Job ID = 14171855 SRX = SRX9986162 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: 00:05:15 22070623 reads; of these: 22070623 (100.00%) were unpaired; of these: 2636079 (11.94%) aligned 0 times 14110440 (63.93%) aligned exactly 1 time 5324104 (24.12%) aligned >1 times 88.06% overall alignment rate Time searching: 00:05:15 Overall time: 00:05:15 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] 4489635 / 19434544 = 0.2310 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 13:20:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX9986162/SRX9986162.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX9986162/SRX9986162.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX9986162/SRX9986162.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX9986162/SRX9986162.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 13:20:15: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:20:15: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:20:19: 1000000 INFO @ Sat, 11 Dec 2021 13:20:24: 2000000 INFO @ Sat, 11 Dec 2021 13:20:28: 3000000 INFO @ Sat, 11 Dec 2021 13:20:33: 4000000 INFO @ Sat, 11 Dec 2021 13:20:37: 5000000 INFO @ Sat, 11 Dec 2021 13:20:42: 6000000 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 13:20:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX9986162/SRX9986162.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX9986162/SRX9986162.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX9986162/SRX9986162.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX9986162/SRX9986162.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 13:20:44: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:20:44: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:20:47: 7000000 INFO @ Sat, 11 Dec 2021 13:20:49: 1000000 INFO @ Sat, 11 Dec 2021 13:20:51: 8000000 INFO @ Sat, 11 Dec 2021 13:20:54: 2000000 INFO @ Sat, 11 Dec 2021 13:20:56: 9000000 INFO @ Sat, 11 Dec 2021 13:20:58: 3000000 INFO @ Sat, 11 Dec 2021 13:21:00: 10000000 INFO @ Sat, 11 Dec 2021 13:21:03: 4000000 INFO @ Sat, 11 Dec 2021 13:21:05: 11000000 INFO @ Sat, 11 Dec 2021 13:21:08: 5000000 INFO @ Sat, 11 Dec 2021 13:21:10: 12000000 INFO @ Sat, 11 Dec 2021 13:21:12: 6000000 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 13:21:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX9986162/SRX9986162.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX9986162/SRX9986162.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX9986162/SRX9986162.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX9986162/SRX9986162.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 13:21:14: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:21:14: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:21:15: 13000000 INFO @ Sat, 11 Dec 2021 13:21:17: 7000000 INFO @ Sat, 11 Dec 2021 13:21:19: 1000000 INFO @ Sat, 11 Dec 2021 13:21:19: 14000000 INFO @ Sat, 11 Dec 2021 13:21:22: 8000000 INFO @ Sat, 11 Dec 2021 13:21:24: 2000000 INFO @ Sat, 11 Dec 2021 13:21:24: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 13:21:24: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 13:21:24: #1 total tags in treatment: 14944909 INFO @ Sat, 11 Dec 2021 13:21:24: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:21:24: #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 13:21:25: #1 tags after filtering in treatment: 14944837 INFO @ Sat, 11 Dec 2021 13:21:25: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 13:21:25: #1 finished! INFO @ Sat, 11 Dec 2021 13:21:25: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:21:25: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:21:26: #2 number of paired peaks: 123 WARNING @ Sat, 11 Dec 2021 13:21:26: Fewer paired peaks (123) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 123 pairs to build model! INFO @ Sat, 11 Dec 2021 13:21:26: start model_add_line... INFO @ Sat, 11 Dec 2021 13:21:26: start X-correlation... INFO @ Sat, 11 Dec 2021 13:21:26: end of X-cor INFO @ Sat, 11 Dec 2021 13:21:26: #2 finished! INFO @ Sat, 11 Dec 2021 13:21:26: #2 predicted fragment length is 48 bps INFO @ Sat, 11 Dec 2021 13:21:26: #2 alternative fragment length(s) may be 23,48,67,105,494,529,586 bps INFO @ Sat, 11 Dec 2021 13:21:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX9986162/SRX9986162.05_model.r WARNING @ Sat, 11 Dec 2021 13:21:26: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 13:21:26: #2 You may need to consider one of the other alternative d(s): 23,48,67,105,494,529,586 WARNING @ Sat, 11 Dec 2021 13:21:26: #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 13:21:26: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:21:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 13:21:26: 9000000 INFO @ Sat, 11 Dec 2021 13:21:29: 3000000 INFO @ Sat, 11 Dec 2021 13:21:31: 10000000 INFO @ Sat, 11 Dec 2021 13:21:33: 4000000 INFO @ Sat, 11 Dec 2021 13:21:36: 11000000 INFO @ Sat, 11 Dec 2021 13:21:38: 5000000 INFO @ Sat, 11 Dec 2021 13:21:40: 12000000 INFO @ Sat, 11 Dec 2021 13:21:43: 6000000 INFO @ Sat, 11 Dec 2021 13:21:45: 13000000 INFO @ Sat, 11 Dec 2021 13:21:48: 7000000 INFO @ Sat, 11 Dec 2021 13:21:50: 14000000 INFO @ Sat, 11 Dec 2021 13:21:52: 8000000 INFO @ Sat, 11 Dec 2021 13:21:52: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:21:54: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 13:21:54: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 13:21:54: #1 total tags in treatment: 14944909 INFO @ Sat, 11 Dec 2021 13:21:54: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:21:54: #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 13:21:55: #1 tags after filtering in treatment: 14944837 INFO @ Sat, 11 Dec 2021 13:21:55: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 13:21:55: #1 finished! INFO @ Sat, 11 Dec 2021 13:21:55: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:21:55: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:21:56: #2 number of paired peaks: 123 WARNING @ Sat, 11 Dec 2021 13:21:56: Fewer paired peaks (123) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 123 pairs to build model! INFO @ Sat, 11 Dec 2021 13:21:56: start model_add_line... INFO @ Sat, 11 Dec 2021 13:21:56: start X-correlation... INFO @ Sat, 11 Dec 2021 13:21:56: end of X-cor INFO @ Sat, 11 Dec 2021 13:21:56: #2 finished! INFO @ Sat, 11 Dec 2021 13:21:56: #2 predicted fragment length is 48 bps INFO @ Sat, 11 Dec 2021 13:21:56: #2 alternative fragment length(s) may be 23,48,67,105,494,529,586 bps INFO @ Sat, 11 Dec 2021 13:21:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX9986162/SRX9986162.10_model.r WARNING @ Sat, 11 Dec 2021 13:21:56: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 13:21:56: #2 You may need to consider one of the other alternative d(s): 23,48,67,105,494,529,586 WARNING @ Sat, 11 Dec 2021 13:21:56: #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 13:21:56: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:21:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 13:21:57: 9000000 INFO @ Sat, 11 Dec 2021 13:22:01: 10000000 INFO @ Sat, 11 Dec 2021 13:22:06: 11000000 INFO @ Sat, 11 Dec 2021 13:22:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX9986162/SRX9986162.05_peaks.xls INFO @ Sat, 11 Dec 2021 13:22:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX9986162/SRX9986162.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:22:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX9986162/SRX9986162.05_summits.bed INFO @ Sat, 11 Dec 2021 13:22:06: Done! pass1 - making usageList (418 chroms): 1 millis pass2 - checking and writing primary data (1410 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 13:22:11: 12000000 INFO @ Sat, 11 Dec 2021 13:22:15: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 13:22:20: 14000000 INFO @ Sat, 11 Dec 2021 13:22:23: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:22:24: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 13:22:24: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 13:22:24: #1 total tags in treatment: 14944909 INFO @ Sat, 11 Dec 2021 13:22:24: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:22:24: #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 13:22:25: #1 tags after filtering in treatment: 14944837 INFO @ Sat, 11 Dec 2021 13:22:25: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 13:22:25: #1 finished! INFO @ Sat, 11 Dec 2021 13:22:25: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:22:25: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:22:26: #2 number of paired peaks: 123 WARNING @ Sat, 11 Dec 2021 13:22:26: Fewer paired peaks (123) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 123 pairs to build model! INFO @ Sat, 11 Dec 2021 13:22:26: start model_add_line... INFO @ Sat, 11 Dec 2021 13:22:26: start X-correlation... INFO @ Sat, 11 Dec 2021 13:22:26: end of X-cor INFO @ Sat, 11 Dec 2021 13:22:26: #2 finished! INFO @ Sat, 11 Dec 2021 13:22:26: #2 predicted fragment length is 48 bps INFO @ Sat, 11 Dec 2021 13:22:26: #2 alternative fragment length(s) may be 23,48,67,105,494,529,586 bps INFO @ Sat, 11 Dec 2021 13:22:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX9986162/SRX9986162.20_model.r WARNING @ Sat, 11 Dec 2021 13:22:26: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 13:22:26: #2 You may need to consider one of the other alternative d(s): 23,48,67,105,494,529,586 WARNING @ Sat, 11 Dec 2021 13:22:26: #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 13:22:26: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:22:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 13:22:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX9986162/SRX9986162.10_peaks.xls INFO @ Sat, 11 Dec 2021 13:22:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX9986162/SRX9986162.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:22:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX9986162/SRX9986162.10_summits.bed INFO @ Sat, 11 Dec 2021 13:22:35: Done! pass1 - making usageList (172 chroms): 1 millis pass2 - checking and writing primary data (380 records, 4 fields): 7 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 13:22:54: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:23:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX9986162/SRX9986162.20_peaks.xls INFO @ Sat, 11 Dec 2021 13:23:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX9986162/SRX9986162.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:23:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX9986162/SRX9986162.20_summits.bed INFO @ Sat, 11 Dec 2021 13:23:07: Done! pass1 - making usageList (53 chroms): 1 millis pass2 - checking and writing primary data (89 records, 4 fields): 3 millis CompletedMACS2peakCalling