Job ID = 16439402 SRX = SRX15206485 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: 00:04:52 22066348 reads; of these: 22066348 (100.00%) were unpaired; of these: 701460 (3.18%) aligned 0 times 18104489 (82.05%) aligned exactly 1 time 3260399 (14.78%) aligned >1 times 96.82% overall alignment rate Time searching: 00:04:52 Overall time: 00:04:52 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 12 files... [bam_rmdupse_core] 1757879 / 21364888 = 0.0823 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/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 15:13:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX15206485/SRX15206485.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX15206485/SRX15206485.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX15206485/SRX15206485.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX15206485/SRX15206485.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 @ Tue, 02 Aug 2022 15:13:07: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:13:07: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:13:13: 1000000 INFO @ Tue, 02 Aug 2022 15:13:19: 2000000 INFO @ Tue, 02 Aug 2022 15:13:24: 3000000 INFO @ Tue, 02 Aug 2022 15:13:30: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 15:13:36: 5000000 INFO @ Tue, 02 Aug 2022 15:13:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX15206485/SRX15206485.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX15206485/SRX15206485.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX15206485/SRX15206485.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX15206485/SRX15206485.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 @ Tue, 02 Aug 2022 15:13:38: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:13:38: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:13:42: 6000000 INFO @ Tue, 02 Aug 2022 15:13:44: 1000000 INFO @ Tue, 02 Aug 2022 15:13:48: 7000000 INFO @ Tue, 02 Aug 2022 15:13:51: 2000000 INFO @ Tue, 02 Aug 2022 15:13:55: 8000000 INFO @ Tue, 02 Aug 2022 15:13:57: 3000000 INFO @ Tue, 02 Aug 2022 15:14:01: 9000000 INFO @ Tue, 02 Aug 2022 15:14:04: 4000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 15:14:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX15206485/SRX15206485.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX15206485/SRX15206485.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX15206485/SRX15206485.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX15206485/SRX15206485.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 @ Tue, 02 Aug 2022 15:14:07: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:14:07: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:14:08: 10000000 INFO @ Tue, 02 Aug 2022 15:14:10: 5000000 INFO @ Tue, 02 Aug 2022 15:14:14: 1000000 INFO @ Tue, 02 Aug 2022 15:14:14: 11000000 INFO @ Tue, 02 Aug 2022 15:14:17: 6000000 INFO @ Tue, 02 Aug 2022 15:14:21: 2000000 INFO @ Tue, 02 Aug 2022 15:14:21: 12000000 INFO @ Tue, 02 Aug 2022 15:14:24: 7000000 INFO @ Tue, 02 Aug 2022 15:14:27: 3000000 INFO @ Tue, 02 Aug 2022 15:14:28: 13000000 INFO @ Tue, 02 Aug 2022 15:14:30: 8000000 INFO @ Tue, 02 Aug 2022 15:14:34: 4000000 INFO @ Tue, 02 Aug 2022 15:14:34: 14000000 INFO @ Tue, 02 Aug 2022 15:14:37: 9000000 INFO @ Tue, 02 Aug 2022 15:14:41: 5000000 INFO @ Tue, 02 Aug 2022 15:14:41: 15000000 INFO @ Tue, 02 Aug 2022 15:14:44: 10000000 INFO @ Tue, 02 Aug 2022 15:14:47: 6000000 INFO @ Tue, 02 Aug 2022 15:14:48: 16000000 INFO @ Tue, 02 Aug 2022 15:14:50: 11000000 INFO @ Tue, 02 Aug 2022 15:14:54: 7000000 INFO @ Tue, 02 Aug 2022 15:14:54: 17000000 INFO @ Tue, 02 Aug 2022 15:14:57: 12000000 INFO @ Tue, 02 Aug 2022 15:15:01: 8000000 INFO @ Tue, 02 Aug 2022 15:15:01: 18000000 INFO @ Tue, 02 Aug 2022 15:15:04: 13000000 INFO @ Tue, 02 Aug 2022 15:15:07: 9000000 INFO @ Tue, 02 Aug 2022 15:15:08: 19000000 INFO @ Tue, 02 Aug 2022 15:15:10: 14000000 INFO @ Tue, 02 Aug 2022 15:15:12: #1 tag size is determined as 50 bps INFO @ Tue, 02 Aug 2022 15:15:12: #1 tag size = 50 INFO @ Tue, 02 Aug 2022 15:15:12: #1 total tags in treatment: 19607009 INFO @ Tue, 02 Aug 2022 15:15:12: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:15:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 15:15:12: #1 tags after filtering in treatment: 19606926 INFO @ Tue, 02 Aug 2022 15:15:12: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 15:15:12: #1 finished! INFO @ Tue, 02 Aug 2022 15:15:12: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:15:12: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:15:14: #2 number of paired peaks: 205 WARNING @ Tue, 02 Aug 2022 15:15:14: Fewer paired peaks (205) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 205 pairs to build model! INFO @ Tue, 02 Aug 2022 15:15:14: start model_add_line... INFO @ Tue, 02 Aug 2022 15:15:14: start X-correlation... INFO @ Tue, 02 Aug 2022 15:15:14: end of X-cor INFO @ Tue, 02 Aug 2022 15:15:14: #2 finished! INFO @ Tue, 02 Aug 2022 15:15:14: #2 predicted fragment length is 62 bps INFO @ Tue, 02 Aug 2022 15:15:14: #2 alternative fragment length(s) may be 2,62 bps INFO @ Tue, 02 Aug 2022 15:15:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX15206485/SRX15206485.05_model.r WARNING @ Tue, 02 Aug 2022 15:15:14: #2 Since the d (62) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 15:15:14: #2 You may need to consider one of the other alternative d(s): 2,62 WARNING @ Tue, 02 Aug 2022 15:15:14: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 15:15:14: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:15:14: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:15:14: 10000000 INFO @ Tue, 02 Aug 2022 15:15:17: 15000000 INFO @ Tue, 02 Aug 2022 15:15:20: 11000000 INFO @ Tue, 02 Aug 2022 15:15:24: 16000000 INFO @ Tue, 02 Aug 2022 15:15:27: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 15:15:30: 17000000 INFO @ Tue, 02 Aug 2022 15:15:34: 13000000 INFO @ Tue, 02 Aug 2022 15:15:37: 18000000 INFO @ Tue, 02 Aug 2022 15:15:41: 14000000 INFO @ Tue, 02 Aug 2022 15:15:44: 19000000 INFO @ Tue, 02 Aug 2022 15:15:48: 15000000 INFO @ Tue, 02 Aug 2022 15:15:48: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:15:49: #1 tag size is determined as 50 bps INFO @ Tue, 02 Aug 2022 15:15:49: #1 tag size = 50 INFO @ Tue, 02 Aug 2022 15:15:49: #1 total tags in treatment: 19607009 INFO @ Tue, 02 Aug 2022 15:15:49: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:15:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 15:15:49: #1 tags after filtering in treatment: 19606926 INFO @ Tue, 02 Aug 2022 15:15:49: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 15:15:49: #1 finished! INFO @ Tue, 02 Aug 2022 15:15:49: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:15:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:15:50: #2 number of paired peaks: 205 WARNING @ Tue, 02 Aug 2022 15:15:50: Fewer paired peaks (205) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 205 pairs to build model! INFO @ Tue, 02 Aug 2022 15:15:50: start model_add_line... INFO @ Tue, 02 Aug 2022 15:15:50: start X-correlation... INFO @ Tue, 02 Aug 2022 15:15:50: end of X-cor INFO @ Tue, 02 Aug 2022 15:15:50: #2 finished! INFO @ Tue, 02 Aug 2022 15:15:50: #2 predicted fragment length is 62 bps INFO @ Tue, 02 Aug 2022 15:15:50: #2 alternative fragment length(s) may be 2,62 bps INFO @ Tue, 02 Aug 2022 15:15:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX15206485/SRX15206485.10_model.r WARNING @ Tue, 02 Aug 2022 15:15:50: #2 Since the d (62) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 15:15:50: #2 You may need to consider one of the other alternative d(s): 2,62 WARNING @ Tue, 02 Aug 2022 15:15:50: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 15:15:50: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:15:50: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:15:54: 16000000 INFO @ Tue, 02 Aug 2022 15:16:00: 17000000 INFO @ Tue, 02 Aug 2022 15:16:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX15206485/SRX15206485.05_peaks.xls INFO @ Tue, 02 Aug 2022 15:16:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX15206485/SRX15206485.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:16:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX15206485/SRX15206485.05_summits.bed INFO @ Tue, 02 Aug 2022 15:16:05: Done! pass1 - making usageList (139 chroms): 1 millis pass2 - checking and writing primary data (439 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 15:16:06: 18000000 INFO @ Tue, 02 Aug 2022 15:16:12: 19000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 15:16:15: #1 tag size is determined as 50 bps INFO @ Tue, 02 Aug 2022 15:16:15: #1 tag size = 50 INFO @ Tue, 02 Aug 2022 15:16:15: #1 total tags in treatment: 19607009 INFO @ Tue, 02 Aug 2022 15:16:15: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:16:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 15:16:16: #1 tags after filtering in treatment: 19606926 INFO @ Tue, 02 Aug 2022 15:16:16: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 15:16:16: #1 finished! INFO @ Tue, 02 Aug 2022 15:16:16: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:16:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:16:17: #2 number of paired peaks: 205 WARNING @ Tue, 02 Aug 2022 15:16:17: Fewer paired peaks (205) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 205 pairs to build model! INFO @ Tue, 02 Aug 2022 15:16:17: start model_add_line... INFO @ Tue, 02 Aug 2022 15:16:17: start X-correlation... INFO @ Tue, 02 Aug 2022 15:16:17: end of X-cor INFO @ Tue, 02 Aug 2022 15:16:17: #2 finished! INFO @ Tue, 02 Aug 2022 15:16:17: #2 predicted fragment length is 62 bps INFO @ Tue, 02 Aug 2022 15:16:17: #2 alternative fragment length(s) may be 2,62 bps INFO @ Tue, 02 Aug 2022 15:16:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX15206485/SRX15206485.20_model.r WARNING @ Tue, 02 Aug 2022 15:16:17: #2 Since the d (62) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 15:16:17: #2 You may need to consider one of the other alternative d(s): 2,62 WARNING @ Tue, 02 Aug 2022 15:16:17: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 15:16:17: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:16:17: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:16:25: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:16:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX15206485/SRX15206485.10_peaks.xls INFO @ Tue, 02 Aug 2022 15:16:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX15206485/SRX15206485.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:16:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX15206485/SRX15206485.10_summits.bed INFO @ Tue, 02 Aug 2022 15:16:42: Done! pass1 - making usageList (99 chroms): 1 millis pass2 - checking and writing primary data (277 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 15:16:52: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:17:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX15206485/SRX15206485.20_peaks.xls INFO @ Tue, 02 Aug 2022 15:17:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX15206485/SRX15206485.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:17:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX15206485/SRX15206485.20_summits.bed INFO @ Tue, 02 Aug 2022 15:17:09: Done! pass1 - making usageList (74 chroms): 1 millis pass2 - checking and writing primary data (189 records, 4 fields): 38 millis CompletedMACS2peakCalling