Job ID = 6368799 SRX = SRX5709765 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:24:51 prefetch.2.10.7: 1) Downloading 'SRR8928715'... 2020-06-16T00:24:51 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:27:57 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:27:57 prefetch.2.10.7: 1) 'SRR8928715' was downloaded successfully 2020-06-16T00:27:57 prefetch.2.10.7: 'SRR8928715' has 0 unresolved dependencies Read 28874592 spots for SRR8928715/SRR8928715.sra Written 28874592 spots for SRR8928715/SRR8928715.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: 00:00:01 Multiseed full-index search: 00:06:01 28874592 reads; of these: 28874592 (100.00%) were unpaired; of these: 2040499 (7.07%) aligned 0 times 22368241 (77.47%) aligned exactly 1 time 4465852 (15.47%) aligned >1 times 92.93% overall alignment rate Time searching: 00:06:02 Overall time: 00:06:02 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] 5654656 / 26834093 = 0.2107 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 09:41:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5709765/SRX5709765.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5709765/SRX5709765.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5709765/SRX5709765.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5709765/SRX5709765.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 09:41:13: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:41:13: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:41:19: 1000000 INFO @ Tue, 16 Jun 2020 09:41:25: 2000000 INFO @ Tue, 16 Jun 2020 09:41:31: 3000000 INFO @ Tue, 16 Jun 2020 09:41:37: 4000000 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 09:41:43: 5000000 INFO @ Tue, 16 Jun 2020 09:41:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5709765/SRX5709765.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5709765/SRX5709765.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5709765/SRX5709765.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5709765/SRX5709765.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 09:41:43: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:41:43: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:41:49: 1000000 INFO @ Tue, 16 Jun 2020 09:41:50: 6000000 INFO @ Tue, 16 Jun 2020 09:41:55: 2000000 INFO @ Tue, 16 Jun 2020 09:41:56: 7000000 INFO @ Tue, 16 Jun 2020 09:42:01: 3000000 INFO @ Tue, 16 Jun 2020 09:42:02: 8000000 INFO @ Tue, 16 Jun 2020 09:42:07: 4000000 INFO @ Tue, 16 Jun 2020 09:42:08: 9000000 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 09:42:12: 5000000 INFO @ Tue, 16 Jun 2020 09:42:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5709765/SRX5709765.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5709765/SRX5709765.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5709765/SRX5709765.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5709765/SRX5709765.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 09:42:13: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:42:13: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:42:15: 10000000 INFO @ Tue, 16 Jun 2020 09:42:18: 6000000 INFO @ Tue, 16 Jun 2020 09:42:20: 1000000 INFO @ Tue, 16 Jun 2020 09:42:21: 11000000 INFO @ Tue, 16 Jun 2020 09:42:24: 7000000 INFO @ Tue, 16 Jun 2020 09:42:26: 2000000 INFO @ Tue, 16 Jun 2020 09:42:27: 12000000 INFO @ Tue, 16 Jun 2020 09:42:30: 8000000 INFO @ Tue, 16 Jun 2020 09:42:33: 3000000 INFO @ Tue, 16 Jun 2020 09:42:34: 13000000 INFO @ Tue, 16 Jun 2020 09:42:36: 9000000 INFO @ Tue, 16 Jun 2020 09:42:39: 4000000 INFO @ Tue, 16 Jun 2020 09:42:40: 14000000 INFO @ Tue, 16 Jun 2020 09:42:42: 10000000 INFO @ Tue, 16 Jun 2020 09:42:46: 5000000 INFO @ Tue, 16 Jun 2020 09:42:47: 15000000 INFO @ Tue, 16 Jun 2020 09:42:47: 11000000 INFO @ Tue, 16 Jun 2020 09:42:52: 6000000 INFO @ Tue, 16 Jun 2020 09:42:53: 16000000 INFO @ Tue, 16 Jun 2020 09:42:53: 12000000 INFO @ Tue, 16 Jun 2020 09:42:58: 7000000 INFO @ Tue, 16 Jun 2020 09:42:59: 13000000 INFO @ Tue, 16 Jun 2020 09:42:59: 17000000 INFO @ Tue, 16 Jun 2020 09:43:05: 8000000 INFO @ Tue, 16 Jun 2020 09:43:05: 14000000 INFO @ Tue, 16 Jun 2020 09:43:06: 18000000 INFO @ Tue, 16 Jun 2020 09:43:11: 15000000 INFO @ Tue, 16 Jun 2020 09:43:11: 9000000 INFO @ Tue, 16 Jun 2020 09:43:12: 19000000 INFO @ Tue, 16 Jun 2020 09:43:17: 16000000 INFO @ Tue, 16 Jun 2020 09:43:18: 10000000 INFO @ Tue, 16 Jun 2020 09:43:19: 20000000 INFO @ Tue, 16 Jun 2020 09:43:22: 17000000 INFO @ Tue, 16 Jun 2020 09:43:24: 11000000 INFO @ Tue, 16 Jun 2020 09:43:25: 21000000 INFO @ Tue, 16 Jun 2020 09:43:26: #1 tag size is determined as 49 bps INFO @ Tue, 16 Jun 2020 09:43:26: #1 tag size = 49 INFO @ Tue, 16 Jun 2020 09:43:26: #1 total tags in treatment: 21179437 INFO @ Tue, 16 Jun 2020 09:43:26: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:43:26: #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 09:43:26: #1 tags after filtering in treatment: 21179437 INFO @ Tue, 16 Jun 2020 09:43:26: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:43:26: #1 finished! INFO @ Tue, 16 Jun 2020 09:43:26: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:43:26: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:43:28: #2 number of paired peaks: 220 WARNING @ Tue, 16 Jun 2020 09:43:28: Fewer paired peaks (220) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 220 pairs to build model! INFO @ Tue, 16 Jun 2020 09:43:28: start model_add_line... INFO @ Tue, 16 Jun 2020 09:43:28: start X-correlation... INFO @ Tue, 16 Jun 2020 09:43:28: end of X-cor INFO @ Tue, 16 Jun 2020 09:43:28: #2 finished! INFO @ Tue, 16 Jun 2020 09:43:28: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:43:28: #2 alternative fragment length(s) may be 1,11 bps INFO @ Tue, 16 Jun 2020 09:43:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5709765/SRX5709765.05_model.r WARNING @ Tue, 16 Jun 2020 09:43:28: #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, 16 Jun 2020 09:43:28: #2 You may need to consider one of the other alternative d(s): 1,11 WARNING @ Tue, 16 Jun 2020 09:43:28: #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 09:43:28: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:43:28: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:43:28: 18000000 INFO @ Tue, 16 Jun 2020 09:43:30: 12000000 INFO @ Tue, 16 Jun 2020 09:43:34: 19000000 INFO @ Tue, 16 Jun 2020 09:43:37: 13000000 INFO @ Tue, 16 Jun 2020 09:43:40: 20000000 INFO @ Tue, 16 Jun 2020 09:43:43: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:43:46: 21000000 INFO @ Tue, 16 Jun 2020 09:43:47: #1 tag size is determined as 49 bps INFO @ Tue, 16 Jun 2020 09:43:47: #1 tag size = 49 INFO @ Tue, 16 Jun 2020 09:43:47: #1 total tags in treatment: 21179437 INFO @ Tue, 16 Jun 2020 09:43:47: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:43:47: #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 09:43:47: #1 tags after filtering in treatment: 21179437 INFO @ Tue, 16 Jun 2020 09:43:47: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:43:47: #1 finished! INFO @ Tue, 16 Jun 2020 09:43:47: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:43:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:43:49: #2 number of paired peaks: 220 WARNING @ Tue, 16 Jun 2020 09:43:49: Fewer paired peaks (220) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 220 pairs to build model! INFO @ Tue, 16 Jun 2020 09:43:49: start model_add_line... INFO @ Tue, 16 Jun 2020 09:43:49: start X-correlation... INFO @ Tue, 16 Jun 2020 09:43:49: end of X-cor INFO @ Tue, 16 Jun 2020 09:43:49: #2 finished! INFO @ Tue, 16 Jun 2020 09:43:49: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:43:49: #2 alternative fragment length(s) may be 1,11 bps INFO @ Tue, 16 Jun 2020 09:43:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5709765/SRX5709765.10_model.r WARNING @ Tue, 16 Jun 2020 09:43:49: #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, 16 Jun 2020 09:43:49: #2 You may need to consider one of the other alternative d(s): 1,11 WARNING @ Tue, 16 Jun 2020 09:43:49: #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 09:43:49: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:43:49: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:43:50: 15000000 INFO @ Tue, 16 Jun 2020 09:43:56: 16000000 INFO @ Tue, 16 Jun 2020 09:43:58: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:44:02: 17000000 INFO @ Tue, 16 Jun 2020 09:44:08: 18000000 INFO @ Tue, 16 Jun 2020 09:44:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5709765/SRX5709765.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:44:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5709765/SRX5709765.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:44:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5709765/SRX5709765.05_summits.bed INFO @ Tue, 16 Jun 2020 09:44:13: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:44:14: 19000000 INFO @ Tue, 16 Jun 2020 09:44:19: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:44:20: 20000000 INFO @ Tue, 16 Jun 2020 09:44:26: 21000000 INFO @ Tue, 16 Jun 2020 09:44:27: #1 tag size is determined as 49 bps INFO @ Tue, 16 Jun 2020 09:44:27: #1 tag size = 49 INFO @ Tue, 16 Jun 2020 09:44:27: #1 total tags in treatment: 21179437 INFO @ Tue, 16 Jun 2020 09:44:27: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:44:27: #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 09:44:27: #1 tags after filtering in treatment: 21179437 INFO @ Tue, 16 Jun 2020 09:44:27: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:44:27: #1 finished! INFO @ Tue, 16 Jun 2020 09:44:27: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:44:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:44:29: #2 number of paired peaks: 220 WARNING @ Tue, 16 Jun 2020 09:44:29: Fewer paired peaks (220) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 220 pairs to build model! INFO @ Tue, 16 Jun 2020 09:44:29: start model_add_line... INFO @ Tue, 16 Jun 2020 09:44:29: start X-correlation... INFO @ Tue, 16 Jun 2020 09:44:29: end of X-cor INFO @ Tue, 16 Jun 2020 09:44:29: #2 finished! INFO @ Tue, 16 Jun 2020 09:44:29: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:44:29: #2 alternative fragment length(s) may be 1,11 bps INFO @ Tue, 16 Jun 2020 09:44:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5709765/SRX5709765.20_model.r WARNING @ Tue, 16 Jun 2020 09:44:29: #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, 16 Jun 2020 09:44:29: #2 You may need to consider one of the other alternative d(s): 1,11 WARNING @ Tue, 16 Jun 2020 09:44:29: #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 09:44:29: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:44:29: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:44:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5709765/SRX5709765.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:44:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5709765/SRX5709765.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:44:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5709765/SRX5709765.10_summits.bed INFO @ Tue, 16 Jun 2020 09:44:34: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:44:59: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:45:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5709765/SRX5709765.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:45:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5709765/SRX5709765.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:45:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5709765/SRX5709765.20_summits.bed INFO @ Tue, 16 Jun 2020 09:45:14: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling