Job ID = 6507751 SRX = SRX277027 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T13:02:26 prefetch.2.10.7: 1) Downloading 'SRR849696'... 2020-06-26T13:02:26 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T13:02:49 prefetch.2.10.7: HTTPS download succeed 2020-06-26T13:02:49 prefetch.2.10.7: 'SRR849696' is valid 2020-06-26T13:02:49 prefetch.2.10.7: 1) 'SRR849696' was downloaded successfully Read 2951621 spots for SRR849696/SRR849696.sra Written 2951621 spots for SRR849696/SRR849696.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: 00:00:26 2951621 reads; of these: 2951621 (100.00%) were unpaired; of these: 707792 (23.98%) aligned 0 times 1922657 (65.14%) aligned exactly 1 time 321172 (10.88%) aligned >1 times 76.02% overall alignment rate Time searching: 00:00:26 Overall time: 00:00:26 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] 137689 / 2243829 = 0.0614 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 22:04:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX277027/SRX277027.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX277027/SRX277027.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX277027/SRX277027.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX277027/SRX277027.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 22:04:22: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:04:22: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:04:28: 1000000 INFO @ Fri, 26 Jun 2020 22:04:33: 2000000 INFO @ Fri, 26 Jun 2020 22:04:33: #1 tag size is determined as 32 bps INFO @ Fri, 26 Jun 2020 22:04:33: #1 tag size = 32 INFO @ Fri, 26 Jun 2020 22:04:33: #1 total tags in treatment: 2106140 INFO @ Fri, 26 Jun 2020 22:04:33: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:04:33: #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 22:04:33: #1 tags after filtering in treatment: 2106140 INFO @ Fri, 26 Jun 2020 22:04:33: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:04:33: #1 finished! INFO @ Fri, 26 Jun 2020 22:04:33: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:04:33: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:04:34: #2 number of paired peaks: 1042 INFO @ Fri, 26 Jun 2020 22:04:34: start model_add_line... INFO @ Fri, 26 Jun 2020 22:04:34: start X-correlation... INFO @ Fri, 26 Jun 2020 22:04:34: end of X-cor INFO @ Fri, 26 Jun 2020 22:04:34: #2 finished! INFO @ Fri, 26 Jun 2020 22:04:34: #2 predicted fragment length is 157 bps INFO @ Fri, 26 Jun 2020 22:04:34: #2 alternative fragment length(s) may be 157 bps INFO @ Fri, 26 Jun 2020 22:04:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX277027/SRX277027.05_model.r INFO @ Fri, 26 Jun 2020 22:04:34: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:04:34: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:04:39: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:04:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX277027/SRX277027.05_peaks.xls INFO @ Fri, 26 Jun 2020 22:04:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX277027/SRX277027.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:04:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX277027/SRX277027.05_summits.bed INFO @ Fri, 26 Jun 2020 22:04:42: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (2080 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 22:04:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX277027/SRX277027.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX277027/SRX277027.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX277027/SRX277027.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX277027/SRX277027.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 22:04:52: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:04:52: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:04:57: 1000000 INFO @ Fri, 26 Jun 2020 22:05:02: 2000000 INFO @ Fri, 26 Jun 2020 22:05:03: #1 tag size is determined as 32 bps INFO @ Fri, 26 Jun 2020 22:05:03: #1 tag size = 32 INFO @ Fri, 26 Jun 2020 22:05:03: #1 total tags in treatment: 2106140 INFO @ Fri, 26 Jun 2020 22:05:03: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:05:03: #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 22:05:03: #1 tags after filtering in treatment: 2106140 INFO @ Fri, 26 Jun 2020 22:05:03: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:05:03: #1 finished! INFO @ Fri, 26 Jun 2020 22:05:03: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:05:03: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:05:03: #2 number of paired peaks: 1042 INFO @ Fri, 26 Jun 2020 22:05:03: start model_add_line... INFO @ Fri, 26 Jun 2020 22:05:03: start X-correlation... INFO @ Fri, 26 Jun 2020 22:05:03: end of X-cor INFO @ Fri, 26 Jun 2020 22:05:03: #2 finished! INFO @ Fri, 26 Jun 2020 22:05:03: #2 predicted fragment length is 157 bps INFO @ Fri, 26 Jun 2020 22:05:03: #2 alternative fragment length(s) may be 157 bps INFO @ Fri, 26 Jun 2020 22:05:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX277027/SRX277027.10_model.r INFO @ Fri, 26 Jun 2020 22:05:03: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:05:03: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:05:08: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:05:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX277027/SRX277027.10_peaks.xls INFO @ Fri, 26 Jun 2020 22:05:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX277027/SRX277027.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:05:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX277027/SRX277027.10_summits.bed INFO @ Fri, 26 Jun 2020 22:05:11: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (904 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 @ Fri, 26 Jun 2020 22:05:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX277027/SRX277027.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX277027/SRX277027.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX277027/SRX277027.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX277027/SRX277027.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 22:05:22: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:05:22: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:05:28: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 22:05:33: 2000000 INFO @ Fri, 26 Jun 2020 22:05:34: #1 tag size is determined as 32 bps INFO @ Fri, 26 Jun 2020 22:05:34: #1 tag size = 32 INFO @ Fri, 26 Jun 2020 22:05:34: #1 total tags in treatment: 2106140 INFO @ Fri, 26 Jun 2020 22:05:34: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:05:34: #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 22:05:34: #1 tags after filtering in treatment: 2106140 INFO @ Fri, 26 Jun 2020 22:05:34: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:05:34: #1 finished! INFO @ Fri, 26 Jun 2020 22:05:34: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:05:34: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:05:34: #2 number of paired peaks: 1042 INFO @ Fri, 26 Jun 2020 22:05:34: start model_add_line... INFO @ Fri, 26 Jun 2020 22:05:34: start X-correlation... INFO @ Fri, 26 Jun 2020 22:05:34: end of X-cor INFO @ Fri, 26 Jun 2020 22:05:34: #2 finished! INFO @ Fri, 26 Jun 2020 22:05:34: #2 predicted fragment length is 157 bps INFO @ Fri, 26 Jun 2020 22:05:34: #2 alternative fragment length(s) may be 157 bps INFO @ Fri, 26 Jun 2020 22:05:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX277027/SRX277027.20_model.r INFO @ Fri, 26 Jun 2020 22:05:34: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:05:34: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 22:05:39: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:05:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX277027/SRX277027.20_peaks.xls INFO @ Fri, 26 Jun 2020 22:05:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX277027/SRX277027.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:05:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX277027/SRX277027.20_summits.bed INFO @ Fri, 26 Jun 2020 22:05:42: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (276 records, 4 fields): 1 millis CompletedMACS2peakCalling