Job ID = 14166979 SRX = SRX7723712 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 48616499 spots for SRR11084668/SRR11084668.sra Written 48616499 spots for SRR11084668/SRR11084668.sra fastq に変換しました。 bowtie でマッピング中... Your job 14167343 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:19:46 48616499 reads; of these: 48616499 (100.00%) were unpaired; of these: 9394680 (19.32%) aligned 0 times 29175131 (60.01%) aligned exactly 1 time 10046688 (20.67%) aligned >1 times 80.68% overall alignment rate Time searching: 00:19:46 Overall time: 00:19:46 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 16 files... [bam_rmdupse_core] 27975548 / 39221819 = 0.7133 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 08:46:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7723712/SRX7723712.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7723712/SRX7723712.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7723712/SRX7723712.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7723712/SRX7723712.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 08:46:48: #1 read tag files... INFO @ Fri, 10 Dec 2021 08:46:48: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 08:46:54: 1000000 INFO @ Fri, 10 Dec 2021 08:47:01: 2000000 INFO @ Fri, 10 Dec 2021 08:47:07: 3000000 INFO @ Fri, 10 Dec 2021 08:47:13: 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 08:47:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7723712/SRX7723712.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7723712/SRX7723712.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7723712/SRX7723712.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7723712/SRX7723712.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 08:47:18: #1 read tag files... INFO @ Fri, 10 Dec 2021 08:47:18: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 08:47:19: 5000000 INFO @ Fri, 10 Dec 2021 08:47:27: 6000000 INFO @ Fri, 10 Dec 2021 08:47:27: 1000000 INFO @ Fri, 10 Dec 2021 08:47:35: 7000000 INFO @ Fri, 10 Dec 2021 08:47:36: 2000000 INFO @ Fri, 10 Dec 2021 08:47:43: 8000000 INFO @ Fri, 10 Dec 2021 08:47:45: 3000000 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 08:47:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7723712/SRX7723712.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7723712/SRX7723712.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7723712/SRX7723712.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7723712/SRX7723712.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 08:47:48: #1 read tag files... INFO @ Fri, 10 Dec 2021 08:47:48: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 08:47:51: 9000000 INFO @ Fri, 10 Dec 2021 08:47:53: 4000000 INFO @ Fri, 10 Dec 2021 08:47:56: 1000000 INFO @ Fri, 10 Dec 2021 08:47:59: 10000000 INFO @ Fri, 10 Dec 2021 08:48:02: 5000000 INFO @ Fri, 10 Dec 2021 08:48:04: 2000000 INFO @ Fri, 10 Dec 2021 08:48:07: 11000000 INFO @ Fri, 10 Dec 2021 08:48:09: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 08:48:09: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 08:48:09: #1 total tags in treatment: 11246271 INFO @ Fri, 10 Dec 2021 08:48:09: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 08:48:09: #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 08:48:09: #1 tags after filtering in treatment: 11246271 INFO @ Fri, 10 Dec 2021 08:48:09: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 08:48:09: #1 finished! INFO @ Fri, 10 Dec 2021 08:48:09: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 08:48:09: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 08:48:10: #2 number of paired peaks: 445 WARNING @ Fri, 10 Dec 2021 08:48:10: Fewer paired peaks (445) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 445 pairs to build model! INFO @ Fri, 10 Dec 2021 08:48:10: start model_add_line... INFO @ Fri, 10 Dec 2021 08:48:10: start X-correlation... INFO @ Fri, 10 Dec 2021 08:48:10: end of X-cor INFO @ Fri, 10 Dec 2021 08:48:10: #2 finished! INFO @ Fri, 10 Dec 2021 08:48:10: #2 predicted fragment length is 73 bps INFO @ Fri, 10 Dec 2021 08:48:10: #2 alternative fragment length(s) may be 73 bps INFO @ Fri, 10 Dec 2021 08:48:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7723712/SRX7723712.05_model.r WARNING @ Fri, 10 Dec 2021 08:48:10: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 08:48:10: #2 You may need to consider one of the other alternative d(s): 73 WARNING @ Fri, 10 Dec 2021 08:48:10: #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 08:48:10: #3 Call peaks... INFO @ Fri, 10 Dec 2021 08:48:10: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 08:48:11: 6000000 INFO @ Fri, 10 Dec 2021 08:48:12: 3000000 INFO @ Fri, 10 Dec 2021 08:48:20: 4000000 INFO @ Fri, 10 Dec 2021 08:48:20: 7000000 INFO @ Fri, 10 Dec 2021 08:48:28: 5000000 INFO @ Fri, 10 Dec 2021 08:48:29: 8000000 INFO @ Fri, 10 Dec 2021 08:48:32: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 08:48:36: 6000000 INFO @ Fri, 10 Dec 2021 08:48:38: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 08:48:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7723712/SRX7723712.05_peaks.xls INFO @ Fri, 10 Dec 2021 08:48:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7723712/SRX7723712.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 08:48:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7723712/SRX7723712.05_summits.bed INFO @ Fri, 10 Dec 2021 08:48:43: Done! INFO @ Fri, 10 Dec 2021 08:48:44: 7000000 pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (9740 records, 4 fields): 140 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 08:48:47: 10000000 INFO @ Fri, 10 Dec 2021 08:48:52: 8000000 INFO @ Fri, 10 Dec 2021 08:48:55: 11000000 INFO @ Fri, 10 Dec 2021 08:48:57: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 08:48:57: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 08:48:57: #1 total tags in treatment: 11246271 INFO @ Fri, 10 Dec 2021 08:48:57: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 08:48:57: #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 08:48:58: #1 tags after filtering in treatment: 11246271 INFO @ Fri, 10 Dec 2021 08:48:58: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 08:48:58: #1 finished! INFO @ Fri, 10 Dec 2021 08:48:58: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 08:48:58: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 08:48:58: #2 number of paired peaks: 445 WARNING @ Fri, 10 Dec 2021 08:48:58: Fewer paired peaks (445) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 445 pairs to build model! INFO @ Fri, 10 Dec 2021 08:48:58: start model_add_line... INFO @ Fri, 10 Dec 2021 08:48:59: start X-correlation... INFO @ Fri, 10 Dec 2021 08:48:59: end of X-cor INFO @ Fri, 10 Dec 2021 08:48:59: #2 finished! INFO @ Fri, 10 Dec 2021 08:48:59: #2 predicted fragment length is 73 bps INFO @ Fri, 10 Dec 2021 08:48:59: #2 alternative fragment length(s) may be 73 bps INFO @ Fri, 10 Dec 2021 08:48:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7723712/SRX7723712.10_model.r WARNING @ Fri, 10 Dec 2021 08:48:59: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 08:48:59: #2 You may need to consider one of the other alternative d(s): 73 WARNING @ Fri, 10 Dec 2021 08:48:59: #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 08:48:59: #3 Call peaks... INFO @ Fri, 10 Dec 2021 08:48:59: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 08:48:59: 9000000 INFO @ Fri, 10 Dec 2021 08:49:05: 10000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 08:49:11: 11000000 INFO @ Fri, 10 Dec 2021 08:49:13: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 08:49:13: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 08:49:13: #1 total tags in treatment: 11246271 INFO @ Fri, 10 Dec 2021 08:49:13: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 08:49:13: #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 08:49:13: #1 tags after filtering in treatment: 11246271 INFO @ Fri, 10 Dec 2021 08:49:13: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 08:49:13: #1 finished! INFO @ Fri, 10 Dec 2021 08:49:13: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 08:49:13: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 08:49:14: #2 number of paired peaks: 445 WARNING @ Fri, 10 Dec 2021 08:49:14: Fewer paired peaks (445) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 445 pairs to build model! INFO @ Fri, 10 Dec 2021 08:49:14: start model_add_line... INFO @ Fri, 10 Dec 2021 08:49:14: start X-correlation... INFO @ Fri, 10 Dec 2021 08:49:14: end of X-cor INFO @ Fri, 10 Dec 2021 08:49:14: #2 finished! INFO @ Fri, 10 Dec 2021 08:49:14: #2 predicted fragment length is 73 bps INFO @ Fri, 10 Dec 2021 08:49:14: #2 alternative fragment length(s) may be 73 bps INFO @ Fri, 10 Dec 2021 08:49:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7723712/SRX7723712.20_model.r WARNING @ Fri, 10 Dec 2021 08:49:14: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 08:49:14: #2 You may need to consider one of the other alternative d(s): 73 WARNING @ Fri, 10 Dec 2021 08:49:14: #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 08:49:14: #3 Call peaks... INFO @ Fri, 10 Dec 2021 08:49:14: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 08:49:20: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 08:49:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7723712/SRX7723712.10_peaks.xls INFO @ Fri, 10 Dec 2021 08:49:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7723712/SRX7723712.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 08:49:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7723712/SRX7723712.10_summits.bed INFO @ Fri, 10 Dec 2021 08:49:31: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2652 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 08:49:36: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 08:49:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7723712/SRX7723712.20_peaks.xls INFO @ Fri, 10 Dec 2021 08:49:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7723712/SRX7723712.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 08:49:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7723712/SRX7723712.20_summits.bed INFO @ Fri, 10 Dec 2021 08:49:47: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (422 records, 4 fields): 2 millis CompletedMACS2peakCalling