Job ID = 14171844 SRX = SRX8512933 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: 00:06:28 11274144 reads; of these: 11274144 (100.00%) were unpaired; of these: 856 (0.01%) aligned 0 times 9958307 (88.33%) aligned exactly 1 time 1314981 (11.66%) aligned >1 times 99.99% overall alignment rate Time searching: 00:06:28 Overall time: 00:06:28 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] 991993 / 11273288 = 0.0880 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 13:18:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8512933/SRX8512933.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8512933/SRX8512933.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8512933/SRX8512933.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8512933/SRX8512933.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 13:18:13: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:18:13: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:18:20: 1000000 INFO @ Sat, 11 Dec 2021 13:18:28: 2000000 INFO @ Sat, 11 Dec 2021 13:18:36: 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 13:18:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8512933/SRX8512933.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8512933/SRX8512933.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8512933/SRX8512933.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8512933/SRX8512933.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 13:18:43: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:18:43: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:18:44: 4000000 INFO @ Sat, 11 Dec 2021 13:18:53: 5000000 INFO @ Sat, 11 Dec 2021 13:18:53: 1000000 INFO @ Sat, 11 Dec 2021 13:19:03: 6000000 INFO @ Sat, 11 Dec 2021 13:19:04: 2000000 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 13:19:12: 7000000 INFO @ Sat, 11 Dec 2021 13:19:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8512933/SRX8512933.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8512933/SRX8512933.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8512933/SRX8512933.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8512933/SRX8512933.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 13:19:13: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:19:13: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:19:15: 3000000 INFO @ Sat, 11 Dec 2021 13:19:22: 8000000 INFO @ Sat, 11 Dec 2021 13:19:23: 1000000 INFO @ Sat, 11 Dec 2021 13:19:25: 4000000 INFO @ Sat, 11 Dec 2021 13:19:32: 9000000 INFO @ Sat, 11 Dec 2021 13:19:33: 2000000 INFO @ Sat, 11 Dec 2021 13:19:36: 5000000 INFO @ Sat, 11 Dec 2021 13:19:42: 10000000 INFO @ Sat, 11 Dec 2021 13:19:43: 3000000 INFO @ Sat, 11 Dec 2021 13:19:45: #1 tag size is determined as 150 bps INFO @ Sat, 11 Dec 2021 13:19:45: #1 tag size = 150 INFO @ Sat, 11 Dec 2021 13:19:45: #1 total tags in treatment: 10281295 INFO @ Sat, 11 Dec 2021 13:19:45: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:19:45: #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 13:19:45: #1 tags after filtering in treatment: 10281027 INFO @ Sat, 11 Dec 2021 13:19:45: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 13:19:45: #1 finished! INFO @ Sat, 11 Dec 2021 13:19:45: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:19:45: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:19:46: #2 number of paired peaks: 264 WARNING @ Sat, 11 Dec 2021 13:19:46: Fewer paired peaks (264) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 264 pairs to build model! INFO @ Sat, 11 Dec 2021 13:19:46: start model_add_line... INFO @ Sat, 11 Dec 2021 13:19:46: start X-correlation... INFO @ Sat, 11 Dec 2021 13:19:46: end of X-cor INFO @ Sat, 11 Dec 2021 13:19:46: #2 finished! INFO @ Sat, 11 Dec 2021 13:19:46: #2 predicted fragment length is 156 bps INFO @ Sat, 11 Dec 2021 13:19:46: #2 alternative fragment length(s) may be 156 bps INFO @ Sat, 11 Dec 2021 13:19:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8512933/SRX8512933.05_model.r WARNING @ Sat, 11 Dec 2021 13:19:46: #2 Since the d (156) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 13:19:46: #2 You may need to consider one of the other alternative d(s): 156 WARNING @ Sat, 11 Dec 2021 13:19:46: #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 13:19:46: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:19:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 13:19:47: 6000000 INFO @ Sat, 11 Dec 2021 13:19:54: 4000000 INFO @ Sat, 11 Dec 2021 13:19:57: 7000000 INFO @ Sat, 11 Dec 2021 13:20:04: 5000000 INFO @ Sat, 11 Dec 2021 13:20:08: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:20:08: 8000000 INFO @ Sat, 11 Dec 2021 13:20:14: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 13:20:18: 9000000 INFO @ Sat, 11 Dec 2021 13:20:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8512933/SRX8512933.05_peaks.xls INFO @ Sat, 11 Dec 2021 13:20:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8512933/SRX8512933.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:20:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8512933/SRX8512933.05_summits.bed INFO @ Sat, 11 Dec 2021 13:20:19: Done! pass1 - making usageList (88 chroms): 1 millis pass2 - checking and writing primary data (3628 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 13:20:24: 7000000 INFO @ Sat, 11 Dec 2021 13:20:29: 10000000 INFO @ Sat, 11 Dec 2021 13:20:32: #1 tag size is determined as 150 bps INFO @ Sat, 11 Dec 2021 13:20:32: #1 tag size = 150 INFO @ Sat, 11 Dec 2021 13:20:32: #1 total tags in treatment: 10281295 INFO @ Sat, 11 Dec 2021 13:20:32: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:20:32: #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 13:20:32: #1 tags after filtering in treatment: 10281027 INFO @ Sat, 11 Dec 2021 13:20:32: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 13:20:32: #1 finished! INFO @ Sat, 11 Dec 2021 13:20:32: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:20:32: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:20:33: #2 number of paired peaks: 264 WARNING @ Sat, 11 Dec 2021 13:20:33: Fewer paired peaks (264) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 264 pairs to build model! INFO @ Sat, 11 Dec 2021 13:20:33: start model_add_line... INFO @ Sat, 11 Dec 2021 13:20:33: start X-correlation... INFO @ Sat, 11 Dec 2021 13:20:33: end of X-cor INFO @ Sat, 11 Dec 2021 13:20:33: #2 finished! INFO @ Sat, 11 Dec 2021 13:20:33: #2 predicted fragment length is 156 bps INFO @ Sat, 11 Dec 2021 13:20:33: #2 alternative fragment length(s) may be 156 bps INFO @ Sat, 11 Dec 2021 13:20:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8512933/SRX8512933.10_model.r WARNING @ Sat, 11 Dec 2021 13:20:33: #2 Since the d (156) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 13:20:33: #2 You may need to consider one of the other alternative d(s): 156 WARNING @ Sat, 11 Dec 2021 13:20:33: #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 13:20:33: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:20:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 13:20:34: 8000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 13:20:43: 9000000 INFO @ Sat, 11 Dec 2021 13:20:53: 10000000 INFO @ Sat, 11 Dec 2021 13:20:54: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:20:55: #1 tag size is determined as 150 bps INFO @ Sat, 11 Dec 2021 13:20:55: #1 tag size = 150 INFO @ Sat, 11 Dec 2021 13:20:55: #1 total tags in treatment: 10281295 INFO @ Sat, 11 Dec 2021 13:20:55: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:20:55: #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 13:20:56: #1 tags after filtering in treatment: 10281027 INFO @ Sat, 11 Dec 2021 13:20:56: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 13:20:56: #1 finished! INFO @ Sat, 11 Dec 2021 13:20:56: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:20:56: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:20:56: #2 number of paired peaks: 264 WARNING @ Sat, 11 Dec 2021 13:20:56: Fewer paired peaks (264) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 264 pairs to build model! INFO @ Sat, 11 Dec 2021 13:20:56: start model_add_line... INFO @ Sat, 11 Dec 2021 13:20:56: start X-correlation... INFO @ Sat, 11 Dec 2021 13:20:56: end of X-cor INFO @ Sat, 11 Dec 2021 13:20:56: #2 finished! INFO @ Sat, 11 Dec 2021 13:20:56: #2 predicted fragment length is 156 bps INFO @ Sat, 11 Dec 2021 13:20:56: #2 alternative fragment length(s) may be 156 bps INFO @ Sat, 11 Dec 2021 13:20:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8512933/SRX8512933.20_model.r WARNING @ Sat, 11 Dec 2021 13:20:56: #2 Since the d (156) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 13:20:56: #2 You may need to consider one of the other alternative d(s): 156 WARNING @ Sat, 11 Dec 2021 13:20:56: #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 13:20:56: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:20:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 13:21:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8512933/SRX8512933.10_peaks.xls INFO @ Sat, 11 Dec 2021 13:21:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8512933/SRX8512933.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:21:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8512933/SRX8512933.10_summits.bed INFO @ Sat, 11 Dec 2021 13:21:04: Done! pass1 - making usageList (50 chroms): 1 millis pass2 - checking and writing primary data (568 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 13:21:17: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:21:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8512933/SRX8512933.20_peaks.xls INFO @ Sat, 11 Dec 2021 13:21:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8512933/SRX8512933.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:21:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8512933/SRX8512933.20_summits.bed INFO @ Sat, 11 Dec 2021 13:21:27: Done! pass1 - making usageList (34 chroms): 1 millis pass2 - checking and writing primary data (108 records, 4 fields): 2 millis CompletedMACS2peakCalling