Job ID = 14170918 SRX = SRX8689044 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: 00:05:42 19117994 reads; of these: 19117994 (100.00%) were unpaired; of these: 731227 (3.82%) aligned 0 times 12041682 (62.99%) aligned exactly 1 time 6345085 (33.19%) aligned >1 times 96.18% overall alignment rate Time searching: 00:05:42 Overall time: 00:05:42 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] 2480901 / 18386767 = 0.1349 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 09:10:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8689044/SRX8689044.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8689044/SRX8689044.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8689044/SRX8689044.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8689044/SRX8689044.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 09:10:23: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:10:23: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:10:29: 1000000 INFO @ Sat, 11 Dec 2021 09:10:35: 2000000 INFO @ Sat, 11 Dec 2021 09:10:41: 3000000 INFO @ Sat, 11 Dec 2021 09:10:46: 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 @ Sat, 11 Dec 2021 09:10:52: 5000000 INFO @ Sat, 11 Dec 2021 09:10:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8689044/SRX8689044.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8689044/SRX8689044.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8689044/SRX8689044.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8689044/SRX8689044.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 09:10:53: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:10:53: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:10:59: 6000000 INFO @ Sat, 11 Dec 2021 09:11:01: 1000000 INFO @ Sat, 11 Dec 2021 09:11:06: 7000000 INFO @ Sat, 11 Dec 2021 09:11:08: 2000000 INFO @ Sat, 11 Dec 2021 09:11:13: 8000000 INFO @ Sat, 11 Dec 2021 09:11:16: 3000000 INFO @ Sat, 11 Dec 2021 09:11:21: 9000000 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 09:11:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8689044/SRX8689044.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8689044/SRX8689044.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8689044/SRX8689044.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8689044/SRX8689044.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 09:11:23: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:11:23: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:11:24: 4000000 INFO @ Sat, 11 Dec 2021 09:11:28: 10000000 INFO @ Sat, 11 Dec 2021 09:11:30: 1000000 INFO @ Sat, 11 Dec 2021 09:11:32: 5000000 INFO @ Sat, 11 Dec 2021 09:11:35: 11000000 INFO @ Sat, 11 Dec 2021 09:11:37: 2000000 INFO @ Sat, 11 Dec 2021 09:11:40: 6000000 INFO @ Sat, 11 Dec 2021 09:11:43: 12000000 INFO @ Sat, 11 Dec 2021 09:11:45: 3000000 INFO @ Sat, 11 Dec 2021 09:11:48: 7000000 INFO @ Sat, 11 Dec 2021 09:11:50: 13000000 INFO @ Sat, 11 Dec 2021 09:11:52: 4000000 INFO @ Sat, 11 Dec 2021 09:11:56: 8000000 INFO @ Sat, 11 Dec 2021 09:11:58: 14000000 INFO @ Sat, 11 Dec 2021 09:11:59: 5000000 INFO @ Sat, 11 Dec 2021 09:12:04: 9000000 INFO @ Sat, 11 Dec 2021 09:12:05: 15000000 INFO @ Sat, 11 Dec 2021 09:12:06: 6000000 INFO @ Sat, 11 Dec 2021 09:12:12: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 09:12:12: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 09:12:12: #1 total tags in treatment: 15905866 INFO @ Sat, 11 Dec 2021 09:12:12: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:12:12: #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 09:12:12: 10000000 INFO @ Sat, 11 Dec 2021 09:12:12: #1 tags after filtering in treatment: 15905866 INFO @ Sat, 11 Dec 2021 09:12:12: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 09:12:12: #1 finished! INFO @ Sat, 11 Dec 2021 09:12:12: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:12:12: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:12:13: #2 number of paired peaks: 328 WARNING @ Sat, 11 Dec 2021 09:12:13: Fewer paired peaks (328) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 328 pairs to build model! INFO @ Sat, 11 Dec 2021 09:12:13: start model_add_line... INFO @ Sat, 11 Dec 2021 09:12:13: 7000000 INFO @ Sat, 11 Dec 2021 09:12:14: start X-correlation... INFO @ Sat, 11 Dec 2021 09:12:14: end of X-cor INFO @ Sat, 11 Dec 2021 09:12:14: #2 finished! INFO @ Sat, 11 Dec 2021 09:12:14: #2 predicted fragment length is 56 bps INFO @ Sat, 11 Dec 2021 09:12:14: #2 alternative fragment length(s) may be 4,56 bps INFO @ Sat, 11 Dec 2021 09:12:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8689044/SRX8689044.05_model.r WARNING @ Sat, 11 Dec 2021 09:12:14: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 09:12:14: #2 You may need to consider one of the other alternative d(s): 4,56 WARNING @ Sat, 11 Dec 2021 09:12:14: #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 09:12:14: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:12:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:12:20: 11000000 INFO @ Sat, 11 Dec 2021 09:12:21: 8000000 INFO @ Sat, 11 Dec 2021 09:12:28: 9000000 INFO @ Sat, 11 Dec 2021 09:12:28: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 09:12:35: 10000000 INFO @ Sat, 11 Dec 2021 09:12:36: 13000000 INFO @ Sat, 11 Dec 2021 09:12:42: 11000000 INFO @ Sat, 11 Dec 2021 09:12:42: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:12:44: 14000000 INFO @ Sat, 11 Dec 2021 09:12:49: 12000000 INFO @ Sat, 11 Dec 2021 09:12:52: 15000000 INFO @ Sat, 11 Dec 2021 09:12:56: 13000000 INFO @ Sat, 11 Dec 2021 09:12:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8689044/SRX8689044.05_peaks.xls INFO @ Sat, 11 Dec 2021 09:12:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8689044/SRX8689044.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:12:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8689044/SRX8689044.05_summits.bed INFO @ Sat, 11 Dec 2021 09:12:56: Done! pass1 - making usageList (924 chroms): 1 millis pass2 - checking and writing primary data (3833 records, 4 fields): 27 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 09:12:59: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 09:12:59: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 09:12:59: #1 total tags in treatment: 15905866 INFO @ Sat, 11 Dec 2021 09:12:59: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:12:59: #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 09:13:00: #1 tags after filtering in treatment: 15905866 INFO @ Sat, 11 Dec 2021 09:13:00: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 09:13:00: #1 finished! INFO @ Sat, 11 Dec 2021 09:13:00: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:13:00: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:13:01: #2 number of paired peaks: 328 WARNING @ Sat, 11 Dec 2021 09:13:01: Fewer paired peaks (328) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 328 pairs to build model! INFO @ Sat, 11 Dec 2021 09:13:01: start model_add_line... INFO @ Sat, 11 Dec 2021 09:13:01: start X-correlation... INFO @ Sat, 11 Dec 2021 09:13:01: end of X-cor INFO @ Sat, 11 Dec 2021 09:13:01: #2 finished! INFO @ Sat, 11 Dec 2021 09:13:01: #2 predicted fragment length is 56 bps INFO @ Sat, 11 Dec 2021 09:13:01: #2 alternative fragment length(s) may be 4,56 bps INFO @ Sat, 11 Dec 2021 09:13:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8689044/SRX8689044.10_model.r WARNING @ Sat, 11 Dec 2021 09:13:01: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 09:13:01: #2 You may need to consider one of the other alternative d(s): 4,56 WARNING @ Sat, 11 Dec 2021 09:13:01: #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 09:13:01: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:13:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:13:03: 14000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 09:13:09: 15000000 INFO @ Sat, 11 Dec 2021 09:13:14: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 09:13:14: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 09:13:14: #1 total tags in treatment: 15905866 INFO @ Sat, 11 Dec 2021 09:13:14: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:13:14: #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 09:13:14: #1 tags after filtering in treatment: 15905866 INFO @ Sat, 11 Dec 2021 09:13:14: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 09:13:14: #1 finished! INFO @ Sat, 11 Dec 2021 09:13:14: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:13:14: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:13:15: #2 number of paired peaks: 328 WARNING @ Sat, 11 Dec 2021 09:13:15: Fewer paired peaks (328) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 328 pairs to build model! INFO @ Sat, 11 Dec 2021 09:13:15: start model_add_line... INFO @ Sat, 11 Dec 2021 09:13:16: start X-correlation... INFO @ Sat, 11 Dec 2021 09:13:16: end of X-cor INFO @ Sat, 11 Dec 2021 09:13:16: #2 finished! INFO @ Sat, 11 Dec 2021 09:13:16: #2 predicted fragment length is 56 bps INFO @ Sat, 11 Dec 2021 09:13:16: #2 alternative fragment length(s) may be 4,56 bps INFO @ Sat, 11 Dec 2021 09:13:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8689044/SRX8689044.20_model.r WARNING @ Sat, 11 Dec 2021 09:13:16: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 09:13:16: #2 You may need to consider one of the other alternative d(s): 4,56 WARNING @ Sat, 11 Dec 2021 09:13:16: #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 09:13:16: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:13:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:13:29: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:13:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8689044/SRX8689044.10_peaks.xls INFO @ Sat, 11 Dec 2021 09:13:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8689044/SRX8689044.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:13:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8689044/SRX8689044.10_summits.bed INFO @ Sat, 11 Dec 2021 09:13:44: Done! INFO @ Sat, 11 Dec 2021 09:13:44: #3 Call peaks for each chromosome... pass1 - making usageList (704 chroms): 1 millis pass2 - checking and writing primary data (2090 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 09:13:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8689044/SRX8689044.20_peaks.xls INFO @ Sat, 11 Dec 2021 09:13:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8689044/SRX8689044.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:13:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8689044/SRX8689044.20_summits.bed INFO @ Sat, 11 Dec 2021 09:13:58: Done! pass1 - making usageList (286 chroms): 1 millis pass2 - checking and writing primary data (538 records, 4 fields): 8 millis CompletedMACS2peakCalling