14000000 INFO @ Wed, 08 Dec 2021 22:53:57: 16000000 INFO @ Wed, 08 Dec 2021 22:53:59: 18000000 INFO @ Wed, 08 Dec 2021 22:54:04: 17000000 INFO @ Wed, 08 Dec 2021 22:54:04: 15000000 INFO @ Wed, 08 Dec 2021 22:54:09: 19000000 INFO @ Wed, 08 Dec 2021 22:54:11: 18000000 INFO @ Wed, 08 Dec 2021 22:54:15: 16000000 INFO @ Wed, 08 Dec 2021 22:54:18: 19000000 INFO @ Wed, 08 Dec 2021 22:54:20: 20000000 INFO @ Wed, 08 Dec 2021 22:54:25: 17000000 INFO @ Wed, 08 Dec 2021 22:54:25: 20000000 INFO @ Wed, 08 Dec 2021 22:54:30: 21000000 INFO @ Wed, 08 Dec 2021 22:54:33: 21000000 INFO @ Wed, 08 Dec 2021 22:54:36: 18000000 INFO @ Wed, 08 Dec 2021 22:54:40: 22000000 INFO @ Wed, 08 Dec 2021 22:54:41: 22000000 INFO @ Wed, 08 Dec 2021 22:54:46: 19000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 22:54:48: 23000000 INFO @ Wed, 08 Dec 2021 22:54:51: 23000000 INFO @ Wed, 08 Dec 2021 22:54:55: 24000000 INFO @ Wed, 08 Dec 2021 22:54:56: 20000000 INFO @ Wed, 08 Dec 2021 22:55:01: 24000000 INFO @ Wed, 08 Dec 2021 22:55:03: 25000000 INFO @ Wed, 08 Dec 2021 22:55:07: 21000000 INFO @ Wed, 08 Dec 2021 22:55:10: 26000000 INFO @ Wed, 08 Dec 2021 22:55:12: 25000000 INFO @ Wed, 08 Dec 2021 22:55:17: 22000000 INFO @ Wed, 08 Dec 2021 22:55:18: 27000000 INFO @ Wed, 08 Dec 2021 22:55:22: 26000000 INFO @ Wed, 08 Dec 2021 22:55:25: 28000000 INFO @ Wed, 08 Dec 2021 22:55:27: 23000000 INFO @ Wed, 08 Dec 2021 22:55:32: 27000000 INFO @ Wed, 08 Dec 2021 22:55:32: 29000000 INFO @ Wed, 08 Dec 2021 22:55:37: 24000000 INFO @ Wed, 08 Dec 2021 22:55:39: 30000000 INFO @ Wed, 08 Dec 2021 22:55:41: 28000000 INFO @ Wed, 08 Dec 2021 22:55:42: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 22:55:42: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 22:55:42: #1 total tags in treatment: 30265770 INFO @ Wed, 08 Dec 2021 22:55:42: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 22:55:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 22:55:42: #1 tags after filtering in treatment: 30265770 INFO @ Wed, 08 Dec 2021 22:55:42: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 22:55:42: #1 finished! INFO @ Wed, 08 Dec 2021 22:55:42: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 22:55:42: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 22:55:45: #2 number of paired peaks: 123 WARNING @ Wed, 08 Dec 2021 22:55:45: Fewer paired peaks (123) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 123 pairs to build model! INFO @ Wed, 08 Dec 2021 22:55:45: start model_add_line... INFO @ Wed, 08 Dec 2021 22:55:45: start X-correlation... INFO @ Wed, 08 Dec 2021 22:55:45: end of X-cor INFO @ Wed, 08 Dec 2021 22:55:45: #2 finished! INFO @ Wed, 08 Dec 2021 22:55:45: #2 predicted fragment length is 0 bps INFO @ Wed, 08 Dec 2021 22:55:45: #2 alternative fragment length(s) may be 0,21,42,237,369,429,507,531,550,583 bps INFO @ Wed, 08 Dec 2021 22:55:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8845634/SRX8845634.20_model.r WARNING @ Wed, 08 Dec 2021 22:55:45: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 22:55:45: #2 You may need to consider one of the other alternative d(s): 0,21,42,237,369,429,507,531,550,583 WARNING @ Wed, 08 Dec 2021 22:55:45: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 22:55:45: #3 Call peaks... INFO @ Wed, 08 Dec 2021 22:55:45: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 22:55:47: 25000000 INFO @ Wed, 08 Dec 2021 22:55:51: 29000000 INFO @ Wed, 08 Dec 2021 22:55:57: 26000000 INFO @ Wed, 08 Dec 2021 22:56:00: 30000000 INFO @ Wed, 08 Dec 2021 22:56:03: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 22:56:03: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 22:56:03: #1 total tags in treatment: 30265770 INFO @ Wed, 08 Dec 2021 22:56:03: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 22:56:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 22:56:03: #1 tags after filtering in treatment: 30265770 INFO @ Wed, 08 Dec 2021 22:56:03: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 22:56:03: #1 finished! INFO @ Wed, 08 Dec 2021 22:56:03: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 22:56:03: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 22:56:06: #2 number of paired peaks: 123 WARNING @ Wed, 08 Dec 2021 22:56:06: Fewer paired peaks (123) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 123 pairs to build model! INFO @ Wed, 08 Dec 2021 22:56:06: start model_add_line... INFO @ Wed, 08 Dec 2021 22:56:06: start X-correlation... INFO @ Wed, 08 Dec 2021 22:56:06: 27000000 INFO @ Wed, 08 Dec 2021 22:56:06: end of X-cor INFO @ Wed, 08 Dec 2021 22:56:06: #2 finished! INFO @ Wed, 08 Dec 2021 22:56:06: #2 predicted fragment length is 0 bps INFO @ Wed, 08 Dec 2021 22:56:06: #2 alternative fragment length(s) may be 0,21,42,237,369,429,507,531,550,583 bps INFO @ Wed, 08 Dec 2021 22:56:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8845634/SRX8845634.05_model.r WARNING @ Wed, 08 Dec 2021 22:56:06: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 22:56:06: #2 You may need to consider one of the other alternative d(s): 0,21,42,237,369,429,507,531,550,583 WARNING @ Wed, 08 Dec 2021 22:56:06: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 22:56:06: #3 Call peaks... INFO @ Wed, 08 Dec 2021 22:56:06: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 /var/spool/uge/at076/job_scripts/14159523: line 297: 63122 Terminated MACS $i /var/spool/uge/at076/job_scripts/14159523: line 297: 65510 Terminated MACS $i /var/spool/uge/at076/job_scripts/14159523: line 297: 2757 Terminated MACS $i ls: cannot access SRX8845634.05.bed: No such file or directory mv: cannot stat ‘SRX8845634.05.bed’: No such file or directory mv: cannot stat ‘SRX8845634.05.bb’: No such file or directory ls: cannot access SRX8845634.10.bed: No such file or directory mv: cannot stat ‘SRX8845634.10.bed’: No such file or directory mv: cannot stat ‘SRX8845634.10.bb’: No such file or directory ls: cannot access SRX8845634.20.bed: No such file or directory mv: cannot stat ‘SRX8845634.20.bed’: No such file or directory mv: cannot stat ‘SRX8845634.20.bb’: No such file or directory