Job ID = 6367266 SRX = SRX323687 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:23:31 prefetch.2.10.7: 1) Downloading 'SRR935761'... 2020-06-15T23:23:31 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:24:38 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:24:39 prefetch.2.10.7: 'SRR935761' is valid 2020-06-15T23:24:39 prefetch.2.10.7: 1) 'SRR935761' was downloaded successfully Read 27905418 spots for SRR935761/SRR935761.sra Written 27905418 spots for SRR935761/SRR935761.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: 00:04:09 27905418 reads; of these: 27905418 (100.00%) were unpaired; of these: 680345 (2.44%) aligned 0 times 22387333 (80.23%) aligned exactly 1 time 4837740 (17.34%) aligned >1 times 97.56% overall alignment rate Time searching: 00:04:09 Overall time: 00:04:09 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] 5234282 / 27225073 = 0.1923 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 08:35:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX323687/SRX323687.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX323687/SRX323687.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX323687/SRX323687.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX323687/SRX323687.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 08:35:06: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:35:06: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:35:11: 1000000 INFO @ Tue, 16 Jun 2020 08:35:15: 2000000 INFO @ Tue, 16 Jun 2020 08:35:20: 3000000 INFO @ Tue, 16 Jun 2020 08:35:25: 4000000 INFO @ Tue, 16 Jun 2020 08:35:30: 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 08:35:35: 6000000 INFO @ Tue, 16 Jun 2020 08:35:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX323687/SRX323687.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX323687/SRX323687.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX323687/SRX323687.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX323687/SRX323687.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 08:35:36: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:35:36: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:35:41: 7000000 INFO @ Tue, 16 Jun 2020 08:35:42: 1000000 INFO @ Tue, 16 Jun 2020 08:35:46: 8000000 INFO @ Tue, 16 Jun 2020 08:35:49: 2000000 INFO @ Tue, 16 Jun 2020 08:35:52: 9000000 INFO @ Tue, 16 Jun 2020 08:35:55: 3000000 INFO @ Tue, 16 Jun 2020 08:35:58: 10000000 INFO @ Tue, 16 Jun 2020 08:36:02: 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 08:36:04: 11000000 INFO @ Tue, 16 Jun 2020 08:36:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX323687/SRX323687.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX323687/SRX323687.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX323687/SRX323687.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX323687/SRX323687.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 08:36:06: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:36:06: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:36:09: 5000000 INFO @ Tue, 16 Jun 2020 08:36:10: 12000000 INFO @ Tue, 16 Jun 2020 08:36:12: 1000000 INFO @ Tue, 16 Jun 2020 08:36:15: 6000000 INFO @ Tue, 16 Jun 2020 08:36:16: 13000000 INFO @ Tue, 16 Jun 2020 08:36:18: 2000000 INFO @ Tue, 16 Jun 2020 08:36:22: 7000000 INFO @ Tue, 16 Jun 2020 08:36:22: 14000000 INFO @ Tue, 16 Jun 2020 08:36:24: 3000000 INFO @ Tue, 16 Jun 2020 08:36:28: 15000000 INFO @ Tue, 16 Jun 2020 08:36:29: 8000000 INFO @ Tue, 16 Jun 2020 08:36:30: 4000000 INFO @ Tue, 16 Jun 2020 08:36:34: 16000000 INFO @ Tue, 16 Jun 2020 08:36:35: 9000000 INFO @ Tue, 16 Jun 2020 08:36:36: 5000000 INFO @ Tue, 16 Jun 2020 08:36:40: 17000000 INFO @ Tue, 16 Jun 2020 08:36:42: 10000000 INFO @ Tue, 16 Jun 2020 08:36:42: 6000000 INFO @ Tue, 16 Jun 2020 08:36:46: 18000000 INFO @ Tue, 16 Jun 2020 08:36:48: 7000000 INFO @ Tue, 16 Jun 2020 08:36:49: 11000000 INFO @ Tue, 16 Jun 2020 08:36:52: 19000000 INFO @ Tue, 16 Jun 2020 08:36:54: 8000000 INFO @ Tue, 16 Jun 2020 08:36:55: 12000000 INFO @ Tue, 16 Jun 2020 08:36:59: 20000000 INFO @ Tue, 16 Jun 2020 08:37:00: 9000000 INFO @ Tue, 16 Jun 2020 08:37:02: 13000000 INFO @ Tue, 16 Jun 2020 08:37:05: 21000000 INFO @ Tue, 16 Jun 2020 08:37:07: 10000000 INFO @ Tue, 16 Jun 2020 08:37:09: 14000000 INFO @ Tue, 16 Jun 2020 08:37:11: #1 tag size is determined as 28 bps INFO @ Tue, 16 Jun 2020 08:37:11: #1 tag size = 28 INFO @ Tue, 16 Jun 2020 08:37:11: #1 total tags in treatment: 21990791 INFO @ Tue, 16 Jun 2020 08:37:11: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:37:11: #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 08:37:11: #1 tags after filtering in treatment: 21990791 INFO @ Tue, 16 Jun 2020 08:37:11: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:37:11: #1 finished! INFO @ Tue, 16 Jun 2020 08:37:11: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:37:11: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:37:13: #2 number of paired peaks: 148 WARNING @ Tue, 16 Jun 2020 08:37:13: Fewer paired peaks (148) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 148 pairs to build model! INFO @ Tue, 16 Jun 2020 08:37:13: start model_add_line... INFO @ Tue, 16 Jun 2020 08:37:13: 11000000 INFO @ Tue, 16 Jun 2020 08:37:13: start X-correlation... INFO @ Tue, 16 Jun 2020 08:37:13: end of X-cor INFO @ Tue, 16 Jun 2020 08:37:13: #2 finished! INFO @ Tue, 16 Jun 2020 08:37:13: #2 predicted fragment length is 0 bps INFO @ Tue, 16 Jun 2020 08:37:13: #2 alternative fragment length(s) may be 0,27,533,558 bps INFO @ Tue, 16 Jun 2020 08:37:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX323687/SRX323687.05_model.r WARNING @ Tue, 16 Jun 2020 08:37:13: #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 08:37:13: #2 You may need to consider one of the other alternative d(s): 0,27,533,558 WARNING @ Tue, 16 Jun 2020 08:37:13: #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 08:37:13: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:37:13: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:37:16: 15000000 INFO @ Tue, 16 Jun 2020 08:37:19: 12000000 INFO @ Tue, 16 Jun 2020 08:37:22: 16000000 INFO @ Tue, 16 Jun 2020 08:37:25: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:37:29: 17000000 INFO @ Tue, 16 Jun 2020 08:37:31: 14000000 INFO @ Tue, 16 Jun 2020 08:37:36: 18000000 INFO @ Tue, 16 Jun 2020 08:37:38: 15000000 INFO @ Tue, 16 Jun 2020 08:37:43: 19000000 INFO @ Tue, 16 Jun 2020 08:37:44: 16000000 INFO @ Tue, 16 Jun 2020 08:37:49: 20000000 INFO @ Tue, 16 Jun 2020 08:37:50: 17000000 INFO @ Tue, 16 Jun 2020 08:37:56: 21000000 INFO @ Tue, 16 Jun 2020 08:37:57: 18000000 INFO @ Tue, 16 Jun 2020 08:38:03: #1 tag size is determined as 28 bps INFO @ Tue, 16 Jun 2020 08:38:03: #1 tag size = 28 INFO @ Tue, 16 Jun 2020 08:38:03: #1 total tags in treatment: 21990791 INFO @ Tue, 16 Jun 2020 08:38:03: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:38:03: #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 08:38:03: 19000000 INFO @ Tue, 16 Jun 2020 08:38:03: #1 tags after filtering in treatment: 21990791 INFO @ Tue, 16 Jun 2020 08:38:03: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:38:03: #1 finished! INFO @ Tue, 16 Jun 2020 08:38:03: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:38:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:38:04: #2 number of paired peaks: 148 WARNING @ Tue, 16 Jun 2020 08:38:04: Fewer paired peaks (148) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 148 pairs to build model! INFO @ Tue, 16 Jun 2020 08:38:04: start model_add_line... INFO @ Tue, 16 Jun 2020 08:38:05: start X-correlation... INFO @ Tue, 16 Jun 2020 08:38:05: end of X-cor INFO @ Tue, 16 Jun 2020 08:38:05: #2 finished! INFO @ Tue, 16 Jun 2020 08:38:05: #2 predicted fragment length is 0 bps INFO @ Tue, 16 Jun 2020 08:38:05: #2 alternative fragment length(s) may be 0,27,533,558 bps INFO @ Tue, 16 Jun 2020 08:38:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX323687/SRX323687.10_model.r WARNING @ Tue, 16 Jun 2020 08:38:05: #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 08:38:05: #2 You may need to consider one of the other alternative d(s): 0,27,533,558 WARNING @ Tue, 16 Jun 2020 08:38:05: #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 08:38:05: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:38:05: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:38:09: 20000000 INFO @ Tue, 16 Jun 2020 08:38:14: 21000000 BigWig に変換しました。 /var/spool/uge/at158/job_scripts/6367266: line 271: 62073 Terminated MACS $i /var/spool/uge/at158/job_scripts/6367266: line 271: 68411 Terminated MACS $i /var/spool/uge/at158/job_scripts/6367266: line 271: 77612 Terminated MACS $i ls: cannot access SRX323687.05.bed: No such file or directory mv: cannot stat ‘SRX323687.05.bed’: No such file or directory mv: cannot stat ‘SRX323687.05.bb’: No such file or directory ls: cannot access SRX323687.10.bed: No such file or directory mv: cannot stat ‘SRX323687.10.bed’: No such file or directory mv: cannot stat ‘SRX323687.10.bb’: No such file or directory ls: cannot access SRX323687.20.bed: No such file or directory mv: cannot stat ‘SRX323687.20.bed’: No such file or directory mv: cannot stat ‘SRX323687.20.bb’: No such file or directory