Job ID = 14160842 SRX = SRX10569206 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: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:05:25 13046990 reads; of these: 13046990 (100.00%) were unpaired; of these: 12003245 (92.00%) aligned 0 times 823135 (6.31%) aligned exactly 1 time 220610 (1.69%) aligned >1 times 8.00% overall alignment rate Time searching: 00:05:26 Overall time: 00:05:26 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] 161461 / 1043745 = 0.1547 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 @ Thu, 09 Dec 2021 04:37:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10569206/SRX10569206.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10569206/SRX10569206.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10569206/SRX10569206.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10569206/SRX10569206.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 @ Thu, 09 Dec 2021 04:37:06: #1 read tag files... INFO @ Thu, 09 Dec 2021 04:37:06: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 04:37:14: #1 tag size is determined as 75 bps INFO @ Thu, 09 Dec 2021 04:37:14: #1 tag size = 75 INFO @ Thu, 09 Dec 2021 04:37:14: #1 total tags in treatment: 882284 INFO @ Thu, 09 Dec 2021 04:37:14: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 04:37:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 04:37:14: #1 tags after filtering in treatment: 882284 INFO @ Thu, 09 Dec 2021 04:37:14: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 04:37:14: #1 finished! INFO @ Thu, 09 Dec 2021 04:37:14: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 04:37:14: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 04:37:14: #2 number of paired peaks: 464 WARNING @ Thu, 09 Dec 2021 04:37:14: Fewer paired peaks (464) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 464 pairs to build model! INFO @ Thu, 09 Dec 2021 04:37:14: start model_add_line... INFO @ Thu, 09 Dec 2021 04:37:14: start X-correlation... INFO @ Thu, 09 Dec 2021 04:37:14: end of X-cor INFO @ Thu, 09 Dec 2021 04:37:14: #2 finished! INFO @ Thu, 09 Dec 2021 04:37:14: #2 predicted fragment length is 65 bps INFO @ Thu, 09 Dec 2021 04:37:14: #2 alternative fragment length(s) may be 65,250,468,485 bps INFO @ Thu, 09 Dec 2021 04:37:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10569206/SRX10569206.05_model.r WARNING @ Thu, 09 Dec 2021 04:37:14: #2 Since the d (65) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 04:37:14: #2 You may need to consider one of the other alternative d(s): 65,250,468,485 WARNING @ Thu, 09 Dec 2021 04:37:14: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 04:37:14: #3 Call peaks... INFO @ Thu, 09 Dec 2021 04:37:14: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 04:37:17: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 04:37:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10569206/SRX10569206.05_peaks.xls INFO @ Thu, 09 Dec 2021 04:37:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10569206/SRX10569206.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 04:37:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10569206/SRX10569206.05_summits.bed INFO @ Thu, 09 Dec 2021 04:37:19: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (287 records, 4 fields): 2 millis CompletedMACS2peakCalling 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 @ Thu, 09 Dec 2021 04:37:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10569206/SRX10569206.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10569206/SRX10569206.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10569206/SRX10569206.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10569206/SRX10569206.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 @ Thu, 09 Dec 2021 04:37:36: #1 read tag files... INFO @ Thu, 09 Dec 2021 04:37:36: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 04:37:45: #1 tag size is determined as 75 bps INFO @ Thu, 09 Dec 2021 04:37:45: #1 tag size = 75 INFO @ Thu, 09 Dec 2021 04:37:45: #1 total tags in treatment: 882284 INFO @ Thu, 09 Dec 2021 04:37:45: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 04:37:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 04:37:45: #1 tags after filtering in treatment: 882284 INFO @ Thu, 09 Dec 2021 04:37:45: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 04:37:45: #1 finished! INFO @ Thu, 09 Dec 2021 04:37:45: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 04:37:45: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 04:37:45: #2 number of paired peaks: 464 WARNING @ Thu, 09 Dec 2021 04:37:45: Fewer paired peaks (464) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 464 pairs to build model! INFO @ Thu, 09 Dec 2021 04:37:45: start model_add_line... INFO @ Thu, 09 Dec 2021 04:37:45: start X-correlation... INFO @ Thu, 09 Dec 2021 04:37:45: end of X-cor INFO @ Thu, 09 Dec 2021 04:37:45: #2 finished! INFO @ Thu, 09 Dec 2021 04:37:45: #2 predicted fragment length is 65 bps INFO @ Thu, 09 Dec 2021 04:37:45: #2 alternative fragment length(s) may be 65,250,468,485 bps INFO @ Thu, 09 Dec 2021 04:37:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10569206/SRX10569206.10_model.r WARNING @ Thu, 09 Dec 2021 04:37:45: #2 Since the d (65) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 04:37:45: #2 You may need to consider one of the other alternative d(s): 65,250,468,485 WARNING @ Thu, 09 Dec 2021 04:37:45: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 04:37:45: #3 Call peaks... INFO @ Thu, 09 Dec 2021 04:37:45: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 04:37:48: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 04:37:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10569206/SRX10569206.10_peaks.xls INFO @ Thu, 09 Dec 2021 04:37:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10569206/SRX10569206.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 04:37:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10569206/SRX10569206.10_summits.bed INFO @ Thu, 09 Dec 2021 04:37:50: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (158 records, 4 fields): 3 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 @ Thu, 09 Dec 2021 04:38:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10569206/SRX10569206.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10569206/SRX10569206.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10569206/SRX10569206.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10569206/SRX10569206.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 @ Thu, 09 Dec 2021 04:38:06: #1 read tag files... INFO @ Thu, 09 Dec 2021 04:38:06: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 04:38:14: #1 tag size is determined as 75 bps INFO @ Thu, 09 Dec 2021 04:38:14: #1 tag size = 75 INFO @ Thu, 09 Dec 2021 04:38:14: #1 total tags in treatment: 882284 INFO @ Thu, 09 Dec 2021 04:38:14: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 04:38:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 04:38:14: #1 tags after filtering in treatment: 882284 INFO @ Thu, 09 Dec 2021 04:38:14: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 04:38:14: #1 finished! INFO @ Thu, 09 Dec 2021 04:38:14: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 04:38:14: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 04:38:14: #2 number of paired peaks: 464 WARNING @ Thu, 09 Dec 2021 04:38:14: Fewer paired peaks (464) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 464 pairs to build model! INFO @ Thu, 09 Dec 2021 04:38:14: start model_add_line... INFO @ Thu, 09 Dec 2021 04:38:14: start X-correlation... INFO @ Thu, 09 Dec 2021 04:38:14: end of X-cor INFO @ Thu, 09 Dec 2021 04:38:14: #2 finished! INFO @ Thu, 09 Dec 2021 04:38:14: #2 predicted fragment length is 65 bps INFO @ Thu, 09 Dec 2021 04:38:14: #2 alternative fragment length(s) may be 65,250,468,485 bps INFO @ Thu, 09 Dec 2021 04:38:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10569206/SRX10569206.20_model.r WARNING @ Thu, 09 Dec 2021 04:38:14: #2 Since the d (65) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 04:38:14: #2 You may need to consider one of the other alternative d(s): 65,250,468,485 WARNING @ Thu, 09 Dec 2021 04:38:14: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 04:38:14: #3 Call peaks... INFO @ Thu, 09 Dec 2021 04:38:14: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 04:38:17: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 04:38:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10569206/SRX10569206.20_peaks.xls INFO @ Thu, 09 Dec 2021 04:38:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10569206/SRX10569206.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 04:38:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10569206/SRX10569206.20_summits.bed INFO @ Thu, 09 Dec 2021 04:38:18: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (77 records, 4 fields): 1 millis CompletedMACS2peakCalling