Job ID = 6626403 SRX = SRX7262200 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: 00:00:57 4163318 reads; of these: 4163318 (100.00%) were unpaired; of these: 183366 (4.40%) aligned 0 times 3141502 (75.46%) aligned exactly 1 time 838450 (20.14%) aligned >1 times 95.60% overall alignment rate Time searching: 00:00:57 Overall time: 00:00:57 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] 242120 / 3979952 = 0.0608 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 14 Jul 2020 06:59:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7262200/SRX7262200.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7262200/SRX7262200.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7262200/SRX7262200.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7262200/SRX7262200.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, 14 Jul 2020 06:59:38: #1 read tag files... INFO @ Tue, 14 Jul 2020 06:59:38: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 06:59:43: 1000000 INFO @ Tue, 14 Jul 2020 06:59:48: 2000000 INFO @ Tue, 14 Jul 2020 06:59:53: 3000000 INFO @ Tue, 14 Jul 2020 06:59:56: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 06:59:56: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 06:59:56: #1 total tags in treatment: 3737832 INFO @ Tue, 14 Jul 2020 06:59:56: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 06:59:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 06:59:56: #1 tags after filtering in treatment: 3737832 INFO @ Tue, 14 Jul 2020 06:59:56: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 06:59:56: #1 finished! INFO @ Tue, 14 Jul 2020 06:59:56: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 06:59:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 06:59:56: #2 number of paired peaks: 496 WARNING @ Tue, 14 Jul 2020 06:59:56: Fewer paired peaks (496) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 496 pairs to build model! INFO @ Tue, 14 Jul 2020 06:59:56: start model_add_line... INFO @ Tue, 14 Jul 2020 06:59:56: start X-correlation... INFO @ Tue, 14 Jul 2020 06:59:56: end of X-cor INFO @ Tue, 14 Jul 2020 06:59:56: #2 finished! INFO @ Tue, 14 Jul 2020 06:59:56: #2 predicted fragment length is 48 bps INFO @ Tue, 14 Jul 2020 06:59:56: #2 alternative fragment length(s) may be 48,510 bps INFO @ Tue, 14 Jul 2020 06:59:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7262200/SRX7262200.05_model.r WARNING @ Tue, 14 Jul 2020 06:59:56: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 06:59:56: #2 You may need to consider one of the other alternative d(s): 48,510 WARNING @ Tue, 14 Jul 2020 06:59:56: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 06:59:56: #3 Call peaks... INFO @ Tue, 14 Jul 2020 06:59:56: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:00:04: #3 Call peaks for each chromosome... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 14 Jul 2020 07:00:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7262200/SRX7262200.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7262200/SRX7262200.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7262200/SRX7262200.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7262200/SRX7262200.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, 14 Jul 2020 07:00:08: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:00:08: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:00:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7262200/SRX7262200.05_peaks.xls INFO @ Tue, 14 Jul 2020 07:00:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7262200/SRX7262200.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:00:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7262200/SRX7262200.05_summits.bed INFO @ Tue, 14 Jul 2020 07:00:08: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (534 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 07:00:13: 1000000 INFO @ Tue, 14 Jul 2020 07:00:18: 2000000 INFO @ Tue, 14 Jul 2020 07:00:22: 3000000 INFO @ Tue, 14 Jul 2020 07:00:26: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 07:00:26: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 07:00:26: #1 total tags in treatment: 3737832 INFO @ Tue, 14 Jul 2020 07:00:26: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:00:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 07:00:26: #1 tags after filtering in treatment: 3737832 INFO @ Tue, 14 Jul 2020 07:00:26: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:00:26: #1 finished! INFO @ Tue, 14 Jul 2020 07:00:26: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:00:26: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:00:26: #2 number of paired peaks: 496 WARNING @ Tue, 14 Jul 2020 07:00:26: Fewer paired peaks (496) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 496 pairs to build model! INFO @ Tue, 14 Jul 2020 07:00:26: start model_add_line... INFO @ Tue, 14 Jul 2020 07:00:26: start X-correlation... INFO @ Tue, 14 Jul 2020 07:00:26: end of X-cor INFO @ Tue, 14 Jul 2020 07:00:26: #2 finished! INFO @ Tue, 14 Jul 2020 07:00:26: #2 predicted fragment length is 48 bps INFO @ Tue, 14 Jul 2020 07:00:26: #2 alternative fragment length(s) may be 48,510 bps INFO @ Tue, 14 Jul 2020 07:00:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7262200/SRX7262200.10_model.r WARNING @ Tue, 14 Jul 2020 07:00:26: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 07:00:26: #2 You may need to consider one of the other alternative d(s): 48,510 WARNING @ Tue, 14 Jul 2020 07:00:26: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 07:00:26: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:00:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:00:34: #3 Call peaks for each chromosome... BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 14 Jul 2020 07:00:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7262200/SRX7262200.10_peaks.xls INFO @ Tue, 14 Jul 2020 07:00:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7262200/SRX7262200.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:00:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7262200/SRX7262200.10_summits.bed INFO @ Tue, 14 Jul 2020 07:00:38: Done! INFO @ Tue, 14 Jul 2020 07:00:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7262200/SRX7262200.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7262200/SRX7262200.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7262200/SRX7262200.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7262200/SRX7262200.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, 14 Jul 2020 07:00:38: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:00:38: #1 read treatment tags... pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (318 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 07:00:43: 1000000 INFO @ Tue, 14 Jul 2020 07:00:47: 2000000 INFO @ Tue, 14 Jul 2020 07:00:52: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 07:00:55: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 07:00:55: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 07:00:55: #1 total tags in treatment: 3737832 INFO @ Tue, 14 Jul 2020 07:00:55: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:00:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 07:00:55: #1 tags after filtering in treatment: 3737832 INFO @ Tue, 14 Jul 2020 07:00:55: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:00:55: #1 finished! INFO @ Tue, 14 Jul 2020 07:00:55: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:00:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:00:55: #2 number of paired peaks: 496 WARNING @ Tue, 14 Jul 2020 07:00:55: Fewer paired peaks (496) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 496 pairs to build model! INFO @ Tue, 14 Jul 2020 07:00:55: start model_add_line... INFO @ Tue, 14 Jul 2020 07:00:55: start X-correlation... INFO @ Tue, 14 Jul 2020 07:00:56: end of X-cor INFO @ Tue, 14 Jul 2020 07:00:56: #2 finished! INFO @ Tue, 14 Jul 2020 07:00:56: #2 predicted fragment length is 48 bps INFO @ Tue, 14 Jul 2020 07:00:56: #2 alternative fragment length(s) may be 48,510 bps INFO @ Tue, 14 Jul 2020 07:00:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7262200/SRX7262200.20_model.r WARNING @ Tue, 14 Jul 2020 07:00:56: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 07:00:56: #2 You may need to consider one of the other alternative d(s): 48,510 WARNING @ Tue, 14 Jul 2020 07:00:56: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 07:00:56: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:00:56: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:01:03: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 07:01:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7262200/SRX7262200.20_peaks.xls INFO @ Tue, 14 Jul 2020 07:01:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7262200/SRX7262200.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:01:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7262200/SRX7262200.20_summits.bed INFO @ Tue, 14 Jul 2020 07:01:07: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (139 records, 4 fields): 8 millis CompletedMACS2peakCalling