Job ID = 6368413 SRX = SRX495092 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:25:17 prefetch.2.10.7: 1) Downloading 'SRR1198624'... 2020-06-16T00:25:17 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:27:16 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:27:17 prefetch.2.10.7: 'SRR1198624' is valid 2020-06-16T00:27:17 prefetch.2.10.7: 1) 'SRR1198624' was downloaded successfully Read 11245765 spots for SRR1198624/SRR1198624.sra Written 11245765 spots for SRR1198624/SRR1198624.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: 00:01:56 11245765 reads; of these: 11245765 (100.00%) were unpaired; of these: 1924710 (17.11%) aligned 0 times 7808886 (69.44%) aligned exactly 1 time 1512169 (13.45%) aligned >1 times 82.89% overall alignment rate Time searching: 00:01:57 Overall time: 00:01:57 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] 5625992 / 9321055 = 0.6036 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 09:31:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495092/SRX495092.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495092/SRX495092.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495092/SRX495092.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495092/SRX495092.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 09:31:51: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:31:51: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:31:56: 1000000 INFO @ Tue, 16 Jun 2020 09:32:01: 2000000 INFO @ Tue, 16 Jun 2020 09:32:06: 3000000 INFO @ Tue, 16 Jun 2020 09:32:10: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:32:10: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:32:10: #1 total tags in treatment: 3695063 INFO @ Tue, 16 Jun 2020 09:32:10: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:32:10: #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 09:32:10: #1 tags after filtering in treatment: 3695063 INFO @ Tue, 16 Jun 2020 09:32:10: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:32:10: #1 finished! INFO @ Tue, 16 Jun 2020 09:32:10: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:32:10: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:32:10: #2 number of paired peaks: 807 WARNING @ Tue, 16 Jun 2020 09:32:10: Fewer paired peaks (807) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 807 pairs to build model! INFO @ Tue, 16 Jun 2020 09:32:10: start model_add_line... INFO @ Tue, 16 Jun 2020 09:32:10: start X-correlation... INFO @ Tue, 16 Jun 2020 09:32:10: end of X-cor INFO @ Tue, 16 Jun 2020 09:32:10: #2 finished! INFO @ Tue, 16 Jun 2020 09:32:10: #2 predicted fragment length is 129 bps INFO @ Tue, 16 Jun 2020 09:32:10: #2 alternative fragment length(s) may be 129 bps INFO @ Tue, 16 Jun 2020 09:32:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495092/SRX495092.05_model.r INFO @ Tue, 16 Jun 2020 09:32:10: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:32:10: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:32:19: #3 Call peaks for each chromosome... 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 09:32:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495092/SRX495092.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495092/SRX495092.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495092/SRX495092.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495092/SRX495092.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 09:32:21: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:32:21: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:32:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495092/SRX495092.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:32:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495092/SRX495092.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:32:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495092/SRX495092.05_summits.bed INFO @ Tue, 16 Jun 2020 09:32:23: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1668 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:32:26: 1000000 INFO @ Tue, 16 Jun 2020 09:32:31: 2000000 INFO @ Tue, 16 Jun 2020 09:32:37: 3000000 INFO @ Tue, 16 Jun 2020 09:32:40: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:32:40: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:32:40: #1 total tags in treatment: 3695063 INFO @ Tue, 16 Jun 2020 09:32:40: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:32:40: #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 09:32:40: #1 tags after filtering in treatment: 3695063 INFO @ Tue, 16 Jun 2020 09:32:40: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:32:40: #1 finished! INFO @ Tue, 16 Jun 2020 09:32:40: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:32:40: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:32:40: #2 number of paired peaks: 807 WARNING @ Tue, 16 Jun 2020 09:32:40: Fewer paired peaks (807) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 807 pairs to build model! INFO @ Tue, 16 Jun 2020 09:32:40: start model_add_line... INFO @ Tue, 16 Jun 2020 09:32:41: start X-correlation... INFO @ Tue, 16 Jun 2020 09:32:41: end of X-cor INFO @ Tue, 16 Jun 2020 09:32:41: #2 finished! INFO @ Tue, 16 Jun 2020 09:32:41: #2 predicted fragment length is 129 bps INFO @ Tue, 16 Jun 2020 09:32:41: #2 alternative fragment length(s) may be 129 bps INFO @ Tue, 16 Jun 2020 09:32:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495092/SRX495092.10_model.r INFO @ Tue, 16 Jun 2020 09:32:41: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:32:41: #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 09:32:50: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:32:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495092/SRX495092.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495092/SRX495092.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495092/SRX495092.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495092/SRX495092.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 09:32:51: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:32:51: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:32:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495092/SRX495092.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:32:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495092/SRX495092.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:32:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495092/SRX495092.10_summits.bed INFO @ Tue, 16 Jun 2020 09:32:54: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (726 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:32:56: 1000000 INFO @ Tue, 16 Jun 2020 09:33:01: 2000000 INFO @ Tue, 16 Jun 2020 09:33:07: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:33:10: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:33:10: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:33:10: #1 total tags in treatment: 3695063 INFO @ Tue, 16 Jun 2020 09:33:10: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:33:10: #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 09:33:10: #1 tags after filtering in treatment: 3695063 INFO @ Tue, 16 Jun 2020 09:33:10: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:33:10: #1 finished! INFO @ Tue, 16 Jun 2020 09:33:10: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:33:10: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:33:11: #2 number of paired peaks: 807 WARNING @ Tue, 16 Jun 2020 09:33:11: Fewer paired peaks (807) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 807 pairs to build model! INFO @ Tue, 16 Jun 2020 09:33:11: start model_add_line... INFO @ Tue, 16 Jun 2020 09:33:11: start X-correlation... INFO @ Tue, 16 Jun 2020 09:33:11: end of X-cor INFO @ Tue, 16 Jun 2020 09:33:11: #2 finished! INFO @ Tue, 16 Jun 2020 09:33:11: #2 predicted fragment length is 129 bps INFO @ Tue, 16 Jun 2020 09:33:11: #2 alternative fragment length(s) may be 129 bps INFO @ Tue, 16 Jun 2020 09:33:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495092/SRX495092.20_model.r INFO @ Tue, 16 Jun 2020 09:33:11: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:33:11: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:33:20: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:33:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495092/SRX495092.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:33:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495092/SRX495092.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:33:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495092/SRX495092.20_summits.bed INFO @ Tue, 16 Jun 2020 09:33:24: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (265 records, 4 fields): 2 millis CompletedMACS2peakCalling