Job ID = 16440120 SRX = SRX10987325 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: 00:04:47 39550014 reads; of these: 39550014 (100.00%) were unpaired; of these: 39272518 (99.30%) aligned 0 times 191450 (0.48%) aligned exactly 1 time 86046 (0.22%) aligned >1 times 0.70% overall alignment rate Time searching: 00:04:47 Overall time: 00:04:47 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] 15005 / 277496 = 0.0541 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 17:20:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX10987325/SRX10987325.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX10987325/SRX10987325.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX10987325/SRX10987325.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX10987325/SRX10987325.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 @ Tue, 02 Aug 2022 17:20:42: #1 read tag files... INFO @ Tue, 02 Aug 2022 17:20:42: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 17:20:44: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 17:20:44: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 17:20:44: #1 total tags in treatment: 262491 INFO @ Tue, 02 Aug 2022 17:20:44: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 17:20:44: #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 17:20:44: #1 tags after filtering in treatment: 261972 INFO @ Tue, 02 Aug 2022 17:20:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 17:20:44: #1 finished! INFO @ Tue, 02 Aug 2022 17:20:44: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 17:20:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 17:20:44: #2 number of paired peaks: 1775 INFO @ Tue, 02 Aug 2022 17:20:44: start model_add_line... INFO @ Tue, 02 Aug 2022 17:20:44: start X-correlation... INFO @ Tue, 02 Aug 2022 17:20:44: end of X-cor INFO @ Tue, 02 Aug 2022 17:20:44: #2 finished! INFO @ Tue, 02 Aug 2022 17:20:44: #2 predicted fragment length is 78 bps INFO @ Tue, 02 Aug 2022 17:20:44: #2 alternative fragment length(s) may be 78,121,158,184,242,293,467 bps INFO @ Tue, 02 Aug 2022 17:20:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX10987325/SRX10987325.05_model.r WARNING @ Tue, 02 Aug 2022 17:20:44: #2 Since the d (78) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 17:20:44: #2 You may need to consider one of the other alternative d(s): 78,121,158,184,242,293,467 WARNING @ Tue, 02 Aug 2022 17:20:44: #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 17:20:44: #3 Call peaks... INFO @ Tue, 02 Aug 2022 17:20:44: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 17:20:45: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 17:20:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX10987325/SRX10987325.05_peaks.xls INFO @ Tue, 02 Aug 2022 17:20:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX10987325/SRX10987325.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 17:20:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX10987325/SRX10987325.05_summits.bed INFO @ Tue, 02 Aug 2022 17:20:46: Done! pass1 - making usageList (55 chroms): 1 millis pass2 - checking and writing primary data (95 records, 4 fields): 54 millis CompletedMACS2peakCalling 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 17:21:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX10987325/SRX10987325.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX10987325/SRX10987325.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX10987325/SRX10987325.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX10987325/SRX10987325.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 @ Tue, 02 Aug 2022 17:21:11: #1 read tag files... INFO @ Tue, 02 Aug 2022 17:21:11: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 17:21:13: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 17:21:13: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 17:21:13: #1 total tags in treatment: 262491 INFO @ Tue, 02 Aug 2022 17:21:13: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 17:21:13: #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 17:21:13: #1 tags after filtering in treatment: 261972 INFO @ Tue, 02 Aug 2022 17:21:13: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 17:21:13: #1 finished! INFO @ Tue, 02 Aug 2022 17:21:13: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 17:21:13: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 17:21:13: #2 number of paired peaks: 1775 INFO @ Tue, 02 Aug 2022 17:21:13: start model_add_line... INFO @ Tue, 02 Aug 2022 17:21:13: start X-correlation... INFO @ Tue, 02 Aug 2022 17:21:13: end of X-cor INFO @ Tue, 02 Aug 2022 17:21:13: #2 finished! INFO @ Tue, 02 Aug 2022 17:21:13: #2 predicted fragment length is 78 bps INFO @ Tue, 02 Aug 2022 17:21:13: #2 alternative fragment length(s) may be 78,121,158,184,242,293,467 bps INFO @ Tue, 02 Aug 2022 17:21:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX10987325/SRX10987325.10_model.r WARNING @ Tue, 02 Aug 2022 17:21:13: #2 Since the d (78) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 17:21:13: #2 You may need to consider one of the other alternative d(s): 78,121,158,184,242,293,467 WARNING @ Tue, 02 Aug 2022 17:21:13: #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 17:21:13: #3 Call peaks... INFO @ Tue, 02 Aug 2022 17:21:13: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 17:21:14: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 17:21:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX10987325/SRX10987325.10_peaks.xls INFO @ Tue, 02 Aug 2022 17:21:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX10987325/SRX10987325.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 17:21:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX10987325/SRX10987325.10_summits.bed INFO @ Tue, 02 Aug 2022 17:21:15: Done! pass1 - making usageList (31 chroms): 1 millis pass2 - checking and writing primary data (46 records, 4 fields): 56 millis CompletedMACS2peakCalling 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 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 17:21:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX10987325/SRX10987325.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX10987325/SRX10987325.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX10987325/SRX10987325.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX10987325/SRX10987325.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 @ Tue, 02 Aug 2022 17:21:41: #1 read tag files... INFO @ Tue, 02 Aug 2022 17:21:41: #1 read treatment tags... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 17:21:43: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 17:21:43: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 17:21:43: #1 total tags in treatment: 262491 INFO @ Tue, 02 Aug 2022 17:21:43: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 17:21:43: #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 17:21:43: #1 tags after filtering in treatment: 261972 INFO @ Tue, 02 Aug 2022 17:21:43: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 17:21:43: #1 finished! INFO @ Tue, 02 Aug 2022 17:21:43: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 17:21:43: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 17:21:43: #2 number of paired peaks: 1775 INFO @ Tue, 02 Aug 2022 17:21:43: start model_add_line... INFO @ Tue, 02 Aug 2022 17:21:43: start X-correlation... INFO @ Tue, 02 Aug 2022 17:21:43: end of X-cor INFO @ Tue, 02 Aug 2022 17:21:43: #2 finished! INFO @ Tue, 02 Aug 2022 17:21:43: #2 predicted fragment length is 78 bps INFO @ Tue, 02 Aug 2022 17:21:43: #2 alternative fragment length(s) may be 78,121,158,184,242,293,467 bps INFO @ Tue, 02 Aug 2022 17:21:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX10987325/SRX10987325.20_model.r WARNING @ Tue, 02 Aug 2022 17:21:43: #2 Since the d (78) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 17:21:43: #2 You may need to consider one of the other alternative d(s): 78,121,158,184,242,293,467 WARNING @ Tue, 02 Aug 2022 17:21:43: #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 17:21:43: #3 Call peaks... INFO @ Tue, 02 Aug 2022 17:21:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 17:21:44: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 17:21:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX10987325/SRX10987325.20_peaks.xls INFO @ Tue, 02 Aug 2022 17:21:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX10987325/SRX10987325.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 17:21:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX10987325/SRX10987325.20_summits.bed INFO @ Tue, 02 Aug 2022 17:21:45: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (18 records, 4 fields): 20 millis CompletedMACS2peakCalling