Job ID = 14158191 SRX = SRX6717197 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 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: 00:07:39 52724146 reads; of these: 52724146 (100.00%) were unpaired; of these: 46356579 (87.92%) aligned 0 times 5785602 (10.97%) aligned exactly 1 time 581965 (1.10%) aligned >1 times 12.08% overall alignment rate Time searching: 00:07:39 Overall time: 00:07:39 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] 2602206 / 6367567 = 0.4087 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 08 Dec 2021 14:47:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX6717197/SRX6717197.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX6717197/SRX6717197.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX6717197/SRX6717197.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX6717197/SRX6717197.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 @ Wed, 08 Dec 2021 14:47:18: #1 read tag files... INFO @ Wed, 08 Dec 2021 14:47:18: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 14:47:24: 1000000 INFO @ Wed, 08 Dec 2021 14:47:30: 2000000 INFO @ Wed, 08 Dec 2021 14:47:37: 3000000 INFO @ Wed, 08 Dec 2021 14:47:41: #1 tag size is determined as 62 bps INFO @ Wed, 08 Dec 2021 14:47:41: #1 tag size = 62 INFO @ Wed, 08 Dec 2021 14:47:41: #1 total tags in treatment: 3765361 INFO @ Wed, 08 Dec 2021 14:47:41: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 14:47:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 14:47:41: #1 tags after filtering in treatment: 3765361 INFO @ Wed, 08 Dec 2021 14:47:41: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 14:47:41: #1 finished! INFO @ Wed, 08 Dec 2021 14:47:41: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 14:47:41: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 14:47:42: #2 number of paired peaks: 3824 INFO @ Wed, 08 Dec 2021 14:47:42: start model_add_line... INFO @ Wed, 08 Dec 2021 14:47:42: start X-correlation... INFO @ Wed, 08 Dec 2021 14:47:42: end of X-cor INFO @ Wed, 08 Dec 2021 14:47:42: #2 finished! INFO @ Wed, 08 Dec 2021 14:47:42: #2 predicted fragment length is 176 bps INFO @ Wed, 08 Dec 2021 14:47:42: #2 alternative fragment length(s) may be 176 bps INFO @ Wed, 08 Dec 2021 14:47:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX6717197/SRX6717197.05_model.r INFO @ Wed, 08 Dec 2021 14:47:42: #3 Call peaks... INFO @ Wed, 08 Dec 2021 14:47:42: #3 Pre-compute pvalue-qvalue table... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 08 Dec 2021 14:47:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX6717197/SRX6717197.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX6717197/SRX6717197.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX6717197/SRX6717197.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX6717197/SRX6717197.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 @ Wed, 08 Dec 2021 14:47:48: #1 read tag files... INFO @ Wed, 08 Dec 2021 14:47:48: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 14:47:52: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 14:47:54: 1000000 INFO @ Wed, 08 Dec 2021 14:47:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX6717197/SRX6717197.05_peaks.xls INFO @ Wed, 08 Dec 2021 14:47:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX6717197/SRX6717197.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 14:47:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX6717197/SRX6717197.05_summits.bed INFO @ Wed, 08 Dec 2021 14:47:57: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (10154 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 14:48:00: 2000000 INFO @ Wed, 08 Dec 2021 14:48:07: 3000000 INFO @ Wed, 08 Dec 2021 14:48:11: #1 tag size is determined as 62 bps INFO @ Wed, 08 Dec 2021 14:48:11: #1 tag size = 62 INFO @ Wed, 08 Dec 2021 14:48:11: #1 total tags in treatment: 3765361 INFO @ Wed, 08 Dec 2021 14:48:11: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 14:48:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 14:48:11: #1 tags after filtering in treatment: 3765361 INFO @ Wed, 08 Dec 2021 14:48:11: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 14:48:11: #1 finished! INFO @ Wed, 08 Dec 2021 14:48:11: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 14:48:11: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 14:48:12: #2 number of paired peaks: 3824 INFO @ Wed, 08 Dec 2021 14:48:12: start model_add_line... INFO @ Wed, 08 Dec 2021 14:48:12: start X-correlation... INFO @ Wed, 08 Dec 2021 14:48:12: end of X-cor INFO @ Wed, 08 Dec 2021 14:48:12: #2 finished! INFO @ Wed, 08 Dec 2021 14:48:12: #2 predicted fragment length is 176 bps INFO @ Wed, 08 Dec 2021 14:48:12: #2 alternative fragment length(s) may be 176 bps INFO @ Wed, 08 Dec 2021 14:48:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX6717197/SRX6717197.10_model.r INFO @ Wed, 08 Dec 2021 14:48:12: #3 Call peaks... INFO @ Wed, 08 Dec 2021 14:48:12: #3 Pre-compute pvalue-qvalue table... BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 08 Dec 2021 14:48:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX6717197/SRX6717197.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX6717197/SRX6717197.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX6717197/SRX6717197.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX6717197/SRX6717197.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 @ Wed, 08 Dec 2021 14:48:18: #1 read tag files... INFO @ Wed, 08 Dec 2021 14:48:18: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 14:48:22: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 14:48:24: 1000000 INFO @ Wed, 08 Dec 2021 14:48:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX6717197/SRX6717197.10_peaks.xls INFO @ Wed, 08 Dec 2021 14:48:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX6717197/SRX6717197.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 14:48:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX6717197/SRX6717197.10_summits.bed INFO @ Wed, 08 Dec 2021 14:48:27: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (6620 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 14:48:30: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 14:48:37: 3000000 INFO @ Wed, 08 Dec 2021 14:48:42: #1 tag size is determined as 62 bps INFO @ Wed, 08 Dec 2021 14:48:42: #1 tag size = 62 INFO @ Wed, 08 Dec 2021 14:48:42: #1 total tags in treatment: 3765361 INFO @ Wed, 08 Dec 2021 14:48:42: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 14:48:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 14:48:42: #1 tags after filtering in treatment: 3765361 INFO @ Wed, 08 Dec 2021 14:48:42: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 14:48:42: #1 finished! INFO @ Wed, 08 Dec 2021 14:48:42: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 14:48:42: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 14:48:42: #2 number of paired peaks: 3824 INFO @ Wed, 08 Dec 2021 14:48:42: start model_add_line... INFO @ Wed, 08 Dec 2021 14:48:42: start X-correlation... INFO @ Wed, 08 Dec 2021 14:48:42: end of X-cor INFO @ Wed, 08 Dec 2021 14:48:42: #2 finished! INFO @ Wed, 08 Dec 2021 14:48:42: #2 predicted fragment length is 176 bps INFO @ Wed, 08 Dec 2021 14:48:42: #2 alternative fragment length(s) may be 176 bps INFO @ Wed, 08 Dec 2021 14:48:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX6717197/SRX6717197.20_model.r INFO @ Wed, 08 Dec 2021 14:48:42: #3 Call peaks... INFO @ Wed, 08 Dec 2021 14:48:42: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 14:48:53: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 14:48:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX6717197/SRX6717197.20_peaks.xls INFO @ Wed, 08 Dec 2021 14:48:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX6717197/SRX6717197.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 14:48:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX6717197/SRX6717197.20_summits.bed INFO @ Wed, 08 Dec 2021 14:48:57: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3813 records, 4 fields): 6 millis CompletedMACS2peakCalling