Job ID = 6366228 SRX = SRX080082 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:37:10 prefetch.2.10.7: 1) Downloading 'SRR298902'... 2020-06-15T22:37:10 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:38:03 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:38:04 prefetch.2.10.7: 'SRR298902' is valid 2020-06-15T22:38:04 prefetch.2.10.7: 1) 'SRR298902' was downloaded successfully Read 6303653 spots for SRR298902/SRR298902.sra Written 6303653 spots for SRR298902/SRR298902.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: 00:00:39 6303653 reads; of these: 6303653 (100.00%) were unpaired; of these: 3764536 (59.72%) aligned 0 times 2183421 (34.64%) aligned exactly 1 time 355696 (5.64%) aligned >1 times 40.28% overall alignment rate Time searching: 00:00:39 Overall time: 00:00:39 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] 587090 / 2539117 = 0.2312 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 07:40:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX080082/SRX080082.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX080082/SRX080082.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX080082/SRX080082.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX080082/SRX080082.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 07:40:06: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:40:06: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:40:12: 1000000 INFO @ Tue, 16 Jun 2020 07:40:17: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 07:40:17: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 07:40:17: #1 total tags in treatment: 1952027 INFO @ Tue, 16 Jun 2020 07:40:17: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:40:17: #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 07:40:17: #1 tags after filtering in treatment: 1952027 INFO @ Tue, 16 Jun 2020 07:40:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:40:17: #1 finished! INFO @ Tue, 16 Jun 2020 07:40:17: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:40:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:40:17: #2 number of paired peaks: 2386 INFO @ Tue, 16 Jun 2020 07:40:17: start model_add_line... INFO @ Tue, 16 Jun 2020 07:40:17: start X-correlation... INFO @ Tue, 16 Jun 2020 07:40:17: end of X-cor INFO @ Tue, 16 Jun 2020 07:40:17: #2 finished! INFO @ Tue, 16 Jun 2020 07:40:17: #2 predicted fragment length is 139 bps INFO @ Tue, 16 Jun 2020 07:40:17: #2 alternative fragment length(s) may be 139 bps INFO @ Tue, 16 Jun 2020 07:40:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX080082/SRX080082.05_model.r INFO @ Tue, 16 Jun 2020 07:40:17: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:40:17: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:40:23: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:40:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX080082/SRX080082.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:40:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX080082/SRX080082.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:40:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX080082/SRX080082.05_summits.bed INFO @ Tue, 16 Jun 2020 07:40:25: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3701 records, 4 fields): 6 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 07:40:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX080082/SRX080082.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX080082/SRX080082.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX080082/SRX080082.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX080082/SRX080082.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 07:40:36: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:40:36: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:40:42: 1000000 INFO @ Tue, 16 Jun 2020 07:40:47: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 07:40:47: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 07:40:47: #1 total tags in treatment: 1952027 INFO @ Tue, 16 Jun 2020 07:40:47: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:40:47: #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 07:40:47: #1 tags after filtering in treatment: 1952027 INFO @ Tue, 16 Jun 2020 07:40:47: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:40:47: #1 finished! INFO @ Tue, 16 Jun 2020 07:40:47: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:40:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:40:47: #2 number of paired peaks: 2386 INFO @ Tue, 16 Jun 2020 07:40:47: start model_add_line... INFO @ Tue, 16 Jun 2020 07:40:47: start X-correlation... INFO @ Tue, 16 Jun 2020 07:40:47: end of X-cor INFO @ Tue, 16 Jun 2020 07:40:47: #2 finished! INFO @ Tue, 16 Jun 2020 07:40:47: #2 predicted fragment length is 139 bps INFO @ Tue, 16 Jun 2020 07:40:47: #2 alternative fragment length(s) may be 139 bps INFO @ Tue, 16 Jun 2020 07:40:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX080082/SRX080082.10_model.r INFO @ Tue, 16 Jun 2020 07:40:47: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:40:47: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:40:52: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:40:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX080082/SRX080082.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:40:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX080082/SRX080082.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:40:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX080082/SRX080082.10_summits.bed INFO @ Tue, 16 Jun 2020 07:40:55: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2669 records, 4 fields): 4 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 07:41:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX080082/SRX080082.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX080082/SRX080082.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX080082/SRX080082.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX080082/SRX080082.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 07:41:07: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:41:07: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:41:13: 1000000 BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:41:18: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 07:41:18: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 07:41:18: #1 total tags in treatment: 1952027 INFO @ Tue, 16 Jun 2020 07:41:18: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:41:18: #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 07:41:18: #1 tags after filtering in treatment: 1952027 INFO @ Tue, 16 Jun 2020 07:41:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:41:18: #1 finished! INFO @ Tue, 16 Jun 2020 07:41:18: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:41:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:41:18: #2 number of paired peaks: 2386 INFO @ Tue, 16 Jun 2020 07:41:18: start model_add_line... INFO @ Tue, 16 Jun 2020 07:41:18: start X-correlation... INFO @ Tue, 16 Jun 2020 07:41:18: end of X-cor INFO @ Tue, 16 Jun 2020 07:41:18: #2 finished! INFO @ Tue, 16 Jun 2020 07:41:18: #2 predicted fragment length is 139 bps INFO @ Tue, 16 Jun 2020 07:41:18: #2 alternative fragment length(s) may be 139 bps INFO @ Tue, 16 Jun 2020 07:41:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX080082/SRX080082.20_model.r INFO @ Tue, 16 Jun 2020 07:41:18: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:41:18: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:41:24: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:41:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX080082/SRX080082.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:41:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX080082/SRX080082.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:41:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX080082/SRX080082.20_summits.bed INFO @ Tue, 16 Jun 2020 07:41:26: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1692 records, 4 fields): 3 millis CompletedMACS2peakCalling