Job ID = 6529109 SRX = SRX495113 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: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:05:32 30788149 reads; of these: 30788149 (100.00%) were unpaired; of these: 169820 (0.55%) aligned 0 times 25275368 (82.09%) aligned exactly 1 time 5342961 (17.35%) aligned >1 times 99.45% overall alignment rate Time searching: 00:05:33 Overall time: 00:05:33 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] 4711476 / 30618329 = 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, 30 Jun 2020 01:19:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495113/SRX495113.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495113/SRX495113.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495113/SRX495113.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495113/SRX495113.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, 30 Jun 2020 01:19:28: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:19:28: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:19:33: 1000000 INFO @ Tue, 30 Jun 2020 01:19:38: 2000000 INFO @ Tue, 30 Jun 2020 01:19:43: 3000000 INFO @ Tue, 30 Jun 2020 01:19:48: 4000000 INFO @ Tue, 30 Jun 2020 01:19:53: 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, 30 Jun 2020 01:19:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495113/SRX495113.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495113/SRX495113.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495113/SRX495113.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495113/SRX495113.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, 30 Jun 2020 01:19:58: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:19:58: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:19:59: 6000000 INFO @ Tue, 30 Jun 2020 01:20:03: 1000000 INFO @ Tue, 30 Jun 2020 01:20:04: 7000000 INFO @ Tue, 30 Jun 2020 01:20:09: 2000000 INFO @ Tue, 30 Jun 2020 01:20:09: 8000000 INFO @ Tue, 30 Jun 2020 01:20:14: 3000000 INFO @ Tue, 30 Jun 2020 01:20:14: 9000000 INFO @ Tue, 30 Jun 2020 01:20:20: 4000000 INFO @ Tue, 30 Jun 2020 01:20:20: 10000000 INFO @ Tue, 30 Jun 2020 01:20:25: 11000000 INFO @ Tue, 30 Jun 2020 01:20:25: 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, 30 Jun 2020 01:20:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495113/SRX495113.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495113/SRX495113.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495113/SRX495113.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495113/SRX495113.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, 30 Jun 2020 01:20:28: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:20:28: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:20:30: 6000000 INFO @ Tue, 30 Jun 2020 01:20:31: 12000000 INFO @ Tue, 30 Jun 2020 01:20:34: 1000000 INFO @ Tue, 30 Jun 2020 01:20:36: 7000000 INFO @ Tue, 30 Jun 2020 01:20:36: 13000000 INFO @ Tue, 30 Jun 2020 01:20:40: 2000000 INFO @ Tue, 30 Jun 2020 01:20:41: 8000000 INFO @ Tue, 30 Jun 2020 01:20:42: 14000000 INFO @ Tue, 30 Jun 2020 01:20:46: 3000000 INFO @ Tue, 30 Jun 2020 01:20:47: 9000000 INFO @ Tue, 30 Jun 2020 01:20:48: 15000000 INFO @ Tue, 30 Jun 2020 01:20:51: 4000000 INFO @ Tue, 30 Jun 2020 01:20:52: 10000000 INFO @ Tue, 30 Jun 2020 01:20:54: 16000000 INFO @ Tue, 30 Jun 2020 01:20:57: 5000000 INFO @ Tue, 30 Jun 2020 01:20:58: 11000000 INFO @ Tue, 30 Jun 2020 01:21:00: 17000000 INFO @ Tue, 30 Jun 2020 01:21:03: 12000000 INFO @ Tue, 30 Jun 2020 01:21:03: 6000000 INFO @ Tue, 30 Jun 2020 01:21:05: 18000000 INFO @ Tue, 30 Jun 2020 01:21:09: 13000000 INFO @ Tue, 30 Jun 2020 01:21:09: 7000000 INFO @ Tue, 30 Jun 2020 01:21:11: 19000000 INFO @ Tue, 30 Jun 2020 01:21:14: 14000000 INFO @ Tue, 30 Jun 2020 01:21:15: 8000000 INFO @ Tue, 30 Jun 2020 01:21:17: 20000000 INFO @ Tue, 30 Jun 2020 01:21:19: 15000000 INFO @ Tue, 30 Jun 2020 01:21:21: 9000000 INFO @ Tue, 30 Jun 2020 01:21:22: 21000000 INFO @ Tue, 30 Jun 2020 01:21:25: 16000000 INFO @ Tue, 30 Jun 2020 01:21:27: 10000000 INFO @ Tue, 30 Jun 2020 01:21:28: 22000000 INFO @ Tue, 30 Jun 2020 01:21:31: 17000000 INFO @ Tue, 30 Jun 2020 01:21:32: 11000000 INFO @ Tue, 30 Jun 2020 01:21:34: 23000000 INFO @ Tue, 30 Jun 2020 01:21:36: 18000000 INFO @ Tue, 30 Jun 2020 01:21:38: 12000000 INFO @ Tue, 30 Jun 2020 01:21:39: 24000000 INFO @ Tue, 30 Jun 2020 01:21:41: 19000000 INFO @ Tue, 30 Jun 2020 01:21:44: 13000000 INFO @ Tue, 30 Jun 2020 01:21:45: 25000000 INFO @ Tue, 30 Jun 2020 01:21:47: 20000000 INFO @ Tue, 30 Jun 2020 01:21:50: 14000000 INFO @ Tue, 30 Jun 2020 01:21:51: #1 tag size is determined as 36 bps INFO @ Tue, 30 Jun 2020 01:21:51: #1 tag size = 36 INFO @ Tue, 30 Jun 2020 01:21:51: #1 total tags in treatment: 25906853 INFO @ Tue, 30 Jun 2020 01:21:51: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:21:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 01:21:51: #1 tags after filtering in treatment: 25906853 INFO @ Tue, 30 Jun 2020 01:21:51: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:21:51: #1 finished! INFO @ Tue, 30 Jun 2020 01:21:51: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:21:51: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:21:52: 21000000 INFO @ Tue, 30 Jun 2020 01:21:53: #2 number of paired peaks: 145 WARNING @ Tue, 30 Jun 2020 01:21:53: Fewer paired peaks (145) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 145 pairs to build model! INFO @ Tue, 30 Jun 2020 01:21:53: start model_add_line... INFO @ Tue, 30 Jun 2020 01:21:53: start X-correlation... INFO @ Tue, 30 Jun 2020 01:21:53: end of X-cor INFO @ Tue, 30 Jun 2020 01:21:53: #2 finished! INFO @ Tue, 30 Jun 2020 01:21:53: #2 predicted fragment length is 1 bps INFO @ Tue, 30 Jun 2020 01:21:53: #2 alternative fragment length(s) may be 1,14,18,30,213,435,460,478,572 bps INFO @ Tue, 30 Jun 2020 01:21:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495113/SRX495113.05_model.r WARNING @ Tue, 30 Jun 2020 01:21:53: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:21:53: #2 You may need to consider one of the other alternative d(s): 1,14,18,30,213,435,460,478,572 WARNING @ Tue, 30 Jun 2020 01:21:53: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 01:21:53: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:21:53: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:21:55: 15000000 INFO @ Tue, 30 Jun 2020 01:21:57: 22000000 INFO @ Tue, 30 Jun 2020 01:22:00: 16000000 INFO @ Tue, 30 Jun 2020 01:22:03: 23000000 INFO @ Tue, 30 Jun 2020 01:22:06: 17000000 INFO @ Tue, 30 Jun 2020 01:22:08: 24000000 INFO @ Tue, 30 Jun 2020 01:22:13: 18000000 INFO @ Tue, 30 Jun 2020 01:22:14: 25000000 INFO @ Tue, 30 Jun 2020 01:22:19: 19000000 INFO @ Tue, 30 Jun 2020 01:22:19: #1 tag size is determined as 36 bps INFO @ Tue, 30 Jun 2020 01:22:19: #1 tag size = 36 INFO @ Tue, 30 Jun 2020 01:22:19: #1 total tags in treatment: 25906853 INFO @ Tue, 30 Jun 2020 01:22:19: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:22:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 01:22:20: #1 tags after filtering in treatment: 25906853 INFO @ Tue, 30 Jun 2020 01:22:20: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:22:20: #1 finished! INFO @ Tue, 30 Jun 2020 01:22:20: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:22:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:22:22: #2 number of paired peaks: 145 WARNING @ Tue, 30 Jun 2020 01:22:22: Fewer paired peaks (145) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 145 pairs to build model! INFO @ Tue, 30 Jun 2020 01:22:22: start model_add_line... INFO @ Tue, 30 Jun 2020 01:22:22: start X-correlation... INFO @ Tue, 30 Jun 2020 01:22:22: end of X-cor INFO @ Tue, 30 Jun 2020 01:22:22: #2 finished! INFO @ Tue, 30 Jun 2020 01:22:22: #2 predicted fragment length is 1 bps INFO @ Tue, 30 Jun 2020 01:22:22: #2 alternative fragment length(s) may be 1,14,18,30,213,435,460,478,572 bps INFO @ Tue, 30 Jun 2020 01:22:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495113/SRX495113.10_model.r WARNING @ Tue, 30 Jun 2020 01:22:22: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:22:22: #2 You may need to consider one of the other alternative d(s): 1,14,18,30,213,435,460,478,572 WARNING @ Tue, 30 Jun 2020 01:22:22: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 01:22:22: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:22:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:22:24: 20000000 INFO @ Tue, 30 Jun 2020 01:22:27: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:22:30: 21000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 01:22:36: 22000000 INFO @ Tue, 30 Jun 2020 01:22:42: 23000000 INFO @ Tue, 30 Jun 2020 01:22:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495113/SRX495113.05_peaks.xls INFO @ Tue, 30 Jun 2020 01:22:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495113/SRX495113.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:22:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495113/SRX495113.05_summits.bed INFO @ Tue, 30 Jun 2020 01:22:43: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 01:22:48: 24000000 INFO @ Tue, 30 Jun 2020 01:22:54: 25000000 INFO @ Tue, 30 Jun 2020 01:22:56: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:23:00: #1 tag size is determined as 36 bps INFO @ Tue, 30 Jun 2020 01:23:00: #1 tag size = 36 INFO @ Tue, 30 Jun 2020 01:23:00: #1 total tags in treatment: 25906853 INFO @ Tue, 30 Jun 2020 01:23:00: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:23:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 01:23:00: #1 tags after filtering in treatment: 25906853 INFO @ Tue, 30 Jun 2020 01:23:00: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:23:00: #1 finished! INFO @ Tue, 30 Jun 2020 01:23:00: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:23:00: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:23:02: #2 number of paired peaks: 145 WARNING @ Tue, 30 Jun 2020 01:23:02: Fewer paired peaks (145) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 145 pairs to build model! INFO @ Tue, 30 Jun 2020 01:23:02: start model_add_line... INFO @ Tue, 30 Jun 2020 01:23:02: start X-correlation... INFO @ Tue, 30 Jun 2020 01:23:02: end of X-cor INFO @ Tue, 30 Jun 2020 01:23:02: #2 finished! INFO @ Tue, 30 Jun 2020 01:23:02: #2 predicted fragment length is 1 bps INFO @ Tue, 30 Jun 2020 01:23:02: #2 alternative fragment length(s) may be 1,14,18,30,213,435,460,478,572 bps INFO @ Tue, 30 Jun 2020 01:23:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495113/SRX495113.20_model.r WARNING @ Tue, 30 Jun 2020 01:23:02: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:23:02: #2 You may need to consider one of the other alternative d(s): 1,14,18,30,213,435,460,478,572 WARNING @ Tue, 30 Jun 2020 01:23:02: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 01:23:02: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:23:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:23:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495113/SRX495113.10_peaks.xls INFO @ Tue, 30 Jun 2020 01:23:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495113/SRX495113.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:23:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495113/SRX495113.10_summits.bed INFO @ Tue, 30 Jun 2020 01:23:12: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 01:23:37: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 01:23:53: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495113/SRX495113.20_peaks.xls INFO @ Tue, 30 Jun 2020 01:23:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495113/SRX495113.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:23:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495113/SRX495113.20_summits.bed INFO @ Tue, 30 Jun 2020 01:23:53: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling