Job ID = 6368573 SRX = SRX5020799 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:35:16 prefetch.2.10.7: 1) Downloading 'SRR8201422'... 2020-06-16T00:35:16 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:36:43 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:36:44 prefetch.2.10.7: 'SRR8201422' is valid 2020-06-16T00:36:44 prefetch.2.10.7: 1) 'SRR8201422' was downloaded successfully Read 8209981 spots for SRR8201422/SRR8201422.sra Written 8209981 spots for SRR8201422/SRR8201422.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:02:04 8209981 reads; of these: 8209981 (100.00%) were unpaired; of these: 100709 (1.23%) aligned 0 times 6697905 (81.58%) aligned exactly 1 time 1411367 (17.19%) aligned >1 times 98.77% overall alignment rate Time searching: 00:02:05 Overall time: 00:02:05 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] 479423 / 8109272 = 0.0591 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 09:41:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020799/SRX5020799.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020799/SRX5020799.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020799/SRX5020799.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020799/SRX5020799.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 09:41:57: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:41:57: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:42:05: 1000000 INFO @ Tue, 16 Jun 2020 09:42:12: 2000000 INFO @ Tue, 16 Jun 2020 09:42:19: 3000000 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 09:42:26: 4000000 INFO @ Tue, 16 Jun 2020 09:42:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020799/SRX5020799.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020799/SRX5020799.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020799/SRX5020799.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020799/SRX5020799.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 09:42:27: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:42:27: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:42:34: 5000000 INFO @ Tue, 16 Jun 2020 09:42:34: 1000000 INFO @ Tue, 16 Jun 2020 09:42:41: 2000000 INFO @ Tue, 16 Jun 2020 09:42:42: 6000000 INFO @ Tue, 16 Jun 2020 09:42:48: 3000000 INFO @ Tue, 16 Jun 2020 09:42:49: 7000000 INFO @ Tue, 16 Jun 2020 09:42:54: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:42:54: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:42:54: #1 total tags in treatment: 7629849 INFO @ Tue, 16 Jun 2020 09:42:54: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:42:54: #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 09:42:54: #1 tags after filtering in treatment: 7629849 INFO @ Tue, 16 Jun 2020 09:42:54: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:42:54: #1 finished! INFO @ Tue, 16 Jun 2020 09:42:54: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:42:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:42:55: #2 number of paired peaks: 388 WARNING @ Tue, 16 Jun 2020 09:42:55: Fewer paired peaks (388) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 388 pairs to build model! INFO @ Tue, 16 Jun 2020 09:42:55: start model_add_line... INFO @ Tue, 16 Jun 2020 09:42:55: start X-correlation... INFO @ Tue, 16 Jun 2020 09:42:55: end of X-cor INFO @ Tue, 16 Jun 2020 09:42:55: #2 finished! INFO @ Tue, 16 Jun 2020 09:42:55: #2 predicted fragment length is 50 bps INFO @ Tue, 16 Jun 2020 09:42:55: #2 alternative fragment length(s) may be 4,50,595 bps INFO @ Tue, 16 Jun 2020 09:42:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020799/SRX5020799.05_model.r WARNING @ Tue, 16 Jun 2020 09:42:55: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:42:55: #2 You may need to consider one of the other alternative d(s): 4,50,595 WARNING @ Tue, 16 Jun 2020 09:42:55: #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 09:42:55: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:42:55: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:42:55: 4000000 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 09:42:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020799/SRX5020799.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020799/SRX5020799.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020799/SRX5020799.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020799/SRX5020799.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 09:42:57: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:42:57: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:43:02: 5000000 INFO @ Tue, 16 Jun 2020 09:43:04: 1000000 INFO @ Tue, 16 Jun 2020 09:43:08: 6000000 INFO @ Tue, 16 Jun 2020 09:43:11: 2000000 INFO @ Tue, 16 Jun 2020 09:43:11: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:43:15: 7000000 INFO @ Tue, 16 Jun 2020 09:43:17: 3000000 INFO @ Tue, 16 Jun 2020 09:43:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020799/SRX5020799.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:43:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020799/SRX5020799.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:43:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020799/SRX5020799.05_summits.bed INFO @ Tue, 16 Jun 2020 09:43:19: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (580 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:43:19: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:43:19: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:43:19: #1 total tags in treatment: 7629849 INFO @ Tue, 16 Jun 2020 09:43:19: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:43:19: #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 09:43:19: #1 tags after filtering in treatment: 7629849 INFO @ Tue, 16 Jun 2020 09:43:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:43:19: #1 finished! INFO @ Tue, 16 Jun 2020 09:43:19: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:43:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:43:20: #2 number of paired peaks: 388 WARNING @ Tue, 16 Jun 2020 09:43:20: Fewer paired peaks (388) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 388 pairs to build model! INFO @ Tue, 16 Jun 2020 09:43:20: start model_add_line... INFO @ Tue, 16 Jun 2020 09:43:20: start X-correlation... INFO @ Tue, 16 Jun 2020 09:43:20: end of X-cor INFO @ Tue, 16 Jun 2020 09:43:20: #2 finished! INFO @ Tue, 16 Jun 2020 09:43:20: #2 predicted fragment length is 50 bps INFO @ Tue, 16 Jun 2020 09:43:20: #2 alternative fragment length(s) may be 4,50,595 bps INFO @ Tue, 16 Jun 2020 09:43:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020799/SRX5020799.10_model.r WARNING @ Tue, 16 Jun 2020 09:43:20: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:43:20: #2 You may need to consider one of the other alternative d(s): 4,50,595 WARNING @ Tue, 16 Jun 2020 09:43:20: #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 09:43:20: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:43:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:43:24: 4000000 INFO @ Tue, 16 Jun 2020 09:43:30: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:43:36: 6000000 INFO @ Tue, 16 Jun 2020 09:43:37: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:43:42: 7000000 INFO @ Tue, 16 Jun 2020 09:43:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020799/SRX5020799.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:43:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020799/SRX5020799.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:43:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020799/SRX5020799.10_summits.bed INFO @ Tue, 16 Jun 2020 09:43:45: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (363 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:43:46: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:43:46: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:43:46: #1 total tags in treatment: 7629849 INFO @ Tue, 16 Jun 2020 09:43:46: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:43:46: #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 09:43:46: #1 tags after filtering in treatment: 7629849 INFO @ Tue, 16 Jun 2020 09:43:46: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:43:46: #1 finished! INFO @ Tue, 16 Jun 2020 09:43:46: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:43:46: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:43:46: #2 number of paired peaks: 388 WARNING @ Tue, 16 Jun 2020 09:43:46: Fewer paired peaks (388) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 388 pairs to build model! INFO @ Tue, 16 Jun 2020 09:43:46: start model_add_line... INFO @ Tue, 16 Jun 2020 09:43:46: start X-correlation... INFO @ Tue, 16 Jun 2020 09:43:46: end of X-cor INFO @ Tue, 16 Jun 2020 09:43:46: #2 finished! INFO @ Tue, 16 Jun 2020 09:43:46: #2 predicted fragment length is 50 bps INFO @ Tue, 16 Jun 2020 09:43:46: #2 alternative fragment length(s) may be 4,50,595 bps INFO @ Tue, 16 Jun 2020 09:43:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020799/SRX5020799.20_model.r WARNING @ Tue, 16 Jun 2020 09:43:46: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:43:46: #2 You may need to consider one of the other alternative d(s): 4,50,595 WARNING @ Tue, 16 Jun 2020 09:43:46: #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 09:43:46: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:43:46: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:44:02: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:44:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020799/SRX5020799.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:44:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020799/SRX5020799.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:44:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020799/SRX5020799.20_summits.bed INFO @ Tue, 16 Jun 2020 09:44:11: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (154 records, 4 fields): 1 millis CompletedMACS2peakCalling