Job ID = 6368468 SRX = SRX5020698 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:14:47 prefetch.2.10.7: 1) Downloading 'SRR8201321'... 2020-06-16T00:14:47 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:15:15 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:15:16 prefetch.2.10.7: 'SRR8201321' is valid 2020-06-16T00:15:16 prefetch.2.10.7: 1) 'SRR8201321' was downloaded successfully 2020-06-16T00:15:16 prefetch.2.10.7: 'SRR8201321' has 0 unresolved dependencies Read 5534775 spots for SRR8201321/SRR8201321.sra Written 5534775 spots for SRR8201321/SRR8201321.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: 00:01:14 5534775 reads; of these: 5534775 (100.00%) were unpaired; of these: 157437 (2.84%) aligned 0 times 4255651 (76.89%) aligned exactly 1 time 1121687 (20.27%) aligned >1 times 97.16% overall alignment rate Time searching: 00:01:14 Overall time: 00:01:14 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] 531940 / 5377338 = 0.0989 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 09:18:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020698/SRX5020698.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020698/SRX5020698.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020698/SRX5020698.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020698/SRX5020698.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 09:18:38: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:18:38: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:18:42: 1000000 INFO @ Tue, 16 Jun 2020 09:18:47: 2000000 INFO @ Tue, 16 Jun 2020 09:18:52: 3000000 INFO @ Tue, 16 Jun 2020 09:18:57: 4000000 INFO @ Tue, 16 Jun 2020 09:19:01: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:19:01: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:19:01: #1 total tags in treatment: 4845398 INFO @ Tue, 16 Jun 2020 09:19:01: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:19:01: #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 09:19:01: #1 tags after filtering in treatment: 4845398 INFO @ Tue, 16 Jun 2020 09:19:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:19:01: #1 finished! INFO @ Tue, 16 Jun 2020 09:19:01: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:19:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:19:01: #2 number of paired peaks: 520 WARNING @ Tue, 16 Jun 2020 09:19:01: Fewer paired peaks (520) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 520 pairs to build model! INFO @ Tue, 16 Jun 2020 09:19:01: start model_add_line... INFO @ Tue, 16 Jun 2020 09:19:01: start X-correlation... INFO @ Tue, 16 Jun 2020 09:19:01: end of X-cor INFO @ Tue, 16 Jun 2020 09:19:01: #2 finished! INFO @ Tue, 16 Jun 2020 09:19:01: #2 predicted fragment length is 57 bps INFO @ Tue, 16 Jun 2020 09:19:01: #2 alternative fragment length(s) may be 57 bps INFO @ Tue, 16 Jun 2020 09:19:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020698/SRX5020698.05_model.r WARNING @ Tue, 16 Jun 2020 09:19:01: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:19:01: #2 You may need to consider one of the other alternative d(s): 57 WARNING @ Tue, 16 Jun 2020 09:19:01: #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 09:19:01: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:19:01: #3 Pre-compute pvalue-qvalue table... 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/SRX5020698/SRX5020698.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020698/SRX5020698.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020698/SRX5020698.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020698/SRX5020698.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 09:19:11: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:19:13: 1000000 INFO @ Tue, 16 Jun 2020 09:19:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020698/SRX5020698.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:19:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020698/SRX5020698.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:19:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020698/SRX5020698.05_summits.bed INFO @ Tue, 16 Jun 2020 09:19:16: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (599 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:19:17: 2000000 INFO @ Tue, 16 Jun 2020 09:19:22: 3000000 INFO @ Tue, 16 Jun 2020 09:19:26: 4000000 INFO @ Tue, 16 Jun 2020 09:19:30: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:19:30: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:19:30: #1 total tags in treatment: 4845398 INFO @ Tue, 16 Jun 2020 09:19:30: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:19:30: #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 09:19:30: #1 tags after filtering in treatment: 4845398 INFO @ Tue, 16 Jun 2020 09:19:30: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:19:30: #1 finished! INFO @ Tue, 16 Jun 2020 09:19:30: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:19:30: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:19:31: #2 number of paired peaks: 520 WARNING @ Tue, 16 Jun 2020 09:19:31: Fewer paired peaks (520) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 520 pairs to build model! INFO @ Tue, 16 Jun 2020 09:19:31: start model_add_line... INFO @ Tue, 16 Jun 2020 09:19:31: start X-correlation... INFO @ Tue, 16 Jun 2020 09:19:31: end of X-cor INFO @ Tue, 16 Jun 2020 09:19:31: #2 finished! INFO @ Tue, 16 Jun 2020 09:19:31: #2 predicted fragment length is 57 bps INFO @ Tue, 16 Jun 2020 09:19:31: #2 alternative fragment length(s) may be 57 bps INFO @ Tue, 16 Jun 2020 09:19:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020698/SRX5020698.10_model.r WARNING @ Tue, 16 Jun 2020 09:19:31: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:19:31: #2 You may need to consider one of the other alternative d(s): 57 WARNING @ Tue, 16 Jun 2020 09:19:31: #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 09:19:31: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:19:31: #3 Pre-compute pvalue-qvalue table... 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 09:19:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020698/SRX5020698.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020698/SRX5020698.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020698/SRX5020698.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020698/SRX5020698.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 09:19:38: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:19:38: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:19:41: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:19:43: 1000000 INFO @ Tue, 16 Jun 2020 09:19:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020698/SRX5020698.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:19:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020698/SRX5020698.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:19:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020698/SRX5020698.10_summits.bed INFO @ Tue, 16 Jun 2020 09:19:47: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (303 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:19:48: 2000000 INFO @ Tue, 16 Jun 2020 09:19:52: 3000000 INFO @ Tue, 16 Jun 2020 09:19:57: 4000000 INFO @ Tue, 16 Jun 2020 09:20:02: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:20:02: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:20:02: #1 total tags in treatment: 4845398 INFO @ Tue, 16 Jun 2020 09:20:02: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:20:02: #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 09:20:02: #1 tags after filtering in treatment: 4845398 INFO @ Tue, 16 Jun 2020 09:20:02: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:20:02: #1 finished! INFO @ Tue, 16 Jun 2020 09:20:02: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:20:02: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:20:02: #2 number of paired peaks: 520 WARNING @ Tue, 16 Jun 2020 09:20:02: Fewer paired peaks (520) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 520 pairs to build model! INFO @ Tue, 16 Jun 2020 09:20:02: start model_add_line... INFO @ Tue, 16 Jun 2020 09:20:02: start X-correlation... INFO @ Tue, 16 Jun 2020 09:20:02: end of X-cor INFO @ Tue, 16 Jun 2020 09:20:02: #2 finished! INFO @ Tue, 16 Jun 2020 09:20:02: #2 predicted fragment length is 57 bps INFO @ Tue, 16 Jun 2020 09:20:02: #2 alternative fragment length(s) may be 57 bps INFO @ Tue, 16 Jun 2020 09:20:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020698/SRX5020698.20_model.r WARNING @ Tue, 16 Jun 2020 09:20:02: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:20:02: #2 You may need to consider one of the other alternative d(s): 57 WARNING @ Tue, 16 Jun 2020 09:20:02: #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 09:20:02: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:20:02: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:20:12: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:20:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020698/SRX5020698.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:20:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020698/SRX5020698.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:20:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020698/SRX5020698.20_summits.bed INFO @ Tue, 16 Jun 2020 09:20:18: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (145 records, 4 fields): 1 millis CompletedMACS2peakCalling