Job ID = 12265067 SRX = SRX7246258 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: 00:06:41 25617132 reads; of these: 25617132 (100.00%) were unpaired; of these: 919493 (3.59%) aligned 0 times 21652189 (84.52%) aligned exactly 1 time 3045450 (11.89%) aligned >1 times 96.41% overall alignment rate Time searching: 00:06:41 Overall time: 00:06:41 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 12 files... [bam_rmdupse_core] 12695648 / 24697639 = 0.5140 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 06:19:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7246258/SRX7246258.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7246258/SRX7246258.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7246258/SRX7246258.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7246258/SRX7246258.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 06:19:44: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:19:44: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:19:54: 1000000 INFO @ Sat, 03 Apr 2021 06:20:04: 2000000 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 06:20:14: 3000000 INFO @ Sat, 03 Apr 2021 06:20:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7246258/SRX7246258.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7246258/SRX7246258.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7246258/SRX7246258.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7246258/SRX7246258.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 06:20:14: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:20:14: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:20:23: 4000000 INFO @ Sat, 03 Apr 2021 06:20:25: 1000000 INFO @ Sat, 03 Apr 2021 06:20:33: 5000000 INFO @ Sat, 03 Apr 2021 06:20:35: 2000000 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 06:20:43: 6000000 INFO @ Sat, 03 Apr 2021 06:20:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7246258/SRX7246258.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7246258/SRX7246258.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7246258/SRX7246258.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7246258/SRX7246258.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 06:20:44: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:20:44: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:20:45: 3000000 INFO @ Sat, 03 Apr 2021 06:20:52: 1000000 INFO @ Sat, 03 Apr 2021 06:20:54: 7000000 INFO @ Sat, 03 Apr 2021 06:20:56: 4000000 INFO @ Sat, 03 Apr 2021 06:20:59: 2000000 INFO @ Sat, 03 Apr 2021 06:21:05: 8000000 INFO @ Sat, 03 Apr 2021 06:21:07: 3000000 INFO @ Sat, 03 Apr 2021 06:21:07: 5000000 INFO @ Sat, 03 Apr 2021 06:21:14: 4000000 INFO @ Sat, 03 Apr 2021 06:21:15: 9000000 INFO @ Sat, 03 Apr 2021 06:21:16: 6000000 INFO @ Sat, 03 Apr 2021 06:21:21: 5000000 INFO @ Sat, 03 Apr 2021 06:21:25: 10000000 INFO @ Sat, 03 Apr 2021 06:21:27: 7000000 INFO @ Sat, 03 Apr 2021 06:21:29: 6000000 INFO @ Sat, 03 Apr 2021 06:21:36: 7000000 INFO @ Sat, 03 Apr 2021 06:21:36: 11000000 INFO @ Sat, 03 Apr 2021 06:21:38: 8000000 INFO @ Sat, 03 Apr 2021 06:21:43: 8000000 INFO @ Sat, 03 Apr 2021 06:21:47: 12000000 INFO @ Sat, 03 Apr 2021 06:21:47: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 06:21:47: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 06:21:47: #1 total tags in treatment: 12001991 INFO @ Sat, 03 Apr 2021 06:21:47: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:21:47: #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 06:21:47: #1 tags after filtering in treatment: 12001991 INFO @ Sat, 03 Apr 2021 06:21:47: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:21:47: #1 finished! INFO @ Sat, 03 Apr 2021 06:21:47: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:21:47: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:21:48: 9000000 INFO @ Sat, 03 Apr 2021 06:21:48: #2 number of paired peaks: 610 WARNING @ Sat, 03 Apr 2021 06:21:48: Fewer paired peaks (610) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 610 pairs to build model! INFO @ Sat, 03 Apr 2021 06:21:48: start model_add_line... INFO @ Sat, 03 Apr 2021 06:21:48: start X-correlation... INFO @ Sat, 03 Apr 2021 06:21:48: end of X-cor INFO @ Sat, 03 Apr 2021 06:21:48: #2 finished! INFO @ Sat, 03 Apr 2021 06:21:48: #2 predicted fragment length is 98 bps INFO @ Sat, 03 Apr 2021 06:21:48: #2 alternative fragment length(s) may be 98 bps INFO @ Sat, 03 Apr 2021 06:21:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7246258/SRX7246258.05_model.r WARNING @ Sat, 03 Apr 2021 06:21:48: #2 Since the d (98) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:21:48: #2 You may need to consider one of the other alternative d(s): 98 WARNING @ Sat, 03 Apr 2021 06:21:48: #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 06:21:48: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:21:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:21:51: 9000000 INFO @ Sat, 03 Apr 2021 06:21:57: 10000000 INFO @ Sat, 03 Apr 2021 06:21:58: 10000000 INFO @ Sat, 03 Apr 2021 06:22:05: 11000000 INFO @ Sat, 03 Apr 2021 06:22:06: 11000000 INFO @ Sat, 03 Apr 2021 06:22:13: 12000000 INFO @ Sat, 03 Apr 2021 06:22:13: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 06:22:13: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 06:22:13: #1 total tags in treatment: 12001991 INFO @ Sat, 03 Apr 2021 06:22:13: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:22:13: #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 06:22:13: #1 tags after filtering in treatment: 12001991 INFO @ Sat, 03 Apr 2021 06:22:13: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:22:13: #1 finished! INFO @ Sat, 03 Apr 2021 06:22:13: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:22:13: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:22:14: #2 number of paired peaks: 610 WARNING @ Sat, 03 Apr 2021 06:22:14: Fewer paired peaks (610) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 610 pairs to build model! INFO @ Sat, 03 Apr 2021 06:22:14: start model_add_line... INFO @ Sat, 03 Apr 2021 06:22:14: start X-correlation... INFO @ Sat, 03 Apr 2021 06:22:14: end of X-cor INFO @ Sat, 03 Apr 2021 06:22:14: #2 finished! INFO @ Sat, 03 Apr 2021 06:22:14: #2 predicted fragment length is 98 bps INFO @ Sat, 03 Apr 2021 06:22:14: #2 alternative fragment length(s) may be 98 bps INFO @ Sat, 03 Apr 2021 06:22:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7246258/SRX7246258.20_model.r WARNING @ Sat, 03 Apr 2021 06:22:14: #2 Since the d (98) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:22:14: #2 You may need to consider one of the other alternative d(s): 98 WARNING @ Sat, 03 Apr 2021 06:22:14: #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 06:22:14: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:22:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:22:15: 12000000 INFO @ Sat, 03 Apr 2021 06:22:15: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 06:22:15: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 06:22:15: #1 total tags in treatment: 12001991 INFO @ Sat, 03 Apr 2021 06:22:15: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:22:15: #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 06:22:16: #1 tags after filtering in treatment: 12001991 INFO @ Sat, 03 Apr 2021 06:22:16: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:22:16: #1 finished! INFO @ Sat, 03 Apr 2021 06:22:16: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:22:16: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:22:17: #2 number of paired peaks: 610 WARNING @ Sat, 03 Apr 2021 06:22:17: Fewer paired peaks (610) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 610 pairs to build model! INFO @ Sat, 03 Apr 2021 06:22:17: start model_add_line... INFO @ Sat, 03 Apr 2021 06:22:17: start X-correlation... INFO @ Sat, 03 Apr 2021 06:22:17: end of X-cor INFO @ Sat, 03 Apr 2021 06:22:17: #2 finished! INFO @ Sat, 03 Apr 2021 06:22:17: #2 predicted fragment length is 98 bps INFO @ Sat, 03 Apr 2021 06:22:17: #2 alternative fragment length(s) may be 98 bps INFO @ Sat, 03 Apr 2021 06:22:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7246258/SRX7246258.10_model.r WARNING @ Sat, 03 Apr 2021 06:22:17: #2 Since the d (98) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:22:17: #2 You may need to consider one of the other alternative d(s): 98 WARNING @ Sat, 03 Apr 2021 06:22:17: #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 06:22:17: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:22:17: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 06:22:23: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:22:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7246258/SRX7246258.05_peaks.xls INFO @ Sat, 03 Apr 2021 06:22:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7246258/SRX7246258.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:22:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7246258/SRX7246258.05_summits.bed INFO @ Sat, 03 Apr 2021 06:22:41: Done! pass1 - making usageList (7 chroms): 5 millis pass2 - checking and writing primary data (8215 records, 4 fields): 31 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:22:50: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:22:51: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 06:23:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7246258/SRX7246258.20_peaks.xls INFO @ Sat, 03 Apr 2021 06:23:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7246258/SRX7246258.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:23:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7246258/SRX7246258.20_summits.bed INFO @ Sat, 03 Apr 2021 06:23:09: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (2348 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:23:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7246258/SRX7246258.10_peaks.xls INFO @ Sat, 03 Apr 2021 06:23:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7246258/SRX7246258.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:23:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7246258/SRX7246258.10_summits.bed INFO @ Sat, 03 Apr 2021 06:23:09: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (5235 records, 4 fields): 10 millis CompletedMACS2peakCalling