Job ID = 6369000 SRX = SRX982066 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:37:31 prefetch.2.10.7: 1) Downloading 'SRR1956542'... 2020-06-16T00:37:31 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:38:28 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:38:29 prefetch.2.10.7: 'SRR1956542' is valid 2020-06-16T00:38:29 prefetch.2.10.7: 1) 'SRR1956542' was downloaded successfully Read 6126417 spots for SRR1956542/SRR1956542.sra Written 6126417 spots for SRR1956542/SRR1956542.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: 00:01:21 6126417 reads; of these: 6126417 (100.00%) were unpaired; of these: 606239 (9.90%) aligned 0 times 4555862 (74.36%) aligned exactly 1 time 964316 (15.74%) aligned >1 times 90.10% overall alignment rate Time searching: 00:01:21 Overall time: 00:01:21 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] 756483 / 5520178 = 0.1370 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 09:42:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX982066/SRX982066.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX982066/SRX982066.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX982066/SRX982066.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX982066/SRX982066.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 09:42:01: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:42:01: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:42:07: 1000000 INFO @ Tue, 16 Jun 2020 09:42:14: 2000000 INFO @ Tue, 16 Jun 2020 09:42:20: 3000000 INFO @ Tue, 16 Jun 2020 09:42:26: 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 09:42:30: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:42:30: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:42:30: #1 total tags in treatment: 4763695 INFO @ Tue, 16 Jun 2020 09:42:30: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:42:30: #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 09:42:30: #1 tags after filtering in treatment: 4763695 INFO @ Tue, 16 Jun 2020 09:42:30: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:42:30: #1 finished! INFO @ Tue, 16 Jun 2020 09:42:30: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:42:30: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:42:31: #2 number of paired peaks: 484 WARNING @ Tue, 16 Jun 2020 09:42:31: Fewer paired peaks (484) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 484 pairs to build model! INFO @ Tue, 16 Jun 2020 09:42:31: start model_add_line... INFO @ Tue, 16 Jun 2020 09:42:31: start X-correlation... INFO @ Tue, 16 Jun 2020 09:42:31: end of X-cor INFO @ Tue, 16 Jun 2020 09:42:31: #2 finished! INFO @ Tue, 16 Jun 2020 09:42:31: #2 predicted fragment length is 57 bps INFO @ Tue, 16 Jun 2020 09:42:31: #2 alternative fragment length(s) may be 57 bps INFO @ Tue, 16 Jun 2020 09:42:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX982066/SRX982066.05_model.r WARNING @ Tue, 16 Jun 2020 09:42:31: #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 09:42:31: #2 You may need to consider one of the other alternative d(s): 57 WARNING @ Tue, 16 Jun 2020 09:42:31: #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 09:42:31: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:42:31: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:42:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX982066/SRX982066.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX982066/SRX982066.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX982066/SRX982066.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX982066/SRX982066.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 09:42:31: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:42:31: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:42:38: 1000000 INFO @ Tue, 16 Jun 2020 09:42:42: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:42:44: 2000000 INFO @ Tue, 16 Jun 2020 09:42:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX982066/SRX982066.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:42:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX982066/SRX982066.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:42:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX982066/SRX982066.05_summits.bed INFO @ Tue, 16 Jun 2020 09:42:47: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (563 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:42:51: 3000000 INFO @ Tue, 16 Jun 2020 09:42:58: 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 09:43:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX982066/SRX982066.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX982066/SRX982066.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX982066/SRX982066.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX982066/SRX982066.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 09:43:01: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:43:01: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:43:03: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:43:03: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:43:03: #1 total tags in treatment: 4763695 INFO @ Tue, 16 Jun 2020 09:43:03: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:43:03: #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 09:43:03: #1 tags after filtering in treatment: 4763695 INFO @ Tue, 16 Jun 2020 09:43:03: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:43:03: #1 finished! INFO @ Tue, 16 Jun 2020 09:43:03: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:43:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:43:03: #2 number of paired peaks: 484 WARNING @ Tue, 16 Jun 2020 09:43:03: Fewer paired peaks (484) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 484 pairs to build model! INFO @ Tue, 16 Jun 2020 09:43:03: start model_add_line... INFO @ Tue, 16 Jun 2020 09:43:03: start X-correlation... INFO @ Tue, 16 Jun 2020 09:43:03: end of X-cor INFO @ Tue, 16 Jun 2020 09:43:03: #2 finished! INFO @ Tue, 16 Jun 2020 09:43:03: #2 predicted fragment length is 57 bps INFO @ Tue, 16 Jun 2020 09:43:03: #2 alternative fragment length(s) may be 57 bps INFO @ Tue, 16 Jun 2020 09:43:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX982066/SRX982066.10_model.r WARNING @ Tue, 16 Jun 2020 09:43:03: #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 09:43:03: #2 You may need to consider one of the other alternative d(s): 57 WARNING @ Tue, 16 Jun 2020 09:43:03: #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 09:43:03: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:43:03: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:43:08: 1000000 INFO @ Tue, 16 Jun 2020 09:43:14: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:43:15: 2000000 INFO @ Tue, 16 Jun 2020 09:43:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX982066/SRX982066.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:43:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX982066/SRX982066.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:43:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX982066/SRX982066.10_summits.bed INFO @ Tue, 16 Jun 2020 09:43:19: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (323 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:43:21: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:43:28: 4000000 INFO @ Tue, 16 Jun 2020 09:43:33: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:43:33: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:43:33: #1 total tags in treatment: 4763695 INFO @ Tue, 16 Jun 2020 09:43:33: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:43:33: #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 09:43:33: #1 tags after filtering in treatment: 4763695 INFO @ Tue, 16 Jun 2020 09:43:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:43:33: #1 finished! INFO @ Tue, 16 Jun 2020 09:43:33: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:43:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:43:33: #2 number of paired peaks: 484 WARNING @ Tue, 16 Jun 2020 09:43:33: Fewer paired peaks (484) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 484 pairs to build model! INFO @ Tue, 16 Jun 2020 09:43:33: start model_add_line... INFO @ Tue, 16 Jun 2020 09:43:33: start X-correlation... INFO @ Tue, 16 Jun 2020 09:43:33: end of X-cor INFO @ Tue, 16 Jun 2020 09:43:33: #2 finished! INFO @ Tue, 16 Jun 2020 09:43:33: #2 predicted fragment length is 57 bps INFO @ Tue, 16 Jun 2020 09:43:33: #2 alternative fragment length(s) may be 57 bps INFO @ Tue, 16 Jun 2020 09:43:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX982066/SRX982066.20_model.r WARNING @ Tue, 16 Jun 2020 09:43:33: #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 09:43:33: #2 You may need to consider one of the other alternative d(s): 57 WARNING @ Tue, 16 Jun 2020 09:43:33: #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 09:43:33: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:43:33: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:43:44: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:43:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX982066/SRX982066.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:43:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX982066/SRX982066.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:43:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX982066/SRX982066.20_summits.bed INFO @ Tue, 16 Jun 2020 09:43:49: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (154 records, 4 fields): 2 millis CompletedMACS2peakCalling