Job ID = 10165874 SRX = SRX7879261 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 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: 00:00:01 Multiseed full-index search: 00:05:34 24822282 reads; of these: 24822282 (100.00%) were unpaired; of these: 507701 (2.05%) aligned 0 times 20433768 (82.32%) aligned exactly 1 time 3880813 (15.63%) aligned >1 times 97.95% overall alignment rate Time searching: 00:05:35 Overall time: 00:05:35 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] 3544882 / 24314581 = 0.1458 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 @ Thu, 08 Oct 2020 20:17:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7879261/SRX7879261.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7879261/SRX7879261.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7879261/SRX7879261.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7879261/SRX7879261.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 @ Thu, 08 Oct 2020 20:17:11: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:17:11: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:17:20: 1000000 INFO @ Thu, 08 Oct 2020 20:17:28: 2000000 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 @ Thu, 08 Oct 2020 20:17:36: 3000000 INFO @ Thu, 08 Oct 2020 20:17:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7879261/SRX7879261.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7879261/SRX7879261.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7879261/SRX7879261.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7879261/SRX7879261.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 @ Thu, 08 Oct 2020 20:17:38: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:17:38: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:17:45: 4000000 INFO @ Thu, 08 Oct 2020 20:17:47: 1000000 INFO @ Thu, 08 Oct 2020 20:17:53: 5000000 INFO @ Thu, 08 Oct 2020 20:17:55: 2000000 INFO @ Thu, 08 Oct 2020 20:18:02: 6000000 INFO @ Thu, 08 Oct 2020 20:18:04: 3000000 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 @ Thu, 08 Oct 2020 20:18:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7879261/SRX7879261.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7879261/SRX7879261.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7879261/SRX7879261.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7879261/SRX7879261.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 @ Thu, 08 Oct 2020 20:18:08: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:18:08: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:18:10: 7000000 INFO @ Thu, 08 Oct 2020 20:18:12: 4000000 INFO @ Thu, 08 Oct 2020 20:18:17: 1000000 INFO @ Thu, 08 Oct 2020 20:18:19: 8000000 INFO @ Thu, 08 Oct 2020 20:18:21: 5000000 INFO @ Thu, 08 Oct 2020 20:18:26: 2000000 INFO @ Thu, 08 Oct 2020 20:18:28: 9000000 INFO @ Thu, 08 Oct 2020 20:18:29: 6000000 INFO @ Thu, 08 Oct 2020 20:18:35: 3000000 INFO @ Thu, 08 Oct 2020 20:18:36: 10000000 INFO @ Thu, 08 Oct 2020 20:18:38: 7000000 INFO @ Thu, 08 Oct 2020 20:18:43: 4000000 INFO @ Thu, 08 Oct 2020 20:18:45: 11000000 INFO @ Thu, 08 Oct 2020 20:18:46: 8000000 INFO @ Thu, 08 Oct 2020 20:18:52: 5000000 INFO @ Thu, 08 Oct 2020 20:18:53: 12000000 INFO @ Thu, 08 Oct 2020 20:18:55: 9000000 INFO @ Thu, 08 Oct 2020 20:19:00: 6000000 INFO @ Thu, 08 Oct 2020 20:19:02: 13000000 INFO @ Thu, 08 Oct 2020 20:19:03: 10000000 INFO @ Thu, 08 Oct 2020 20:19:09: 7000000 INFO @ Thu, 08 Oct 2020 20:19:11: 14000000 INFO @ Thu, 08 Oct 2020 20:19:12: 11000000 INFO @ Thu, 08 Oct 2020 20:19:18: 8000000 INFO @ Thu, 08 Oct 2020 20:19:19: 15000000 INFO @ Thu, 08 Oct 2020 20:19:20: 12000000 INFO @ Thu, 08 Oct 2020 20:19:26: 9000000 INFO @ Thu, 08 Oct 2020 20:19:28: 16000000 INFO @ Thu, 08 Oct 2020 20:19:28: 13000000 INFO @ Thu, 08 Oct 2020 20:19:34: 10000000 INFO @ Thu, 08 Oct 2020 20:19:36: 17000000 INFO @ Thu, 08 Oct 2020 20:19:37: 14000000 INFO @ Thu, 08 Oct 2020 20:19:43: 11000000 INFO @ Thu, 08 Oct 2020 20:19:45: 18000000 INFO @ Thu, 08 Oct 2020 20:19:45: 15000000 INFO @ Thu, 08 Oct 2020 20:19:51: 12000000 INFO @ Thu, 08 Oct 2020 20:19:54: 19000000 INFO @ Thu, 08 Oct 2020 20:19:54: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 08 Oct 2020 20:20:00: 13000000 INFO @ Thu, 08 Oct 2020 20:20:02: 20000000 INFO @ Thu, 08 Oct 2020 20:20:03: 17000000 INFO @ Thu, 08 Oct 2020 20:20:08: 14000000 INFO @ Thu, 08 Oct 2020 20:20:09: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 20:20:09: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 20:20:09: #1 total tags in treatment: 20769699 INFO @ Thu, 08 Oct 2020 20:20:09: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:20:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 20:20:09: #1 tags after filtering in treatment: 20769699 INFO @ Thu, 08 Oct 2020 20:20:09: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:20:09: #1 finished! INFO @ Thu, 08 Oct 2020 20:20:09: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:20:09: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:20:10: #2 number of paired peaks: 188 WARNING @ Thu, 08 Oct 2020 20:20:10: Fewer paired peaks (188) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 188 pairs to build model! INFO @ Thu, 08 Oct 2020 20:20:10: start model_add_line... INFO @ Thu, 08 Oct 2020 20:20:11: start X-correlation... INFO @ Thu, 08 Oct 2020 20:20:11: end of X-cor INFO @ Thu, 08 Oct 2020 20:20:11: #2 finished! INFO @ Thu, 08 Oct 2020 20:20:11: #2 predicted fragment length is 0 bps INFO @ Thu, 08 Oct 2020 20:20:11: #2 alternative fragment length(s) may be 0,12,45,142,508,532 bps INFO @ Thu, 08 Oct 2020 20:20:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7879261/SRX7879261.05_model.r WARNING @ Thu, 08 Oct 2020 20:20:11: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:20:11: #2 You may need to consider one of the other alternative d(s): 0,12,45,142,508,532 WARNING @ Thu, 08 Oct 2020 20:20:11: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 20:20:11: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:20:11: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:20:11: 18000000 INFO @ Thu, 08 Oct 2020 20:20:17: 15000000 INFO @ Thu, 08 Oct 2020 20:20:19: 19000000 INFO @ Thu, 08 Oct 2020 20:20:25: 16000000 INFO @ Thu, 08 Oct 2020 20:20:27: 20000000 INFO @ Thu, 08 Oct 2020 20:20:34: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 20:20:34: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 20:20:34: #1 total tags in treatment: 20769699 INFO @ Thu, 08 Oct 2020 20:20:34: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:20:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 20:20:34: 17000000 INFO @ Thu, 08 Oct 2020 20:20:34: #1 tags after filtering in treatment: 20769699 INFO @ Thu, 08 Oct 2020 20:20:34: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:20:34: #1 finished! INFO @ Thu, 08 Oct 2020 20:20:34: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:20:34: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:20:35: #2 number of paired peaks: 188 WARNING @ Thu, 08 Oct 2020 20:20:35: Fewer paired peaks (188) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 188 pairs to build model! INFO @ Thu, 08 Oct 2020 20:20:35: start model_add_line... INFO @ Thu, 08 Oct 2020 20:20:35: start X-correlation... INFO @ Thu, 08 Oct 2020 20:20:35: end of X-cor INFO @ Thu, 08 Oct 2020 20:20:35: #2 finished! INFO @ Thu, 08 Oct 2020 20:20:35: #2 predicted fragment length is 0 bps INFO @ Thu, 08 Oct 2020 20:20:35: #2 alternative fragment length(s) may be 0,12,45,142,508,532 bps INFO @ Thu, 08 Oct 2020 20:20:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7879261/SRX7879261.10_model.r WARNING @ Thu, 08 Oct 2020 20:20:36: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:20:36: #2 You may need to consider one of the other alternative d(s): 0,12,45,142,508,532 WARNING @ Thu, 08 Oct 2020 20:20:36: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 20:20:36: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:20:36: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:20:42: 18000000 INFO @ Thu, 08 Oct 2020 20:20:50: 19000000 BigWig に変換しました。 /var/spool/uge/it026/job_scripts/10165874: line 297: 3904 Terminated MACS $i /var/spool/uge/it026/job_scripts/10165874: line 297: 4006 Terminated MACS $i /var/spool/uge/it026/job_scripts/10165874: line 297: 4339 Terminated MACS $i ls: cannot access SRX7879261.05.bed: No such file or directory mv: cannot stat ‘SRX7879261.05.bed’: No such file or directory mv: cannot stat ‘SRX7879261.05.bb’: No such file or directory ls: cannot access SRX7879261.10.bed: No such file or directory mv: cannot stat ‘SRX7879261.10.bed’: No such file or directory mv: cannot stat ‘SRX7879261.10.bb’: No such file or directory ls: cannot access SRX7879261.20.bed: No such file or directory mv: cannot stat ‘SRX7879261.20.bed’: No such file or directory mv: cannot stat ‘SRX7879261.20.bb’: No such file or directory