Job ID = 6367990 SRX = SRX463082 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:04:00 prefetch.2.10.7: 1) Downloading 'SRR1159144'... 2020-06-16T00:04:00 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:05:05 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:05:05 prefetch.2.10.7: 'SRR1159144' is valid 2020-06-16T00:05:05 prefetch.2.10.7: 1) 'SRR1159144' was downloaded successfully Read 8602844 spots for SRR1159144/SRR1159144.sra Written 8602844 spots for SRR1159144/SRR1159144.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:01:19 8602844 reads; of these: 8602844 (100.00%) were unpaired; of these: 241696 (2.81%) aligned 0 times 7184890 (83.52%) aligned exactly 1 time 1176258 (13.67%) aligned >1 times 97.19% overall alignment rate Time searching: 00:01:20 Overall time: 00:01:20 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] 608201 / 8361148 = 0.0727 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 09:09:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX463082/SRX463082.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX463082/SRX463082.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX463082/SRX463082.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX463082/SRX463082.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 09:09:03: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:09:03: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:09:08: 1000000 INFO @ Tue, 16 Jun 2020 09:09:14: 2000000 INFO @ Tue, 16 Jun 2020 09:09:19: 3000000 INFO @ Tue, 16 Jun 2020 09:09:25: 4000000 INFO @ Tue, 16 Jun 2020 09:09:31: 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 09:09:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX463082/SRX463082.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX463082/SRX463082.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX463082/SRX463082.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX463082/SRX463082.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 09:09:33: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:09:33: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:09:36: 6000000 INFO @ Tue, 16 Jun 2020 09:09:38: 1000000 INFO @ Tue, 16 Jun 2020 09:09:42: 7000000 INFO @ Tue, 16 Jun 2020 09:09:44: 2000000 INFO @ Tue, 16 Jun 2020 09:09:47: #1 tag size is determined as 35 bps INFO @ Tue, 16 Jun 2020 09:09:47: #1 tag size = 35 INFO @ Tue, 16 Jun 2020 09:09:47: #1 total tags in treatment: 7752947 INFO @ Tue, 16 Jun 2020 09:09:47: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:09:47: #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 09:09:47: #1 tags after filtering in treatment: 7752947 INFO @ Tue, 16 Jun 2020 09:09:47: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:09:47: #1 finished! INFO @ Tue, 16 Jun 2020 09:09:47: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:09:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:09:47: #2 number of paired peaks: 291 WARNING @ Tue, 16 Jun 2020 09:09:47: Fewer paired peaks (291) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 291 pairs to build model! INFO @ Tue, 16 Jun 2020 09:09:47: start model_add_line... INFO @ Tue, 16 Jun 2020 09:09:47: start X-correlation... INFO @ Tue, 16 Jun 2020 09:09:48: end of X-cor INFO @ Tue, 16 Jun 2020 09:09:48: #2 finished! INFO @ Tue, 16 Jun 2020 09:09:48: #2 predicted fragment length is 110 bps INFO @ Tue, 16 Jun 2020 09:09:48: #2 alternative fragment length(s) may be 4,81,84,101,110 bps INFO @ Tue, 16 Jun 2020 09:09:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX463082/SRX463082.05_model.r INFO @ Tue, 16 Jun 2020 09:09:48: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:09:48: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:09:49: 3000000 INFO @ Tue, 16 Jun 2020 09:09:54: 4000000 INFO @ Tue, 16 Jun 2020 09:09:59: 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 09:10:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX463082/SRX463082.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX463082/SRX463082.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX463082/SRX463082.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX463082/SRX463082.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 09:10:03: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:10:03: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:10:03: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:10:05: 6000000 INFO @ Tue, 16 Jun 2020 09:10:09: 1000000 INFO @ Tue, 16 Jun 2020 09:10:10: 7000000 INFO @ Tue, 16 Jun 2020 09:10:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX463082/SRX463082.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:10:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX463082/SRX463082.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:10:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX463082/SRX463082.05_summits.bed INFO @ Tue, 16 Jun 2020 09:10:12: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3984 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:10:14: #1 tag size is determined as 35 bps INFO @ Tue, 16 Jun 2020 09:10:14: #1 tag size = 35 INFO @ Tue, 16 Jun 2020 09:10:14: #1 total tags in treatment: 7752947 INFO @ Tue, 16 Jun 2020 09:10:14: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:10:14: #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 09:10:14: #1 tags after filtering in treatment: 7752947 INFO @ Tue, 16 Jun 2020 09:10:14: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:10:14: #1 finished! INFO @ Tue, 16 Jun 2020 09:10:14: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:10:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:10:15: 2000000 INFO @ Tue, 16 Jun 2020 09:10:15: #2 number of paired peaks: 291 WARNING @ Tue, 16 Jun 2020 09:10:15: Fewer paired peaks (291) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 291 pairs to build model! INFO @ Tue, 16 Jun 2020 09:10:15: start model_add_line... INFO @ Tue, 16 Jun 2020 09:10:15: start X-correlation... INFO @ Tue, 16 Jun 2020 09:10:15: end of X-cor INFO @ Tue, 16 Jun 2020 09:10:15: #2 finished! INFO @ Tue, 16 Jun 2020 09:10:15: #2 predicted fragment length is 110 bps INFO @ Tue, 16 Jun 2020 09:10:15: #2 alternative fragment length(s) may be 4,81,84,101,110 bps INFO @ Tue, 16 Jun 2020 09:10:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX463082/SRX463082.10_model.r INFO @ Tue, 16 Jun 2020 09:10:15: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:10:15: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:10:20: 3000000 INFO @ Tue, 16 Jun 2020 09:10:26: 4000000 INFO @ Tue, 16 Jun 2020 09:10:30: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:10:32: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:10:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX463082/SRX463082.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:10:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX463082/SRX463082.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:10:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX463082/SRX463082.10_summits.bed INFO @ Tue, 16 Jun 2020 09:10:38: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1468 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:10:38: 6000000 INFO @ Tue, 16 Jun 2020 09:10:44: 7000000 INFO @ Tue, 16 Jun 2020 09:10:48: #1 tag size is determined as 35 bps INFO @ Tue, 16 Jun 2020 09:10:48: #1 tag size = 35 INFO @ Tue, 16 Jun 2020 09:10:48: #1 total tags in treatment: 7752947 INFO @ Tue, 16 Jun 2020 09:10:48: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:10:48: #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 09:10:48: #1 tags after filtering in treatment: 7752947 INFO @ Tue, 16 Jun 2020 09:10:48: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:10:48: #1 finished! INFO @ Tue, 16 Jun 2020 09:10:48: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:10:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:10:49: #2 number of paired peaks: 291 WARNING @ Tue, 16 Jun 2020 09:10:49: Fewer paired peaks (291) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 291 pairs to build model! INFO @ Tue, 16 Jun 2020 09:10:49: start model_add_line... INFO @ Tue, 16 Jun 2020 09:10:49: start X-correlation... INFO @ Tue, 16 Jun 2020 09:10:49: end of X-cor INFO @ Tue, 16 Jun 2020 09:10:49: #2 finished! INFO @ Tue, 16 Jun 2020 09:10:49: #2 predicted fragment length is 110 bps INFO @ Tue, 16 Jun 2020 09:10:49: #2 alternative fragment length(s) may be 4,81,84,101,110 bps INFO @ Tue, 16 Jun 2020 09:10:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX463082/SRX463082.20_model.r INFO @ Tue, 16 Jun 2020 09:10:49: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:10:49: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:11:04: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:11:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX463082/SRX463082.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:11:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX463082/SRX463082.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:11:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX463082/SRX463082.20_summits.bed INFO @ Tue, 16 Jun 2020 09:11:12: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (276 records, 4 fields): 1 millis CompletedMACS2peakCalling