Job ID = 6366091 SRX = SRX059269 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:13:27 prefetch.2.10.7: 1) Downloading 'SRR190709'... 2020-06-15T22:13:27 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:14:05 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:14:06 prefetch.2.10.7: 'SRR190709' is valid 2020-06-15T22:14:06 prefetch.2.10.7: 1) 'SRR190709' was downloaded successfully Read 8549506 spots for SRR190709/SRR190709.sra Written 8549506 spots for SRR190709/SRR190709.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: 00:00:53 8549506 reads; of these: 8549506 (100.00%) were unpaired; of these: 5018460 (58.70%) aligned 0 times 2868546 (33.55%) aligned exactly 1 time 662500 (7.75%) aligned >1 times 41.30% overall alignment rate Time searching: 00:00:53 Overall time: 00:00:53 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] 926900 / 3531046 = 0.2625 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 07:16:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX059269/SRX059269.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX059269/SRX059269.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX059269/SRX059269.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX059269/SRX059269.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 07:16:45: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:16:45: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:16:51: 1000000 INFO @ Tue, 16 Jun 2020 07:16:57: 2000000 INFO @ Tue, 16 Jun 2020 07:17:00: #1 tag size is determined as 28 bps INFO @ Tue, 16 Jun 2020 07:17:00: #1 tag size = 28 INFO @ Tue, 16 Jun 2020 07:17:00: #1 total tags in treatment: 2604146 INFO @ Tue, 16 Jun 2020 07:17:00: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:17:00: #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 07:17:00: #1 tags after filtering in treatment: 2604146 INFO @ Tue, 16 Jun 2020 07:17:00: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:17:00: #1 finished! INFO @ Tue, 16 Jun 2020 07:17:00: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:17:00: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:17:00: #2 number of paired peaks: 851 WARNING @ Tue, 16 Jun 2020 07:17:00: Fewer paired peaks (851) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 851 pairs to build model! INFO @ Tue, 16 Jun 2020 07:17:00: start model_add_line... INFO @ Tue, 16 Jun 2020 07:17:00: start X-correlation... INFO @ Tue, 16 Jun 2020 07:17:00: end of X-cor INFO @ Tue, 16 Jun 2020 07:17:00: #2 finished! INFO @ Tue, 16 Jun 2020 07:17:00: #2 predicted fragment length is 149 bps INFO @ Tue, 16 Jun 2020 07:17:00: #2 alternative fragment length(s) may be 149 bps INFO @ Tue, 16 Jun 2020 07:17:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX059269/SRX059269.05_model.r INFO @ Tue, 16 Jun 2020 07:17:00: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:17:00: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:17:06: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:17:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX059269/SRX059269.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:17:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX059269/SRX059269.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:17:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX059269/SRX059269.05_summits.bed INFO @ Tue, 16 Jun 2020 07:17:09: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1184 records, 4 fields): 3 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 07:17:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX059269/SRX059269.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX059269/SRX059269.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX059269/SRX059269.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX059269/SRX059269.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 07:17:15: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:17:15: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:17:21: 1000000 INFO @ Tue, 16 Jun 2020 07:17:26: 2000000 INFO @ Tue, 16 Jun 2020 07:17:29: #1 tag size is determined as 28 bps INFO @ Tue, 16 Jun 2020 07:17:29: #1 tag size = 28 INFO @ Tue, 16 Jun 2020 07:17:29: #1 total tags in treatment: 2604146 INFO @ Tue, 16 Jun 2020 07:17:29: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:17:29: #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 07:17:30: #1 tags after filtering in treatment: 2604146 INFO @ Tue, 16 Jun 2020 07:17:30: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:17:30: #1 finished! INFO @ Tue, 16 Jun 2020 07:17:30: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:17:30: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:17:30: #2 number of paired peaks: 851 WARNING @ Tue, 16 Jun 2020 07:17:30: Fewer paired peaks (851) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 851 pairs to build model! INFO @ Tue, 16 Jun 2020 07:17:30: start model_add_line... INFO @ Tue, 16 Jun 2020 07:17:30: start X-correlation... INFO @ Tue, 16 Jun 2020 07:17:30: end of X-cor INFO @ Tue, 16 Jun 2020 07:17:30: #2 finished! INFO @ Tue, 16 Jun 2020 07:17:30: #2 predicted fragment length is 149 bps INFO @ Tue, 16 Jun 2020 07:17:30: #2 alternative fragment length(s) may be 149 bps INFO @ Tue, 16 Jun 2020 07:17:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX059269/SRX059269.10_model.r INFO @ Tue, 16 Jun 2020 07:17:30: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:17:30: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:17:36: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:17:39: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX059269/SRX059269.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:17:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX059269/SRX059269.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:17:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX059269/SRX059269.10_summits.bed INFO @ Tue, 16 Jun 2020 07:17:39: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (759 records, 4 fields): 2 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 07:17:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX059269/SRX059269.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX059269/SRX059269.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX059269/SRX059269.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX059269/SRX059269.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 07:17:45: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:17:45: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:17:51: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:17:56: 2000000 INFO @ Tue, 16 Jun 2020 07:18:00: #1 tag size is determined as 28 bps INFO @ Tue, 16 Jun 2020 07:18:00: #1 tag size = 28 INFO @ Tue, 16 Jun 2020 07:18:00: #1 total tags in treatment: 2604146 INFO @ Tue, 16 Jun 2020 07:18:00: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:18:00: #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 07:18:00: #1 tags after filtering in treatment: 2604146 INFO @ Tue, 16 Jun 2020 07:18:00: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:18:00: #1 finished! INFO @ Tue, 16 Jun 2020 07:18:00: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:18:00: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:18:00: #2 number of paired peaks: 851 WARNING @ Tue, 16 Jun 2020 07:18:00: Fewer paired peaks (851) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 851 pairs to build model! INFO @ Tue, 16 Jun 2020 07:18:00: start model_add_line... INFO @ Tue, 16 Jun 2020 07:18:00: start X-correlation... INFO @ Tue, 16 Jun 2020 07:18:00: end of X-cor INFO @ Tue, 16 Jun 2020 07:18:00: #2 finished! INFO @ Tue, 16 Jun 2020 07:18:00: #2 predicted fragment length is 149 bps INFO @ Tue, 16 Jun 2020 07:18:00: #2 alternative fragment length(s) may be 149 bps INFO @ Tue, 16 Jun 2020 07:18:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX059269/SRX059269.20_model.r INFO @ Tue, 16 Jun 2020 07:18:00: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:18:00: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:18:06: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:18:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX059269/SRX059269.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:18:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX059269/SRX059269.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:18:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX059269/SRX059269.20_summits.bed INFO @ Tue, 16 Jun 2020 07:18:09: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (440 records, 4 fields): 1 millis CompletedMACS2peakCalling