Job ID = 6366071 SRX = SRX059243 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:37:51 prefetch.2.10.7: 1) Downloading 'SRR190683'... 2020-06-15T22:37:51 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:38:30 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:38:30 prefetch.2.10.7: 'SRR190683' is valid 2020-06-15T22:38:30 prefetch.2.10.7: 1) 'SRR190683' was downloaded successfully Read 7751700 spots for SRR190683/SRR190683.sra Written 7751700 spots for SRR190683/SRR190683.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: 00:01:06 7751700 reads; of these: 7751700 (100.00%) were unpaired; of these: 974566 (12.57%) aligned 0 times 5728445 (73.90%) aligned exactly 1 time 1048689 (13.53%) aligned >1 times 87.43% overall alignment rate Time searching: 00:01:06 Overall time: 00:01:06 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] 2569925 / 6777134 = 0.3792 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 07:41:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX059243/SRX059243.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX059243/SRX059243.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX059243/SRX059243.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX059243/SRX059243.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 07:41:38: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:41:38: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:41:43: 1000000 INFO @ Tue, 16 Jun 2020 07:41:49: 2000000 INFO @ Tue, 16 Jun 2020 07:41:55: 3000000 INFO @ Tue, 16 Jun 2020 07:42:00: 4000000 INFO @ Tue, 16 Jun 2020 07:42:01: #1 tag size is determined as 28 bps INFO @ Tue, 16 Jun 2020 07:42:01: #1 tag size = 28 INFO @ Tue, 16 Jun 2020 07:42:01: #1 total tags in treatment: 4207209 INFO @ Tue, 16 Jun 2020 07:42:01: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:42:01: #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 07:42:01: #1 tags after filtering in treatment: 4207209 INFO @ Tue, 16 Jun 2020 07:42:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:42:01: #1 finished! INFO @ Tue, 16 Jun 2020 07:42:01: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:42:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:42:02: #2 number of paired peaks: 1104 INFO @ Tue, 16 Jun 2020 07:42:02: start model_add_line... INFO @ Tue, 16 Jun 2020 07:42:02: start X-correlation... INFO @ Tue, 16 Jun 2020 07:42:02: end of X-cor INFO @ Tue, 16 Jun 2020 07:42:02: #2 finished! INFO @ Tue, 16 Jun 2020 07:42:02: #2 predicted fragment length is 139 bps INFO @ Tue, 16 Jun 2020 07:42:02: #2 alternative fragment length(s) may be 139 bps INFO @ Tue, 16 Jun 2020 07:42:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX059243/SRX059243.05_model.r INFO @ Tue, 16 Jun 2020 07:42:02: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:42:02: #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 07:42:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX059243/SRX059243.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX059243/SRX059243.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX059243/SRX059243.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX059243/SRX059243.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 07:42:08: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:42:08: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:42:13: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:42:14: 1000000 INFO @ Tue, 16 Jun 2020 07:42:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX059243/SRX059243.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:42:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX059243/SRX059243.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:42:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX059243/SRX059243.05_summits.bed INFO @ Tue, 16 Jun 2020 07:42:19: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1056 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:42:20: 2000000 INFO @ Tue, 16 Jun 2020 07:42:25: 3000000 INFO @ Tue, 16 Jun 2020 07:42:31: 4000000 INFO @ Tue, 16 Jun 2020 07:42:32: #1 tag size is determined as 28 bps INFO @ Tue, 16 Jun 2020 07:42:32: #1 tag size = 28 INFO @ Tue, 16 Jun 2020 07:42:32: #1 total tags in treatment: 4207209 INFO @ Tue, 16 Jun 2020 07:42:32: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:42:32: #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 07:42:32: #1 tags after filtering in treatment: 4207209 INFO @ Tue, 16 Jun 2020 07:42:32: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:42:32: #1 finished! INFO @ Tue, 16 Jun 2020 07:42:32: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:42:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:42:32: #2 number of paired peaks: 1104 INFO @ Tue, 16 Jun 2020 07:42:32: start model_add_line... INFO @ Tue, 16 Jun 2020 07:42:32: start X-correlation... INFO @ Tue, 16 Jun 2020 07:42:32: end of X-cor INFO @ Tue, 16 Jun 2020 07:42:32: #2 finished! INFO @ Tue, 16 Jun 2020 07:42:32: #2 predicted fragment length is 139 bps INFO @ Tue, 16 Jun 2020 07:42:32: #2 alternative fragment length(s) may be 139 bps INFO @ Tue, 16 Jun 2020 07:42:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX059243/SRX059243.10_model.r INFO @ Tue, 16 Jun 2020 07:42:32: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:42:32: #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 07:42:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX059243/SRX059243.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX059243/SRX059243.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX059243/SRX059243.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX059243/SRX059243.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 07:42:38: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:42:38: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:42:43: 1000000 INFO @ Tue, 16 Jun 2020 07:42:44: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:42:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX059243/SRX059243.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:42:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX059243/SRX059243.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:42:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX059243/SRX059243.10_summits.bed INFO @ Tue, 16 Jun 2020 07:42:49: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (666 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:42:50: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:42:56: 3000000 INFO @ Tue, 16 Jun 2020 07:43:02: 4000000 INFO @ Tue, 16 Jun 2020 07:43:03: #1 tag size is determined as 28 bps INFO @ Tue, 16 Jun 2020 07:43:03: #1 tag size = 28 INFO @ Tue, 16 Jun 2020 07:43:03: #1 total tags in treatment: 4207209 INFO @ Tue, 16 Jun 2020 07:43:03: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:43:03: #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 07:43:03: #1 tags after filtering in treatment: 4207209 INFO @ Tue, 16 Jun 2020 07:43:03: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:43:03: #1 finished! INFO @ Tue, 16 Jun 2020 07:43:03: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:43:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:43:03: #2 number of paired peaks: 1104 INFO @ Tue, 16 Jun 2020 07:43:03: start model_add_line... INFO @ Tue, 16 Jun 2020 07:43:03: start X-correlation... INFO @ Tue, 16 Jun 2020 07:43:03: end of X-cor INFO @ Tue, 16 Jun 2020 07:43:03: #2 finished! INFO @ Tue, 16 Jun 2020 07:43:03: #2 predicted fragment length is 139 bps INFO @ Tue, 16 Jun 2020 07:43:03: #2 alternative fragment length(s) may be 139 bps INFO @ Tue, 16 Jun 2020 07:43:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX059243/SRX059243.20_model.r INFO @ Tue, 16 Jun 2020 07:43:03: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:43:03: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:43:15: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:43:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX059243/SRX059243.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:43:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX059243/SRX059243.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:43:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX059243/SRX059243.20_summits.bed INFO @ Tue, 16 Jun 2020 07:43:20: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (311 records, 4 fields): 1 millis CompletedMACS2peakCalling