Job ID = 6368377 SRX = SRX495057 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:09:39 prefetch.2.10.7: 1) Downloading 'SRR1198589'... 2020-06-16T00:09:39 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:11:43 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:11:44 prefetch.2.10.7: 'SRR1198589' is valid 2020-06-16T00:11:44 prefetch.2.10.7: 1) 'SRR1198589' was downloaded successfully Read 13338445 spots for SRR1198589/SRR1198589.sra Written 13338445 spots for SRR1198589/SRR1198589.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: 00:02:39 13338445 reads; of these: 13338445 (100.00%) were unpaired; of these: 88339 (0.66%) aligned 0 times 10992864 (82.41%) aligned exactly 1 time 2257242 (16.92%) aligned >1 times 99.34% overall alignment rate Time searching: 00:02:39 Overall time: 00:02:39 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_rmdupse_core] 2114500 / 13250106 = 0.1596 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 09:18:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495057/SRX495057.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495057/SRX495057.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495057/SRX495057.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495057/SRX495057.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 09:18:37: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:18:37: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:18:42: 1000000 INFO @ Tue, 16 Jun 2020 09:18:48: 2000000 INFO @ Tue, 16 Jun 2020 09:18:53: 3000000 INFO @ Tue, 16 Jun 2020 09:18:59: 4000000 INFO @ Tue, 16 Jun 2020 09:19:04: 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 09:19:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495057/SRX495057.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495057/SRX495057.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495057/SRX495057.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495057/SRX495057.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 09:19:08: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:19:08: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:19:10: 6000000 INFO @ Tue, 16 Jun 2020 09:19:14: 1000000 INFO @ Tue, 16 Jun 2020 09:19:16: 7000000 INFO @ Tue, 16 Jun 2020 09:19:20: 2000000 INFO @ Tue, 16 Jun 2020 09:19:22: 8000000 INFO @ Tue, 16 Jun 2020 09:19:27: 3000000 INFO @ Tue, 16 Jun 2020 09:19:28: 9000000 INFO @ Tue, 16 Jun 2020 09:19:33: 4000000 INFO @ Tue, 16 Jun 2020 09:19:35: 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 09:19:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495057/SRX495057.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495057/SRX495057.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495057/SRX495057.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495057/SRX495057.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 09:19:37: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:19:37: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:19:39: 5000000 INFO @ Tue, 16 Jun 2020 09:19:41: 11000000 INFO @ Tue, 16 Jun 2020 09:19:42: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:19:42: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:19:42: #1 total tags in treatment: 11135606 INFO @ Tue, 16 Jun 2020 09:19:42: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:19:42: #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 09:19:42: #1 tags after filtering in treatment: 11135606 INFO @ Tue, 16 Jun 2020 09:19:42: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:19:42: #1 finished! INFO @ Tue, 16 Jun 2020 09:19:42: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:19:42: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:19:43: #2 number of paired peaks: 375 WARNING @ Tue, 16 Jun 2020 09:19:43: Fewer paired peaks (375) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 375 pairs to build model! INFO @ Tue, 16 Jun 2020 09:19:43: start model_add_line... INFO @ Tue, 16 Jun 2020 09:19:43: start X-correlation... INFO @ Tue, 16 Jun 2020 09:19:43: end of X-cor INFO @ Tue, 16 Jun 2020 09:19:43: #2 finished! INFO @ Tue, 16 Jun 2020 09:19:43: #2 predicted fragment length is 48 bps INFO @ Tue, 16 Jun 2020 09:19:43: #2 alternative fragment length(s) may be 2,48,560,589 bps INFO @ Tue, 16 Jun 2020 09:19:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495057/SRX495057.05_model.r WARNING @ Tue, 16 Jun 2020 09:19:43: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:19:43: #2 You may need to consider one of the other alternative d(s): 2,48,560,589 WARNING @ Tue, 16 Jun 2020 09:19:43: #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 09:19:43: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:19:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:19:43: 1000000 INFO @ Tue, 16 Jun 2020 09:19:45: 6000000 INFO @ Tue, 16 Jun 2020 09:19:50: 2000000 INFO @ Tue, 16 Jun 2020 09:19:52: 7000000 INFO @ Tue, 16 Jun 2020 09:19:56: 3000000 INFO @ Tue, 16 Jun 2020 09:19:58: 8000000 INFO @ Tue, 16 Jun 2020 09:20:02: 4000000 INFO @ Tue, 16 Jun 2020 09:20:04: 9000000 INFO @ Tue, 16 Jun 2020 09:20:04: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:20:08: 5000000 INFO @ Tue, 16 Jun 2020 09:20:10: 10000000 INFO @ Tue, 16 Jun 2020 09:20:14: 6000000 INFO @ Tue, 16 Jun 2020 09:20:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495057/SRX495057.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:20:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495057/SRX495057.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:20:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495057/SRX495057.05_summits.bed INFO @ Tue, 16 Jun 2020 09:20:15: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1036 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:20:16: 11000000 INFO @ Tue, 16 Jun 2020 09:20:17: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:20:17: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:20:17: #1 total tags in treatment: 11135606 INFO @ Tue, 16 Jun 2020 09:20:17: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:20:17: #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 09:20:17: #1 tags after filtering in treatment: 11135606 INFO @ Tue, 16 Jun 2020 09:20:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:20:17: #1 finished! INFO @ Tue, 16 Jun 2020 09:20:17: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:20:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:20:18: #2 number of paired peaks: 375 WARNING @ Tue, 16 Jun 2020 09:20:18: Fewer paired peaks (375) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 375 pairs to build model! INFO @ Tue, 16 Jun 2020 09:20:18: start model_add_line... INFO @ Tue, 16 Jun 2020 09:20:18: start X-correlation... INFO @ Tue, 16 Jun 2020 09:20:18: end of X-cor INFO @ Tue, 16 Jun 2020 09:20:18: #2 finished! INFO @ Tue, 16 Jun 2020 09:20:18: #2 predicted fragment length is 48 bps INFO @ Tue, 16 Jun 2020 09:20:18: #2 alternative fragment length(s) may be 2,48,560,589 bps INFO @ Tue, 16 Jun 2020 09:20:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495057/SRX495057.10_model.r WARNING @ Tue, 16 Jun 2020 09:20:18: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:20:18: #2 You may need to consider one of the other alternative d(s): 2,48,560,589 WARNING @ Tue, 16 Jun 2020 09:20:18: #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 09:20:18: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:20:18: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:20:20: 7000000 INFO @ Tue, 16 Jun 2020 09:20:26: 8000000 INFO @ Tue, 16 Jun 2020 09:20:32: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:20:37: 10000000 INFO @ Tue, 16 Jun 2020 09:20:38: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:20:43: 11000000 INFO @ Tue, 16 Jun 2020 09:20:44: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:20:44: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:20:44: #1 total tags in treatment: 11135606 INFO @ Tue, 16 Jun 2020 09:20:44: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:20:44: #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 09:20:44: #1 tags after filtering in treatment: 11135606 INFO @ Tue, 16 Jun 2020 09:20:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:20:44: #1 finished! INFO @ Tue, 16 Jun 2020 09:20:44: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:20:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:20:45: #2 number of paired peaks: 375 WARNING @ Tue, 16 Jun 2020 09:20:45: Fewer paired peaks (375) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 375 pairs to build model! INFO @ Tue, 16 Jun 2020 09:20:45: start model_add_line... INFO @ Tue, 16 Jun 2020 09:20:45: start X-correlation... INFO @ Tue, 16 Jun 2020 09:20:45: end of X-cor INFO @ Tue, 16 Jun 2020 09:20:45: #2 finished! INFO @ Tue, 16 Jun 2020 09:20:45: #2 predicted fragment length is 48 bps INFO @ Tue, 16 Jun 2020 09:20:45: #2 alternative fragment length(s) may be 2,48,560,589 bps INFO @ Tue, 16 Jun 2020 09:20:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495057/SRX495057.20_model.r WARNING @ Tue, 16 Jun 2020 09:20:45: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:20:45: #2 You may need to consider one of the other alternative d(s): 2,48,560,589 WARNING @ Tue, 16 Jun 2020 09:20:45: #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 09:20:45: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:20:45: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:20:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495057/SRX495057.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:20:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495057/SRX495057.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:20:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495057/SRX495057.10_summits.bed INFO @ Tue, 16 Jun 2020 09:20:49: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (405 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:21:05: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:21:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495057/SRX495057.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:21:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495057/SRX495057.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:21:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495057/SRX495057.20_summits.bed INFO @ Tue, 16 Jun 2020 09:21:15: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (157 records, 4 fields): 1 millis CompletedMACS2peakCalling