Job ID = 6368497 SRX = SRX5020727 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:11:35 prefetch.2.10.7: 1) Downloading 'SRR8201350'... 2020-06-16T00:11:35 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:12:33 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:12:33 prefetch.2.10.7: 'SRR8201350' is valid 2020-06-16T00:12:33 prefetch.2.10.7: 1) 'SRR8201350' was downloaded successfully Read 5756432 spots for SRR8201350/SRR8201350.sra Written 5756432 spots for SRR8201350/SRR8201350.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: 00:01:18 5756432 reads; of these: 5756432 (100.00%) were unpaired; of these: 194218 (3.37%) aligned 0 times 4718878 (81.98%) aligned exactly 1 time 843336 (14.65%) aligned >1 times 96.63% overall alignment rate Time searching: 00:01:18 Overall time: 00:01:18 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] 325109 / 5562214 = 0.0584 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 09:16:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020727/SRX5020727.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020727/SRX5020727.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020727/SRX5020727.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020727/SRX5020727.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 09:16:38: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:16:38: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:16:43: 1000000 INFO @ Tue, 16 Jun 2020 09:16:49: 2000000 INFO @ Tue, 16 Jun 2020 09:16:54: 3000000 INFO @ Tue, 16 Jun 2020 09:17:00: 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 09:17:05: 5000000 INFO @ Tue, 16 Jun 2020 09:17:07: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:17:07: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:17:07: #1 total tags in treatment: 5237105 INFO @ Tue, 16 Jun 2020 09:17:07: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:17:07: #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 09:17:07: #1 tags after filtering in treatment: 5237105 INFO @ Tue, 16 Jun 2020 09:17:07: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:17:07: #1 finished! INFO @ Tue, 16 Jun 2020 09:17:07: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:17:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:17:07: #2 number of paired peaks: 279 WARNING @ Tue, 16 Jun 2020 09:17:07: Fewer paired peaks (279) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 279 pairs to build model! INFO @ Tue, 16 Jun 2020 09:17:07: start model_add_line... INFO @ Tue, 16 Jun 2020 09:17:07: start X-correlation... INFO @ Tue, 16 Jun 2020 09:17:07: end of X-cor INFO @ Tue, 16 Jun 2020 09:17:07: #2 finished! INFO @ Tue, 16 Jun 2020 09:17:07: #2 predicted fragment length is 52 bps INFO @ Tue, 16 Jun 2020 09:17:07: #2 alternative fragment length(s) may be 52,541 bps INFO @ Tue, 16 Jun 2020 09:17:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020727/SRX5020727.05_model.r WARNING @ Tue, 16 Jun 2020 09:17:07: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:17:07: #2 You may need to consider one of the other alternative d(s): 52,541 WARNING @ Tue, 16 Jun 2020 09:17:07: #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 09:17:07: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:17:07: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:17:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020727/SRX5020727.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020727/SRX5020727.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020727/SRX5020727.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020727/SRX5020727.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 09:17:08: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:17:08: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:17:13: 1000000 INFO @ Tue, 16 Jun 2020 09:17:17: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:17:18: 2000000 INFO @ Tue, 16 Jun 2020 09:17:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020727/SRX5020727.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:17:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020727/SRX5020727.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:17:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020727/SRX5020727.05_summits.bed INFO @ Tue, 16 Jun 2020 09:17:23: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (358 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:17:24: 3000000 INFO @ Tue, 16 Jun 2020 09:17:29: 4000000 INFO @ Tue, 16 Jun 2020 09:17:35: 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 09:17:36: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:17:36: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:17:36: #1 total tags in treatment: 5237105 INFO @ Tue, 16 Jun 2020 09:17:36: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:17:36: #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 09:17:36: #1 tags after filtering in treatment: 5237105 INFO @ Tue, 16 Jun 2020 09:17:36: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:17:36: #1 finished! INFO @ Tue, 16 Jun 2020 09:17:36: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:17:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:17:36: #2 number of paired peaks: 279 WARNING @ Tue, 16 Jun 2020 09:17:36: Fewer paired peaks (279) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 279 pairs to build model! INFO @ Tue, 16 Jun 2020 09:17:36: start model_add_line... INFO @ Tue, 16 Jun 2020 09:17:36: start X-correlation... INFO @ Tue, 16 Jun 2020 09:17:36: end of X-cor INFO @ Tue, 16 Jun 2020 09:17:36: #2 finished! INFO @ Tue, 16 Jun 2020 09:17:36: #2 predicted fragment length is 52 bps INFO @ Tue, 16 Jun 2020 09:17:36: #2 alternative fragment length(s) may be 52,541 bps INFO @ Tue, 16 Jun 2020 09:17:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020727/SRX5020727.10_model.r WARNING @ Tue, 16 Jun 2020 09:17:36: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:17:36: #2 You may need to consider one of the other alternative d(s): 52,541 WARNING @ Tue, 16 Jun 2020 09:17:36: #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 09:17:36: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:17:36: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:17:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020727/SRX5020727.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020727/SRX5020727.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020727/SRX5020727.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020727/SRX5020727.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 09:17:38: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:17:38: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:17:43: 1000000 INFO @ Tue, 16 Jun 2020 09:17:46: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:17:48: 2000000 INFO @ Tue, 16 Jun 2020 09:17:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020727/SRX5020727.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:17:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020727/SRX5020727.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:17:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020727/SRX5020727.10_summits.bed INFO @ Tue, 16 Jun 2020 09:17:52: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (213 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:17:54: 3000000 INFO @ Tue, 16 Jun 2020 09:18:00: 4000000 INFO @ Tue, 16 Jun 2020 09:18:07: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:18:08: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:18:08: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:18:08: #1 total tags in treatment: 5237105 INFO @ Tue, 16 Jun 2020 09:18:08: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:18:08: #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 09:18:08: #1 tags after filtering in treatment: 5237105 INFO @ Tue, 16 Jun 2020 09:18:08: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:18:08: #1 finished! INFO @ Tue, 16 Jun 2020 09:18:08: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:18:08: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:18:09: #2 number of paired peaks: 279 WARNING @ Tue, 16 Jun 2020 09:18:09: Fewer paired peaks (279) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 279 pairs to build model! INFO @ Tue, 16 Jun 2020 09:18:09: start model_add_line... INFO @ Tue, 16 Jun 2020 09:18:09: start X-correlation... INFO @ Tue, 16 Jun 2020 09:18:09: end of X-cor INFO @ Tue, 16 Jun 2020 09:18:09: #2 finished! INFO @ Tue, 16 Jun 2020 09:18:09: #2 predicted fragment length is 52 bps INFO @ Tue, 16 Jun 2020 09:18:09: #2 alternative fragment length(s) may be 52,541 bps INFO @ Tue, 16 Jun 2020 09:18:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020727/SRX5020727.20_model.r WARNING @ Tue, 16 Jun 2020 09:18:09: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:18:09: #2 You may need to consider one of the other alternative d(s): 52,541 WARNING @ Tue, 16 Jun 2020 09:18:09: #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 09:18:09: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:18:09: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:18:19: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:18:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020727/SRX5020727.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:18:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020727/SRX5020727.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:18:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020727/SRX5020727.20_summits.bed INFO @ Tue, 16 Jun 2020 09:18:24: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (87 records, 4 fields): 1 millis CompletedMACS2peakCalling