Job ID = 6367147 SRX = SRX277105 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:17:46 prefetch.2.10.7: 1) Downloading 'SRR849781'... 2020-06-15T23:17:46 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:18:14 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:18:14 prefetch.2.10.7: 'SRR849781' is valid 2020-06-15T23:18:14 prefetch.2.10.7: 1) 'SRR849781' was downloaded successfully Read 7612569 spots for SRR849781/SRR849781.sra Written 7612569 spots for SRR849781/SRR849781.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: 00:00:56 7612569 reads; of these: 7612569 (100.00%) were unpaired; of these: 2444671 (32.11%) aligned 0 times 4493595 (59.03%) aligned exactly 1 time 674303 (8.86%) aligned >1 times 67.89% overall alignment rate Time searching: 00:00:56 Overall time: 00:00:56 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] 759211 / 5167898 = 0.1469 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 08:21:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX277105/SRX277105.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX277105/SRX277105.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX277105/SRX277105.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX277105/SRX277105.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 08:21:02: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:21:02: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:21:07: 1000000 INFO @ Tue, 16 Jun 2020 08:21:13: 2000000 INFO @ Tue, 16 Jun 2020 08:21:19: 3000000 INFO @ Tue, 16 Jun 2020 08:21:24: 4000000 INFO @ Tue, 16 Jun 2020 08:21:26: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:21:26: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:21:26: #1 total tags in treatment: 4408687 INFO @ Tue, 16 Jun 2020 08:21:26: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:21:26: #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 08:21:27: #1 tags after filtering in treatment: 4408687 INFO @ Tue, 16 Jun 2020 08:21:27: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:21:27: #1 finished! INFO @ Tue, 16 Jun 2020 08:21:27: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:21:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:21:27: #2 number of paired peaks: 1293 INFO @ Tue, 16 Jun 2020 08:21:27: start model_add_line... INFO @ Tue, 16 Jun 2020 08:21:27: start X-correlation... INFO @ Tue, 16 Jun 2020 08:21:27: end of X-cor INFO @ Tue, 16 Jun 2020 08:21:27: #2 finished! INFO @ Tue, 16 Jun 2020 08:21:27: #2 predicted fragment length is 165 bps INFO @ Tue, 16 Jun 2020 08:21:27: #2 alternative fragment length(s) may be 165 bps INFO @ Tue, 16 Jun 2020 08:21:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX277105/SRX277105.05_model.r INFO @ Tue, 16 Jun 2020 08:21:27: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:21:27: #3 Pre-compute pvalue-qvalue table... 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 08:21:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX277105/SRX277105.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX277105/SRX277105.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX277105/SRX277105.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX277105/SRX277105.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 08:21:32: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:21:32: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:21:38: 1000000 INFO @ Tue, 16 Jun 2020 08:21:38: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:21:43: 2000000 INFO @ Tue, 16 Jun 2020 08:21:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX277105/SRX277105.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:21:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX277105/SRX277105.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:21:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX277105/SRX277105.05_summits.bed INFO @ Tue, 16 Jun 2020 08:21:43: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3905 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:21:49: 3000000 INFO @ Tue, 16 Jun 2020 08:21:55: 4000000 INFO @ Tue, 16 Jun 2020 08:21:57: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:21:57: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:21:57: #1 total tags in treatment: 4408687 INFO @ Tue, 16 Jun 2020 08:21:57: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:21:57: #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 08:21:57: #1 tags after filtering in treatment: 4408687 INFO @ Tue, 16 Jun 2020 08:21:57: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:21:57: #1 finished! INFO @ Tue, 16 Jun 2020 08:21:57: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:21:57: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:21:57: #2 number of paired peaks: 1293 INFO @ Tue, 16 Jun 2020 08:21:57: start model_add_line... INFO @ Tue, 16 Jun 2020 08:21:57: start X-correlation... INFO @ Tue, 16 Jun 2020 08:21:57: end of X-cor INFO @ Tue, 16 Jun 2020 08:21:57: #2 finished! INFO @ Tue, 16 Jun 2020 08:21:57: #2 predicted fragment length is 165 bps INFO @ Tue, 16 Jun 2020 08:21:57: #2 alternative fragment length(s) may be 165 bps INFO @ Tue, 16 Jun 2020 08:21:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX277105/SRX277105.10_model.r INFO @ Tue, 16 Jun 2020 08:21:57: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:21:57: #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 08:22:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX277105/SRX277105.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX277105/SRX277105.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX277105/SRX277105.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX277105/SRX277105.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 08:22:02: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:22:02: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:22:08: 1000000 INFO @ Tue, 16 Jun 2020 08:22:08: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:22:13: 2000000 INFO @ Tue, 16 Jun 2020 08:22:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX277105/SRX277105.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:22:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX277105/SRX277105.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:22:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX277105/SRX277105.10_summits.bed INFO @ Tue, 16 Jun 2020 08:22:14: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2197 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:22:18: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:22:24: 4000000 INFO @ Tue, 16 Jun 2020 08:22:26: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:22:26: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:22:26: #1 total tags in treatment: 4408687 INFO @ Tue, 16 Jun 2020 08:22:26: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:22:26: #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 08:22:26: #1 tags after filtering in treatment: 4408687 INFO @ Tue, 16 Jun 2020 08:22:26: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:22:26: #1 finished! INFO @ Tue, 16 Jun 2020 08:22:26: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:22:26: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:22:27: #2 number of paired peaks: 1293 INFO @ Tue, 16 Jun 2020 08:22:27: start model_add_line... INFO @ Tue, 16 Jun 2020 08:22:27: start X-correlation... INFO @ Tue, 16 Jun 2020 08:22:27: end of X-cor INFO @ Tue, 16 Jun 2020 08:22:27: #2 finished! INFO @ Tue, 16 Jun 2020 08:22:27: #2 predicted fragment length is 165 bps INFO @ Tue, 16 Jun 2020 08:22:27: #2 alternative fragment length(s) may be 165 bps INFO @ Tue, 16 Jun 2020 08:22:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX277105/SRX277105.20_model.r INFO @ Tue, 16 Jun 2020 08:22:27: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:22:27: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:22:38: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:22:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX277105/SRX277105.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:22:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX277105/SRX277105.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:22:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX277105/SRX277105.20_summits.bed INFO @ Tue, 16 Jun 2020 08:22:44: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (959 records, 4 fields): 2 millis CompletedMACS2peakCalling