Job ID = 6507979 SRX = SRX554720 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T13:39:12 prefetch.2.10.7: 1) Downloading 'SRR1301068'... 2020-06-26T13:39:12 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T13:39:39 prefetch.2.10.7: HTTPS download succeed 2020-06-26T13:39:39 prefetch.2.10.7: 'SRR1301068' is valid 2020-06-26T13:39:39 prefetch.2.10.7: 1) 'SRR1301068' was downloaded successfully Read 1829269 spots for SRR1301068/SRR1301068.sra Written 1829269 spots for SRR1301068/SRR1301068.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:00:30 1829269 reads; of these: 1829269 (100.00%) were unpaired; of these: 127168 (6.95%) aligned 0 times 1421644 (77.72%) aligned exactly 1 time 280457 (15.33%) aligned >1 times 93.05% overall alignment rate Time searching: 00:00:31 Overall time: 00:00:31 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] 493715 / 1702101 = 0.2901 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 @ Fri, 26 Jun 2020 22:41:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX554720/SRX554720.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX554720/SRX554720.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX554720/SRX554720.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX554720/SRX554720.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 @ Fri, 26 Jun 2020 22:41:14: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:41:14: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:41:20: 1000000 INFO @ Fri, 26 Jun 2020 22:41:21: #1 tag size is determined as 51 bps INFO @ Fri, 26 Jun 2020 22:41:21: #1 tag size = 51 INFO @ Fri, 26 Jun 2020 22:41:21: #1 total tags in treatment: 1208386 INFO @ Fri, 26 Jun 2020 22:41:21: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:41:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 22:41:21: #1 tags after filtering in treatment: 1208386 INFO @ Fri, 26 Jun 2020 22:41:21: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:41:21: #1 finished! INFO @ Fri, 26 Jun 2020 22:41:21: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:41:21: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:41:22: #2 number of paired peaks: 1701 INFO @ Fri, 26 Jun 2020 22:41:22: start model_add_line... INFO @ Fri, 26 Jun 2020 22:41:22: start X-correlation... INFO @ Fri, 26 Jun 2020 22:41:22: end of X-cor INFO @ Fri, 26 Jun 2020 22:41:22: #2 finished! INFO @ Fri, 26 Jun 2020 22:41:22: #2 predicted fragment length is 163 bps INFO @ Fri, 26 Jun 2020 22:41:22: #2 alternative fragment length(s) may be 163 bps INFO @ Fri, 26 Jun 2020 22:41:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX554720/SRX554720.05_model.r INFO @ Fri, 26 Jun 2020 22:41:22: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:41:22: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:41:25: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:41:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX554720/SRX554720.05_peaks.xls INFO @ Fri, 26 Jun 2020 22:41:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX554720/SRX554720.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:41:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX554720/SRX554720.05_summits.bed INFO @ Fri, 26 Jun 2020 22:41:26: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (761 records, 4 fields): 4 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 @ Fri, 26 Jun 2020 22:41:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX554720/SRX554720.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX554720/SRX554720.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX554720/SRX554720.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX554720/SRX554720.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 @ Fri, 26 Jun 2020 22:41:44: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:41:44: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:41:50: 1000000 INFO @ Fri, 26 Jun 2020 22:41:52: #1 tag size is determined as 51 bps INFO @ Fri, 26 Jun 2020 22:41:52: #1 tag size = 51 INFO @ Fri, 26 Jun 2020 22:41:52: #1 total tags in treatment: 1208386 INFO @ Fri, 26 Jun 2020 22:41:52: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:41:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 22:41:52: #1 tags after filtering in treatment: 1208386 INFO @ Fri, 26 Jun 2020 22:41:52: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:41:52: #1 finished! INFO @ Fri, 26 Jun 2020 22:41:52: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:41:52: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:41:52: #2 number of paired peaks: 1701 INFO @ Fri, 26 Jun 2020 22:41:52: start model_add_line... INFO @ Fri, 26 Jun 2020 22:41:52: start X-correlation... INFO @ Fri, 26 Jun 2020 22:41:52: end of X-cor INFO @ Fri, 26 Jun 2020 22:41:52: #2 finished! INFO @ Fri, 26 Jun 2020 22:41:52: #2 predicted fragment length is 163 bps INFO @ Fri, 26 Jun 2020 22:41:52: #2 alternative fragment length(s) may be 163 bps INFO @ Fri, 26 Jun 2020 22:41:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX554720/SRX554720.10_model.r INFO @ Fri, 26 Jun 2020 22:41:52: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:41:52: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:41:55: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:41:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX554720/SRX554720.10_peaks.xls INFO @ Fri, 26 Jun 2020 22:41:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX554720/SRX554720.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:41:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX554720/SRX554720.10_summits.bed INFO @ Fri, 26 Jun 2020 22:41:57: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (365 records, 4 fields): 1 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 @ Fri, 26 Jun 2020 22:42:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX554720/SRX554720.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX554720/SRX554720.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX554720/SRX554720.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX554720/SRX554720.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 @ Fri, 26 Jun 2020 22:42:14: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:42:14: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 22:42:21: 1000000 INFO @ Fri, 26 Jun 2020 22:42:22: #1 tag size is determined as 51 bps INFO @ Fri, 26 Jun 2020 22:42:22: #1 tag size = 51 INFO @ Fri, 26 Jun 2020 22:42:22: #1 total tags in treatment: 1208386 INFO @ Fri, 26 Jun 2020 22:42:22: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:42:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 22:42:22: #1 tags after filtering in treatment: 1208386 INFO @ Fri, 26 Jun 2020 22:42:22: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:42:22: #1 finished! INFO @ Fri, 26 Jun 2020 22:42:22: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:42:22: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:42:22: #2 number of paired peaks: 1701 INFO @ Fri, 26 Jun 2020 22:42:22: start model_add_line... INFO @ Fri, 26 Jun 2020 22:42:22: start X-correlation... INFO @ Fri, 26 Jun 2020 22:42:22: end of X-cor INFO @ Fri, 26 Jun 2020 22:42:22: #2 finished! INFO @ Fri, 26 Jun 2020 22:42:22: #2 predicted fragment length is 163 bps INFO @ Fri, 26 Jun 2020 22:42:22: #2 alternative fragment length(s) may be 163 bps INFO @ Fri, 26 Jun 2020 22:42:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX554720/SRX554720.20_model.r INFO @ Fri, 26 Jun 2020 22:42:22: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:42:22: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 22:42:25: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:42:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX554720/SRX554720.20_peaks.xls INFO @ Fri, 26 Jun 2020 22:42:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX554720/SRX554720.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:42:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX554720/SRX554720.20_summits.bed INFO @ Fri, 26 Jun 2020 22:42:27: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (175 records, 4 fields): 2 millis CompletedMACS2peakCalling