Job ID = 16436119 SRX = SRX13110351 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: 00:03:46 12742419 reads; of these: 12742419 (100.00%) were unpaired; of these: 748029 (5.87%) aligned 0 times 10451815 (82.02%) aligned exactly 1 time 1542575 (12.11%) aligned >1 times 94.13% overall alignment rate Time searching: 00:03:46 Overall time: 00:03:46 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_sort_core] merging from 8 files... [bam_rmdupse_core] 2162460 / 11994390 = 0.1803 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 11:02:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX13110351/SRX13110351.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX13110351/SRX13110351.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX13110351/SRX13110351.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX13110351/SRX13110351.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 11:02:04: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:02:04: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:02:10: 1000000 INFO @ Tue, 02 Aug 2022 11:02:16: 2000000 INFO @ Tue, 02 Aug 2022 11:02:22: 3000000 INFO @ Tue, 02 Aug 2022 11:02:28: 4000000 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 11:02:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX13110351/SRX13110351.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX13110351/SRX13110351.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX13110351/SRX13110351.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX13110351/SRX13110351.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 11:02:33: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:02:33: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:02:34: 5000000 INFO @ Tue, 02 Aug 2022 11:02:41: 6000000 INFO @ Tue, 02 Aug 2022 11:02:42: 1000000 INFO @ Tue, 02 Aug 2022 11:02:48: 7000000 INFO @ Tue, 02 Aug 2022 11:02:50: 2000000 INFO @ Tue, 02 Aug 2022 11:02:55: 8000000 INFO @ Tue, 02 Aug 2022 11:02:58: 3000000 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 11:03:02: 9000000 INFO @ Tue, 02 Aug 2022 11:03:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX13110351/SRX13110351.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX13110351/SRX13110351.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX13110351/SRX13110351.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX13110351/SRX13110351.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 11:03:04: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:03:04: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:03:06: 4000000 INFO @ Tue, 02 Aug 2022 11:03:08: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 11:03:08: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 11:03:08: #1 total tags in treatment: 9831930 INFO @ Tue, 02 Aug 2022 11:03:08: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:03:08: #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 11:03:08: #1 tags after filtering in treatment: 9831930 INFO @ Tue, 02 Aug 2022 11:03:08: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 11:03:08: #1 finished! INFO @ Tue, 02 Aug 2022 11:03:08: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:03:08: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:03:09: #2 number of paired peaks: 1897 INFO @ Tue, 02 Aug 2022 11:03:09: start model_add_line... INFO @ Tue, 02 Aug 2022 11:03:09: start X-correlation... INFO @ Tue, 02 Aug 2022 11:03:09: end of X-cor INFO @ Tue, 02 Aug 2022 11:03:09: #2 finished! INFO @ Tue, 02 Aug 2022 11:03:09: #2 predicted fragment length is 236 bps INFO @ Tue, 02 Aug 2022 11:03:09: #2 alternative fragment length(s) may be 236 bps INFO @ Tue, 02 Aug 2022 11:03:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX13110351/SRX13110351.05_model.r INFO @ Tue, 02 Aug 2022 11:03:09: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:03:09: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:03:12: 1000000 INFO @ Tue, 02 Aug 2022 11:03:14: 5000000 INFO @ Tue, 02 Aug 2022 11:03:20: 2000000 INFO @ Tue, 02 Aug 2022 11:03:22: 6000000 INFO @ Tue, 02 Aug 2022 11:03:28: 3000000 INFO @ Tue, 02 Aug 2022 11:03:31: 7000000 INFO @ Tue, 02 Aug 2022 11:03:34: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:03:37: 4000000 INFO @ Tue, 02 Aug 2022 11:03:38: 8000000 INFO @ Tue, 02 Aug 2022 11:03:45: 5000000 INFO @ Tue, 02 Aug 2022 11:03:46: 9000000 INFO @ Tue, 02 Aug 2022 11:03:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX13110351/SRX13110351.05_peaks.xls INFO @ Tue, 02 Aug 2022 11:03:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX13110351/SRX13110351.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:03:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX13110351/SRX13110351.05_summits.bed INFO @ Tue, 02 Aug 2022 11:03:47: Done! pass1 - making usageList (7 chroms): 1 millis BedGraph に変換しました。 BigWig に変換中... pass2 - checking and writing primary data (9351 records, 4 fields): 347 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 11:03:53: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 11:03:53: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 11:03:53: #1 total tags in treatment: 9831930 INFO @ Tue, 02 Aug 2022 11:03:53: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:03:53: #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 11:03:53: 6000000 INFO @ Tue, 02 Aug 2022 11:03:53: #1 tags after filtering in treatment: 9831930 INFO @ Tue, 02 Aug 2022 11:03:53: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 11:03:53: #1 finished! INFO @ Tue, 02 Aug 2022 11:03:53: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:03:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:03:54: #2 number of paired peaks: 1897 INFO @ Tue, 02 Aug 2022 11:03:54: start model_add_line... INFO @ Tue, 02 Aug 2022 11:03:54: start X-correlation... INFO @ Tue, 02 Aug 2022 11:03:54: end of X-cor INFO @ Tue, 02 Aug 2022 11:03:54: #2 finished! INFO @ Tue, 02 Aug 2022 11:03:54: #2 predicted fragment length is 236 bps INFO @ Tue, 02 Aug 2022 11:03:54: #2 alternative fragment length(s) may be 236 bps INFO @ Tue, 02 Aug 2022 11:03:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX13110351/SRX13110351.10_model.r INFO @ Tue, 02 Aug 2022 11:03:54: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:03:54: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:04:01: 7000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 11:04:08: 8000000 INFO @ Tue, 02 Aug 2022 11:04:16: 9000000 INFO @ Tue, 02 Aug 2022 11:04:21: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:04:22: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 11:04:22: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 11:04:22: #1 total tags in treatment: 9831930 INFO @ Tue, 02 Aug 2022 11:04:22: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:04:22: #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 11:04:22: #1 tags after filtering in treatment: 9831930 INFO @ Tue, 02 Aug 2022 11:04:22: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 11:04:22: #1 finished! INFO @ Tue, 02 Aug 2022 11:04:22: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:04:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:04:23: #2 number of paired peaks: 1897 INFO @ Tue, 02 Aug 2022 11:04:23: start model_add_line... INFO @ Tue, 02 Aug 2022 11:04:23: start X-correlation... INFO @ Tue, 02 Aug 2022 11:04:23: end of X-cor INFO @ Tue, 02 Aug 2022 11:04:23: #2 finished! INFO @ Tue, 02 Aug 2022 11:04:23: #2 predicted fragment length is 236 bps INFO @ Tue, 02 Aug 2022 11:04:23: #2 alternative fragment length(s) may be 236 bps INFO @ Tue, 02 Aug 2022 11:04:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX13110351/SRX13110351.20_model.r INFO @ Tue, 02 Aug 2022 11:04:23: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:04:23: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:04:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX13110351/SRX13110351.10_peaks.xls INFO @ Tue, 02 Aug 2022 11:04:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX13110351/SRX13110351.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:04:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX13110351/SRX13110351.10_summits.bed INFO @ Tue, 02 Aug 2022 11:04:34: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (6719 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 11:04:48: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:05:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX13110351/SRX13110351.20_peaks.xls INFO @ Tue, 02 Aug 2022 11:05:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX13110351/SRX13110351.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:05:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX13110351/SRX13110351.20_summits.bed INFO @ Tue, 02 Aug 2022 11:05:01: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4167 records, 4 fields): 21 millis CompletedMACS2peakCalling