Job ID = 6368164 SRX = SRX494848 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:11:20 prefetch.2.10.7: 1) Downloading 'SRR1198380'... 2020-06-16T00:11:20 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:14:26 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:14:26 prefetch.2.10.7: 1) 'SRR1198380' was downloaded successfully Read 30788149 spots for SRR1198380/SRR1198380.sra Written 30788149 spots for SRR1198380/SRR1198380.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: 00:05:16 30788149 reads; of these: 30788149 (100.00%) were unpaired; of these: 169816 (0.55%) aligned 0 times 25275412 (82.09%) aligned exactly 1 time 5342921 (17.35%) aligned >1 times 99.45% overall alignment rate Time searching: 00:05:16 Overall time: 00:05:16 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 8 files... [bam_rmdupse_core] 4711722 / 30618333 = 0.1539 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 09:27:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494848/SRX494848.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494848/SRX494848.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494848/SRX494848.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494848/SRX494848.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 09:27:35: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:27:35: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:27:40: 1000000 INFO @ Tue, 16 Jun 2020 09:27:46: 2000000 INFO @ Tue, 16 Jun 2020 09:27:51: 3000000 INFO @ Tue, 16 Jun 2020 09:27:56: 4000000 INFO @ Tue, 16 Jun 2020 09:28:01: 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, 16 Jun 2020 09:28:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494848/SRX494848.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494848/SRX494848.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494848/SRX494848.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494848/SRX494848.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 09:28:05: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:28:05: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:28:06: 6000000 INFO @ Tue, 16 Jun 2020 09:28:11: 1000000 INFO @ Tue, 16 Jun 2020 09:28:12: 7000000 INFO @ Tue, 16 Jun 2020 09:28:17: 2000000 INFO @ Tue, 16 Jun 2020 09:28:18: 8000000 INFO @ Tue, 16 Jun 2020 09:28:23: 9000000 INFO @ Tue, 16 Jun 2020 09:28:23: 3000000 INFO @ Tue, 16 Jun 2020 09:28:29: 10000000 INFO @ Tue, 16 Jun 2020 09:28:29: 4000000 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 09:28:34: 11000000 INFO @ Tue, 16 Jun 2020 09:28:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494848/SRX494848.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494848/SRX494848.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494848/SRX494848.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494848/SRX494848.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 09:28:35: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:28:35: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:28:35: 5000000 INFO @ Tue, 16 Jun 2020 09:28:40: 12000000 INFO @ Tue, 16 Jun 2020 09:28:41: 1000000 INFO @ Tue, 16 Jun 2020 09:28:41: 6000000 INFO @ Tue, 16 Jun 2020 09:28:46: 13000000 INFO @ Tue, 16 Jun 2020 09:28:47: 2000000 INFO @ Tue, 16 Jun 2020 09:28:47: 7000000 INFO @ Tue, 16 Jun 2020 09:28:51: 14000000 INFO @ Tue, 16 Jun 2020 09:28:53: 3000000 INFO @ Tue, 16 Jun 2020 09:28:53: 8000000 INFO @ Tue, 16 Jun 2020 09:28:57: 15000000 INFO @ Tue, 16 Jun 2020 09:28:58: 4000000 INFO @ Tue, 16 Jun 2020 09:28:59: 9000000 INFO @ Tue, 16 Jun 2020 09:29:02: 16000000 INFO @ Tue, 16 Jun 2020 09:29:04: 5000000 INFO @ Tue, 16 Jun 2020 09:29:05: 10000000 INFO @ Tue, 16 Jun 2020 09:29:08: 17000000 INFO @ Tue, 16 Jun 2020 09:29:10: 6000000 INFO @ Tue, 16 Jun 2020 09:29:11: 11000000 INFO @ Tue, 16 Jun 2020 09:29:14: 18000000 INFO @ Tue, 16 Jun 2020 09:29:16: 7000000 INFO @ Tue, 16 Jun 2020 09:29:17: 12000000 INFO @ Tue, 16 Jun 2020 09:29:19: 19000000 INFO @ Tue, 16 Jun 2020 09:29:22: 8000000 INFO @ Tue, 16 Jun 2020 09:29:23: 13000000 INFO @ Tue, 16 Jun 2020 09:29:25: 20000000 INFO @ Tue, 16 Jun 2020 09:29:27: 9000000 INFO @ Tue, 16 Jun 2020 09:29:29: 14000000 INFO @ Tue, 16 Jun 2020 09:29:30: 21000000 INFO @ Tue, 16 Jun 2020 09:29:33: 10000000 INFO @ Tue, 16 Jun 2020 09:29:35: 15000000 INFO @ Tue, 16 Jun 2020 09:29:36: 22000000 INFO @ Tue, 16 Jun 2020 09:29:39: 11000000 INFO @ Tue, 16 Jun 2020 09:29:41: 16000000 INFO @ Tue, 16 Jun 2020 09:29:42: 23000000 INFO @ Tue, 16 Jun 2020 09:29:45: 12000000 INFO @ Tue, 16 Jun 2020 09:29:47: 17000000 INFO @ Tue, 16 Jun 2020 09:29:47: 24000000 INFO @ Tue, 16 Jun 2020 09:29:51: 13000000 INFO @ Tue, 16 Jun 2020 09:29:53: 25000000 INFO @ Tue, 16 Jun 2020 09:29:53: 18000000 INFO @ Tue, 16 Jun 2020 09:29:56: 14000000 INFO @ Tue, 16 Jun 2020 09:29:58: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 09:29:58: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 09:29:58: #1 total tags in treatment: 25906611 INFO @ Tue, 16 Jun 2020 09:29:58: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:29:58: #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 09:29:59: #1 tags after filtering in treatment: 25906611 INFO @ Tue, 16 Jun 2020 09:29:59: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:29:59: #1 finished! INFO @ Tue, 16 Jun 2020 09:29:59: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:29:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:29:59: 19000000 INFO @ Tue, 16 Jun 2020 09:30:00: #2 number of paired peaks: 143 WARNING @ Tue, 16 Jun 2020 09:30:00: Fewer paired peaks (143) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 143 pairs to build model! INFO @ Tue, 16 Jun 2020 09:30:00: start model_add_line... INFO @ Tue, 16 Jun 2020 09:30:00: start X-correlation... INFO @ Tue, 16 Jun 2020 09:30:01: end of X-cor INFO @ Tue, 16 Jun 2020 09:30:01: #2 finished! INFO @ Tue, 16 Jun 2020 09:30:01: #2 predicted fragment length is 0 bps INFO @ Tue, 16 Jun 2020 09:30:01: #2 alternative fragment length(s) may be 0,30,99,145,308,339,483,516,550 bps INFO @ Tue, 16 Jun 2020 09:30:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494848/SRX494848.05_model.r WARNING @ Tue, 16 Jun 2020 09:30:01: #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 09:30:01: #2 You may need to consider one of the other alternative d(s): 0,30,99,145,308,339,483,516,550 WARNING @ Tue, 16 Jun 2020 09:30:01: #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 09:30:01: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:30:01: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:30:02: 15000000 INFO @ Tue, 16 Jun 2020 09:30:05: 20000000 INFO @ Tue, 16 Jun 2020 09:30:07: 16000000 INFO @ Tue, 16 Jun 2020 09:30:11: 21000000 INFO @ Tue, 16 Jun 2020 09:30:13: 17000000 INFO @ Tue, 16 Jun 2020 09:30:17: 22000000 INFO @ Tue, 16 Jun 2020 09:30:19: 18000000 INFO @ Tue, 16 Jun 2020 09:30:23: 23000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:30:24: 19000000 INFO @ Tue, 16 Jun 2020 09:30:29: 24000000 INFO @ Tue, 16 Jun 2020 09:30:30: 20000000 INFO @ Tue, 16 Jun 2020 09:30:35: 25000000 INFO @ Tue, 16 Jun 2020 09:30:36: 21000000 INFO @ Tue, 16 Jun 2020 09:30:40: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 09:30:40: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 09:30:40: #1 total tags in treatment: 25906611 INFO @ Tue, 16 Jun 2020 09:30:40: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:30:40: #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 09:30:41: #1 tags after filtering in treatment: 25906611 INFO @ Tue, 16 Jun 2020 09:30:41: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:30:41: #1 finished! INFO @ Tue, 16 Jun 2020 09:30:41: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:30:41: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:30:41: 22000000 INFO @ Tue, 16 Jun 2020 09:30:43: #2 number of paired peaks: 143 WARNING @ Tue, 16 Jun 2020 09:30:43: Fewer paired peaks (143) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 143 pairs to build model! INFO @ Tue, 16 Jun 2020 09:30:43: start model_add_line... INFO @ Tue, 16 Jun 2020 09:30:43: start X-correlation... INFO @ Tue, 16 Jun 2020 09:30:43: end of X-cor INFO @ Tue, 16 Jun 2020 09:30:43: #2 finished! INFO @ Tue, 16 Jun 2020 09:30:43: #2 predicted fragment length is 0 bps INFO @ Tue, 16 Jun 2020 09:30:43: #2 alternative fragment length(s) may be 0,30,99,145,308,339,483,516,550 bps INFO @ Tue, 16 Jun 2020 09:30:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494848/SRX494848.10_model.r WARNING @ Tue, 16 Jun 2020 09:30:43: #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 09:30:43: #2 You may need to consider one of the other alternative d(s): 0,30,99,145,308,339,483,516,550 WARNING @ Tue, 16 Jun 2020 09:30:43: #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 09:30:43: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:30:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:30:47: 23000000 INFO @ Tue, 16 Jun 2020 09:30:52: 24000000 INFO @ Tue, 16 Jun 2020 09:30:57: 25000000 INFO @ Tue, 16 Jun 2020 09:31:02: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 09:31:02: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 09:31:02: #1 total tags in treatment: 25906611 INFO @ Tue, 16 Jun 2020 09:31:02: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:31:02: #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 09:31:03: #1 tags after filtering in treatment: 25906611 INFO @ Tue, 16 Jun 2020 09:31:03: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:31:03: #1 finished! INFO @ Tue, 16 Jun 2020 09:31:03: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:31:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:31:05: #2 number of paired peaks: 143 WARNING @ Tue, 16 Jun 2020 09:31:05: Fewer paired peaks (143) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 143 pairs to build model! INFO @ Tue, 16 Jun 2020 09:31:05: start model_add_line... INFO @ Tue, 16 Jun 2020 09:31:05: start X-correlation... INFO @ Tue, 16 Jun 2020 09:31:05: end of X-cor INFO @ Tue, 16 Jun 2020 09:31:05: #2 finished! INFO @ Tue, 16 Jun 2020 09:31:05: #2 predicted fragment length is 0 bps INFO @ Tue, 16 Jun 2020 09:31:05: #2 alternative fragment length(s) may be 0,30,99,145,308,339,483,516,550 bps INFO @ Tue, 16 Jun 2020 09:31:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494848/SRX494848.20_model.r WARNING @ Tue, 16 Jun 2020 09:31:05: #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, 16 Jun 2020 09:31:05: #2 You may need to consider one of the other alternative d(s): 0,30,99,145,308,339,483,516,550 WARNING @ Tue, 16 Jun 2020 09:31:05: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 09:31:05: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:31:05: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 /var/spool/uge/at162/job_scripts/6368164: line 271: 78686 Terminated MACS $i /var/spool/uge/at162/job_scripts/6368164: line 271: 108827 Terminated MACS $i /var/spool/uge/at162/job_scripts/6368164: line 271: 126638 Terminated MACS $i ls: cannot access SRX494848.05.bed: No such file or directory mv: cannot stat ‘SRX494848.05.bed’: No such file or directory mv: cannot stat ‘SRX494848.05.bb’: No such file or directory ls: cannot access SRX494848.10.bed: No such file or directory mv: cannot stat ‘SRX494848.10.bed’: No such file or directory mv: cannot stat ‘SRX494848.10.bb’: No such file or directory ls: cannot access SRX494848.20.bed: No such file or directory mv: cannot stat ‘SRX494848.20.bed’: No such file or directory mv: cannot stat ‘SRX494848.20.bb’: No such file or directory