Job ID = 16435591 SRX = SRX13110343 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: 00:03:13 16519686 reads; of these: 16519686 (100.00%) were unpaired; of these: 8973821 (54.32%) aligned 0 times 6633676 (40.16%) aligned exactly 1 time 912189 (5.52%) aligned >1 times 45.68% overall alignment rate Time searching: 00:03:13 Overall time: 00:03:13 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] 1029900 / 7545865 = 0.1365 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 10:57:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX13110343/SRX13110343.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX13110343/SRX13110343.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX13110343/SRX13110343.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX13110343/SRX13110343.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 10:57:23: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:57:23: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:57:29: 1000000 INFO @ Tue, 02 Aug 2022 10:57:36: 2000000 INFO @ Tue, 02 Aug 2022 10:57:43: 3000000 INFO @ Tue, 02 Aug 2022 10:57:50: 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 10:57:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX13110343/SRX13110343.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX13110343/SRX13110343.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX13110343/SRX13110343.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX13110343/SRX13110343.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 10:57:53: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:57:53: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:57:57: 5000000 INFO @ Tue, 02 Aug 2022 10:58:01: 1000000 INFO @ Tue, 02 Aug 2022 10:58:05: 6000000 INFO @ Tue, 02 Aug 2022 10:58:08: 2000000 INFO @ Tue, 02 Aug 2022 10:58:08: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:58:08: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:58:08: #1 total tags in treatment: 6515965 INFO @ Tue, 02 Aug 2022 10:58:08: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:58:08: #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 10:58:09: #1 tags after filtering in treatment: 6515965 INFO @ Tue, 02 Aug 2022 10:58:09: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:58:09: #1 finished! INFO @ Tue, 02 Aug 2022 10:58:09: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:58:09: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:58:09: #2 number of paired peaks: 1070 INFO @ Tue, 02 Aug 2022 10:58:09: start model_add_line... INFO @ Tue, 02 Aug 2022 10:58:09: start X-correlation... INFO @ Tue, 02 Aug 2022 10:58:09: end of X-cor INFO @ Tue, 02 Aug 2022 10:58:09: #2 finished! INFO @ Tue, 02 Aug 2022 10:58:09: #2 predicted fragment length is 189 bps INFO @ Tue, 02 Aug 2022 10:58:09: #2 alternative fragment length(s) may be 189 bps INFO @ Tue, 02 Aug 2022 10:58:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX13110343/SRX13110343.05_model.r INFO @ Tue, 02 Aug 2022 10:58:09: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:58:09: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:58:15: 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 10:58:22: 4000000 INFO @ Tue, 02 Aug 2022 10:58:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX13110343/SRX13110343.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX13110343/SRX13110343.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX13110343/SRX13110343.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX13110343/SRX13110343.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 10:58:23: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:58:23: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:58:25: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:58:29: 5000000 INFO @ Tue, 02 Aug 2022 10:58:31: 1000000 INFO @ Tue, 02 Aug 2022 10:58:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX13110343/SRX13110343.05_peaks.xls INFO @ Tue, 02 Aug 2022 10:58:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX13110343/SRX13110343.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:58:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX13110343/SRX13110343.05_summits.bed INFO @ Tue, 02 Aug 2022 10:58:33: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (5442 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:58:36: 6000000 INFO @ Tue, 02 Aug 2022 10:58:40: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:58:40: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:58:40: #1 total tags in treatment: 6515965 INFO @ Tue, 02 Aug 2022 10:58:40: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:58:40: #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 10:58:40: #1 tags after filtering in treatment: 6515965 INFO @ Tue, 02 Aug 2022 10:58:40: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:58:40: #1 finished! INFO @ Tue, 02 Aug 2022 10:58:40: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:58:40: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:58:40: 2000000 INFO @ Tue, 02 Aug 2022 10:58:40: #2 number of paired peaks: 1070 INFO @ Tue, 02 Aug 2022 10:58:40: start model_add_line... INFO @ Tue, 02 Aug 2022 10:58:40: start X-correlation... INFO @ Tue, 02 Aug 2022 10:58:40: end of X-cor INFO @ Tue, 02 Aug 2022 10:58:40: #2 finished! INFO @ Tue, 02 Aug 2022 10:58:40: #2 predicted fragment length is 189 bps INFO @ Tue, 02 Aug 2022 10:58:40: #2 alternative fragment length(s) may be 189 bps INFO @ Tue, 02 Aug 2022 10:58:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX13110343/SRX13110343.10_model.r INFO @ Tue, 02 Aug 2022 10:58:40: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:58:40: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:58:49: 3000000 INFO @ Tue, 02 Aug 2022 10:58:55: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:58:58: 4000000 INFO @ Tue, 02 Aug 2022 10:59:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX13110343/SRX13110343.10_peaks.xls INFO @ Tue, 02 Aug 2022 10:59:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX13110343/SRX13110343.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:59:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX13110343/SRX13110343.10_summits.bed INFO @ Tue, 02 Aug 2022 10:59:02: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3047 records, 4 fields): 18 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 10:59:07: 5000000 INFO @ Tue, 02 Aug 2022 10:59:16: 6000000 INFO @ Tue, 02 Aug 2022 10:59:20: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:59:20: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:59:20: #1 total tags in treatment: 6515965 INFO @ Tue, 02 Aug 2022 10:59:20: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:59:20: #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 10:59:20: #1 tags after filtering in treatment: 6515965 INFO @ Tue, 02 Aug 2022 10:59:20: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:59:20: #1 finished! INFO @ Tue, 02 Aug 2022 10:59:20: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:59:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:59:20: #2 number of paired peaks: 1070 INFO @ Tue, 02 Aug 2022 10:59:20: start model_add_line... INFO @ Tue, 02 Aug 2022 10:59:20: start X-correlation... INFO @ Tue, 02 Aug 2022 10:59:20: end of X-cor INFO @ Tue, 02 Aug 2022 10:59:20: #2 finished! INFO @ Tue, 02 Aug 2022 10:59:20: #2 predicted fragment length is 189 bps INFO @ Tue, 02 Aug 2022 10:59:20: #2 alternative fragment length(s) may be 189 bps INFO @ Tue, 02 Aug 2022 10:59:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX13110343/SRX13110343.20_model.r INFO @ Tue, 02 Aug 2022 10:59:20: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:59:20: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 10:59:36: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:59:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX13110343/SRX13110343.20_peaks.xls INFO @ Tue, 02 Aug 2022 10:59:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX13110343/SRX13110343.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:59:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX13110343/SRX13110343.20_summits.bed INFO @ Tue, 02 Aug 2022 10:59:44: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1327 records, 4 fields): 34 millis CompletedMACS2peakCalling