Job ID = 14158082 SRX = SRX10040020 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: 00:02:08 7173756 reads; of these: 7173756 (100.00%) were unpaired; of these: 188958 (2.63%) aligned 0 times 5683601 (79.23%) aligned exactly 1 time 1301197 (18.14%) aligned >1 times 97.37% overall alignment rate Time searching: 00:02:08 Overall time: 00:02:08 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] 652385 / 6984798 = 0.0934 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 14:21:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10040020/SRX10040020.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10040020/SRX10040020.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10040020/SRX10040020.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10040020/SRX10040020.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 14:21:56: #1 read tag files... INFO @ Wed, 08 Dec 2021 14:21:56: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 14:22:02: 1000000 INFO @ Wed, 08 Dec 2021 14:22:08: 2000000 INFO @ Wed, 08 Dec 2021 14:22:14: 3000000 INFO @ Wed, 08 Dec 2021 14:22:20: 4000000 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 14:22:25: 5000000 INFO @ Wed, 08 Dec 2021 14:22:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10040020/SRX10040020.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10040020/SRX10040020.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10040020/SRX10040020.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10040020/SRX10040020.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 14:22:26: #1 read tag files... INFO @ Wed, 08 Dec 2021 14:22:26: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 14:22:32: 6000000 INFO @ Wed, 08 Dec 2021 14:22:33: 1000000 INFO @ Wed, 08 Dec 2021 14:22:34: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 14:22:34: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 14:22:34: #1 total tags in treatment: 6332413 INFO @ Wed, 08 Dec 2021 14:22:34: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 14:22:34: #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 14:22:34: #1 tags after filtering in treatment: 6332413 INFO @ Wed, 08 Dec 2021 14:22:34: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 14:22:34: #1 finished! INFO @ Wed, 08 Dec 2021 14:22:34: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 14:22:34: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 14:22:35: #2 number of paired peaks: 368 WARNING @ Wed, 08 Dec 2021 14:22:35: Fewer paired peaks (368) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 368 pairs to build model! INFO @ Wed, 08 Dec 2021 14:22:35: start model_add_line... INFO @ Wed, 08 Dec 2021 14:22:35: start X-correlation... INFO @ Wed, 08 Dec 2021 14:22:35: end of X-cor INFO @ Wed, 08 Dec 2021 14:22:35: #2 finished! INFO @ Wed, 08 Dec 2021 14:22:35: #2 predicted fragment length is 52 bps INFO @ Wed, 08 Dec 2021 14:22:35: #2 alternative fragment length(s) may be 4,52,530 bps INFO @ Wed, 08 Dec 2021 14:22:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10040020/SRX10040020.05_model.r WARNING @ Wed, 08 Dec 2021 14:22:35: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 14:22:35: #2 You may need to consider one of the other alternative d(s): 4,52,530 WARNING @ Wed, 08 Dec 2021 14:22:35: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 14:22:35: #3 Call peaks... INFO @ Wed, 08 Dec 2021 14:22:35: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 14:22:39: 2000000 INFO @ Wed, 08 Dec 2021 14:22:46: 3000000 INFO @ Wed, 08 Dec 2021 14:22:47: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 14:22:52: 4000000 INFO @ Wed, 08 Dec 2021 14:22:53: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10040020/SRX10040020.05_peaks.xls INFO @ Wed, 08 Dec 2021 14:22:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10040020/SRX10040020.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 14:22:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10040020/SRX10040020.05_summits.bed INFO @ Wed, 08 Dec 2021 14:22:53: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (544 records, 4 fields): 2 millis CompletedMACS2peakCalling 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 14:22:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10040020/SRX10040020.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10040020/SRX10040020.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10040020/SRX10040020.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10040020/SRX10040020.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 14:22:56: #1 read tag files... INFO @ Wed, 08 Dec 2021 14:22:56: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 14:22:58: 5000000 INFO @ Wed, 08 Dec 2021 14:23:03: 1000000 INFO @ Wed, 08 Dec 2021 14:23:05: 6000000 INFO @ Wed, 08 Dec 2021 14:23:07: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 14:23:07: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 14:23:07: #1 total tags in treatment: 6332413 INFO @ Wed, 08 Dec 2021 14:23:07: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 14:23:07: #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 14:23:07: #1 tags after filtering in treatment: 6332413 INFO @ Wed, 08 Dec 2021 14:23:07: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 14:23:07: #1 finished! INFO @ Wed, 08 Dec 2021 14:23:07: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 14:23:07: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 14:23:08: #2 number of paired peaks: 368 WARNING @ Wed, 08 Dec 2021 14:23:08: Fewer paired peaks (368) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 368 pairs to build model! INFO @ Wed, 08 Dec 2021 14:23:08: start model_add_line... INFO @ Wed, 08 Dec 2021 14:23:08: start X-correlation... INFO @ Wed, 08 Dec 2021 14:23:08: end of X-cor INFO @ Wed, 08 Dec 2021 14:23:08: #2 finished! INFO @ Wed, 08 Dec 2021 14:23:08: #2 predicted fragment length is 52 bps INFO @ Wed, 08 Dec 2021 14:23:08: #2 alternative fragment length(s) may be 4,52,530 bps INFO @ Wed, 08 Dec 2021 14:23:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10040020/SRX10040020.10_model.r WARNING @ Wed, 08 Dec 2021 14:23:08: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 14:23:08: #2 You may need to consider one of the other alternative d(s): 4,52,530 WARNING @ Wed, 08 Dec 2021 14:23:08: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 14:23:08: #3 Call peaks... INFO @ Wed, 08 Dec 2021 14:23:08: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 14:23:09: 2000000 INFO @ Wed, 08 Dec 2021 14:23:16: 3000000 INFO @ Wed, 08 Dec 2021 14:23:20: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 14:23:22: 4000000 INFO @ Wed, 08 Dec 2021 14:23:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10040020/SRX10040020.10_peaks.xls INFO @ Wed, 08 Dec 2021 14:23:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10040020/SRX10040020.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 14:23:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10040020/SRX10040020.10_summits.bed INFO @ Wed, 08 Dec 2021 14:23:26: Done! BedGraph に変換しました。 BigWig に変換中... pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (321 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 14:23:28: 5000000 INFO @ Wed, 08 Dec 2021 14:23:34: 6000000 INFO @ Wed, 08 Dec 2021 14:23:36: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 14:23:36: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 14:23:36: #1 total tags in treatment: 6332413 INFO @ Wed, 08 Dec 2021 14:23:36: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 14:23:36: #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 14:23:37: #1 tags after filtering in treatment: 6332413 INFO @ Wed, 08 Dec 2021 14:23:37: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 14:23:37: #1 finished! INFO @ Wed, 08 Dec 2021 14:23:37: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 14:23:37: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 14:23:37: #2 number of paired peaks: 368 WARNING @ Wed, 08 Dec 2021 14:23:37: Fewer paired peaks (368) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 368 pairs to build model! INFO @ Wed, 08 Dec 2021 14:23:37: start model_add_line... INFO @ Wed, 08 Dec 2021 14:23:37: start X-correlation... INFO @ Wed, 08 Dec 2021 14:23:37: end of X-cor INFO @ Wed, 08 Dec 2021 14:23:37: #2 finished! INFO @ Wed, 08 Dec 2021 14:23:37: #2 predicted fragment length is 52 bps INFO @ Wed, 08 Dec 2021 14:23:37: #2 alternative fragment length(s) may be 4,52,530 bps INFO @ Wed, 08 Dec 2021 14:23:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10040020/SRX10040020.20_model.r WARNING @ Wed, 08 Dec 2021 14:23:37: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 14:23:37: #2 You may need to consider one of the other alternative d(s): 4,52,530 WARNING @ Wed, 08 Dec 2021 14:23:37: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 14:23:37: #3 Call peaks... INFO @ Wed, 08 Dec 2021 14:23:37: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 14:23:50: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 14:23:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10040020/SRX10040020.20_peaks.xls INFO @ Wed, 08 Dec 2021 14:23:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10040020/SRX10040020.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 14:23:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10040020/SRX10040020.20_summits.bed INFO @ Wed, 08 Dec 2021 14:23:56: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (122 records, 4 fields): 2 millis CompletedMACS2peakCalling