Job ID = 16434971 SRX = SRX11633391 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: 00:03:33 9789573 reads; of these: 9789573 (100.00%) were unpaired; of these: 542639 (5.54%) aligned 0 times 7927842 (80.98%) aligned exactly 1 time 1319092 (13.47%) aligned >1 times 94.46% overall alignment rate Time searching: 00:03:33 Overall time: 00:03:33 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] 515576 / 9246934 = 0.0558 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 10:30:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX11633391/SRX11633391.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX11633391/SRX11633391.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX11633391/SRX11633391.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX11633391/SRX11633391.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 10:30:04: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:30:04: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:30:12: 1000000 INFO @ Tue, 02 Aug 2022 10:30:20: 2000000 INFO @ Tue, 02 Aug 2022 10:30:28: 3000000 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 10:30:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX11633391/SRX11633391.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX11633391/SRX11633391.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX11633391/SRX11633391.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX11633391/SRX11633391.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 10:30:33: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:30:33: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:30:36: 4000000 INFO @ Tue, 02 Aug 2022 10:30:42: 1000000 INFO @ Tue, 02 Aug 2022 10:30:45: 5000000 INFO @ Tue, 02 Aug 2022 10:30:51: 2000000 INFO @ Tue, 02 Aug 2022 10:30:53: 6000000 INFO @ Tue, 02 Aug 2022 10:31:00: 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 10:31:02: 7000000 INFO @ Tue, 02 Aug 2022 10:31:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX11633391/SRX11633391.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX11633391/SRX11633391.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX11633391/SRX11633391.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX11633391/SRX11633391.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 10:31:04: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:31:04: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:31:08: 4000000 INFO @ Tue, 02 Aug 2022 10:31:10: 8000000 INFO @ Tue, 02 Aug 2022 10:31:12: 1000000 INFO @ Tue, 02 Aug 2022 10:31:16: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 10:31:16: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 10:31:16: #1 total tags in treatment: 8731358 INFO @ Tue, 02 Aug 2022 10:31:16: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:31:16: #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 10:31:16: #1 tags after filtering in treatment: 8731358 INFO @ Tue, 02 Aug 2022 10:31:16: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:31:16: #1 finished! INFO @ Tue, 02 Aug 2022 10:31:16: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:31:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:31:17: 5000000 INFO @ Tue, 02 Aug 2022 10:31:17: #2 number of paired peaks: 263 WARNING @ Tue, 02 Aug 2022 10:31:17: Fewer paired peaks (263) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 263 pairs to build model! INFO @ Tue, 02 Aug 2022 10:31:17: start model_add_line... INFO @ Tue, 02 Aug 2022 10:31:17: start X-correlation... INFO @ Tue, 02 Aug 2022 10:31:17: end of X-cor INFO @ Tue, 02 Aug 2022 10:31:17: #2 finished! INFO @ Tue, 02 Aug 2022 10:31:17: #2 predicted fragment length is 61 bps INFO @ Tue, 02 Aug 2022 10:31:17: #2 alternative fragment length(s) may be 4,61 bps INFO @ Tue, 02 Aug 2022 10:31:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX11633391/SRX11633391.05_model.r WARNING @ Tue, 02 Aug 2022 10:31:17: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:31:17: #2 You may need to consider one of the other alternative d(s): 4,61 WARNING @ Tue, 02 Aug 2022 10:31:17: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 10:31:17: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:31:17: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:31:21: 2000000 INFO @ Tue, 02 Aug 2022 10:31:26: 6000000 INFO @ Tue, 02 Aug 2022 10:31:30: 3000000 INFO @ Tue, 02 Aug 2022 10:31:33: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:31:34: 7000000 INFO @ Tue, 02 Aug 2022 10:31:38: 4000000 INFO @ Tue, 02 Aug 2022 10:31:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX11633391/SRX11633391.05_peaks.xls INFO @ Tue, 02 Aug 2022 10:31:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX11633391/SRX11633391.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:31:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX11633391/SRX11633391.05_summits.bed INFO @ Tue, 02 Aug 2022 10:31:42: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (433 records, 4 fields): 27 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:31:43: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 10:31:46: 5000000 INFO @ Tue, 02 Aug 2022 10:31:49: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 10:31:49: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 10:31:49: #1 total tags in treatment: 8731358 INFO @ Tue, 02 Aug 2022 10:31:49: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:31:49: #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 10:31:49: #1 tags after filtering in treatment: 8731358 INFO @ Tue, 02 Aug 2022 10:31:49: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:31:49: #1 finished! INFO @ Tue, 02 Aug 2022 10:31:49: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:31:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:31:50: #2 number of paired peaks: 263 WARNING @ Tue, 02 Aug 2022 10:31:50: Fewer paired peaks (263) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 263 pairs to build model! INFO @ Tue, 02 Aug 2022 10:31:50: start model_add_line... INFO @ Tue, 02 Aug 2022 10:31:50: start X-correlation... INFO @ Tue, 02 Aug 2022 10:31:50: end of X-cor INFO @ Tue, 02 Aug 2022 10:31:50: #2 finished! INFO @ Tue, 02 Aug 2022 10:31:50: #2 predicted fragment length is 61 bps INFO @ Tue, 02 Aug 2022 10:31:50: #2 alternative fragment length(s) may be 4,61 bps INFO @ Tue, 02 Aug 2022 10:31:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX11633391/SRX11633391.10_model.r WARNING @ Tue, 02 Aug 2022 10:31:50: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:31:50: #2 You may need to consider one of the other alternative d(s): 4,61 WARNING @ Tue, 02 Aug 2022 10:31:50: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 10:31:50: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:31:50: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:31:54: 6000000 INFO @ Tue, 02 Aug 2022 10:32:02: 7000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 10:32:06: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:32:09: 8000000 INFO @ Tue, 02 Aug 2022 10:32:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX11633391/SRX11633391.10_peaks.xls INFO @ Tue, 02 Aug 2022 10:32:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX11633391/SRX11633391.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:32:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX11633391/SRX11633391.10_summits.bed INFO @ Tue, 02 Aug 2022 10:32:14: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (294 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:32:15: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 10:32:15: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 10:32:15: #1 total tags in treatment: 8731358 INFO @ Tue, 02 Aug 2022 10:32:15: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:32:15: #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 10:32:15: #1 tags after filtering in treatment: 8731358 INFO @ Tue, 02 Aug 2022 10:32:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:32:15: #1 finished! INFO @ Tue, 02 Aug 2022 10:32:15: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:32:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:32:15: #2 number of paired peaks: 263 WARNING @ Tue, 02 Aug 2022 10:32:15: Fewer paired peaks (263) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 263 pairs to build model! INFO @ Tue, 02 Aug 2022 10:32:15: start model_add_line... INFO @ Tue, 02 Aug 2022 10:32:15: start X-correlation... INFO @ Tue, 02 Aug 2022 10:32:16: end of X-cor INFO @ Tue, 02 Aug 2022 10:32:16: #2 finished! INFO @ Tue, 02 Aug 2022 10:32:16: #2 predicted fragment length is 61 bps INFO @ Tue, 02 Aug 2022 10:32:16: #2 alternative fragment length(s) may be 4,61 bps INFO @ Tue, 02 Aug 2022 10:32:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX11633391/SRX11633391.20_model.r WARNING @ Tue, 02 Aug 2022 10:32:16: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:32:16: #2 You may need to consider one of the other alternative d(s): 4,61 WARNING @ Tue, 02 Aug 2022 10:32:16: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 10:32:16: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:32:16: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:32:32: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:32:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX11633391/SRX11633391.20_peaks.xls INFO @ Tue, 02 Aug 2022 10:32:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX11633391/SRX11633391.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:32:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX11633391/SRX11633391.20_summits.bed INFO @ Tue, 02 Aug 2022 10:32:40: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (159 records, 4 fields): 75 millis CompletedMACS2peakCalling