Job ID = 6368905 SRX = SRX6720167 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:33:06 prefetch.2.10.7: 1) Downloading 'SRR9972863'... 2020-06-16T00:33:06 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:34:01 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:34:02 prefetch.2.10.7: 'SRR9972863' is valid 2020-06-16T00:34:02 prefetch.2.10.7: 1) 'SRR9972863' was downloaded successfully 2020-06-16T00:34:02 prefetch.2.10.7: 'SRR9972863' has 0 unresolved dependencies Read 10512400 spots for SRR9972863/SRR9972863.sra Written 10512400 spots for SRR9972863/SRR9972863.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: 00:01:55 10512400 reads; of these: 10512400 (100.00%) were unpaired; of these: 2735474 (26.02%) aligned 0 times 6561559 (62.42%) aligned exactly 1 time 1215367 (11.56%) aligned >1 times 73.98% overall alignment rate Time searching: 00:01:55 Overall time: 00:01:55 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] 2688887 / 7776926 = 0.3458 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 09:39:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX6720167/SRX6720167.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX6720167/SRX6720167.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX6720167/SRX6720167.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX6720167/SRX6720167.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 09:39:45: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:39:45: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:39:50: 1000000 INFO @ Tue, 16 Jun 2020 09:39:55: 2000000 INFO @ Tue, 16 Jun 2020 09:40:01: 3000000 INFO @ Tue, 16 Jun 2020 09:40:06: 4000000 INFO @ Tue, 16 Jun 2020 09:40:11: 5000000 INFO @ Tue, 16 Jun 2020 09:40:11: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:40:11: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:40:11: #1 total tags in treatment: 5088039 INFO @ Tue, 16 Jun 2020 09:40:11: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:40:11: #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 09:40:11: #1 tags after filtering in treatment: 5088039 INFO @ Tue, 16 Jun 2020 09:40:11: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:40:11: #1 finished! INFO @ Tue, 16 Jun 2020 09:40:11: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:40:11: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:40:12: #2 number of paired peaks: 435 WARNING @ Tue, 16 Jun 2020 09:40:12: Fewer paired peaks (435) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 435 pairs to build model! INFO @ Tue, 16 Jun 2020 09:40:12: start model_add_line... INFO @ Tue, 16 Jun 2020 09:40:12: start X-correlation... INFO @ Tue, 16 Jun 2020 09:40:12: end of X-cor INFO @ Tue, 16 Jun 2020 09:40:12: #2 finished! INFO @ Tue, 16 Jun 2020 09:40:12: #2 predicted fragment length is 51 bps INFO @ Tue, 16 Jun 2020 09:40:12: #2 alternative fragment length(s) may be 4,51 bps INFO @ Tue, 16 Jun 2020 09:40:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX6720167/SRX6720167.05_model.r WARNING @ Tue, 16 Jun 2020 09:40:12: #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 09:40:12: #2 You may need to consider one of the other alternative d(s): 4,51 WARNING @ Tue, 16 Jun 2020 09:40:12: #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 09:40:12: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:40:12: #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 @ Tue, 16 Jun 2020 09:40:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX6720167/SRX6720167.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX6720167/SRX6720167.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX6720167/SRX6720167.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX6720167/SRX6720167.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 09:40:15: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:40:15: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:40:20: 1000000 INFO @ Tue, 16 Jun 2020 09:40:21: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:40:25: 2000000 INFO @ Tue, 16 Jun 2020 09:40:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX6720167/SRX6720167.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:40:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX6720167/SRX6720167.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:40:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX6720167/SRX6720167.05_summits.bed INFO @ Tue, 16 Jun 2020 09:40:26: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (631 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:40:31: 3000000 INFO @ Tue, 16 Jun 2020 09:40:36: 4000000 INFO @ Tue, 16 Jun 2020 09:40:41: 5000000 INFO @ Tue, 16 Jun 2020 09:40:41: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:40:41: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:40:41: #1 total tags in treatment: 5088039 INFO @ Tue, 16 Jun 2020 09:40:41: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:40:41: #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 09:40:41: #1 tags after filtering in treatment: 5088039 INFO @ Tue, 16 Jun 2020 09:40:41: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:40:41: #1 finished! INFO @ Tue, 16 Jun 2020 09:40:41: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:40:41: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:40:42: #2 number of paired peaks: 435 WARNING @ Tue, 16 Jun 2020 09:40:42: Fewer paired peaks (435) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 435 pairs to build model! INFO @ Tue, 16 Jun 2020 09:40:42: start model_add_line... INFO @ Tue, 16 Jun 2020 09:40:42: start X-correlation... INFO @ Tue, 16 Jun 2020 09:40:42: end of X-cor INFO @ Tue, 16 Jun 2020 09:40:42: #2 finished! INFO @ Tue, 16 Jun 2020 09:40:42: #2 predicted fragment length is 51 bps INFO @ Tue, 16 Jun 2020 09:40:42: #2 alternative fragment length(s) may be 4,51 bps INFO @ Tue, 16 Jun 2020 09:40:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX6720167/SRX6720167.10_model.r WARNING @ Tue, 16 Jun 2020 09:40:42: #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 09:40:42: #2 You may need to consider one of the other alternative d(s): 4,51 WARNING @ Tue, 16 Jun 2020 09:40:42: #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 09:40:42: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:40:42: #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 @ Tue, 16 Jun 2020 09:40:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX6720167/SRX6720167.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX6720167/SRX6720167.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX6720167/SRX6720167.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX6720167/SRX6720167.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 09:40:45: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:40:45: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:40:50: 1000000 INFO @ Tue, 16 Jun 2020 09:40:52: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:40:55: 2000000 INFO @ Tue, 16 Jun 2020 09:40:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX6720167/SRX6720167.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:40:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX6720167/SRX6720167.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:40:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX6720167/SRX6720167.10_summits.bed INFO @ Tue, 16 Jun 2020 09:40:57: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (406 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:41:01: 3000000 INFO @ Tue, 16 Jun 2020 09:41:06: 4000000 INFO @ Tue, 16 Jun 2020 09:41:11: 5000000 INFO @ Tue, 16 Jun 2020 09:41:11: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:41:11: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:41:11: #1 total tags in treatment: 5088039 INFO @ Tue, 16 Jun 2020 09:41:11: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:41:11: #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 09:41:11: #1 tags after filtering in treatment: 5088039 INFO @ Tue, 16 Jun 2020 09:41:11: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:41:11: #1 finished! INFO @ Tue, 16 Jun 2020 09:41:11: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:41:11: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:41:12: #2 number of paired peaks: 435 WARNING @ Tue, 16 Jun 2020 09:41:12: Fewer paired peaks (435) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 435 pairs to build model! INFO @ Tue, 16 Jun 2020 09:41:12: start model_add_line... INFO @ Tue, 16 Jun 2020 09:41:12: start X-correlation... INFO @ Tue, 16 Jun 2020 09:41:12: end of X-cor INFO @ Tue, 16 Jun 2020 09:41:12: #2 finished! INFO @ Tue, 16 Jun 2020 09:41:12: #2 predicted fragment length is 51 bps INFO @ Tue, 16 Jun 2020 09:41:12: #2 alternative fragment length(s) may be 4,51 bps INFO @ Tue, 16 Jun 2020 09:41:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX6720167/SRX6720167.20_model.r WARNING @ Tue, 16 Jun 2020 09:41:12: #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 09:41:12: #2 You may need to consider one of the other alternative d(s): 4,51 WARNING @ Tue, 16 Jun 2020 09:41:12: #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 09:41:12: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:41:12: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:41:22: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:41:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX6720167/SRX6720167.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:41:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX6720167/SRX6720167.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:41:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX6720167/SRX6720167.20_summits.bed INFO @ Tue, 16 Jun 2020 09:41:27: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (151 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。