Job ID = 12265446 SRX = SRX5010759 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: 00:05:00 19123450 reads; of these: 19123450 (100.00%) were unpaired; of these: 683396 (3.57%) aligned 0 times 14931544 (78.08%) aligned exactly 1 time 3508510 (18.35%) aligned >1 times 96.43% overall alignment rate Time searching: 00:05:00 Overall time: 00:05:00 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_sort_core] merging from 8 files... [bam_rmdupse_core] 10615368 / 18440054 = 0.5757 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/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 07:13:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5010759/SRX5010759.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5010759/SRX5010759.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5010759/SRX5010759.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5010759/SRX5010759.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, 03 Apr 2021 07:13:05: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:13:05: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:13:11: 1000000 INFO @ Sat, 03 Apr 2021 07:13:17: 2000000 INFO @ Sat, 03 Apr 2021 07:13:23: 3000000 INFO @ Sat, 03 Apr 2021 07:13:29: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 07:13:35: 5000000 INFO @ Sat, 03 Apr 2021 07:13:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5010759/SRX5010759.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5010759/SRX5010759.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5010759/SRX5010759.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5010759/SRX5010759.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, 03 Apr 2021 07:13:35: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:13:35: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:13:41: 6000000 INFO @ Sat, 03 Apr 2021 07:13:42: 1000000 INFO @ Sat, 03 Apr 2021 07:13:48: 7000000 INFO @ Sat, 03 Apr 2021 07:13:48: 2000000 INFO @ Sat, 03 Apr 2021 07:13:53: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 07:13:53: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 07:13:53: #1 total tags in treatment: 7824686 INFO @ Sat, 03 Apr 2021 07:13:53: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:13:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 07:13:54: #1 tags after filtering in treatment: 7824565 INFO @ Sat, 03 Apr 2021 07:13:54: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 07:13:54: #1 finished! INFO @ Sat, 03 Apr 2021 07:13:54: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:13:54: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:13:54: #2 number of paired peaks: 708 WARNING @ Sat, 03 Apr 2021 07:13:54: Fewer paired peaks (708) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 708 pairs to build model! INFO @ Sat, 03 Apr 2021 07:13:54: start model_add_line... INFO @ Sat, 03 Apr 2021 07:13:55: start X-correlation... INFO @ Sat, 03 Apr 2021 07:13:55: end of X-cor INFO @ Sat, 03 Apr 2021 07:13:55: #2 finished! INFO @ Sat, 03 Apr 2021 07:13:55: #2 predicted fragment length is 47 bps INFO @ Sat, 03 Apr 2021 07:13:55: #2 alternative fragment length(s) may be 4,47,556 bps INFO @ Sat, 03 Apr 2021 07:13:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5010759/SRX5010759.05_model.r WARNING @ Sat, 03 Apr 2021 07:13:55: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:13:55: #2 You may need to consider one of the other alternative d(s): 4,47,556 WARNING @ Sat, 03 Apr 2021 07:13:55: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 07:13:55: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:13:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:13:55: 3000000 INFO @ Sat, 03 Apr 2021 07:14:01: 4000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 07:14:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5010759/SRX5010759.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5010759/SRX5010759.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5010759/SRX5010759.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5010759/SRX5010759.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, 03 Apr 2021 07:14:05: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:14:05: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:14:07: 5000000 INFO @ Sat, 03 Apr 2021 07:14:12: 1000000 INFO @ Sat, 03 Apr 2021 07:14:13: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:14:14: 6000000 INFO @ Sat, 03 Apr 2021 07:14:18: 2000000 INFO @ Sat, 03 Apr 2021 07:14:20: 7000000 INFO @ Sat, 03 Apr 2021 07:14:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5010759/SRX5010759.05_peaks.xls INFO @ Sat, 03 Apr 2021 07:14:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5010759/SRX5010759.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:14:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5010759/SRX5010759.05_summits.bed INFO @ Sat, 03 Apr 2021 07:14:22: Done! pass1 - making usageList (393 chroms): 2 millis pass2 - checking and writing primary data (2669 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 07:14:25: 3000000 INFO @ Sat, 03 Apr 2021 07:14:26: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 07:14:26: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 07:14:26: #1 total tags in treatment: 7824686 INFO @ Sat, 03 Apr 2021 07:14:26: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:14:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 07:14:26: #1 tags after filtering in treatment: 7824565 INFO @ Sat, 03 Apr 2021 07:14:26: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 07:14:26: #1 finished! INFO @ Sat, 03 Apr 2021 07:14:26: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:14:26: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:14:27: #2 number of paired peaks: 708 WARNING @ Sat, 03 Apr 2021 07:14:27: Fewer paired peaks (708) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 708 pairs to build model! INFO @ Sat, 03 Apr 2021 07:14:27: start model_add_line... INFO @ Sat, 03 Apr 2021 07:14:27: start X-correlation... INFO @ Sat, 03 Apr 2021 07:14:27: end of X-cor INFO @ Sat, 03 Apr 2021 07:14:27: #2 finished! INFO @ Sat, 03 Apr 2021 07:14:27: #2 predicted fragment length is 47 bps INFO @ Sat, 03 Apr 2021 07:14:27: #2 alternative fragment length(s) may be 4,47,556 bps INFO @ Sat, 03 Apr 2021 07:14:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5010759/SRX5010759.10_model.r WARNING @ Sat, 03 Apr 2021 07:14:27: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:14:27: #2 You may need to consider one of the other alternative d(s): 4,47,556 WARNING @ Sat, 03 Apr 2021 07:14:27: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 07:14:27: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:14:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:14:31: 4000000 INFO @ Sat, 03 Apr 2021 07:14:37: 5000000 INFO @ Sat, 03 Apr 2021 07:14:43: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 07:14:46: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:14:49: 7000000 INFO @ Sat, 03 Apr 2021 07:14:54: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 07:14:54: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 07:14:54: #1 total tags in treatment: 7824686 INFO @ Sat, 03 Apr 2021 07:14:54: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:14:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 07:14:54: #1 tags after filtering in treatment: 7824565 INFO @ Sat, 03 Apr 2021 07:14:54: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 07:14:54: #1 finished! INFO @ Sat, 03 Apr 2021 07:14:54: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:14:54: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:14:55: #2 number of paired peaks: 708 WARNING @ Sat, 03 Apr 2021 07:14:55: Fewer paired peaks (708) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 708 pairs to build model! INFO @ Sat, 03 Apr 2021 07:14:55: start model_add_line... INFO @ Sat, 03 Apr 2021 07:14:55: start X-correlation... INFO @ Sat, 03 Apr 2021 07:14:55: end of X-cor INFO @ Sat, 03 Apr 2021 07:14:55: #2 finished! INFO @ Sat, 03 Apr 2021 07:14:55: #2 predicted fragment length is 47 bps INFO @ Sat, 03 Apr 2021 07:14:55: #2 alternative fragment length(s) may be 4,47,556 bps INFO @ Sat, 03 Apr 2021 07:14:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5010759/SRX5010759.20_model.r WARNING @ Sat, 03 Apr 2021 07:14:55: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:14:55: #2 You may need to consider one of the other alternative d(s): 4,47,556 WARNING @ Sat, 03 Apr 2021 07:14:55: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 07:14:55: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:14:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:14:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5010759/SRX5010759.10_peaks.xls INFO @ Sat, 03 Apr 2021 07:14:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5010759/SRX5010759.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:14:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5010759/SRX5010759.10_summits.bed INFO @ Sat, 03 Apr 2021 07:14:55: Done! pass1 - making usageList (216 chroms): 1 millis pass2 - checking and writing primary data (892 records, 4 fields): 10 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 07:15:13: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:15:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5010759/SRX5010759.20_peaks.xls INFO @ Sat, 03 Apr 2021 07:15:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5010759/SRX5010759.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:15:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5010759/SRX5010759.20_summits.bed INFO @ Sat, 03 Apr 2021 07:15:22: Done! pass1 - making usageList (92 chroms): 1 millis pass2 - checking and writing primary data (225 records, 4 fields): 4 millis CompletedMACS2peakCalling