Job ID = 6366238 SRX = SRX080092 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:53:11 prefetch.2.10.7: 1) Downloading 'SRR298912'... 2020-06-15T22:53:11 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:53:34 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:53:35 prefetch.2.10.7: 'SRR298912' is valid 2020-06-15T22:53:35 prefetch.2.10.7: 1) 'SRR298912' was downloaded successfully Read 2955703 spots for SRR298912/SRR298912.sra Written 2955703 spots for SRR298912/SRR298912.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: 00:00:17 2955703 reads; of these: 2955703 (100.00%) were unpaired; of these: 1645742 (55.68%) aligned 0 times 1105005 (37.39%) aligned exactly 1 time 204956 (6.93%) aligned >1 times 44.32% overall alignment rate Time searching: 00:00:17 Overall time: 00:00:17 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] 178149 / 1309961 = 0.1360 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 07:54:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX080092/SRX080092.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX080092/SRX080092.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX080092/SRX080092.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX080092/SRX080092.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 07:54:46: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:54:46: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:54:51: 1000000 INFO @ Tue, 16 Jun 2020 07:54:52: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 07:54:52: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 07:54:52: #1 total tags in treatment: 1131812 INFO @ Tue, 16 Jun 2020 07:54:52: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:54:52: #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 07:54:52: #1 tags after filtering in treatment: 1131812 INFO @ Tue, 16 Jun 2020 07:54:52: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:54:52: #1 finished! INFO @ Tue, 16 Jun 2020 07:54:52: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:54:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:54:52: #2 number of paired peaks: 1106 INFO @ Tue, 16 Jun 2020 07:54:52: start model_add_line... INFO @ Tue, 16 Jun 2020 07:54:52: start X-correlation... INFO @ Tue, 16 Jun 2020 07:54:52: end of X-cor INFO @ Tue, 16 Jun 2020 07:54:52: #2 finished! INFO @ Tue, 16 Jun 2020 07:54:52: #2 predicted fragment length is 145 bps INFO @ Tue, 16 Jun 2020 07:54:52: #2 alternative fragment length(s) may be 145 bps INFO @ Tue, 16 Jun 2020 07:54:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX080092/SRX080092.05_model.r INFO @ Tue, 16 Jun 2020 07:54:52: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:54:52: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:54:55: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:54:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX080092/SRX080092.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:54:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX080092/SRX080092.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:54:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX080092/SRX080092.05_summits.bed INFO @ Tue, 16 Jun 2020 07:54:57: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1171 records, 4 fields): 3 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 07:55:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX080092/SRX080092.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX080092/SRX080092.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX080092/SRX080092.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX080092/SRX080092.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 07:55:16: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:55:16: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:55:21: 1000000 INFO @ Tue, 16 Jun 2020 07:55:22: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 07:55:22: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 07:55:22: #1 total tags in treatment: 1131812 INFO @ Tue, 16 Jun 2020 07:55:22: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:55:22: #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 07:55:22: #1 tags after filtering in treatment: 1131812 INFO @ Tue, 16 Jun 2020 07:55:22: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:55:22: #1 finished! INFO @ Tue, 16 Jun 2020 07:55:22: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:55:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:55:22: #2 number of paired peaks: 1106 INFO @ Tue, 16 Jun 2020 07:55:22: start model_add_line... INFO @ Tue, 16 Jun 2020 07:55:22: start X-correlation... INFO @ Tue, 16 Jun 2020 07:55:22: end of X-cor INFO @ Tue, 16 Jun 2020 07:55:22: #2 finished! INFO @ Tue, 16 Jun 2020 07:55:22: #2 predicted fragment length is 145 bps INFO @ Tue, 16 Jun 2020 07:55:22: #2 alternative fragment length(s) may be 145 bps INFO @ Tue, 16 Jun 2020 07:55:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX080092/SRX080092.10_model.r INFO @ Tue, 16 Jun 2020 07:55:22: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:55:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:55:25: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:55:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX080092/SRX080092.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:55:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX080092/SRX080092.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:55:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX080092/SRX080092.10_summits.bed INFO @ Tue, 16 Jun 2020 07:55:26: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (752 records, 4 fields): 2 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 07:55:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX080092/SRX080092.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX080092/SRX080092.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX080092/SRX080092.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX080092/SRX080092.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 07:55:46: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:55:46: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:55:51: 1000000 INFO @ Tue, 16 Jun 2020 07:55:52: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 07:55:52: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 07:55:52: #1 total tags in treatment: 1131812 INFO @ Tue, 16 Jun 2020 07:55:52: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:55:52: #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 07:55:52: #1 tags after filtering in treatment: 1131812 INFO @ Tue, 16 Jun 2020 07:55:52: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:55:52: #1 finished! INFO @ Tue, 16 Jun 2020 07:55:52: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:55:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:55:52: #2 number of paired peaks: 1106 INFO @ Tue, 16 Jun 2020 07:55:52: start model_add_line... INFO @ Tue, 16 Jun 2020 07:55:52: start X-correlation... INFO @ Tue, 16 Jun 2020 07:55:52: end of X-cor INFO @ Tue, 16 Jun 2020 07:55:52: #2 finished! INFO @ Tue, 16 Jun 2020 07:55:52: #2 predicted fragment length is 145 bps INFO @ Tue, 16 Jun 2020 07:55:52: #2 alternative fragment length(s) may be 145 bps INFO @ Tue, 16 Jun 2020 07:55:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX080092/SRX080092.20_model.r INFO @ Tue, 16 Jun 2020 07:55:52: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:55:52: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:55:55: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:55:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX080092/SRX080092.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:55:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX080092/SRX080092.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:55:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX080092/SRX080092.20_summits.bed INFO @ Tue, 16 Jun 2020 07:55:57: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (457 records, 4 fields): 1 millis CompletedMACS2peakCalling