Job ID = 14167870 SRX = SRX8688922 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: 00:02:12 5728010 reads; of these: 5728010 (100.00%) were unpaired; of these: 228456 (3.99%) aligned 0 times 3787520 (66.12%) aligned exactly 1 time 1712034 (29.89%) aligned >1 times 96.01% overall alignment rate Time searching: 00:02:12 Overall time: 00:02:12 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] 559258 / 5499554 = 0.1017 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 13:40:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8688922/SRX8688922.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8688922/SRX8688922.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8688922/SRX8688922.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8688922/SRX8688922.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 13:40:09: #1 read tag files... INFO @ Fri, 10 Dec 2021 13:40:09: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 13:40:15: 1000000 INFO @ Fri, 10 Dec 2021 13:40:20: 2000000 INFO @ Fri, 10 Dec 2021 13:40:26: 3000000 INFO @ Fri, 10 Dec 2021 13:40:32: 4000000 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 13:40:38: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 13:40:38: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 13:40:38: #1 total tags in treatment: 4940296 INFO @ Fri, 10 Dec 2021 13:40:38: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 13:40:38: #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 13:40:38: #1 tags after filtering in treatment: 4940287 INFO @ Fri, 10 Dec 2021 13:40:38: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 13:40:38: #1 finished! INFO @ Fri, 10 Dec 2021 13:40:38: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 13:40:38: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 13:40:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8688922/SRX8688922.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8688922/SRX8688922.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8688922/SRX8688922.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8688922/SRX8688922.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 13:40:39: #1 read tag files... INFO @ Fri, 10 Dec 2021 13:40:39: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 13:40:39: #2 number of paired peaks: 487 WARNING @ Fri, 10 Dec 2021 13:40:39: Fewer paired peaks (487) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 487 pairs to build model! INFO @ Fri, 10 Dec 2021 13:40:39: start model_add_line... INFO @ Fri, 10 Dec 2021 13:40:39: start X-correlation... INFO @ Fri, 10 Dec 2021 13:40:39: end of X-cor INFO @ Fri, 10 Dec 2021 13:40:39: #2 finished! INFO @ Fri, 10 Dec 2021 13:40:39: #2 predicted fragment length is 66 bps INFO @ Fri, 10 Dec 2021 13:40:39: #2 alternative fragment length(s) may be 66 bps INFO @ Fri, 10 Dec 2021 13:40:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8688922/SRX8688922.05_model.r WARNING @ Fri, 10 Dec 2021 13:40:39: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 13:40:39: #2 You may need to consider one of the other alternative d(s): 66 WARNING @ Fri, 10 Dec 2021 13:40:39: #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 13:40:39: #3 Call peaks... INFO @ Fri, 10 Dec 2021 13:40:39: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 13:40:45: 1000000 INFO @ Fri, 10 Dec 2021 13:40:49: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 13:40:51: 2000000 INFO @ Fri, 10 Dec 2021 13:40:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8688922/SRX8688922.05_peaks.xls INFO @ Fri, 10 Dec 2021 13:40:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8688922/SRX8688922.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 13:40:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8688922/SRX8688922.05_summits.bed INFO @ Fri, 10 Dec 2021 13:40:55: Done! pass1 - making usageList (449 chroms): 1 millis pass2 - checking and writing primary data (1102 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 13:40:56: 3000000 INFO @ Fri, 10 Dec 2021 13:41:02: 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 13:41:08: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 13:41:08: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 13:41:08: #1 total tags in treatment: 4940296 INFO @ Fri, 10 Dec 2021 13:41:08: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 13:41:08: #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 13:41:09: #1 tags after filtering in treatment: 4940287 INFO @ Fri, 10 Dec 2021 13:41:09: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 13:41:09: #1 finished! INFO @ Fri, 10 Dec 2021 13:41:09: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 13:41:09: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 13:41:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8688922/SRX8688922.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8688922/SRX8688922.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8688922/SRX8688922.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8688922/SRX8688922.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 13:41:09: #1 read tag files... INFO @ Fri, 10 Dec 2021 13:41:09: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 13:41:09: #2 number of paired peaks: 487 WARNING @ Fri, 10 Dec 2021 13:41:09: Fewer paired peaks (487) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 487 pairs to build model! INFO @ Fri, 10 Dec 2021 13:41:09: start model_add_line... INFO @ Fri, 10 Dec 2021 13:41:09: start X-correlation... INFO @ Fri, 10 Dec 2021 13:41:09: end of X-cor INFO @ Fri, 10 Dec 2021 13:41:09: #2 finished! INFO @ Fri, 10 Dec 2021 13:41:09: #2 predicted fragment length is 66 bps INFO @ Fri, 10 Dec 2021 13:41:09: #2 alternative fragment length(s) may be 66 bps INFO @ Fri, 10 Dec 2021 13:41:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8688922/SRX8688922.10_model.r WARNING @ Fri, 10 Dec 2021 13:41:09: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 13:41:09: #2 You may need to consider one of the other alternative d(s): 66 WARNING @ Fri, 10 Dec 2021 13:41:09: #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 13:41:09: #3 Call peaks... INFO @ Fri, 10 Dec 2021 13:41:09: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 13:41:15: 1000000 INFO @ Fri, 10 Dec 2021 13:41:20: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 13:41:20: 2000000 INFO @ Fri, 10 Dec 2021 13:41:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8688922/SRX8688922.10_peaks.xls INFO @ Fri, 10 Dec 2021 13:41:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8688922/SRX8688922.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 13:41:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8688922/SRX8688922.10_summits.bed INFO @ Fri, 10 Dec 2021 13:41:25: Done! pass1 - making usageList (211 chroms): 1 millis pass2 - checking and writing primary data (421 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 13:41:26: 3000000 INFO @ Fri, 10 Dec 2021 13:41:32: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 13:41:38: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 13:41:38: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 13:41:38: #1 total tags in treatment: 4940296 INFO @ Fri, 10 Dec 2021 13:41:38: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 13:41:38: #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 13:41:39: #1 tags after filtering in treatment: 4940287 INFO @ Fri, 10 Dec 2021 13:41:39: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 13:41:39: #1 finished! INFO @ Fri, 10 Dec 2021 13:41:39: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 13:41:39: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 13:41:39: #2 number of paired peaks: 487 WARNING @ Fri, 10 Dec 2021 13:41:39: Fewer paired peaks (487) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 487 pairs to build model! INFO @ Fri, 10 Dec 2021 13:41:39: start model_add_line... INFO @ Fri, 10 Dec 2021 13:41:39: start X-correlation... INFO @ Fri, 10 Dec 2021 13:41:39: end of X-cor INFO @ Fri, 10 Dec 2021 13:41:39: #2 finished! INFO @ Fri, 10 Dec 2021 13:41:39: #2 predicted fragment length is 66 bps INFO @ Fri, 10 Dec 2021 13:41:39: #2 alternative fragment length(s) may be 66 bps INFO @ Fri, 10 Dec 2021 13:41:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8688922/SRX8688922.20_model.r WARNING @ Fri, 10 Dec 2021 13:41:39: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 13:41:39: #2 You may need to consider one of the other alternative d(s): 66 WARNING @ Fri, 10 Dec 2021 13:41:39: #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 13:41:39: #3 Call peaks... INFO @ Fri, 10 Dec 2021 13:41:39: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 13:41:50: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 13:41:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8688922/SRX8688922.20_peaks.xls INFO @ Fri, 10 Dec 2021 13:41:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8688922/SRX8688922.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 13:41:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8688922/SRX8688922.20_summits.bed INFO @ Fri, 10 Dec 2021 13:41:55: Done! pass1 - making usageList (112 chroms): 1 millis pass2 - checking and writing primary data (224 records, 4 fields): 5 millis CompletedMACS2peakCalling