Job ID = 6368574 SRX = SRX5020800 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:20:51 prefetch.2.10.7: 1) Downloading 'SRR8201423'... 2020-06-16T00:20:51 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:22:11 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:22:12 prefetch.2.10.7: 'SRR8201423' is valid 2020-06-16T00:22:12 prefetch.2.10.7: 1) 'SRR8201423' was downloaded successfully Read 8133712 spots for SRR8201423/SRR8201423.sra Written 8133712 spots for SRR8201423/SRR8201423.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: 00:01:48 8133712 reads; of these: 8133712 (100.00%) were unpaired; of these: 112202 (1.38%) aligned 0 times 6594742 (81.08%) aligned exactly 1 time 1426768 (17.54%) aligned >1 times 98.62% overall alignment rate Time searching: 00:01:48 Overall time: 00:01:48 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] 497328 / 8021510 = 0.0620 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 09:26:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020800/SRX5020800.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020800/SRX5020800.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020800/SRX5020800.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020800/SRX5020800.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 09:26:52: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:26:52: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:26:57: 1000000 INFO @ Tue, 16 Jun 2020 09:27:03: 2000000 INFO @ Tue, 16 Jun 2020 09:27:09: 3000000 INFO @ Tue, 16 Jun 2020 09:27:14: 4000000 INFO @ Tue, 16 Jun 2020 09:27:20: 5000000 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 09:27:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020800/SRX5020800.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020800/SRX5020800.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020800/SRX5020800.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020800/SRX5020800.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 09:27:22: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:27:22: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:27:26: 6000000 INFO @ Tue, 16 Jun 2020 09:27:28: 1000000 INFO @ Tue, 16 Jun 2020 09:27:32: 7000000 INFO @ Tue, 16 Jun 2020 09:27:34: 2000000 INFO @ Tue, 16 Jun 2020 09:27:35: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:27:35: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:27:35: #1 total tags in treatment: 7524182 INFO @ Tue, 16 Jun 2020 09:27:35: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:27:35: #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 09:27:35: #1 tags after filtering in treatment: 7524182 INFO @ Tue, 16 Jun 2020 09:27:35: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:27:35: #1 finished! INFO @ Tue, 16 Jun 2020 09:27:35: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:27:35: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:27:36: #2 number of paired peaks: 397 WARNING @ Tue, 16 Jun 2020 09:27:36: Fewer paired peaks (397) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 397 pairs to build model! INFO @ Tue, 16 Jun 2020 09:27:36: start model_add_line... INFO @ Tue, 16 Jun 2020 09:27:36: start X-correlation... INFO @ Tue, 16 Jun 2020 09:27:36: end of X-cor INFO @ Tue, 16 Jun 2020 09:27:36: #2 finished! INFO @ Tue, 16 Jun 2020 09:27:36: #2 predicted fragment length is 51 bps INFO @ Tue, 16 Jun 2020 09:27:36: #2 alternative fragment length(s) may be 4,51 bps INFO @ Tue, 16 Jun 2020 09:27:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020800/SRX5020800.05_model.r WARNING @ Tue, 16 Jun 2020 09:27:36: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:27:36: #2 You may need to consider one of the other alternative d(s): 4,51 WARNING @ Tue, 16 Jun 2020 09:27:36: #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 09:27:36: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:27:36: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:27:40: 3000000 INFO @ Tue, 16 Jun 2020 09:27:46: 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 09:27:50: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:27:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020800/SRX5020800.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020800/SRX5020800.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020800/SRX5020800.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020800/SRX5020800.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 09:27:52: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:27:52: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:27:52: 5000000 INFO @ Tue, 16 Jun 2020 09:27:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020800/SRX5020800.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:27:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020800/SRX5020800.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:27:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020800/SRX5020800.05_summits.bed INFO @ Tue, 16 Jun 2020 09:27:58: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (603 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:27:58: 1000000 INFO @ Tue, 16 Jun 2020 09:27:59: 6000000 INFO @ Tue, 16 Jun 2020 09:28:05: 2000000 INFO @ Tue, 16 Jun 2020 09:28:05: 7000000 INFO @ Tue, 16 Jun 2020 09:28:08: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:28:08: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:28:08: #1 total tags in treatment: 7524182 INFO @ Tue, 16 Jun 2020 09:28:08: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:28:08: #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 09:28:08: #1 tags after filtering in treatment: 7524182 INFO @ Tue, 16 Jun 2020 09:28:08: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:28:08: #1 finished! INFO @ Tue, 16 Jun 2020 09:28:08: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:28:08: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:28:09: #2 number of paired peaks: 397 WARNING @ Tue, 16 Jun 2020 09:28:09: Fewer paired peaks (397) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 397 pairs to build model! INFO @ Tue, 16 Jun 2020 09:28:09: start model_add_line... INFO @ Tue, 16 Jun 2020 09:28:09: start X-correlation... INFO @ Tue, 16 Jun 2020 09:28:09: end of X-cor INFO @ Tue, 16 Jun 2020 09:28:09: #2 finished! INFO @ Tue, 16 Jun 2020 09:28:09: #2 predicted fragment length is 51 bps INFO @ Tue, 16 Jun 2020 09:28:09: #2 alternative fragment length(s) may be 4,51 bps INFO @ Tue, 16 Jun 2020 09:28:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020800/SRX5020800.10_model.r WARNING @ Tue, 16 Jun 2020 09:28:09: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:28:09: #2 You may need to consider one of the other alternative d(s): 4,51 WARNING @ Tue, 16 Jun 2020 09:28:09: #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 09:28:09: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:28:09: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:28:11: 3000000 INFO @ Tue, 16 Jun 2020 09:28:17: 4000000 INFO @ Tue, 16 Jun 2020 09:28:23: 5000000 INFO @ Tue, 16 Jun 2020 09:28:24: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:28:28: 6000000 INFO @ Tue, 16 Jun 2020 09:28:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020800/SRX5020800.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:28:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020800/SRX5020800.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:28:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020800/SRX5020800.10_summits.bed INFO @ Tue, 16 Jun 2020 09:28:31: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (374 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:28:34: 7000000 INFO @ Tue, 16 Jun 2020 09:28:37: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:28:37: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:28:37: #1 total tags in treatment: 7524182 INFO @ Tue, 16 Jun 2020 09:28:37: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:28:37: #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 09:28:37: #1 tags after filtering in treatment: 7524182 INFO @ Tue, 16 Jun 2020 09:28:37: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:28:37: #1 finished! INFO @ Tue, 16 Jun 2020 09:28:37: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:28:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:28:38: #2 number of paired peaks: 397 WARNING @ Tue, 16 Jun 2020 09:28:38: Fewer paired peaks (397) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 397 pairs to build model! INFO @ Tue, 16 Jun 2020 09:28:38: start model_add_line... INFO @ Tue, 16 Jun 2020 09:28:38: start X-correlation... INFO @ Tue, 16 Jun 2020 09:28:38: end of X-cor INFO @ Tue, 16 Jun 2020 09:28:38: #2 finished! INFO @ Tue, 16 Jun 2020 09:28:38: #2 predicted fragment length is 51 bps INFO @ Tue, 16 Jun 2020 09:28:38: #2 alternative fragment length(s) may be 4,51 bps INFO @ Tue, 16 Jun 2020 09:28:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020800/SRX5020800.20_model.r WARNING @ Tue, 16 Jun 2020 09:28:38: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:28:38: #2 You may need to consider one of the other alternative d(s): 4,51 WARNING @ Tue, 16 Jun 2020 09:28:38: #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 09:28:38: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:28:38: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:28:53: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:29:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020800/SRX5020800.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:29:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020800/SRX5020800.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:29:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020800/SRX5020800.20_summits.bed INFO @ Tue, 16 Jun 2020 09:29:00: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (154 records, 4 fields): 1 millis CompletedMACS2peakCalling