Job ID = 6507943 SRX = SRX495103 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T13:48:27 prefetch.2.10.7: 1) Downloading 'SRR1198635'... 2020-06-26T13:48:27 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T13:50:19 prefetch.2.10.7: HTTPS download succeed 2020-06-26T13:50:19 prefetch.2.10.7: 1) 'SRR1198635' was downloaded successfully Read 14545777 spots for SRR1198635/SRR1198635.sra Written 14545777 spots for SRR1198635/SRR1198635.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: 00:02:14 14545777 reads; of these: 14545777 (100.00%) were unpaired; of these: 4615237 (31.73%) aligned 0 times 8469183 (58.22%) aligned exactly 1 time 1461357 (10.05%) aligned >1 times 68.27% overall alignment rate Time searching: 00:02:14 Overall time: 00:02:14 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] 5189874 / 9930540 = 0.5226 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 @ Fri, 26 Jun 2020 22:56:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495103/SRX495103.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495103/SRX495103.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495103/SRX495103.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495103/SRX495103.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 @ Fri, 26 Jun 2020 22:56:07: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:56:07: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:56:12: 1000000 INFO @ Fri, 26 Jun 2020 22:56:17: 2000000 INFO @ Fri, 26 Jun 2020 22:56:22: 3000000 INFO @ Fri, 26 Jun 2020 22:56:27: 4000000 INFO @ Fri, 26 Jun 2020 22:56:31: #1 tag size is determined as 42 bps INFO @ Fri, 26 Jun 2020 22:56:31: #1 tag size = 42 INFO @ Fri, 26 Jun 2020 22:56:31: #1 total tags in treatment: 4740666 INFO @ Fri, 26 Jun 2020 22:56:31: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:56:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 22:56:31: #1 tags after filtering in treatment: 4740666 INFO @ Fri, 26 Jun 2020 22:56:31: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:56:31: #1 finished! INFO @ Fri, 26 Jun 2020 22:56:31: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:56:31: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:56:32: #2 number of paired peaks: 613 WARNING @ Fri, 26 Jun 2020 22:56:32: Fewer paired peaks (613) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 613 pairs to build model! INFO @ Fri, 26 Jun 2020 22:56:32: start model_add_line... INFO @ Fri, 26 Jun 2020 22:56:32: start X-correlation... INFO @ Fri, 26 Jun 2020 22:56:32: end of X-cor INFO @ Fri, 26 Jun 2020 22:56:32: #2 finished! INFO @ Fri, 26 Jun 2020 22:56:32: #2 predicted fragment length is 47 bps INFO @ Fri, 26 Jun 2020 22:56:32: #2 alternative fragment length(s) may be 3,47 bps INFO @ Fri, 26 Jun 2020 22:56:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495103/SRX495103.05_model.r WARNING @ Fri, 26 Jun 2020 22:56:32: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 22:56:32: #2 You may need to consider one of the other alternative d(s): 3,47 WARNING @ Fri, 26 Jun 2020 22:56:32: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 22:56:32: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:56:32: #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 @ Fri, 26 Jun 2020 22:56:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495103/SRX495103.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495103/SRX495103.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495103/SRX495103.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495103/SRX495103.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 @ Fri, 26 Jun 2020 22:56:37: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:56:37: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:56:42: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:56:42: 1000000 INFO @ Fri, 26 Jun 2020 22:56:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495103/SRX495103.05_peaks.xls INFO @ Fri, 26 Jun 2020 22:56:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495103/SRX495103.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:56:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495103/SRX495103.05_summits.bed INFO @ Fri, 26 Jun 2020 22:56:47: Done! INFO @ Fri, 26 Jun 2020 22:56:47: 2000000 pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (688 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 22:56:52: 3000000 INFO @ Fri, 26 Jun 2020 22:56:57: 4000000 INFO @ Fri, 26 Jun 2020 22:57:00: #1 tag size is determined as 42 bps INFO @ Fri, 26 Jun 2020 22:57:00: #1 tag size = 42 INFO @ Fri, 26 Jun 2020 22:57:00: #1 total tags in treatment: 4740666 INFO @ Fri, 26 Jun 2020 22:57:00: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:57:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 22:57:00: #1 tags after filtering in treatment: 4740666 INFO @ Fri, 26 Jun 2020 22:57:00: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:57:00: #1 finished! INFO @ Fri, 26 Jun 2020 22:57:00: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:57:00: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:57:01: #2 number of paired peaks: 613 WARNING @ Fri, 26 Jun 2020 22:57:01: Fewer paired peaks (613) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 613 pairs to build model! INFO @ Fri, 26 Jun 2020 22:57:01: start model_add_line... INFO @ Fri, 26 Jun 2020 22:57:01: start X-correlation... INFO @ Fri, 26 Jun 2020 22:57:01: end of X-cor INFO @ Fri, 26 Jun 2020 22:57:01: #2 finished! INFO @ Fri, 26 Jun 2020 22:57:01: #2 predicted fragment length is 47 bps INFO @ Fri, 26 Jun 2020 22:57:01: #2 alternative fragment length(s) may be 3,47 bps INFO @ Fri, 26 Jun 2020 22:57:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495103/SRX495103.10_model.r WARNING @ Fri, 26 Jun 2020 22:57:01: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 22:57:01: #2 You may need to consider one of the other alternative d(s): 3,47 WARNING @ Fri, 26 Jun 2020 22:57:01: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 22:57:01: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:57:01: #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 @ Fri, 26 Jun 2020 22:57:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495103/SRX495103.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495103/SRX495103.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495103/SRX495103.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495103/SRX495103.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 @ Fri, 26 Jun 2020 22:57:07: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:57:07: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:57:10: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:57:12: 1000000 INFO @ Fri, 26 Jun 2020 22:57:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495103/SRX495103.10_peaks.xls INFO @ Fri, 26 Jun 2020 22:57:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495103/SRX495103.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:57:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495103/SRX495103.10_summits.bed INFO @ Fri, 26 Jun 2020 22:57:15: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (396 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 22:57:17: 2000000 INFO @ Fri, 26 Jun 2020 22:57:23: 3000000 INFO @ Fri, 26 Jun 2020 22:57:28: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 22:57:32: #1 tag size is determined as 42 bps INFO @ Fri, 26 Jun 2020 22:57:32: #1 tag size = 42 INFO @ Fri, 26 Jun 2020 22:57:32: #1 total tags in treatment: 4740666 INFO @ Fri, 26 Jun 2020 22:57:32: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:57:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 22:57:32: #1 tags after filtering in treatment: 4740666 INFO @ Fri, 26 Jun 2020 22:57:32: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:57:32: #1 finished! INFO @ Fri, 26 Jun 2020 22:57:32: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:57:32: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:57:32: #2 number of paired peaks: 613 WARNING @ Fri, 26 Jun 2020 22:57:32: Fewer paired peaks (613) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 613 pairs to build model! INFO @ Fri, 26 Jun 2020 22:57:32: start model_add_line... INFO @ Fri, 26 Jun 2020 22:57:32: start X-correlation... INFO @ Fri, 26 Jun 2020 22:57:32: end of X-cor INFO @ Fri, 26 Jun 2020 22:57:32: #2 finished! INFO @ Fri, 26 Jun 2020 22:57:32: #2 predicted fragment length is 47 bps INFO @ Fri, 26 Jun 2020 22:57:32: #2 alternative fragment length(s) may be 3,47 bps INFO @ Fri, 26 Jun 2020 22:57:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495103/SRX495103.20_model.r WARNING @ Fri, 26 Jun 2020 22:57:32: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 22:57:32: #2 You may need to consider one of the other alternative d(s): 3,47 WARNING @ Fri, 26 Jun 2020 22:57:32: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 22:57:32: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:57:32: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:57:42: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 22:57:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495103/SRX495103.20_peaks.xls INFO @ Fri, 26 Jun 2020 22:57:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495103/SRX495103.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:57:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495103/SRX495103.20_summits.bed INFO @ Fri, 26 Jun 2020 22:57:47: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (146 records, 4 fields): 1 millis CompletedMACS2peakCalling