Job ID = 6368688 SRX = SRX5402714 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:24:10 prefetch.2.10.7: 1) Downloading 'SRR8602948'... 2020-06-16T00:24:10 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:27:50 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:27:50 prefetch.2.10.7: 1) 'SRR8602948' was downloaded successfully Read 30585176 spots for SRR8602948/SRR8602948.sra Written 30585176 spots for SRR8602948/SRR8602948.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: 00:06:30 30585176 reads; of these: 30585176 (100.00%) were unpaired; of these: 2494572 (8.16%) aligned 0 times 24366726 (79.67%) aligned exactly 1 time 3723878 (12.18%) aligned >1 times 91.84% overall alignment rate Time searching: 00:06:30 Overall time: 00:06:30 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] 6002518 / 28090604 = 0.2137 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 09:44:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402714/SRX5402714.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402714/SRX5402714.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402714/SRX5402714.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402714/SRX5402714.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 09:44:37: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:44:37: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:44:41: 1000000 INFO @ Tue, 16 Jun 2020 09:44:46: 2000000 INFO @ Tue, 16 Jun 2020 09:44:51: 3000000 INFO @ Tue, 16 Jun 2020 09:44:56: 4000000 INFO @ Tue, 16 Jun 2020 09:45:00: 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 09:45:05: 6000000 INFO @ Tue, 16 Jun 2020 09:45:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402714/SRX5402714.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402714/SRX5402714.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402714/SRX5402714.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402714/SRX5402714.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 09:45:07: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:45:07: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:45:10: 7000000 INFO @ Tue, 16 Jun 2020 09:45:12: 1000000 INFO @ Tue, 16 Jun 2020 09:45:15: 8000000 INFO @ Tue, 16 Jun 2020 09:45:17: 2000000 INFO @ Tue, 16 Jun 2020 09:45:20: 9000000 INFO @ Tue, 16 Jun 2020 09:45:22: 3000000 INFO @ Tue, 16 Jun 2020 09:45:25: 10000000 INFO @ Tue, 16 Jun 2020 09:45:27: 4000000 INFO @ Tue, 16 Jun 2020 09:45:31: 11000000 INFO @ Tue, 16 Jun 2020 09:45:32: 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, 16 Jun 2020 09:45:36: 12000000 INFO @ Tue, 16 Jun 2020 09:45:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402714/SRX5402714.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402714/SRX5402714.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402714/SRX5402714.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402714/SRX5402714.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 09:45:37: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:45:37: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:45:38: 6000000 INFO @ Tue, 16 Jun 2020 09:45:41: 13000000 INFO @ Tue, 16 Jun 2020 09:45:42: 1000000 INFO @ Tue, 16 Jun 2020 09:45:43: 7000000 INFO @ Tue, 16 Jun 2020 09:45:47: 14000000 INFO @ Tue, 16 Jun 2020 09:45:48: 2000000 INFO @ Tue, 16 Jun 2020 09:45:49: 8000000 INFO @ Tue, 16 Jun 2020 09:45:53: 15000000 INFO @ Tue, 16 Jun 2020 09:45:54: 3000000 INFO @ Tue, 16 Jun 2020 09:45:55: 9000000 INFO @ Tue, 16 Jun 2020 09:45:59: 16000000 INFO @ Tue, 16 Jun 2020 09:46:00: 4000000 INFO @ Tue, 16 Jun 2020 09:46:00: 10000000 INFO @ Tue, 16 Jun 2020 09:46:04: 17000000 INFO @ Tue, 16 Jun 2020 09:46:05: 5000000 INFO @ Tue, 16 Jun 2020 09:46:06: 11000000 INFO @ Tue, 16 Jun 2020 09:46:10: 18000000 INFO @ Tue, 16 Jun 2020 09:46:11: 6000000 INFO @ Tue, 16 Jun 2020 09:46:12: 12000000 INFO @ Tue, 16 Jun 2020 09:46:15: 19000000 INFO @ Tue, 16 Jun 2020 09:46:17: 7000000 INFO @ Tue, 16 Jun 2020 09:46:17: 13000000 INFO @ Tue, 16 Jun 2020 09:46:21: 20000000 INFO @ Tue, 16 Jun 2020 09:46:22: 8000000 INFO @ Tue, 16 Jun 2020 09:46:23: 14000000 INFO @ Tue, 16 Jun 2020 09:46:27: 21000000 INFO @ Tue, 16 Jun 2020 09:46:28: 9000000 INFO @ Tue, 16 Jun 2020 09:46:29: 15000000 INFO @ Tue, 16 Jun 2020 09:46:33: 22000000 INFO @ Tue, 16 Jun 2020 09:46:34: 10000000 INFO @ Tue, 16 Jun 2020 09:46:34: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:46:34: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:46:34: #1 total tags in treatment: 22088086 INFO @ Tue, 16 Jun 2020 09:46:34: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:46:34: #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 09:46:34: #1 tags after filtering in treatment: 22088086 INFO @ Tue, 16 Jun 2020 09:46:34: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:46:34: #1 finished! INFO @ Tue, 16 Jun 2020 09:46:34: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:46:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:46:35: 16000000 INFO @ Tue, 16 Jun 2020 09:46:36: #2 number of paired peaks: 164 WARNING @ Tue, 16 Jun 2020 09:46:36: Fewer paired peaks (164) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 164 pairs to build model! INFO @ Tue, 16 Jun 2020 09:46:36: start model_add_line... INFO @ Tue, 16 Jun 2020 09:46:36: start X-correlation... INFO @ Tue, 16 Jun 2020 09:46:36: end of X-cor INFO @ Tue, 16 Jun 2020 09:46:36: #2 finished! INFO @ Tue, 16 Jun 2020 09:46:36: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:46:36: #2 alternative fragment length(s) may be 1,34,52,576,597 bps INFO @ Tue, 16 Jun 2020 09:46:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402714/SRX5402714.05_model.r WARNING @ Tue, 16 Jun 2020 09:46:36: #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 09:46:36: #2 You may need to consider one of the other alternative d(s): 1,34,52,576,597 WARNING @ Tue, 16 Jun 2020 09:46:36: #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 09:46:36: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:46:36: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:46:39: 11000000 INFO @ Tue, 16 Jun 2020 09:46:40: 17000000 INFO @ Tue, 16 Jun 2020 09:46:44: 12000000 INFO @ Tue, 16 Jun 2020 09:46:45: 18000000 INFO @ Tue, 16 Jun 2020 09:46:50: 13000000 INFO @ Tue, 16 Jun 2020 09:46:51: 19000000 INFO @ Tue, 16 Jun 2020 09:46:55: 14000000 INFO @ Tue, 16 Jun 2020 09:46:56: 20000000 INFO @ Tue, 16 Jun 2020 09:47:00: 15000000 INFO @ Tue, 16 Jun 2020 09:47:01: 21000000 INFO @ Tue, 16 Jun 2020 09:47:05: 16000000 INFO @ Tue, 16 Jun 2020 09:47:06: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:47:07: 22000000 INFO @ Tue, 16 Jun 2020 09:47:07: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:47:07: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:47:07: #1 total tags in treatment: 22088086 INFO @ Tue, 16 Jun 2020 09:47:07: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:47:07: #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 09:47:08: #1 tags after filtering in treatment: 22088086 INFO @ Tue, 16 Jun 2020 09:47:08: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:47:08: #1 finished! INFO @ Tue, 16 Jun 2020 09:47:08: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:47:08: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:47:09: #2 number of paired peaks: 164 WARNING @ Tue, 16 Jun 2020 09:47:09: Fewer paired peaks (164) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 164 pairs to build model! INFO @ Tue, 16 Jun 2020 09:47:09: start model_add_line... INFO @ Tue, 16 Jun 2020 09:47:09: start X-correlation... INFO @ Tue, 16 Jun 2020 09:47:09: end of X-cor INFO @ Tue, 16 Jun 2020 09:47:09: #2 finished! INFO @ Tue, 16 Jun 2020 09:47:09: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:47:09: #2 alternative fragment length(s) may be 1,34,52,576,597 bps INFO @ Tue, 16 Jun 2020 09:47:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402714/SRX5402714.10_model.r WARNING @ Tue, 16 Jun 2020 09:47:09: #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 09:47:09: #2 You may need to consider one of the other alternative d(s): 1,34,52,576,597 WARNING @ Tue, 16 Jun 2020 09:47:09: #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 09:47:09: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:47:09: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:47:10: 17000000 INFO @ Tue, 16 Jun 2020 09:47:15: 18000000 INFO @ Tue, 16 Jun 2020 09:47:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402714/SRX5402714.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:47:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402714/SRX5402714.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:47:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402714/SRX5402714.05_summits.bed INFO @ Tue, 16 Jun 2020 09:47:19: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:47:20: 19000000 INFO @ Tue, 16 Jun 2020 09:47:24: 20000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:47:29: 21000000 INFO @ Tue, 16 Jun 2020 09:47:34: 22000000 INFO @ Tue, 16 Jun 2020 09:47:34: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:47:34: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:47:34: #1 total tags in treatment: 22088086 INFO @ Tue, 16 Jun 2020 09:47:34: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:47:34: #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 09:47:35: #1 tags after filtering in treatment: 22088086 INFO @ Tue, 16 Jun 2020 09:47:35: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:47:35: #1 finished! INFO @ Tue, 16 Jun 2020 09:47:35: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:47:35: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:47:36: #2 number of paired peaks: 164 WARNING @ Tue, 16 Jun 2020 09:47:36: Fewer paired peaks (164) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 164 pairs to build model! INFO @ Tue, 16 Jun 2020 09:47:36: start model_add_line... INFO @ Tue, 16 Jun 2020 09:47:36: start X-correlation... INFO @ Tue, 16 Jun 2020 09:47:36: end of X-cor INFO @ Tue, 16 Jun 2020 09:47:36: #2 finished! INFO @ Tue, 16 Jun 2020 09:47:36: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:47:36: #2 alternative fragment length(s) may be 1,34,52,576,597 bps INFO @ Tue, 16 Jun 2020 09:47:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402714/SRX5402714.20_model.r WARNING @ Tue, 16 Jun 2020 09:47:36: #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 09:47:36: #2 You may need to consider one of the other alternative d(s): 1,34,52,576,597 WARNING @ Tue, 16 Jun 2020 09:47:36: #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 09:47:36: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:47:36: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:47:38: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:47:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402714/SRX5402714.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:47:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402714/SRX5402714.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:47:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402714/SRX5402714.10_summits.bed INFO @ Tue, 16 Jun 2020 09:47:52: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:48:05: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:48:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402714/SRX5402714.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:48:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402714/SRX5402714.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:48:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402714/SRX5402714.20_summits.bed INFO @ Tue, 16 Jun 2020 09:48:19: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BigWig に変換しました。