Job ID = 16435513 SRX = SRX13110329 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: 00:04:38 13248824 reads; of these: 13248824 (100.00%) were unpaired; of these: 775537 (5.85%) aligned 0 times 10680949 (80.62%) aligned exactly 1 time 1792338 (13.53%) aligned >1 times 94.15% overall alignment rate Time searching: 00:04:38 Overall time: 00:04:38 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] 3398536 / 12473287 = 0.2725 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 10:52:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX13110329/SRX13110329.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX13110329/SRX13110329.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX13110329/SRX13110329.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX13110329/SRX13110329.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 10:52:53: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:52:53: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:52:59: 1000000 INFO @ Tue, 02 Aug 2022 10:53:04: 2000000 INFO @ Tue, 02 Aug 2022 10:53:09: 3000000 INFO @ Tue, 02 Aug 2022 10:53:14: 4000000 INFO @ Tue, 02 Aug 2022 10:53:20: 5000000 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 10:53:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX13110329/SRX13110329.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX13110329/SRX13110329.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX13110329/SRX13110329.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX13110329/SRX13110329.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 10:53:23: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:53:23: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:53:26: 6000000 INFO @ Tue, 02 Aug 2022 10:53:29: 1000000 INFO @ Tue, 02 Aug 2022 10:53:31: 7000000 INFO @ Tue, 02 Aug 2022 10:53:36: 2000000 INFO @ Tue, 02 Aug 2022 10:53:37: 8000000 INFO @ Tue, 02 Aug 2022 10:53:43: 3000000 INFO @ Tue, 02 Aug 2022 10:53:43: 9000000 INFO @ Tue, 02 Aug 2022 10:53:43: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:53:43: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:53:43: #1 total tags in treatment: 9074751 INFO @ Tue, 02 Aug 2022 10:53:43: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:53:43: #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 10:53:43: #1 tags after filtering in treatment: 9074751 INFO @ Tue, 02 Aug 2022 10:53:43: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:53:43: #1 finished! INFO @ Tue, 02 Aug 2022 10:53:43: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:53:43: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:53:44: #2 number of paired peaks: 886 WARNING @ Tue, 02 Aug 2022 10:53:44: Fewer paired peaks (886) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 886 pairs to build model! INFO @ Tue, 02 Aug 2022 10:53:44: start model_add_line... INFO @ Tue, 02 Aug 2022 10:53:44: start X-correlation... INFO @ Tue, 02 Aug 2022 10:53:44: end of X-cor INFO @ Tue, 02 Aug 2022 10:53:44: #2 finished! INFO @ Tue, 02 Aug 2022 10:53:44: #2 predicted fragment length is 178 bps INFO @ Tue, 02 Aug 2022 10:53:44: #2 alternative fragment length(s) may be 178 bps INFO @ Tue, 02 Aug 2022 10:53:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX13110329/SRX13110329.05_model.r INFO @ Tue, 02 Aug 2022 10:53:44: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:53:44: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:53:49: 4000000 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 10:53:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX13110329/SRX13110329.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX13110329/SRX13110329.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX13110329/SRX13110329.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX13110329/SRX13110329.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 10:53:53: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:53:53: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:53:55: 5000000 INFO @ Tue, 02 Aug 2022 10:53:59: 1000000 INFO @ Tue, 02 Aug 2022 10:54:02: 6000000 INFO @ Tue, 02 Aug 2022 10:54:05: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:54:05: 2000000 INFO @ Tue, 02 Aug 2022 10:54:09: 7000000 INFO @ Tue, 02 Aug 2022 10:54:11: 3000000 INFO @ Tue, 02 Aug 2022 10:54:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX13110329/SRX13110329.05_peaks.xls INFO @ Tue, 02 Aug 2022 10:54:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX13110329/SRX13110329.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:54:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX13110329/SRX13110329.05_summits.bed INFO @ Tue, 02 Aug 2022 10:54:15: Done! INFO @ Tue, 02 Aug 2022 10:54:15: 8000000 pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2057 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:54:17: 4000000 INFO @ Tue, 02 Aug 2022 10:54:21: 9000000 INFO @ Tue, 02 Aug 2022 10:54:21: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:54:21: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:54:21: #1 total tags in treatment: 9074751 INFO @ Tue, 02 Aug 2022 10:54:21: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:54:21: #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 10:54:21: #1 tags after filtering in treatment: 9074751 INFO @ Tue, 02 Aug 2022 10:54:22: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:54:22: #1 finished! INFO @ Tue, 02 Aug 2022 10:54:22: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:54:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:54:22: #2 number of paired peaks: 886 WARNING @ Tue, 02 Aug 2022 10:54:22: Fewer paired peaks (886) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 886 pairs to build model! INFO @ Tue, 02 Aug 2022 10:54:22: start model_add_line... INFO @ Tue, 02 Aug 2022 10:54:22: start X-correlation... INFO @ Tue, 02 Aug 2022 10:54:22: end of X-cor INFO @ Tue, 02 Aug 2022 10:54:22: #2 finished! INFO @ Tue, 02 Aug 2022 10:54:22: #2 predicted fragment length is 178 bps INFO @ Tue, 02 Aug 2022 10:54:22: #2 alternative fragment length(s) may be 178 bps INFO @ Tue, 02 Aug 2022 10:54:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX13110329/SRX13110329.10_model.r INFO @ Tue, 02 Aug 2022 10:54:22: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:54:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:54:23: 5000000 INFO @ Tue, 02 Aug 2022 10:54:28: 6000000 INFO @ Tue, 02 Aug 2022 10:54:33: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 10:54:38: 8000000 INFO @ Tue, 02 Aug 2022 10:54:42: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:54:44: 9000000 INFO @ Tue, 02 Aug 2022 10:54:44: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:54:44: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:54:44: #1 total tags in treatment: 9074751 INFO @ Tue, 02 Aug 2022 10:54:44: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:54:44: #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 10:54:44: #1 tags after filtering in treatment: 9074751 INFO @ Tue, 02 Aug 2022 10:54:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:54:44: #1 finished! INFO @ Tue, 02 Aug 2022 10:54:44: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:54:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:54:45: #2 number of paired peaks: 886 WARNING @ Tue, 02 Aug 2022 10:54:45: Fewer paired peaks (886) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 886 pairs to build model! INFO @ Tue, 02 Aug 2022 10:54:45: start model_add_line... INFO @ Tue, 02 Aug 2022 10:54:45: start X-correlation... INFO @ Tue, 02 Aug 2022 10:54:45: end of X-cor INFO @ Tue, 02 Aug 2022 10:54:45: #2 finished! INFO @ Tue, 02 Aug 2022 10:54:45: #2 predicted fragment length is 178 bps INFO @ Tue, 02 Aug 2022 10:54:45: #2 alternative fragment length(s) may be 178 bps INFO @ Tue, 02 Aug 2022 10:54:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX13110329/SRX13110329.20_model.r INFO @ Tue, 02 Aug 2022 10:54:45: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:54:45: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:54:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX13110329/SRX13110329.10_peaks.xls INFO @ Tue, 02 Aug 2022 10:54:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX13110329/SRX13110329.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:54:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX13110329/SRX13110329.10_summits.bed INFO @ Tue, 02 Aug 2022 10:54:53: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1337 records, 4 fields): 25 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 10:55:06: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:55:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX13110329/SRX13110329.20_peaks.xls INFO @ Tue, 02 Aug 2022 10:55:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX13110329/SRX13110329.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:55:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX13110329/SRX13110329.20_summits.bed INFO @ Tue, 02 Aug 2022 10:55:16: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (873 records, 4 fields): 16 millis CompletedMACS2peakCalling