Job ID = 14167852 SRX = SRX8688918 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: 00:01:53 6635489 reads; of these: 6635489 (100.00%) were unpaired; of these: 301180 (4.54%) aligned 0 times 4692949 (70.72%) aligned exactly 1 time 1641360 (24.74%) aligned >1 times 95.46% overall alignment rate Time searching: 00:01:53 Overall time: 00:01:53 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] 561339 / 6334309 = 0.0886 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 @ Fri, 10 Dec 2021 13:37:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8688918/SRX8688918.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8688918/SRX8688918.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8688918/SRX8688918.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8688918/SRX8688918.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 @ Fri, 10 Dec 2021 13:37:50: #1 read tag files... INFO @ Fri, 10 Dec 2021 13:37:50: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 13:37:56: 1000000 INFO @ Fri, 10 Dec 2021 13:38:01: 2000000 INFO @ Fri, 10 Dec 2021 13:38:07: 3000000 INFO @ Fri, 10 Dec 2021 13:38:12: 4000000 INFO @ Fri, 10 Dec 2021 13:38:18: 5000000 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 @ Fri, 10 Dec 2021 13:38:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8688918/SRX8688918.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8688918/SRX8688918.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8688918/SRX8688918.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8688918/SRX8688918.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 @ Fri, 10 Dec 2021 13:38:20: #1 read tag files... INFO @ Fri, 10 Dec 2021 13:38:20: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 13:38:23: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 13:38:23: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 13:38:23: #1 total tags in treatment: 5772970 INFO @ Fri, 10 Dec 2021 13:38:23: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 13:38:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 13:38:23: #1 tags after filtering in treatment: 5772772 INFO @ Fri, 10 Dec 2021 13:38:23: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 13:38:23: #1 finished! INFO @ Fri, 10 Dec 2021 13:38:23: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 13:38:23: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 13:38:23: #2 number of paired peaks: 936 WARNING @ Fri, 10 Dec 2021 13:38:23: Fewer paired peaks (936) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 936 pairs to build model! INFO @ Fri, 10 Dec 2021 13:38:23: start model_add_line... INFO @ Fri, 10 Dec 2021 13:38:23: start X-correlation... INFO @ Fri, 10 Dec 2021 13:38:23: end of X-cor INFO @ Fri, 10 Dec 2021 13:38:23: #2 finished! INFO @ Fri, 10 Dec 2021 13:38:23: #2 predicted fragment length is 71 bps INFO @ Fri, 10 Dec 2021 13:38:23: #2 alternative fragment length(s) may be 71,558 bps INFO @ Fri, 10 Dec 2021 13:38:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8688918/SRX8688918.05_model.r WARNING @ Fri, 10 Dec 2021 13:38:23: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 13:38:23: #2 You may need to consider one of the other alternative d(s): 71,558 WARNING @ Fri, 10 Dec 2021 13:38:23: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 13:38:23: #3 Call peaks... INFO @ Fri, 10 Dec 2021 13:38:23: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 13:38:26: 1000000 INFO @ Fri, 10 Dec 2021 13:38:32: 2000000 INFO @ Fri, 10 Dec 2021 13:38:36: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 13:38:38: 3000000 INFO @ Fri, 10 Dec 2021 13:38:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8688918/SRX8688918.05_peaks.xls INFO @ Fri, 10 Dec 2021 13:38:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8688918/SRX8688918.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 13:38:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8688918/SRX8688918.05_summits.bed INFO @ Fri, 10 Dec 2021 13:38:42: Done! pass1 - making usageList (554 chroms): 1 millis pass2 - checking and writing primary data (1923 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 13:38:44: 4000000 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 @ Fri, 10 Dec 2021 13:38:49: 5000000 INFO @ Fri, 10 Dec 2021 13:38:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8688918/SRX8688918.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8688918/SRX8688918.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8688918/SRX8688918.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8688918/SRX8688918.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 @ Fri, 10 Dec 2021 13:38:50: #1 read tag files... INFO @ Fri, 10 Dec 2021 13:38:50: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 13:38:55: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 13:38:55: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 13:38:55: #1 total tags in treatment: 5772970 INFO @ Fri, 10 Dec 2021 13:38:55: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 13:38:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 13:38:55: #1 tags after filtering in treatment: 5772772 INFO @ Fri, 10 Dec 2021 13:38:55: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 13:38:55: #1 finished! INFO @ Fri, 10 Dec 2021 13:38:55: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 13:38:55: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 13:38:55: #2 number of paired peaks: 936 WARNING @ Fri, 10 Dec 2021 13:38:55: Fewer paired peaks (936) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 936 pairs to build model! INFO @ Fri, 10 Dec 2021 13:38:55: start model_add_line... INFO @ Fri, 10 Dec 2021 13:38:55: start X-correlation... INFO @ Fri, 10 Dec 2021 13:38:55: end of X-cor INFO @ Fri, 10 Dec 2021 13:38:55: #2 finished! INFO @ Fri, 10 Dec 2021 13:38:55: #2 predicted fragment length is 71 bps INFO @ Fri, 10 Dec 2021 13:38:55: #2 alternative fragment length(s) may be 71,558 bps INFO @ Fri, 10 Dec 2021 13:38:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8688918/SRX8688918.10_model.r WARNING @ Fri, 10 Dec 2021 13:38:55: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 13:38:55: #2 You may need to consider one of the other alternative d(s): 71,558 WARNING @ Fri, 10 Dec 2021 13:38:55: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 13:38:55: #3 Call peaks... INFO @ Fri, 10 Dec 2021 13:38:55: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 13:38:57: 1000000 INFO @ Fri, 10 Dec 2021 13:39:04: 2000000 INFO @ Fri, 10 Dec 2021 13:39:07: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 13:39:11: 3000000 INFO @ Fri, 10 Dec 2021 13:39:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8688918/SRX8688918.10_peaks.xls INFO @ Fri, 10 Dec 2021 13:39:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8688918/SRX8688918.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 13:39:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8688918/SRX8688918.10_summits.bed INFO @ Fri, 10 Dec 2021 13:39:13: Done! pass1 - making usageList (402 chroms): 1 millis pass2 - checking and writing primary data (929 records, 4 fields): 12 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 13:39:18: 4000000 INFO @ Fri, 10 Dec 2021 13:39:25: 5000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 13:39:31: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 13:39:31: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 13:39:31: #1 total tags in treatment: 5772970 INFO @ Fri, 10 Dec 2021 13:39:31: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 13:39:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 13:39:31: #1 tags after filtering in treatment: 5772772 INFO @ Fri, 10 Dec 2021 13:39:31: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 13:39:31: #1 finished! INFO @ Fri, 10 Dec 2021 13:39:31: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 13:39:31: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 13:39:31: #2 number of paired peaks: 936 WARNING @ Fri, 10 Dec 2021 13:39:31: Fewer paired peaks (936) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 936 pairs to build model! INFO @ Fri, 10 Dec 2021 13:39:31: start model_add_line... INFO @ Fri, 10 Dec 2021 13:39:31: start X-correlation... INFO @ Fri, 10 Dec 2021 13:39:32: end of X-cor INFO @ Fri, 10 Dec 2021 13:39:32: #2 finished! INFO @ Fri, 10 Dec 2021 13:39:32: #2 predicted fragment length is 71 bps INFO @ Fri, 10 Dec 2021 13:39:32: #2 alternative fragment length(s) may be 71,558 bps INFO @ Fri, 10 Dec 2021 13:39:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8688918/SRX8688918.20_model.r WARNING @ Fri, 10 Dec 2021 13:39:32: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 13:39:32: #2 You may need to consider one of the other alternative d(s): 71,558 WARNING @ Fri, 10 Dec 2021 13:39:32: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 13:39:32: #3 Call peaks... INFO @ Fri, 10 Dec 2021 13:39:32: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 13:39:43: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 13:39:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8688918/SRX8688918.20_peaks.xls INFO @ Fri, 10 Dec 2021 13:39:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8688918/SRX8688918.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 13:39:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8688918/SRX8688918.20_summits.bed INFO @ Fri, 10 Dec 2021 13:39:49: Done! pass1 - making usageList (169 chroms): 1 millis pass2 - checking and writing primary data (295 records, 4 fields): 30 millis CompletedMACS2peakCalling