Job ID = 6368550 SRX = SRX5020777 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:29:57 prefetch.2.10.7: 1) Downloading 'SRR8201400'... 2020-06-16T00:29:57 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:31:30 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:31:31 prefetch.2.10.7: 'SRR8201400' is valid 2020-06-16T00:31:31 prefetch.2.10.7: 1) 'SRR8201400' was downloaded successfully 2020-06-16T00:31:31 prefetch.2.10.7: 'SRR8201400' has 0 unresolved dependencies Read 14229397 spots for SRR8201400/SRR8201400.sra Written 14229397 spots for SRR8201400/SRR8201400.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: 00:02:10 14229397 reads; of these: 14229397 (100.00%) were unpaired; of these: 7305265 (51.34%) aligned 0 times 5717886 (40.18%) aligned exactly 1 time 1206246 (8.48%) aligned >1 times 48.66% overall alignment rate Time searching: 00:02:10 Overall time: 00:02:10 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] 1969970 / 6924132 = 0.2845 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 09:36:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020777/SRX5020777.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020777/SRX5020777.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020777/SRX5020777.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020777/SRX5020777.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 09:36:33: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:36:33: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:36:39: 1000000 INFO @ Tue, 16 Jun 2020 09:36:44: 2000000 INFO @ Tue, 16 Jun 2020 09:36:50: 3000000 INFO @ Tue, 16 Jun 2020 09:36:55: 4000000 INFO @ Tue, 16 Jun 2020 09:37:01: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:37:01: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:37:01: #1 total tags in treatment: 4954162 INFO @ Tue, 16 Jun 2020 09:37:01: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:37:01: #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 09:37:01: #1 tags after filtering in treatment: 4954162 INFO @ Tue, 16 Jun 2020 09:37:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:37:01: #1 finished! INFO @ Tue, 16 Jun 2020 09:37:01: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:37:01: #2 looking for paired plus/minus strand peaks... 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 09:37:01: #2 number of paired peaks: 525 WARNING @ Tue, 16 Jun 2020 09:37:01: Fewer paired peaks (525) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 525 pairs to build model! INFO @ Tue, 16 Jun 2020 09:37:01: start model_add_line... INFO @ Tue, 16 Jun 2020 09:37:01: start X-correlation... INFO @ Tue, 16 Jun 2020 09:37:01: end of X-cor INFO @ Tue, 16 Jun 2020 09:37:01: #2 finished! INFO @ Tue, 16 Jun 2020 09:37:01: #2 predicted fragment length is 129 bps INFO @ Tue, 16 Jun 2020 09:37:01: #2 alternative fragment length(s) may be 129 bps INFO @ Tue, 16 Jun 2020 09:37:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020777/SRX5020777.05_model.r INFO @ Tue, 16 Jun 2020 09:37:01: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:37:01: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:37:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020777/SRX5020777.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020777/SRX5020777.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020777/SRX5020777.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020777/SRX5020777.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 09:37:03: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:37:03: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:37:10: 1000000 INFO @ Tue, 16 Jun 2020 09:37:12: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:37:17: 2000000 INFO @ Tue, 16 Jun 2020 09:37:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020777/SRX5020777.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:37:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020777/SRX5020777.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:37:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020777/SRX5020777.05_summits.bed INFO @ Tue, 16 Jun 2020 09:37:18: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1502 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:37:24: 3000000 INFO @ Tue, 16 Jun 2020 09:37:31: 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 09:37:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020777/SRX5020777.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020777/SRX5020777.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020777/SRX5020777.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020777/SRX5020777.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 09:37:33: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:37:33: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:37:38: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:37:38: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:37:38: #1 total tags in treatment: 4954162 INFO @ Tue, 16 Jun 2020 09:37:38: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:37:38: #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 09:37:38: #1 tags after filtering in treatment: 4954162 INFO @ Tue, 16 Jun 2020 09:37:38: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:37:38: #1 finished! INFO @ Tue, 16 Jun 2020 09:37:38: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:37:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:37:38: #2 number of paired peaks: 525 WARNING @ Tue, 16 Jun 2020 09:37:38: Fewer paired peaks (525) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 525 pairs to build model! INFO @ Tue, 16 Jun 2020 09:37:38: start model_add_line... INFO @ Tue, 16 Jun 2020 09:37:38: start X-correlation... INFO @ Tue, 16 Jun 2020 09:37:38: end of X-cor INFO @ Tue, 16 Jun 2020 09:37:38: #2 finished! INFO @ Tue, 16 Jun 2020 09:37:38: #2 predicted fragment length is 129 bps INFO @ Tue, 16 Jun 2020 09:37:38: #2 alternative fragment length(s) may be 129 bps INFO @ Tue, 16 Jun 2020 09:37:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020777/SRX5020777.10_model.r INFO @ Tue, 16 Jun 2020 09:37:38: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:37:38: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:37:40: 1000000 INFO @ Tue, 16 Jun 2020 09:37:46: 2000000 INFO @ Tue, 16 Jun 2020 09:37:49: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:37:52: 3000000 INFO @ Tue, 16 Jun 2020 09:37:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020777/SRX5020777.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:37:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020777/SRX5020777.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:37:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020777/SRX5020777.10_summits.bed INFO @ Tue, 16 Jun 2020 09:37:55: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (871 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:37:58: 4000000 INFO @ Tue, 16 Jun 2020 09:38:04: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:38:04: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:38:04: #1 total tags in treatment: 4954162 INFO @ Tue, 16 Jun 2020 09:38:04: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:38:04: #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 09:38:04: #1 tags after filtering in treatment: 4954162 INFO @ Tue, 16 Jun 2020 09:38:04: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:38:04: #1 finished! INFO @ Tue, 16 Jun 2020 09:38:04: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:38:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:38:04: #2 number of paired peaks: 525 WARNING @ Tue, 16 Jun 2020 09:38:04: Fewer paired peaks (525) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 525 pairs to build model! INFO @ Tue, 16 Jun 2020 09:38:04: start model_add_line... INFO @ Tue, 16 Jun 2020 09:38:04: start X-correlation... INFO @ Tue, 16 Jun 2020 09:38:04: end of X-cor INFO @ Tue, 16 Jun 2020 09:38:04: #2 finished! INFO @ Tue, 16 Jun 2020 09:38:04: #2 predicted fragment length is 129 bps INFO @ Tue, 16 Jun 2020 09:38:04: #2 alternative fragment length(s) may be 129 bps INFO @ Tue, 16 Jun 2020 09:38:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020777/SRX5020777.20_model.r INFO @ Tue, 16 Jun 2020 09:38:04: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:38:04: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:38:16: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:38:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020777/SRX5020777.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:38:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020777/SRX5020777.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:38:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020777/SRX5020777.20_summits.bed INFO @ Tue, 16 Jun 2020 09:38:22: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (406 records, 4 fields): 1 millis CompletedMACS2peakCalling