Job ID = 6367095 SRX = SRX277052 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:22:01 prefetch.2.10.7: 1) Downloading 'SRR849728'... 2020-06-15T23:22:01 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:22:32 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:22:32 prefetch.2.10.7: 'SRR849728' is valid 2020-06-15T23:22:32 prefetch.2.10.7: 1) 'SRR849728' was downloaded successfully Read 6797154 spots for SRR849728/SRR849728.sra Written 6797154 spots for SRR849728/SRR849728.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: 00:00:45 6797154 reads; of these: 6797154 (100.00%) were unpaired; of these: 4355219 (64.07%) aligned 0 times 1970335 (28.99%) aligned exactly 1 time 471600 (6.94%) aligned >1 times 35.93% overall alignment rate Time searching: 00:00:45 Overall time: 00:00:45 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] 143396 / 2441935 = 0.0587 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 08:24:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX277052/SRX277052.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX277052/SRX277052.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX277052/SRX277052.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX277052/SRX277052.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 08:24:35: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:24:35: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:24:42: 1000000 INFO @ Tue, 16 Jun 2020 08:24:48: 2000000 INFO @ Tue, 16 Jun 2020 08:24:49: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:24:49: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:24:49: #1 total tags in treatment: 2298539 INFO @ Tue, 16 Jun 2020 08:24:49: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:24:49: #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 08:24:49: #1 tags after filtering in treatment: 2298539 INFO @ Tue, 16 Jun 2020 08:24:49: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:24:49: #1 finished! INFO @ Tue, 16 Jun 2020 08:24:49: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:24:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:24:50: #2 number of paired peaks: 486 WARNING @ Tue, 16 Jun 2020 08:24:50: Fewer paired peaks (486) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 486 pairs to build model! INFO @ Tue, 16 Jun 2020 08:24:50: start model_add_line... INFO @ Tue, 16 Jun 2020 08:24:50: start X-correlation... INFO @ Tue, 16 Jun 2020 08:24:50: end of X-cor INFO @ Tue, 16 Jun 2020 08:24:50: #2 finished! INFO @ Tue, 16 Jun 2020 08:24:50: #2 predicted fragment length is 35 bps INFO @ Tue, 16 Jun 2020 08:24:50: #2 alternative fragment length(s) may be 4,35,526,595 bps INFO @ Tue, 16 Jun 2020 08:24:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX277052/SRX277052.05_model.r WARNING @ Tue, 16 Jun 2020 08:24:50: #2 Since the d (35) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:24:50: #2 You may need to consider one of the other alternative d(s): 4,35,526,595 WARNING @ Tue, 16 Jun 2020 08:24:50: #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 08:24:50: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:24:50: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:24:55: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:24:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX277052/SRX277052.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:24:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX277052/SRX277052.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:24:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX277052/SRX277052.05_summits.bed INFO @ Tue, 16 Jun 2020 08:24:57: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (562 records, 4 fields): 1 millis CompletedMACS2peakCalling 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 08:25:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX277052/SRX277052.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX277052/SRX277052.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX277052/SRX277052.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX277052/SRX277052.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 08:25:05: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:25:05: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:25:11: 1000000 INFO @ Tue, 16 Jun 2020 08:25:17: 2000000 INFO @ Tue, 16 Jun 2020 08:25:19: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:25:19: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:25:19: #1 total tags in treatment: 2298539 INFO @ Tue, 16 Jun 2020 08:25:19: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:25:19: #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 08:25:19: #1 tags after filtering in treatment: 2298539 INFO @ Tue, 16 Jun 2020 08:25:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:25:19: #1 finished! INFO @ Tue, 16 Jun 2020 08:25:19: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:25:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:25:19: #2 number of paired peaks: 486 WARNING @ Tue, 16 Jun 2020 08:25:19: Fewer paired peaks (486) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 486 pairs to build model! INFO @ Tue, 16 Jun 2020 08:25:19: start model_add_line... INFO @ Tue, 16 Jun 2020 08:25:19: start X-correlation... INFO @ Tue, 16 Jun 2020 08:25:19: end of X-cor INFO @ Tue, 16 Jun 2020 08:25:19: #2 finished! INFO @ Tue, 16 Jun 2020 08:25:19: #2 predicted fragment length is 35 bps INFO @ Tue, 16 Jun 2020 08:25:19: #2 alternative fragment length(s) may be 4,35,526,595 bps INFO @ Tue, 16 Jun 2020 08:25:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX277052/SRX277052.10_model.r WARNING @ Tue, 16 Jun 2020 08:25:19: #2 Since the d (35) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:25:19: #2 You may need to consider one of the other alternative d(s): 4,35,526,595 WARNING @ Tue, 16 Jun 2020 08:25:19: #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 08:25:19: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:25:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:25:24: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:25:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX277052/SRX277052.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:25:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX277052/SRX277052.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:25:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX277052/SRX277052.10_summits.bed INFO @ Tue, 16 Jun 2020 08:25:27: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (256 records, 4 fields): 1 millis CompletedMACS2peakCalling 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 08:25:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX277052/SRX277052.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX277052/SRX277052.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX277052/SRX277052.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX277052/SRX277052.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 08:25:35: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:25:35: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:25:41: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:25:47: 2000000 INFO @ Tue, 16 Jun 2020 08:25:48: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:25:48: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:25:48: #1 total tags in treatment: 2298539 INFO @ Tue, 16 Jun 2020 08:25:48: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:25:48: #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 08:25:49: #1 tags after filtering in treatment: 2298539 INFO @ Tue, 16 Jun 2020 08:25:49: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:25:49: #1 finished! INFO @ Tue, 16 Jun 2020 08:25:49: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:25:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:25:49: #2 number of paired peaks: 486 WARNING @ Tue, 16 Jun 2020 08:25:49: Fewer paired peaks (486) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 486 pairs to build model! INFO @ Tue, 16 Jun 2020 08:25:49: start model_add_line... INFO @ Tue, 16 Jun 2020 08:25:49: start X-correlation... INFO @ Tue, 16 Jun 2020 08:25:49: end of X-cor INFO @ Tue, 16 Jun 2020 08:25:49: #2 finished! INFO @ Tue, 16 Jun 2020 08:25:49: #2 predicted fragment length is 35 bps INFO @ Tue, 16 Jun 2020 08:25:49: #2 alternative fragment length(s) may be 4,35,526,595 bps INFO @ Tue, 16 Jun 2020 08:25:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX277052/SRX277052.20_model.r WARNING @ Tue, 16 Jun 2020 08:25:49: #2 Since the d (35) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:25:49: #2 You may need to consider one of the other alternative d(s): 4,35,526,595 WARNING @ Tue, 16 Jun 2020 08:25:49: #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 08:25:49: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:25:49: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:25:54: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:25:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX277052/SRX277052.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:25:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX277052/SRX277052.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:25:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX277052/SRX277052.20_summits.bed INFO @ Tue, 16 Jun 2020 08:25:56: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (79 records, 4 fields): 1 millis CompletedMACS2peakCalling