Job ID = 6368517 SRX = SRX5020746 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:17:36 prefetch.2.10.7: 1) Downloading 'SRR8201369'... 2020-06-16T00:17:36 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:18:57 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:18:57 prefetch.2.10.7: 'SRR8201369' is valid 2020-06-16T00:18:57 prefetch.2.10.7: 1) 'SRR8201369' was downloaded successfully 2020-06-16T00:18:57 prefetch.2.10.7: 'SRR8201369' has 0 unresolved dependencies Read 7084482 spots for SRR8201369/SRR8201369.sra Written 7084482 spots for SRR8201369/SRR8201369.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: 00:02:22 7084482 reads; of these: 7084482 (100.00%) were unpaired; of these: 1015033 (14.33%) aligned 0 times 4695868 (66.28%) aligned exactly 1 time 1373581 (19.39%) aligned >1 times 85.67% overall alignment rate Time searching: 00:02:23 Overall time: 00:02:23 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] 689430 / 6069449 = 0.1136 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 09:23:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020746/SRX5020746.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020746/SRX5020746.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020746/SRX5020746.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020746/SRX5020746.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 09:23:43: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:23:43: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:23:49: 1000000 INFO @ Tue, 16 Jun 2020 09:23:55: 2000000 INFO @ Tue, 16 Jun 2020 09:24:01: 3000000 INFO @ Tue, 16 Jun 2020 09:24:07: 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 09:24:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020746/SRX5020746.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020746/SRX5020746.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020746/SRX5020746.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020746/SRX5020746.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 09:24:13: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:24:13: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:24:13: 5000000 INFO @ Tue, 16 Jun 2020 09:24:15: #1 tag size is determined as 75 bps INFO @ Tue, 16 Jun 2020 09:24:15: #1 tag size = 75 INFO @ Tue, 16 Jun 2020 09:24:15: #1 total tags in treatment: 5380019 INFO @ Tue, 16 Jun 2020 09:24:15: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:24:15: #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 09:24:15: #1 tags after filtering in treatment: 5380019 INFO @ Tue, 16 Jun 2020 09:24:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:24:15: #1 finished! INFO @ Tue, 16 Jun 2020 09:24:15: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:24:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:24:16: #2 number of paired peaks: 852 WARNING @ Tue, 16 Jun 2020 09:24:16: Fewer paired peaks (852) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 852 pairs to build model! INFO @ Tue, 16 Jun 2020 09:24:16: start model_add_line... INFO @ Tue, 16 Jun 2020 09:24:16: start X-correlation... INFO @ Tue, 16 Jun 2020 09:24:16: end of X-cor INFO @ Tue, 16 Jun 2020 09:24:16: #2 finished! INFO @ Tue, 16 Jun 2020 09:24:16: #2 predicted fragment length is 90 bps INFO @ Tue, 16 Jun 2020 09:24:16: #2 alternative fragment length(s) may be 90,584 bps INFO @ Tue, 16 Jun 2020 09:24:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020746/SRX5020746.05_model.r WARNING @ Tue, 16 Jun 2020 09:24:16: #2 Since the d (90) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:24:16: #2 You may need to consider one of the other alternative d(s): 90,584 WARNING @ Tue, 16 Jun 2020 09:24:16: #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 09:24:16: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:24:16: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:24:18: 1000000 INFO @ Tue, 16 Jun 2020 09:24:23: 2000000 INFO @ Tue, 16 Jun 2020 09:24:28: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:24:29: 3000000 INFO @ Tue, 16 Jun 2020 09:24:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020746/SRX5020746.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:24:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020746/SRX5020746.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:24:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020746/SRX5020746.05_summits.bed INFO @ Tue, 16 Jun 2020 09:24:33: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1597 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:24:34: 4000000 INFO @ Tue, 16 Jun 2020 09:24:39: 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 09:24:41: #1 tag size is determined as 75 bps INFO @ Tue, 16 Jun 2020 09:24:41: #1 tag size = 75 INFO @ Tue, 16 Jun 2020 09:24:41: #1 total tags in treatment: 5380019 INFO @ Tue, 16 Jun 2020 09:24:41: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:24:41: #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 09:24:41: #1 tags after filtering in treatment: 5380019 INFO @ Tue, 16 Jun 2020 09:24:41: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:24:41: #1 finished! INFO @ Tue, 16 Jun 2020 09:24:41: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:24:41: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:24:42: #2 number of paired peaks: 852 WARNING @ Tue, 16 Jun 2020 09:24:42: Fewer paired peaks (852) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 852 pairs to build model! INFO @ Tue, 16 Jun 2020 09:24:42: start model_add_line... INFO @ Tue, 16 Jun 2020 09:24:42: start X-correlation... INFO @ Tue, 16 Jun 2020 09:24:42: end of X-cor INFO @ Tue, 16 Jun 2020 09:24:42: #2 finished! INFO @ Tue, 16 Jun 2020 09:24:42: #2 predicted fragment length is 90 bps INFO @ Tue, 16 Jun 2020 09:24:42: #2 alternative fragment length(s) may be 90,584 bps INFO @ Tue, 16 Jun 2020 09:24:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020746/SRX5020746.10_model.r WARNING @ Tue, 16 Jun 2020 09:24:42: #2 Since the d (90) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:24:42: #2 You may need to consider one of the other alternative d(s): 90,584 WARNING @ Tue, 16 Jun 2020 09:24:42: #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 09:24:42: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:24:42: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:24:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020746/SRX5020746.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020746/SRX5020746.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020746/SRX5020746.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020746/SRX5020746.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 09:24:43: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:24:43: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:24:48: 1000000 INFO @ Tue, 16 Jun 2020 09:24:53: 2000000 INFO @ Tue, 16 Jun 2020 09:24:54: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:24:58: 3000000 INFO @ Tue, 16 Jun 2020 09:24:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020746/SRX5020746.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:24:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020746/SRX5020746.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:24:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020746/SRX5020746.10_summits.bed INFO @ Tue, 16 Jun 2020 09:24:59: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (517 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:25:04: 4000000 INFO @ Tue, 16 Jun 2020 09:25:09: 5000000 INFO @ Tue, 16 Jun 2020 09:25:11: #1 tag size is determined as 75 bps INFO @ Tue, 16 Jun 2020 09:25:11: #1 tag size = 75 INFO @ Tue, 16 Jun 2020 09:25:11: #1 total tags in treatment: 5380019 INFO @ Tue, 16 Jun 2020 09:25:11: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:25:11: #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 09:25:11: #1 tags after filtering in treatment: 5380019 INFO @ Tue, 16 Jun 2020 09:25:11: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:25:11: #1 finished! INFO @ Tue, 16 Jun 2020 09:25:11: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:25:11: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:25:11: #2 number of paired peaks: 852 WARNING @ Tue, 16 Jun 2020 09:25:11: Fewer paired peaks (852) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 852 pairs to build model! INFO @ Tue, 16 Jun 2020 09:25:11: start model_add_line... INFO @ Tue, 16 Jun 2020 09:25:11: start X-correlation... INFO @ Tue, 16 Jun 2020 09:25:11: end of X-cor INFO @ Tue, 16 Jun 2020 09:25:11: #2 finished! INFO @ Tue, 16 Jun 2020 09:25:11: #2 predicted fragment length is 90 bps INFO @ Tue, 16 Jun 2020 09:25:11: #2 alternative fragment length(s) may be 90,584 bps INFO @ Tue, 16 Jun 2020 09:25:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020746/SRX5020746.20_model.r WARNING @ Tue, 16 Jun 2020 09:25:11: #2 Since the d (90) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:25:11: #2 You may need to consider one of the other alternative d(s): 90,584 WARNING @ Tue, 16 Jun 2020 09:25:11: #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 09:25:11: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:25:11: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:25:23: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:25:28: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020746/SRX5020746.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:25:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020746/SRX5020746.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:25:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020746/SRX5020746.20_summits.bed INFO @ Tue, 16 Jun 2020 09:25:28: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (209 records, 4 fields): 2 millis CompletedMACS2peakCalling