Job ID = 16436011 SRX = SRX13110345 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: 00:02:45 13003194 reads; of these: 13003194 (100.00%) were unpaired; of these: 6945067 (53.41%) aligned 0 times 5299640 (40.76%) aligned exactly 1 time 758487 (5.83%) aligned >1 times 46.59% overall alignment rate Time searching: 00:02:45 Overall time: 00:02:45 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] 1360399 / 6058127 = 0.2246 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/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 10:57:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX13110345/SRX13110345.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX13110345/SRX13110345.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX13110345/SRX13110345.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX13110345/SRX13110345.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, 02 Aug 2022 10:57:46: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:57:46: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:57:54: 1000000 INFO @ Tue, 02 Aug 2022 10:58:02: 2000000 INFO @ Tue, 02 Aug 2022 10:58:10: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 10:58:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX13110345/SRX13110345.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX13110345/SRX13110345.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX13110345/SRX13110345.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX13110345/SRX13110345.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, 02 Aug 2022 10:58:16: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:58:16: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:58:18: 4000000 INFO @ Tue, 02 Aug 2022 10:58:23: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:58:23: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:58:23: #1 total tags in treatment: 4697728 INFO @ Tue, 02 Aug 2022 10:58:23: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:58:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 10:58:23: #1 tags after filtering in treatment: 4697728 INFO @ Tue, 02 Aug 2022 10:58:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:58:23: #1 finished! INFO @ Tue, 02 Aug 2022 10:58:23: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:58:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:58:24: #2 number of paired peaks: 2056 INFO @ Tue, 02 Aug 2022 10:58:24: start model_add_line... INFO @ Tue, 02 Aug 2022 10:58:24: start X-correlation... INFO @ Tue, 02 Aug 2022 10:58:24: end of X-cor INFO @ Tue, 02 Aug 2022 10:58:24: #2 finished! INFO @ Tue, 02 Aug 2022 10:58:24: #2 predicted fragment length is 205 bps INFO @ Tue, 02 Aug 2022 10:58:24: #2 alternative fragment length(s) may be 205 bps INFO @ Tue, 02 Aug 2022 10:58:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX13110345/SRX13110345.05_model.r INFO @ Tue, 02 Aug 2022 10:58:24: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:58:24: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:58:25: 1000000 INFO @ Tue, 02 Aug 2022 10:58:33: 2000000 INFO @ Tue, 02 Aug 2022 10:58:36: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:58:40: 3000000 INFO @ Tue, 02 Aug 2022 10:58:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX13110345/SRX13110345.05_peaks.xls INFO @ Tue, 02 Aug 2022 10:58:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX13110345/SRX13110345.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:58:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX13110345/SRX13110345.05_summits.bed INFO @ Tue, 02 Aug 2022 10:58:42: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (5727 records, 4 fields): 22 millis CompletedMACS2peakCalling BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 10:58:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX13110345/SRX13110345.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX13110345/SRX13110345.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX13110345/SRX13110345.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX13110345/SRX13110345.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, 02 Aug 2022 10:58:46: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:58:46: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:58:47: 4000000 INFO @ Tue, 02 Aug 2022 10:58:53: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:58:53: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:58:53: #1 total tags in treatment: 4697728 INFO @ Tue, 02 Aug 2022 10:58:53: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:58:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 10:58:53: #1 tags after filtering in treatment: 4697728 INFO @ Tue, 02 Aug 2022 10:58:53: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:58:53: #1 finished! INFO @ Tue, 02 Aug 2022 10:58:53: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:58:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:58:53: #2 number of paired peaks: 2056 INFO @ Tue, 02 Aug 2022 10:58:53: start model_add_line... INFO @ Tue, 02 Aug 2022 10:58:53: start X-correlation... INFO @ Tue, 02 Aug 2022 10:58:53: end of X-cor INFO @ Tue, 02 Aug 2022 10:58:53: #2 finished! INFO @ Tue, 02 Aug 2022 10:58:53: #2 predicted fragment length is 205 bps INFO @ Tue, 02 Aug 2022 10:58:53: #2 alternative fragment length(s) may be 205 bps INFO @ Tue, 02 Aug 2022 10:58:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX13110345/SRX13110345.10_model.r INFO @ Tue, 02 Aug 2022 10:58:53: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:58:53: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:58:55: 1000000 INFO @ Tue, 02 Aug 2022 10:59:03: 2000000 INFO @ Tue, 02 Aug 2022 10:59:05: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 10:59:10: 3000000 INFO @ Tue, 02 Aug 2022 10:59:10: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX13110345/SRX13110345.10_peaks.xls INFO @ Tue, 02 Aug 2022 10:59:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX13110345/SRX13110345.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:59:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX13110345/SRX13110345.10_summits.bed INFO @ Tue, 02 Aug 2022 10:59:11: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3725 records, 4 fields): 17 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 10:59:18: 4000000 INFO @ Tue, 02 Aug 2022 10:59:23: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:59:23: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:59:23: #1 total tags in treatment: 4697728 INFO @ Tue, 02 Aug 2022 10:59:23: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:59:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 10:59:23: #1 tags after filtering in treatment: 4697728 INFO @ Tue, 02 Aug 2022 10:59:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:59:23: #1 finished! INFO @ Tue, 02 Aug 2022 10:59:23: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:59:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:59:24: #2 number of paired peaks: 2056 INFO @ Tue, 02 Aug 2022 10:59:24: start model_add_line... INFO @ Tue, 02 Aug 2022 10:59:24: start X-correlation... INFO @ Tue, 02 Aug 2022 10:59:24: end of X-cor INFO @ Tue, 02 Aug 2022 10:59:24: #2 finished! INFO @ Tue, 02 Aug 2022 10:59:24: #2 predicted fragment length is 205 bps INFO @ Tue, 02 Aug 2022 10:59:24: #2 alternative fragment length(s) may be 205 bps INFO @ Tue, 02 Aug 2022 10:59:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX13110345/SRX13110345.20_model.r INFO @ Tue, 02 Aug 2022 10:59:24: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:59:24: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:59:36: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:59:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX13110345/SRX13110345.20_peaks.xls INFO @ Tue, 02 Aug 2022 10:59:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX13110345/SRX13110345.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:59:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX13110345/SRX13110345.20_summits.bed INFO @ Tue, 02 Aug 2022 10:59:42: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1877 records, 4 fields): 17 millis CompletedMACS2peakCalling