Job ID = 14170907 SRX = SRX8689038 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: 00:06:48 18402995 reads; of these: 18402995 (100.00%) were unpaired; of these: 547974 (2.98%) aligned 0 times 12808989 (69.60%) aligned exactly 1 time 5046032 (27.42%) aligned >1 times 97.02% overall alignment rate Time searching: 00:06:48 Overall time: 00:06:48 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] 1896016 / 17855021 = 0.1062 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 @ Sat, 11 Dec 2021 09:11:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8689038/SRX8689038.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8689038/SRX8689038.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8689038/SRX8689038.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8689038/SRX8689038.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, 11 Dec 2021 09:11:56: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:11:56: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:12:04: 1000000 INFO @ Sat, 11 Dec 2021 09:12:12: 2000000 INFO @ Sat, 11 Dec 2021 09:12:20: 3000000 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 @ Sat, 11 Dec 2021 09:12:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8689038/SRX8689038.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8689038/SRX8689038.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8689038/SRX8689038.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8689038/SRX8689038.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, 11 Dec 2021 09:12:26: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:12:26: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:12:28: 4000000 INFO @ Sat, 11 Dec 2021 09:12:33: 1000000 INFO @ Sat, 11 Dec 2021 09:12:36: 5000000 INFO @ Sat, 11 Dec 2021 09:12:41: 2000000 INFO @ Sat, 11 Dec 2021 09:12:44: 6000000 INFO @ Sat, 11 Dec 2021 09:12:48: 3000000 INFO @ Sat, 11 Dec 2021 09:12:52: 7000000 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 @ Sat, 11 Dec 2021 09:12:55: 4000000 INFO @ Sat, 11 Dec 2021 09:12:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8689038/SRX8689038.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8689038/SRX8689038.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8689038/SRX8689038.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8689038/SRX8689038.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, 11 Dec 2021 09:12:56: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:12:56: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:12:59: 8000000 INFO @ Sat, 11 Dec 2021 09:13:02: 5000000 INFO @ Sat, 11 Dec 2021 09:13:03: 1000000 INFO @ Sat, 11 Dec 2021 09:13:07: 9000000 INFO @ Sat, 11 Dec 2021 09:13:09: 2000000 INFO @ Sat, 11 Dec 2021 09:13:10: 6000000 INFO @ Sat, 11 Dec 2021 09:13:15: 10000000 INFO @ Sat, 11 Dec 2021 09:13:16: 3000000 INFO @ Sat, 11 Dec 2021 09:13:17: 7000000 INFO @ Sat, 11 Dec 2021 09:13:23: 4000000 INFO @ Sat, 11 Dec 2021 09:13:23: 11000000 INFO @ Sat, 11 Dec 2021 09:13:24: 8000000 INFO @ Sat, 11 Dec 2021 09:13:29: 5000000 INFO @ Sat, 11 Dec 2021 09:13:31: 9000000 INFO @ Sat, 11 Dec 2021 09:13:32: 12000000 INFO @ Sat, 11 Dec 2021 09:13:36: 6000000 INFO @ Sat, 11 Dec 2021 09:13:38: 10000000 INFO @ Sat, 11 Dec 2021 09:13:40: 13000000 INFO @ Sat, 11 Dec 2021 09:13:43: 7000000 INFO @ Sat, 11 Dec 2021 09:13:46: 11000000 INFO @ Sat, 11 Dec 2021 09:13:48: 14000000 INFO @ Sat, 11 Dec 2021 09:13:50: 8000000 INFO @ Sat, 11 Dec 2021 09:13:53: 12000000 INFO @ Sat, 11 Dec 2021 09:13:56: 15000000 INFO @ Sat, 11 Dec 2021 09:13:56: 9000000 INFO @ Sat, 11 Dec 2021 09:14:01: 13000000 INFO @ Sat, 11 Dec 2021 09:14:03: 10000000 INFO @ Sat, 11 Dec 2021 09:14:04: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 09:14:04: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 09:14:04: #1 total tags in treatment: 15959005 INFO @ Sat, 11 Dec 2021 09:14:04: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:14:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 09:14:05: #1 tags after filtering in treatment: 15958915 INFO @ Sat, 11 Dec 2021 09:14:05: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 09:14:05: #1 finished! INFO @ Sat, 11 Dec 2021 09:14:05: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:14:05: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:14:06: #2 number of paired peaks: 846 WARNING @ Sat, 11 Dec 2021 09:14:06: Fewer paired peaks (846) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 846 pairs to build model! INFO @ Sat, 11 Dec 2021 09:14:06: start model_add_line... INFO @ Sat, 11 Dec 2021 09:14:06: start X-correlation... INFO @ Sat, 11 Dec 2021 09:14:06: end of X-cor INFO @ Sat, 11 Dec 2021 09:14:06: #2 finished! INFO @ Sat, 11 Dec 2021 09:14:06: #2 predicted fragment length is 49 bps INFO @ Sat, 11 Dec 2021 09:14:06: #2 alternative fragment length(s) may be 4,49 bps INFO @ Sat, 11 Dec 2021 09:14:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8689038/SRX8689038.05_model.r WARNING @ Sat, 11 Dec 2021 09:14:06: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 09:14:06: #2 You may need to consider one of the other alternative d(s): 4,49 WARNING @ Sat, 11 Dec 2021 09:14:06: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 09:14:06: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:14:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:14:08: 14000000 INFO @ Sat, 11 Dec 2021 09:14:10: 11000000 INFO @ Sat, 11 Dec 2021 09:14:16: 15000000 INFO @ Sat, 11 Dec 2021 09:14:17: 12000000 INFO @ Sat, 11 Dec 2021 09:14:23: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 09:14:23: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 09:14:23: #1 total tags in treatment: 15959005 INFO @ Sat, 11 Dec 2021 09:14:23: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:14:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 09:14:24: #1 tags after filtering in treatment: 15958915 INFO @ Sat, 11 Dec 2021 09:14:24: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 09:14:24: #1 finished! INFO @ Sat, 11 Dec 2021 09:14:24: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:14:24: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:14:24: 13000000 INFO @ Sat, 11 Dec 2021 09:14:25: #2 number of paired peaks: 846 WARNING @ Sat, 11 Dec 2021 09:14:25: Fewer paired peaks (846) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 846 pairs to build model! INFO @ Sat, 11 Dec 2021 09:14:25: start model_add_line... INFO @ Sat, 11 Dec 2021 09:14:25: start X-correlation... INFO @ Sat, 11 Dec 2021 09:14:25: end of X-cor INFO @ Sat, 11 Dec 2021 09:14:25: #2 finished! INFO @ Sat, 11 Dec 2021 09:14:25: #2 predicted fragment length is 49 bps INFO @ Sat, 11 Dec 2021 09:14:25: #2 alternative fragment length(s) may be 4,49 bps INFO @ Sat, 11 Dec 2021 09:14:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8689038/SRX8689038.10_model.r WARNING @ Sat, 11 Dec 2021 09:14:25: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 09:14:25: #2 You may need to consider one of the other alternative d(s): 4,49 WARNING @ Sat, 11 Dec 2021 09:14:25: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 09:14:25: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:14:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:14:31: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 09:14:37: 15000000 INFO @ Sat, 11 Dec 2021 09:14:44: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 09:14:44: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 09:14:44: #1 total tags in treatment: 15959005 INFO @ Sat, 11 Dec 2021 09:14:44: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:14:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 09:14:45: #1 tags after filtering in treatment: 15958915 INFO @ Sat, 11 Dec 2021 09:14:45: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 09:14:45: #1 finished! INFO @ Sat, 11 Dec 2021 09:14:45: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:14:45: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:14:47: #2 number of paired peaks: 846 WARNING @ Sat, 11 Dec 2021 09:14:47: Fewer paired peaks (846) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 846 pairs to build model! INFO @ Sat, 11 Dec 2021 09:14:47: start model_add_line... INFO @ Sat, 11 Dec 2021 09:14:47: start X-correlation... INFO @ Sat, 11 Dec 2021 09:14:47: end of X-cor INFO @ Sat, 11 Dec 2021 09:14:47: #2 finished! INFO @ Sat, 11 Dec 2021 09:14:47: #2 predicted fragment length is 49 bps INFO @ Sat, 11 Dec 2021 09:14:47: #2 alternative fragment length(s) may be 4,49 bps INFO @ Sat, 11 Dec 2021 09:14:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8689038/SRX8689038.20_model.r WARNING @ Sat, 11 Dec 2021 09:14:47: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 09:14:47: #2 You may need to consider one of the other alternative d(s): 4,49 WARNING @ Sat, 11 Dec 2021 09:14:47: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 09:14:47: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:14:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:14:48: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:15:07: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:15:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8689038/SRX8689038.05_peaks.xls INFO @ Sat, 11 Dec 2021 09:15:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8689038/SRX8689038.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:15:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8689038/SRX8689038.05_summits.bed INFO @ Sat, 11 Dec 2021 09:15:07: Done! pass1 - making usageList (706 chroms): 2 millis pass2 - checking and writing primary data (3121 records, 4 fields): 32 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 09:15:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8689038/SRX8689038.10_peaks.xls INFO @ Sat, 11 Dec 2021 09:15:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8689038/SRX8689038.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:15:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8689038/SRX8689038.10_summits.bed INFO @ Sat, 11 Dec 2021 09:15:27: Done! pass1 - making usageList (610 chroms): 2 millis pass2 - checking and writing primary data (2445 records, 4 fields): 28 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 09:15:28: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:15:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8689038/SRX8689038.20_peaks.xls INFO @ Sat, 11 Dec 2021 09:15:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8689038/SRX8689038.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:15:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8689038/SRX8689038.20_summits.bed INFO @ Sat, 11 Dec 2021 09:15:47: Done! pass1 - making usageList (447 chroms): 2 millis pass2 - checking and writing primary data (1133 records, 4 fields): 28 millis CompletedMACS2peakCalling