Job ID = 6368722 SRX = SRX5402746 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:22:24 prefetch.2.10.7: 1) Downloading 'SRR8602980'... 2020-06-16T00:22:24 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:25:43 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:25:43 prefetch.2.10.7: 1) 'SRR8602980' was downloaded successfully Read 29913010 spots for SRR8602980/SRR8602980.sra Written 29913010 spots for SRR8602980/SRR8602980.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: 00:06:13 29913010 reads; of these: 29913010 (100.00%) were unpaired; of these: 7454715 (24.92%) aligned 0 times 15700425 (52.49%) aligned exactly 1 time 6757870 (22.59%) aligned >1 times 75.08% overall alignment rate Time searching: 00:06:13 Overall time: 00:06:13 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] 5294519 / 22458295 = 0.2357 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 09:40:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402746/SRX5402746.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402746/SRX5402746.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402746/SRX5402746.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402746/SRX5402746.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 09:40:23: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:40:23: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:40:28: 1000000 INFO @ Tue, 16 Jun 2020 09:40:33: 2000000 INFO @ Tue, 16 Jun 2020 09:40:38: 3000000 INFO @ Tue, 16 Jun 2020 09:40:43: 4000000 INFO @ Tue, 16 Jun 2020 09:40:48: 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 09:40:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402746/SRX5402746.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402746/SRX5402746.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402746/SRX5402746.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402746/SRX5402746.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 09:40:53: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:40:53: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:40:54: 6000000 INFO @ Tue, 16 Jun 2020 09:40:59: 1000000 INFO @ Tue, 16 Jun 2020 09:40:59: 7000000 INFO @ Tue, 16 Jun 2020 09:41:04: 2000000 INFO @ Tue, 16 Jun 2020 09:41:05: 8000000 INFO @ Tue, 16 Jun 2020 09:41:10: 3000000 INFO @ Tue, 16 Jun 2020 09:41:10: 9000000 INFO @ Tue, 16 Jun 2020 09:41:16: 4000000 INFO @ Tue, 16 Jun 2020 09:41:16: 10000000 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 09:41:21: 5000000 INFO @ Tue, 16 Jun 2020 09:41:22: 11000000 INFO @ Tue, 16 Jun 2020 09:41:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402746/SRX5402746.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402746/SRX5402746.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402746/SRX5402746.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402746/SRX5402746.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 09:41:23: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:41:23: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:41:27: 6000000 INFO @ Tue, 16 Jun 2020 09:41:28: 12000000 INFO @ Tue, 16 Jun 2020 09:41:28: 1000000 INFO @ Tue, 16 Jun 2020 09:41:33: 7000000 INFO @ Tue, 16 Jun 2020 09:41:33: 2000000 INFO @ Tue, 16 Jun 2020 09:41:34: 13000000 INFO @ Tue, 16 Jun 2020 09:41:39: 3000000 INFO @ Tue, 16 Jun 2020 09:41:39: 8000000 INFO @ Tue, 16 Jun 2020 09:41:40: 14000000 INFO @ Tue, 16 Jun 2020 09:41:44: 4000000 INFO @ Tue, 16 Jun 2020 09:41:45: 9000000 INFO @ Tue, 16 Jun 2020 09:41:46: 15000000 INFO @ Tue, 16 Jun 2020 09:41:49: 5000000 INFO @ Tue, 16 Jun 2020 09:41:52: 10000000 INFO @ Tue, 16 Jun 2020 09:41:53: 16000000 INFO @ Tue, 16 Jun 2020 09:41:54: 6000000 INFO @ Tue, 16 Jun 2020 09:41:59: 11000000 INFO @ Tue, 16 Jun 2020 09:41:59: 7000000 INFO @ Tue, 16 Jun 2020 09:41:59: 17000000 INFO @ Tue, 16 Jun 2020 09:42:01: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:42:01: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:42:01: #1 total tags in treatment: 17163776 INFO @ Tue, 16 Jun 2020 09:42:01: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:42:01: #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 09:42:01: #1 tags after filtering in treatment: 17163776 INFO @ Tue, 16 Jun 2020 09:42:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:42:01: #1 finished! INFO @ Tue, 16 Jun 2020 09:42:01: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:42:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:42:02: #2 number of paired peaks: 808 WARNING @ Tue, 16 Jun 2020 09:42:02: Fewer paired peaks (808) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 808 pairs to build model! INFO @ Tue, 16 Jun 2020 09:42:02: start model_add_line... INFO @ Tue, 16 Jun 2020 09:42:02: start X-correlation... INFO @ Tue, 16 Jun 2020 09:42:02: end of X-cor INFO @ Tue, 16 Jun 2020 09:42:02: #2 finished! INFO @ Tue, 16 Jun 2020 09:42:02: #2 predicted fragment length is 2 bps INFO @ Tue, 16 Jun 2020 09:42:02: #2 alternative fragment length(s) may be 2,23,43,594 bps INFO @ Tue, 16 Jun 2020 09:42:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402746/SRX5402746.05_model.r WARNING @ Tue, 16 Jun 2020 09:42:02: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:42:02: #2 You may need to consider one of the other alternative d(s): 2,23,43,594 WARNING @ Tue, 16 Jun 2020 09:42:02: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 09:42:02: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:42:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:42:04: 8000000 INFO @ Tue, 16 Jun 2020 09:42:05: 12000000 INFO @ Tue, 16 Jun 2020 09:42:10: 9000000 INFO @ Tue, 16 Jun 2020 09:42:12: 13000000 INFO @ Tue, 16 Jun 2020 09:42:15: 10000000 INFO @ Tue, 16 Jun 2020 09:42:19: 14000000 INFO @ Tue, 16 Jun 2020 09:42:20: 11000000 INFO @ Tue, 16 Jun 2020 09:42:25: 12000000 INFO @ Tue, 16 Jun 2020 09:42:26: 15000000 INFO @ Tue, 16 Jun 2020 09:42:28: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:42:30: 13000000 INFO @ Tue, 16 Jun 2020 09:42:33: 16000000 INFO @ Tue, 16 Jun 2020 09:42:35: 14000000 INFO @ Tue, 16 Jun 2020 09:42:40: 17000000 INFO @ Tue, 16 Jun 2020 09:42:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402746/SRX5402746.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:42:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402746/SRX5402746.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:42:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402746/SRX5402746.05_summits.bed INFO @ Tue, 16 Jun 2020 09:42:40: Done! INFO @ Tue, 16 Jun 2020 09:42:40: 15000000 pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:42:41: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:42:41: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:42:41: #1 total tags in treatment: 17163776 INFO @ Tue, 16 Jun 2020 09:42:41: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:42:41: #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 09:42:41: #1 tags after filtering in treatment: 17163776 INFO @ Tue, 16 Jun 2020 09:42:41: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:42:41: #1 finished! INFO @ Tue, 16 Jun 2020 09:42:41: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:42:41: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:42:43: #2 number of paired peaks: 808 WARNING @ Tue, 16 Jun 2020 09:42:43: Fewer paired peaks (808) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 808 pairs to build model! INFO @ Tue, 16 Jun 2020 09:42:43: start model_add_line... INFO @ Tue, 16 Jun 2020 09:42:43: start X-correlation... INFO @ Tue, 16 Jun 2020 09:42:43: end of X-cor INFO @ Tue, 16 Jun 2020 09:42:43: #2 finished! INFO @ Tue, 16 Jun 2020 09:42:43: #2 predicted fragment length is 2 bps INFO @ Tue, 16 Jun 2020 09:42:43: #2 alternative fragment length(s) may be 2,23,43,594 bps INFO @ Tue, 16 Jun 2020 09:42:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402746/SRX5402746.10_model.r WARNING @ Tue, 16 Jun 2020 09:42:43: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:42:43: #2 You may need to consider one of the other alternative d(s): 2,23,43,594 WARNING @ Tue, 16 Jun 2020 09:42:43: #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 09:42:43: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:42:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:42:45: 16000000 INFO @ Tue, 16 Jun 2020 09:42:51: 17000000 INFO @ Tue, 16 Jun 2020 09:42:51: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:42:51: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:42:51: #1 total tags in treatment: 17163776 INFO @ Tue, 16 Jun 2020 09:42:51: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:42:51: #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 09:42:52: #1 tags after filtering in treatment: 17163776 INFO @ Tue, 16 Jun 2020 09:42:52: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:42:52: #1 finished! INFO @ Tue, 16 Jun 2020 09:42:52: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:42:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:42:53: #2 number of paired peaks: 808 WARNING @ Tue, 16 Jun 2020 09:42:53: Fewer paired peaks (808) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 808 pairs to build model! INFO @ Tue, 16 Jun 2020 09:42:53: start model_add_line... INFO @ Tue, 16 Jun 2020 09:42:53: start X-correlation... INFO @ Tue, 16 Jun 2020 09:42:53: end of X-cor INFO @ Tue, 16 Jun 2020 09:42:53: #2 finished! INFO @ Tue, 16 Jun 2020 09:42:53: #2 predicted fragment length is 2 bps INFO @ Tue, 16 Jun 2020 09:42:53: #2 alternative fragment length(s) may be 2,23,43,594 bps INFO @ Tue, 16 Jun 2020 09:42:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402746/SRX5402746.20_model.r WARNING @ Tue, 16 Jun 2020 09:42:53: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:42:53: #2 You may need to consider one of the other alternative d(s): 2,23,43,594 WARNING @ Tue, 16 Jun 2020 09:42:53: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 09:42:53: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:42:53: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:43:08: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:43:18: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:43:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402746/SRX5402746.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:43:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402746/SRX5402746.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:43:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402746/SRX5402746.10_summits.bed INFO @ Tue, 16 Jun 2020 09:43:21: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:43:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402746/SRX5402746.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:43:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402746/SRX5402746.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:43:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402746/SRX5402746.20_summits.bed INFO @ Tue, 16 Jun 2020 09:43:31: 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。