Job ID = 12265020 SRX = SRX7246263 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: 00:03:06 16826488 reads; of these: 16826488 (100.00%) were unpaired; of these: 4145671 (24.64%) aligned 0 times 10794256 (64.15%) aligned exactly 1 time 1886561 (11.21%) aligned >1 times 75.36% overall alignment rate Time searching: 00:03:06 Overall time: 00:03:06 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] 4904323 / 12680817 = 0.3868 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/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:10:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7246263/SRX7246263.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7246263/SRX7246263.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7246263/SRX7246263.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7246263/SRX7246263.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 @ Sat, 03 Apr 2021 06:10:50: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:10:50: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:10:57: 1000000 INFO @ Sat, 03 Apr 2021 06:11:03: 2000000 INFO @ Sat, 03 Apr 2021 06:11:09: 3000000 INFO @ Sat, 03 Apr 2021 06:11:15: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:11:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7246263/SRX7246263.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7246263/SRX7246263.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7246263/SRX7246263.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7246263/SRX7246263.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 @ Sat, 03 Apr 2021 06:11:20: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:11:20: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:11:22: 5000000 INFO @ Sat, 03 Apr 2021 06:11:28: 1000000 INFO @ Sat, 03 Apr 2021 06:11:28: 6000000 INFO @ Sat, 03 Apr 2021 06:11:35: 2000000 INFO @ Sat, 03 Apr 2021 06:11:35: 7000000 INFO @ Sat, 03 Apr 2021 06:11:40: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 06:11:40: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 06:11:40: #1 total tags in treatment: 7776494 INFO @ Sat, 03 Apr 2021 06:11:40: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:11:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 06:11:41: #1 tags after filtering in treatment: 7776494 INFO @ Sat, 03 Apr 2021 06:11:41: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:11:41: #1 finished! INFO @ Sat, 03 Apr 2021 06:11:41: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:11:41: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:11:41: #2 number of paired peaks: 714 WARNING @ Sat, 03 Apr 2021 06:11:41: Fewer paired peaks (714) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 714 pairs to build model! INFO @ Sat, 03 Apr 2021 06:11:41: start model_add_line... INFO @ Sat, 03 Apr 2021 06:11:41: start X-correlation... INFO @ Sat, 03 Apr 2021 06:11:41: end of X-cor INFO @ Sat, 03 Apr 2021 06:11:41: #2 finished! INFO @ Sat, 03 Apr 2021 06:11:41: #2 predicted fragment length is 93 bps INFO @ Sat, 03 Apr 2021 06:11:41: #2 alternative fragment length(s) may be 93 bps INFO @ Sat, 03 Apr 2021 06:11:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7246263/SRX7246263.05_model.r WARNING @ Sat, 03 Apr 2021 06:11:41: #2 Since the d (93) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:11:41: #2 You may need to consider one of the other alternative d(s): 93 WARNING @ Sat, 03 Apr 2021 06:11:41: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 06:11:41: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:11:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:11:41: 3000000 INFO @ Sat, 03 Apr 2021 06:11:48: 4000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:11:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7246263/SRX7246263.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7246263/SRX7246263.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7246263/SRX7246263.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7246263/SRX7246263.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 @ Sat, 03 Apr 2021 06:11:50: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:11:50: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:11:54: 5000000 INFO @ Sat, 03 Apr 2021 06:11:57: 1000000 INFO @ Sat, 03 Apr 2021 06:11:58: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:12:02: 6000000 INFO @ Sat, 03 Apr 2021 06:12:04: 2000000 INFO @ Sat, 03 Apr 2021 06:12:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7246263/SRX7246263.05_peaks.xls INFO @ Sat, 03 Apr 2021 06:12:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7246263/SRX7246263.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:12:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7246263/SRX7246263.05_summits.bed INFO @ Sat, 03 Apr 2021 06:12:06: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (6144 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:12:09: 7000000 INFO @ Sat, 03 Apr 2021 06:12:11: 3000000 INFO @ Sat, 03 Apr 2021 06:12:14: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 06:12:14: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 06:12:14: #1 total tags in treatment: 7776494 INFO @ Sat, 03 Apr 2021 06:12:14: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:12:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 06:12:14: #1 tags after filtering in treatment: 7776494 INFO @ Sat, 03 Apr 2021 06:12:14: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:12:14: #1 finished! INFO @ Sat, 03 Apr 2021 06:12:14: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:12:14: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:12:15: #2 number of paired peaks: 714 WARNING @ Sat, 03 Apr 2021 06:12:15: Fewer paired peaks (714) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 714 pairs to build model! INFO @ Sat, 03 Apr 2021 06:12:15: start model_add_line... INFO @ Sat, 03 Apr 2021 06:12:15: start X-correlation... INFO @ Sat, 03 Apr 2021 06:12:15: end of X-cor INFO @ Sat, 03 Apr 2021 06:12:15: #2 finished! INFO @ Sat, 03 Apr 2021 06:12:15: #2 predicted fragment length is 93 bps INFO @ Sat, 03 Apr 2021 06:12:15: #2 alternative fragment length(s) may be 93 bps INFO @ Sat, 03 Apr 2021 06:12:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7246263/SRX7246263.10_model.r WARNING @ Sat, 03 Apr 2021 06:12:15: #2 Since the d (93) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:12:15: #2 You may need to consider one of the other alternative d(s): 93 WARNING @ Sat, 03 Apr 2021 06:12:15: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 06:12:15: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:12:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:12:18: 4000000 INFO @ Sat, 03 Apr 2021 06:12:24: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 06:12:31: 6000000 INFO @ Sat, 03 Apr 2021 06:12:32: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:12:37: 7000000 INFO @ Sat, 03 Apr 2021 06:12:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7246263/SRX7246263.10_peaks.xls INFO @ Sat, 03 Apr 2021 06:12:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7246263/SRX7246263.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:12:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7246263/SRX7246263.10_summits.bed INFO @ Sat, 03 Apr 2021 06:12:41: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3633 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:12:42: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 06:12:42: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 06:12:42: #1 total tags in treatment: 7776494 INFO @ Sat, 03 Apr 2021 06:12:42: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:12:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 06:12:42: #1 tags after filtering in treatment: 7776494 INFO @ Sat, 03 Apr 2021 06:12:42: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:12:42: #1 finished! INFO @ Sat, 03 Apr 2021 06:12:42: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:12:42: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:12:43: #2 number of paired peaks: 714 WARNING @ Sat, 03 Apr 2021 06:12:43: Fewer paired peaks (714) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 714 pairs to build model! INFO @ Sat, 03 Apr 2021 06:12:43: start model_add_line... INFO @ Sat, 03 Apr 2021 06:12:43: start X-correlation... INFO @ Sat, 03 Apr 2021 06:12:43: end of X-cor INFO @ Sat, 03 Apr 2021 06:12:43: #2 finished! INFO @ Sat, 03 Apr 2021 06:12:43: #2 predicted fragment length is 93 bps INFO @ Sat, 03 Apr 2021 06:12:43: #2 alternative fragment length(s) may be 93 bps INFO @ Sat, 03 Apr 2021 06:12:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7246263/SRX7246263.20_model.r WARNING @ Sat, 03 Apr 2021 06:12:43: #2 Since the d (93) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:12:43: #2 You may need to consider one of the other alternative d(s): 93 WARNING @ Sat, 03 Apr 2021 06:12:43: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 06:12:43: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:12:43: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 06:13:00: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:13:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7246263/SRX7246263.20_peaks.xls INFO @ Sat, 03 Apr 2021 06:13:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7246263/SRX7246263.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:13:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7246263/SRX7246263.20_summits.bed INFO @ Sat, 03 Apr 2021 06:13:08: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1542 records, 4 fields): 10 millis CompletedMACS2peakCalling