Job ID = 6368740 SRX = SRX5402764 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:33:30 prefetch.2.10.7: 1) Downloading 'SRR8602998'... 2020-06-16T00:33:30 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:36:55 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:36:55 prefetch.2.10.7: 1) 'SRR8602998' was downloaded successfully Read 32322596 spots for SRR8602998/SRR8602998.sra Written 32322596 spots for SRR8602998/SRR8602998.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: 00:07:06 32322596 reads; of these: 32322596 (100.00%) were unpaired; of these: 3126887 (9.67%) aligned 0 times 23563236 (72.90%) aligned exactly 1 time 5632473 (17.43%) aligned >1 times 90.33% overall alignment rate Time searching: 00:07:06 Overall time: 00:07:06 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 12 files... [bam_rmdupse_core] 4158922 / 29195709 = 0.1424 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 09:52:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402764/SRX5402764.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402764/SRX5402764.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402764/SRX5402764.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402764/SRX5402764.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 09:52:02: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:52:02: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:52:07: 1000000 INFO @ Tue, 16 Jun 2020 09:52:12: 2000000 INFO @ Tue, 16 Jun 2020 09:52:16: 3000000 INFO @ Tue, 16 Jun 2020 09:52:21: 4000000 INFO @ Tue, 16 Jun 2020 09:52:26: 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, 16 Jun 2020 09:52:30: 6000000 INFO @ Tue, 16 Jun 2020 09:52:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402764/SRX5402764.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402764/SRX5402764.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402764/SRX5402764.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402764/SRX5402764.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 09:52:31: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:52:31: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:52:35: 7000000 INFO @ Tue, 16 Jun 2020 09:52:36: 1000000 INFO @ Tue, 16 Jun 2020 09:52:40: 8000000 INFO @ Tue, 16 Jun 2020 09:52:41: 2000000 INFO @ Tue, 16 Jun 2020 09:52:45: 9000000 INFO @ Tue, 16 Jun 2020 09:52:46: 3000000 INFO @ Tue, 16 Jun 2020 09:52:50: 10000000 INFO @ Tue, 16 Jun 2020 09:52:51: 4000000 INFO @ Tue, 16 Jun 2020 09:52:55: 11000000 INFO @ Tue, 16 Jun 2020 09:52:56: 5000000 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 09:53:00: 12000000 INFO @ Tue, 16 Jun 2020 09:53:01: 6000000 INFO @ Tue, 16 Jun 2020 09:53:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402764/SRX5402764.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402764/SRX5402764.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402764/SRX5402764.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402764/SRX5402764.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 09:53:02: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:53:02: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:53:05: 13000000 INFO @ Tue, 16 Jun 2020 09:53:06: 7000000 INFO @ Tue, 16 Jun 2020 09:53:07: 1000000 INFO @ Tue, 16 Jun 2020 09:53:09: 14000000 INFO @ Tue, 16 Jun 2020 09:53:11: 8000000 INFO @ Tue, 16 Jun 2020 09:53:12: 2000000 INFO @ Tue, 16 Jun 2020 09:53:14: 15000000 INFO @ Tue, 16 Jun 2020 09:53:16: 9000000 INFO @ Tue, 16 Jun 2020 09:53:17: 3000000 INFO @ Tue, 16 Jun 2020 09:53:19: 16000000 INFO @ Tue, 16 Jun 2020 09:53:21: 10000000 INFO @ Tue, 16 Jun 2020 09:53:22: 4000000 INFO @ Tue, 16 Jun 2020 09:53:24: 17000000 INFO @ Tue, 16 Jun 2020 09:53:26: 11000000 INFO @ Tue, 16 Jun 2020 09:53:27: 5000000 INFO @ Tue, 16 Jun 2020 09:53:29: 18000000 INFO @ Tue, 16 Jun 2020 09:53:31: 12000000 INFO @ Tue, 16 Jun 2020 09:53:32: 6000000 INFO @ Tue, 16 Jun 2020 09:53:34: 19000000 INFO @ Tue, 16 Jun 2020 09:53:36: 13000000 INFO @ Tue, 16 Jun 2020 09:53:37: 7000000 INFO @ Tue, 16 Jun 2020 09:53:39: 20000000 INFO @ Tue, 16 Jun 2020 09:53:41: 14000000 INFO @ Tue, 16 Jun 2020 09:53:42: 8000000 INFO @ Tue, 16 Jun 2020 09:53:44: 21000000 INFO @ Tue, 16 Jun 2020 09:53:46: 15000000 INFO @ Tue, 16 Jun 2020 09:53:47: 9000000 INFO @ Tue, 16 Jun 2020 09:53:49: 22000000 INFO @ Tue, 16 Jun 2020 09:53:51: 16000000 INFO @ Tue, 16 Jun 2020 09:53:52: 10000000 INFO @ Tue, 16 Jun 2020 09:53:54: 23000000 INFO @ Tue, 16 Jun 2020 09:53:56: 17000000 INFO @ Tue, 16 Jun 2020 09:53:57: 11000000 INFO @ Tue, 16 Jun 2020 09:53:59: 24000000 INFO @ Tue, 16 Jun 2020 09:54:01: 18000000 INFO @ Tue, 16 Jun 2020 09:54:02: 12000000 INFO @ Tue, 16 Jun 2020 09:54:04: 25000000 INFO @ Tue, 16 Jun 2020 09:54:05: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:54:05: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:54:05: #1 total tags in treatment: 25036787 INFO @ Tue, 16 Jun 2020 09:54:05: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:54:05: #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 09:54:05: #1 tags after filtering in treatment: 25036787 INFO @ Tue, 16 Jun 2020 09:54:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:54:05: #1 finished! INFO @ Tue, 16 Jun 2020 09:54:05: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:54:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:54:06: 19000000 INFO @ Tue, 16 Jun 2020 09:54:07: 13000000 INFO @ Tue, 16 Jun 2020 09:54:07: #2 number of paired peaks: 157 WARNING @ Tue, 16 Jun 2020 09:54:07: Fewer paired peaks (157) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 157 pairs to build model! INFO @ Tue, 16 Jun 2020 09:54:07: start model_add_line... INFO @ Tue, 16 Jun 2020 09:54:07: start X-correlation... INFO @ Tue, 16 Jun 2020 09:54:07: end of X-cor INFO @ Tue, 16 Jun 2020 09:54:07: #2 finished! INFO @ Tue, 16 Jun 2020 09:54:07: #2 predicted fragment length is 0 bps INFO @ Tue, 16 Jun 2020 09:54:07: #2 alternative fragment length(s) may be 0,23,545 bps INFO @ Tue, 16 Jun 2020 09:54:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402764/SRX5402764.05_model.r WARNING @ Tue, 16 Jun 2020 09:54:07: #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 09:54:07: #2 You may need to consider one of the other alternative d(s): 0,23,545 WARNING @ Tue, 16 Jun 2020 09:54:07: #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 09:54:07: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:54:07: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:54:11: 20000000 INFO @ Tue, 16 Jun 2020 09:54:11: 14000000 INFO @ Tue, 16 Jun 2020 09:54:16: 21000000 INFO @ Tue, 16 Jun 2020 09:54:16: 15000000 INFO @ Tue, 16 Jun 2020 09:54:21: 22000000 INFO @ Tue, 16 Jun 2020 09:54:21: 16000000 INFO @ Tue, 16 Jun 2020 09:54:26: 23000000 INFO @ Tue, 16 Jun 2020 09:54:26: 17000000 INFO @ Tue, 16 Jun 2020 09:54:31: 18000000 INFO @ Tue, 16 Jun 2020 09:54:31: 24000000 INFO @ Tue, 16 Jun 2020 09:54:36: 19000000 INFO @ Tue, 16 Jun 2020 09:54:37: 25000000 INFO @ Tue, 16 Jun 2020 09:54:37: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:54:37: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:54:37: #1 total tags in treatment: 25036787 INFO @ Tue, 16 Jun 2020 09:54:37: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:54:37: #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 09:54:37: #1 tags after filtering in treatment: 25036787 INFO @ Tue, 16 Jun 2020 09:54:37: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:54:37: #1 finished! INFO @ Tue, 16 Jun 2020 09:54:37: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:54:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:54:39: #2 number of paired peaks: 157 WARNING @ Tue, 16 Jun 2020 09:54:39: Fewer paired peaks (157) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 157 pairs to build model! INFO @ Tue, 16 Jun 2020 09:54:39: start model_add_line... INFO @ Tue, 16 Jun 2020 09:54:39: start X-correlation... INFO @ Tue, 16 Jun 2020 09:54:39: end of X-cor INFO @ Tue, 16 Jun 2020 09:54:39: #2 finished! INFO @ Tue, 16 Jun 2020 09:54:39: #2 predicted fragment length is 0 bps INFO @ Tue, 16 Jun 2020 09:54:39: #2 alternative fragment length(s) may be 0,23,545 bps INFO @ Tue, 16 Jun 2020 09:54:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402764/SRX5402764.10_model.r WARNING @ Tue, 16 Jun 2020 09:54:39: #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 09:54:39: #2 You may need to consider one of the other alternative d(s): 0,23,545 WARNING @ Tue, 16 Jun 2020 09:54:39: #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 09:54:39: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:54:39: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:54:41: 20000000 INFO @ Tue, 16 Jun 2020 09:54:46: 21000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:54:51: 22000000 INFO @ Tue, 16 Jun 2020 09:54:56: 23000000 INFO @ Tue, 16 Jun 2020 09:55:00: 24000000 INFO @ Tue, 16 Jun 2020 09:55:06: 25000000 INFO @ Tue, 16 Jun 2020 09:55:06: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:55:06: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:55:06: #1 total tags in treatment: 25036787 INFO @ Tue, 16 Jun 2020 09:55:06: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:55:06: #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 09:55:06: #1 tags after filtering in treatment: 25036787 INFO @ Tue, 16 Jun 2020 09:55:06: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:55:06: #1 finished! INFO @ Tue, 16 Jun 2020 09:55:06: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:55:06: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:55:08: #2 number of paired peaks: 157 WARNING @ Tue, 16 Jun 2020 09:55:08: Fewer paired peaks (157) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 157 pairs to build model! INFO @ Tue, 16 Jun 2020 09:55:08: start model_add_line... INFO @ Tue, 16 Jun 2020 09:55:08: start X-correlation... INFO @ Tue, 16 Jun 2020 09:55:08: end of X-cor INFO @ Tue, 16 Jun 2020 09:55:08: #2 finished! INFO @ Tue, 16 Jun 2020 09:55:08: #2 predicted fragment length is 0 bps INFO @ Tue, 16 Jun 2020 09:55:08: #2 alternative fragment length(s) may be 0,23,545 bps INFO @ Tue, 16 Jun 2020 09:55:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402764/SRX5402764.20_model.r WARNING @ Tue, 16 Jun 2020 09:55:08: #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 09:55:08: #2 You may need to consider one of the other alternative d(s): 0,23,545 WARNING @ Tue, 16 Jun 2020 09:55:08: #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 09:55:08: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:55:08: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 /var/spool/uge/at162/job_scripts/6368740: line 271: 26022 Terminated MACS $i /var/spool/uge/at162/job_scripts/6368740: line 271: 35690 Terminated MACS $i /var/spool/uge/at162/job_scripts/6368740: line 271: 36096 Terminated MACS $i ls: cannot access SRX5402764.05.bed: No such file or directory mv: cannot stat ‘SRX5402764.05.bed’: No such file or directory mv: cannot stat ‘SRX5402764.05.bb’: No such file or directory ls: cannot access SRX5402764.10.bed: No such file or directory mv: cannot stat ‘SRX5402764.10.bed’: No such file or directory mv: cannot stat ‘SRX5402764.10.bb’: No such file or directory ls: cannot access SRX5402764.20.bed: No such file or directory mv: cannot stat ‘SRX5402764.20.bed’: No such file or directory mv: cannot stat ‘SRX5402764.20.bb’: No such file or directory