Job ID = 6368556 SRX = SRX5020783 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:27:01 prefetch.2.10.7: 1) Downloading 'SRR8201406'... 2020-06-16T00:27:01 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:28:43 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:28:44 prefetch.2.10.7: 'SRR8201406' is valid 2020-06-16T00:28:44 prefetch.2.10.7: 1) 'SRR8201406' was downloaded successfully Read 6972757 spots for SRR8201406/SRR8201406.sra Written 6972757 spots for SRR8201406/SRR8201406.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: 00:01:28 6972757 reads; of these: 6972757 (100.00%) were unpaired; of these: 1541722 (22.11%) aligned 0 times 4455060 (63.89%) aligned exactly 1 time 975975 (14.00%) aligned >1 times 77.89% overall alignment rate Time searching: 00:01:28 Overall time: 00:01:28 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] 501673 / 5431035 = 0.0924 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 09:32:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020783/SRX5020783.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020783/SRX5020783.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020783/SRX5020783.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020783/SRX5020783.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 09:32:31: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:32:31: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:32:37: 1000000 INFO @ Tue, 16 Jun 2020 09:32:42: 2000000 INFO @ Tue, 16 Jun 2020 09:32:48: 3000000 INFO @ Tue, 16 Jun 2020 09:32:54: 4000000 INFO @ Tue, 16 Jun 2020 09:32:59: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:32:59: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:32:59: #1 total tags in treatment: 4929362 INFO @ Tue, 16 Jun 2020 09:32:59: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:32:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) 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 09:32:59: #1 tags after filtering in treatment: 4929362 INFO @ Tue, 16 Jun 2020 09:32:59: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:32:59: #1 finished! INFO @ Tue, 16 Jun 2020 09:32:59: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:32:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:33:00: #2 number of paired peaks: 521 WARNING @ Tue, 16 Jun 2020 09:33:00: Fewer paired peaks (521) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 521 pairs to build model! INFO @ Tue, 16 Jun 2020 09:33:00: start model_add_line... INFO @ Tue, 16 Jun 2020 09:33:00: start X-correlation... INFO @ Tue, 16 Jun 2020 09:33:00: end of X-cor INFO @ Tue, 16 Jun 2020 09:33:00: #2 finished! INFO @ Tue, 16 Jun 2020 09:33:00: #2 predicted fragment length is 63 bps INFO @ Tue, 16 Jun 2020 09:33:00: #2 alternative fragment length(s) may be 63 bps INFO @ Tue, 16 Jun 2020 09:33:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020783/SRX5020783.05_model.r WARNING @ Tue, 16 Jun 2020 09:33:00: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:33:00: #2 You may need to consider one of the other alternative d(s): 63 WARNING @ Tue, 16 Jun 2020 09:33:00: #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 09:33:00: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:33:00: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:33:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020783/SRX5020783.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020783/SRX5020783.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020783/SRX5020783.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020783/SRX5020783.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 09:33:01: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:33:01: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:33:07: 1000000 INFO @ Tue, 16 Jun 2020 09:33:11: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:33:13: 2000000 INFO @ Tue, 16 Jun 2020 09:33:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020783/SRX5020783.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:33:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020783/SRX5020783.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:33:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020783/SRX5020783.05_summits.bed INFO @ Tue, 16 Jun 2020 09:33:17: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (970 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:33:18: 3000000 INFO @ Tue, 16 Jun 2020 09:33:24: 4000000 INFO @ Tue, 16 Jun 2020 09:33:29: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:33:29: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:33:29: #1 total tags in treatment: 4929362 INFO @ Tue, 16 Jun 2020 09:33:29: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:33:29: #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 09:33:29: #1 tags after filtering in treatment: 4929362 INFO @ Tue, 16 Jun 2020 09:33:29: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:33:29: #1 finished! INFO @ Tue, 16 Jun 2020 09:33:29: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:33:29: #2 looking for paired plus/minus strand peaks... 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 09:33:29: #2 number of paired peaks: 521 WARNING @ Tue, 16 Jun 2020 09:33:29: Fewer paired peaks (521) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 521 pairs to build model! INFO @ Tue, 16 Jun 2020 09:33:29: start model_add_line... INFO @ Tue, 16 Jun 2020 09:33:30: start X-correlation... INFO @ Tue, 16 Jun 2020 09:33:30: end of X-cor INFO @ Tue, 16 Jun 2020 09:33:30: #2 finished! INFO @ Tue, 16 Jun 2020 09:33:30: #2 predicted fragment length is 63 bps INFO @ Tue, 16 Jun 2020 09:33:30: #2 alternative fragment length(s) may be 63 bps INFO @ Tue, 16 Jun 2020 09:33:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020783/SRX5020783.10_model.r WARNING @ Tue, 16 Jun 2020 09:33:30: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:33:30: #2 You may need to consider one of the other alternative d(s): 63 WARNING @ Tue, 16 Jun 2020 09:33:30: #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 09:33:30: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:33:30: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:33:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020783/SRX5020783.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020783/SRX5020783.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020783/SRX5020783.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020783/SRX5020783.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 09:33:31: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:33:31: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:33:37: 1000000 INFO @ Tue, 16 Jun 2020 09:33:40: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:33:42: 2000000 INFO @ Tue, 16 Jun 2020 09:33:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020783/SRX5020783.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:33:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020783/SRX5020783.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:33:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020783/SRX5020783.10_summits.bed INFO @ Tue, 16 Jun 2020 09:33:46: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (463 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:33:48: 3000000 INFO @ Tue, 16 Jun 2020 09:33:53: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:33:59: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:33:59: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:33:59: #1 total tags in treatment: 4929362 INFO @ Tue, 16 Jun 2020 09:33:59: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:33:59: #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 09:33:59: #1 tags after filtering in treatment: 4929362 INFO @ Tue, 16 Jun 2020 09:33:59: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:33:59: #1 finished! INFO @ Tue, 16 Jun 2020 09:33:59: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:33:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:33:59: #2 number of paired peaks: 521 WARNING @ Tue, 16 Jun 2020 09:33:59: Fewer paired peaks (521) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 521 pairs to build model! INFO @ Tue, 16 Jun 2020 09:33:59: start model_add_line... INFO @ Tue, 16 Jun 2020 09:33:59: start X-correlation... INFO @ Tue, 16 Jun 2020 09:33:59: end of X-cor INFO @ Tue, 16 Jun 2020 09:33:59: #2 finished! INFO @ Tue, 16 Jun 2020 09:33:59: #2 predicted fragment length is 63 bps INFO @ Tue, 16 Jun 2020 09:33:59: #2 alternative fragment length(s) may be 63 bps INFO @ Tue, 16 Jun 2020 09:33:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020783/SRX5020783.20_model.r WARNING @ Tue, 16 Jun 2020 09:33:59: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:33:59: #2 You may need to consider one of the other alternative d(s): 63 WARNING @ Tue, 16 Jun 2020 09:33:59: #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 09:33:59: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:33:59: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:34:11: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:34:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020783/SRX5020783.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:34:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020783/SRX5020783.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:34:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020783/SRX5020783.20_summits.bed INFO @ Tue, 16 Jun 2020 09:34:16: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (184 records, 4 fields): 1 millis CompletedMACS2peakCalling