Job ID = 16439183 SRX = SRX15206451 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: 00:01:30 2036335 reads; of these: 2036335 (100.00%) were unpaired; of these: 855016 (41.99%) aligned 0 times 982242 (48.24%) aligned exactly 1 time 199077 (9.78%) aligned >1 times 58.01% overall alignment rate Time searching: 00:01:30 Overall time: 00:01:30 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] 204942 / 1181319 = 0.1735 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 14:46:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX15206451/SRX15206451.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX15206451/SRX15206451.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX15206451/SRX15206451.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX15206451/SRX15206451.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 14:46:23: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:46:23: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:46:38: #1 tag size is determined as 100 bps INFO @ Tue, 02 Aug 2022 14:46:38: #1 tag size = 100 INFO @ Tue, 02 Aug 2022 14:46:38: #1 total tags in treatment: 976377 INFO @ Tue, 02 Aug 2022 14:46:38: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:46:38: #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 14:46:38: #1 tags after filtering in treatment: 975933 INFO @ Tue, 02 Aug 2022 14:46:38: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:46:38: #1 finished! INFO @ Tue, 02 Aug 2022 14:46:38: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:46:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:46:38: #2 number of paired peaks: 326 WARNING @ Tue, 02 Aug 2022 14:46:38: Fewer paired peaks (326) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 326 pairs to build model! INFO @ Tue, 02 Aug 2022 14:46:38: start model_add_line... INFO @ Tue, 02 Aug 2022 14:46:39: start X-correlation... INFO @ Tue, 02 Aug 2022 14:46:39: end of X-cor INFO @ Tue, 02 Aug 2022 14:46:39: #2 finished! INFO @ Tue, 02 Aug 2022 14:46:39: #2 predicted fragment length is 114 bps INFO @ Tue, 02 Aug 2022 14:46:39: #2 alternative fragment length(s) may be 114,279,452,527,561 bps INFO @ Tue, 02 Aug 2022 14:46:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX15206451/SRX15206451.05_model.r WARNING @ Tue, 02 Aug 2022 14:46:39: #2 Since the d (114) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:46:39: #2 You may need to consider one of the other alternative d(s): 114,279,452,527,561 WARNING @ Tue, 02 Aug 2022 14:46:39: #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 14:46:39: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:46:39: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:46:42: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:46:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX15206451/SRX15206451.05_peaks.xls INFO @ Tue, 02 Aug 2022 14:46:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX15206451/SRX15206451.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:46:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX15206451/SRX15206451.05_summits.bed INFO @ Tue, 02 Aug 2022 14:46:44: Done! pass1 - making usageList (122 chroms): 1 millis pass2 - checking and writing primary data (214 records, 4 fields): 43 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 14:46:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX15206451/SRX15206451.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX15206451/SRX15206451.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX15206451/SRX15206451.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX15206451/SRX15206451.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 14:46:52: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:46:52: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:47:07: #1 tag size is determined as 100 bps INFO @ Tue, 02 Aug 2022 14:47:07: #1 tag size = 100 INFO @ Tue, 02 Aug 2022 14:47:07: #1 total tags in treatment: 976377 INFO @ Tue, 02 Aug 2022 14:47:07: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:47:07: #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 14:47:07: #1 tags after filtering in treatment: 975933 INFO @ Tue, 02 Aug 2022 14:47:07: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:47:07: #1 finished! INFO @ Tue, 02 Aug 2022 14:47:07: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:47:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:47:07: #2 number of paired peaks: 326 WARNING @ Tue, 02 Aug 2022 14:47:07: Fewer paired peaks (326) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 326 pairs to build model! INFO @ Tue, 02 Aug 2022 14:47:07: start model_add_line... INFO @ Tue, 02 Aug 2022 14:47:07: start X-correlation... INFO @ Tue, 02 Aug 2022 14:47:07: end of X-cor INFO @ Tue, 02 Aug 2022 14:47:07: #2 finished! INFO @ Tue, 02 Aug 2022 14:47:07: #2 predicted fragment length is 114 bps INFO @ Tue, 02 Aug 2022 14:47:07: #2 alternative fragment length(s) may be 114,279,452,527,561 bps INFO @ Tue, 02 Aug 2022 14:47:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX15206451/SRX15206451.10_model.r WARNING @ Tue, 02 Aug 2022 14:47:07: #2 Since the d (114) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:47:07: #2 You may need to consider one of the other alternative d(s): 114,279,452,527,561 WARNING @ Tue, 02 Aug 2022 14:47:07: #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 14:47:07: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:47:07: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:47:11: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:47:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX15206451/SRX15206451.10_peaks.xls INFO @ Tue, 02 Aug 2022 14:47:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX15206451/SRX15206451.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:47:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX15206451/SRX15206451.10_summits.bed INFO @ Tue, 02 Aug 2022 14:47:13: Done! pass1 - making usageList (67 chroms): 2 millis pass2 - checking and writing primary data (114 records, 4 fields): 40 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 INFO @ Tue, 02 Aug 2022 14:47:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX15206451/SRX15206451.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX15206451/SRX15206451.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX15206451/SRX15206451.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX15206451/SRX15206451.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 14:47:22: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:47:22: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 14:47:36: #1 tag size is determined as 100 bps INFO @ Tue, 02 Aug 2022 14:47:36: #1 tag size = 100 INFO @ Tue, 02 Aug 2022 14:47:36: #1 total tags in treatment: 976377 INFO @ Tue, 02 Aug 2022 14:47:36: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:47:36: #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 14:47:36: #1 tags after filtering in treatment: 975933 INFO @ Tue, 02 Aug 2022 14:47:36: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:47:36: #1 finished! INFO @ Tue, 02 Aug 2022 14:47:36: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:47:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:47:36: #2 number of paired peaks: 326 WARNING @ Tue, 02 Aug 2022 14:47:36: Fewer paired peaks (326) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 326 pairs to build model! INFO @ Tue, 02 Aug 2022 14:47:36: start model_add_line... INFO @ Tue, 02 Aug 2022 14:47:36: start X-correlation... INFO @ Tue, 02 Aug 2022 14:47:36: end of X-cor INFO @ Tue, 02 Aug 2022 14:47:36: #2 finished! INFO @ Tue, 02 Aug 2022 14:47:36: #2 predicted fragment length is 114 bps INFO @ Tue, 02 Aug 2022 14:47:36: #2 alternative fragment length(s) may be 114,279,452,527,561 bps INFO @ Tue, 02 Aug 2022 14:47:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX15206451/SRX15206451.20_model.r WARNING @ Tue, 02 Aug 2022 14:47:36: #2 Since the d (114) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:47:36: #2 You may need to consider one of the other alternative d(s): 114,279,452,527,561 WARNING @ Tue, 02 Aug 2022 14:47:36: #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 14:47:36: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:47:36: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:47:40: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:47:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX15206451/SRX15206451.20_peaks.xls INFO @ Tue, 02 Aug 2022 14:47:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX15206451/SRX15206451.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:47:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX15206451/SRX15206451.20_summits.bed INFO @ Tue, 02 Aug 2022 14:47:42: Done! pass1 - making usageList (44 chroms): 2 millis pass2 - checking and writing primary data (60 records, 4 fields): 32 millis CompletedMACS2peakCalling