Job ID = 14170819 SRX = SRX8784755 Genome = dm6 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: 00:02:07 5154683 reads; of these: 5154683 (100.00%) were unpaired; of these: 551714 (10.70%) aligned 0 times 4082731 (79.20%) aligned exactly 1 time 520238 (10.09%) aligned >1 times 89.30% overall alignment rate Time searching: 00:02:07 Overall time: 00:02:07 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_rmdupse_core] 249754 / 4602969 = 0.0543 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 @ Sat, 11 Dec 2021 08:53:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8784755/SRX8784755.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8784755/SRX8784755.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8784755/SRX8784755.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8784755/SRX8784755.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 11 Dec 2021 08:53:35: #1 read tag files... INFO @ Sat, 11 Dec 2021 08:53:35: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 08:53:41: 1000000 INFO @ Sat, 11 Dec 2021 08:53:47: 2000000 INFO @ Sat, 11 Dec 2021 08:53:53: 3000000 INFO @ Sat, 11 Dec 2021 08:53:59: 4000000 INFO @ Sat, 11 Dec 2021 08:54:02: #1 tag size is determined as 100 bps INFO @ Sat, 11 Dec 2021 08:54:02: #1 tag size = 100 INFO @ Sat, 11 Dec 2021 08:54:02: #1 total tags in treatment: 4353215 INFO @ Sat, 11 Dec 2021 08:54:02: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 08:54:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 08:54:02: #1 tags after filtering in treatment: 4352866 INFO @ Sat, 11 Dec 2021 08:54:02: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 08:54:02: #1 finished! INFO @ Sat, 11 Dec 2021 08:54:02: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 08:54:02: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 08:54:02: #2 number of paired peaks: 622 WARNING @ Sat, 11 Dec 2021 08:54:02: Fewer paired peaks (622) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 622 pairs to build model! INFO @ Sat, 11 Dec 2021 08:54:02: start model_add_line... INFO @ Sat, 11 Dec 2021 08:54:02: start X-correlation... INFO @ Sat, 11 Dec 2021 08:54:02: end of X-cor INFO @ Sat, 11 Dec 2021 08:54:02: #2 finished! INFO @ Sat, 11 Dec 2021 08:54:02: #2 predicted fragment length is 196 bps INFO @ Sat, 11 Dec 2021 08:54:02: #2 alternative fragment length(s) may be 196 bps INFO @ Sat, 11 Dec 2021 08:54:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8784755/SRX8784755.05_model.r WARNING @ Sat, 11 Dec 2021 08:54:02: #2 Since the d (196) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 08:54:02: #2 You may need to consider one of the other alternative d(s): 196 WARNING @ Sat, 11 Dec 2021 08:54:02: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 08:54:02: #3 Call peaks... INFO @ Sat, 11 Dec 2021 08:54:02: #3 Pre-compute pvalue-qvalue table... 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 @ Sat, 11 Dec 2021 08:54:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8784755/SRX8784755.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8784755/SRX8784755.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8784755/SRX8784755.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8784755/SRX8784755.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 11 Dec 2021 08:54:05: #1 read tag files... INFO @ Sat, 11 Dec 2021 08:54:05: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 08:54:12: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 08:54:12: 1000000 INFO @ Sat, 11 Dec 2021 08:54:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8784755/SRX8784755.05_peaks.xls INFO @ Sat, 11 Dec 2021 08:54:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8784755/SRX8784755.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 08:54:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8784755/SRX8784755.05_summits.bed INFO @ Sat, 11 Dec 2021 08:54:17: Done! pass1 - making usageList (267 chroms): 2 millis pass2 - checking and writing primary data (4839 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 08:54:19: 2000000 INFO @ Sat, 11 Dec 2021 08:54:26: 3000000 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 @ Sat, 11 Dec 2021 08:54:34: 4000000 INFO @ Sat, 11 Dec 2021 08:54:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8784755/SRX8784755.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8784755/SRX8784755.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8784755/SRX8784755.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8784755/SRX8784755.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 11 Dec 2021 08:54:35: #1 read tag files... INFO @ Sat, 11 Dec 2021 08:54:35: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 08:54:36: #1 tag size is determined as 100 bps INFO @ Sat, 11 Dec 2021 08:54:36: #1 tag size = 100 INFO @ Sat, 11 Dec 2021 08:54:36: #1 total tags in treatment: 4353215 INFO @ Sat, 11 Dec 2021 08:54:36: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 08:54:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 08:54:37: #1 tags after filtering in treatment: 4352866 INFO @ Sat, 11 Dec 2021 08:54:37: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 08:54:37: #1 finished! INFO @ Sat, 11 Dec 2021 08:54:37: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 08:54:37: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 08:54:37: #2 number of paired peaks: 622 WARNING @ Sat, 11 Dec 2021 08:54:37: Fewer paired peaks (622) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 622 pairs to build model! INFO @ Sat, 11 Dec 2021 08:54:37: start model_add_line... INFO @ Sat, 11 Dec 2021 08:54:37: start X-correlation... INFO @ Sat, 11 Dec 2021 08:54:37: end of X-cor INFO @ Sat, 11 Dec 2021 08:54:37: #2 finished! INFO @ Sat, 11 Dec 2021 08:54:37: #2 predicted fragment length is 196 bps INFO @ Sat, 11 Dec 2021 08:54:37: #2 alternative fragment length(s) may be 196 bps INFO @ Sat, 11 Dec 2021 08:54:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8784755/SRX8784755.10_model.r WARNING @ Sat, 11 Dec 2021 08:54:37: #2 Since the d (196) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 08:54:37: #2 You may need to consider one of the other alternative d(s): 196 WARNING @ Sat, 11 Dec 2021 08:54:37: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 08:54:37: #3 Call peaks... INFO @ Sat, 11 Dec 2021 08:54:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 08:54:42: 1000000 INFO @ Sat, 11 Dec 2021 08:54:47: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 08:54:48: 2000000 INFO @ Sat, 11 Dec 2021 08:54:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8784755/SRX8784755.10_peaks.xls INFO @ Sat, 11 Dec 2021 08:54:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8784755/SRX8784755.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 08:54:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8784755/SRX8784755.10_summits.bed INFO @ Sat, 11 Dec 2021 08:54:51: Done! pass1 - making usageList (131 chroms): 1 millis pass2 - checking and writing primary data (1043 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 08:54:54: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 08:55:01: 4000000 INFO @ Sat, 11 Dec 2021 08:55:03: #1 tag size is determined as 100 bps INFO @ Sat, 11 Dec 2021 08:55:03: #1 tag size = 100 INFO @ Sat, 11 Dec 2021 08:55:03: #1 total tags in treatment: 4353215 INFO @ Sat, 11 Dec 2021 08:55:03: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 08:55:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 08:55:04: #1 tags after filtering in treatment: 4352866 INFO @ Sat, 11 Dec 2021 08:55:04: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 08:55:04: #1 finished! INFO @ Sat, 11 Dec 2021 08:55:04: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 08:55:04: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 08:55:04: #2 number of paired peaks: 622 WARNING @ Sat, 11 Dec 2021 08:55:04: Fewer paired peaks (622) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 622 pairs to build model! INFO @ Sat, 11 Dec 2021 08:55:04: start model_add_line... INFO @ Sat, 11 Dec 2021 08:55:04: start X-correlation... INFO @ Sat, 11 Dec 2021 08:55:04: end of X-cor INFO @ Sat, 11 Dec 2021 08:55:04: #2 finished! INFO @ Sat, 11 Dec 2021 08:55:04: #2 predicted fragment length is 196 bps INFO @ Sat, 11 Dec 2021 08:55:04: #2 alternative fragment length(s) may be 196 bps INFO @ Sat, 11 Dec 2021 08:55:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8784755/SRX8784755.20_model.r WARNING @ Sat, 11 Dec 2021 08:55:04: #2 Since the d (196) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 08:55:04: #2 You may need to consider one of the other alternative d(s): 196 WARNING @ Sat, 11 Dec 2021 08:55:04: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 08:55:04: #3 Call peaks... INFO @ Sat, 11 Dec 2021 08:55:04: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 08:55:14: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 08:55:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8784755/SRX8784755.20_peaks.xls INFO @ Sat, 11 Dec 2021 08:55:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8784755/SRX8784755.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 08:55:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8784755/SRX8784755.20_summits.bed INFO @ Sat, 11 Dec 2021 08:55:19: Done! pass1 - making usageList (54 chroms): 1 millis pass2 - checking and writing primary data (130 records, 4 fields): 4 millis CompletedMACS2peakCalling