Job ID = 16438927 SRX = SRX15206501 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: 00:03:32 10328581 reads; of these: 10328581 (100.00%) were unpaired; of these: 259715 (2.51%) aligned 0 times 8467782 (81.98%) aligned exactly 1 time 1601084 (15.50%) aligned >1 times 97.49% overall alignment rate Time searching: 00:03:32 Overall time: 00:03:32 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] 535996 / 10068866 = 0.0532 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 14:17:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX15206501/SRX15206501.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX15206501/SRX15206501.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX15206501/SRX15206501.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX15206501/SRX15206501.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 14:17:26: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:17:26: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:17:32: 1000000 INFO @ Tue, 02 Aug 2022 14:17:37: 2000000 INFO @ Tue, 02 Aug 2022 14:17:42: 3000000 INFO @ Tue, 02 Aug 2022 14:17:48: 4000000 INFO @ Tue, 02 Aug 2022 14:17:53: 5000000 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 14:17:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX15206501/SRX15206501.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX15206501/SRX15206501.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX15206501/SRX15206501.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX15206501/SRX15206501.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 14:17:57: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:17:57: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:17:58: 6000000 INFO @ Tue, 02 Aug 2022 14:18:02: 1000000 INFO @ Tue, 02 Aug 2022 14:18:04: 7000000 INFO @ Tue, 02 Aug 2022 14:18:08: 2000000 INFO @ Tue, 02 Aug 2022 14:18:10: 8000000 INFO @ Tue, 02 Aug 2022 14:18:14: 3000000 INFO @ Tue, 02 Aug 2022 14:18:15: 9000000 INFO @ Tue, 02 Aug 2022 14:18:18: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 14:18:18: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 14:18:18: #1 total tags in treatment: 9532870 INFO @ Tue, 02 Aug 2022 14:18:18: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:18:18: #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 14:18:19: #1 tags after filtering in treatment: 9532690 INFO @ Tue, 02 Aug 2022 14:18:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:18:19: #1 finished! INFO @ Tue, 02 Aug 2022 14:18:19: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:18:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:18:19: 4000000 INFO @ Tue, 02 Aug 2022 14:18:20: #2 number of paired peaks: 260 WARNING @ Tue, 02 Aug 2022 14:18:20: Fewer paired peaks (260) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 260 pairs to build model! INFO @ Tue, 02 Aug 2022 14:18:20: start model_add_line... INFO @ Tue, 02 Aug 2022 14:18:20: start X-correlation... INFO @ Tue, 02 Aug 2022 14:18:20: end of X-cor INFO @ Tue, 02 Aug 2022 14:18:20: #2 finished! INFO @ Tue, 02 Aug 2022 14:18:20: #2 predicted fragment length is 86 bps INFO @ Tue, 02 Aug 2022 14:18:20: #2 alternative fragment length(s) may be 4,86 bps INFO @ Tue, 02 Aug 2022 14:18:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX15206501/SRX15206501.05_model.r WARNING @ Tue, 02 Aug 2022 14:18:20: #2 Since the d (86) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:18:20: #2 You may need to consider one of the other alternative d(s): 4,86 WARNING @ Tue, 02 Aug 2022 14:18:20: #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 14:18:20: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:18:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:18:25: 5000000 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 14:18:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX15206501/SRX15206501.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX15206501/SRX15206501.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX15206501/SRX15206501.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX15206501/SRX15206501.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 14:18:27: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:18:27: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:18:30: 6000000 INFO @ Tue, 02 Aug 2022 14:18:32: 1000000 INFO @ Tue, 02 Aug 2022 14:18:36: 7000000 INFO @ Tue, 02 Aug 2022 14:18:38: 2000000 INFO @ Tue, 02 Aug 2022 14:18:39: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:18:42: 8000000 INFO @ Tue, 02 Aug 2022 14:18:43: 3000000 INFO @ Tue, 02 Aug 2022 14:18:47: 9000000 INFO @ Tue, 02 Aug 2022 14:18:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX15206501/SRX15206501.05_peaks.xls INFO @ Tue, 02 Aug 2022 14:18:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX15206501/SRX15206501.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:18:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX15206501/SRX15206501.05_summits.bed INFO @ Tue, 02 Aug 2022 14:18:49: Done! pass1 - making usageList (229 chroms): 1 millis pass2 - checking and writing primary data (545 records, 4 fields): 33 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:18:49: 4000000 INFO @ Tue, 02 Aug 2022 14:18:50: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 14:18:50: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 14:18:50: #1 total tags in treatment: 9532870 INFO @ Tue, 02 Aug 2022 14:18:50: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:18:50: #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 14:18:51: #1 tags after filtering in treatment: 9532690 INFO @ Tue, 02 Aug 2022 14:18:51: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:18:51: #1 finished! INFO @ Tue, 02 Aug 2022 14:18:51: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:18:51: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:18:52: #2 number of paired peaks: 260 WARNING @ Tue, 02 Aug 2022 14:18:52: Fewer paired peaks (260) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 260 pairs to build model! INFO @ Tue, 02 Aug 2022 14:18:52: start model_add_line... INFO @ Tue, 02 Aug 2022 14:18:52: start X-correlation... INFO @ Tue, 02 Aug 2022 14:18:52: end of X-cor INFO @ Tue, 02 Aug 2022 14:18:52: #2 finished! INFO @ Tue, 02 Aug 2022 14:18:52: #2 predicted fragment length is 86 bps INFO @ Tue, 02 Aug 2022 14:18:52: #2 alternative fragment length(s) may be 4,86 bps INFO @ Tue, 02 Aug 2022 14:18:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX15206501/SRX15206501.10_model.r WARNING @ Tue, 02 Aug 2022 14:18:52: #2 Since the d (86) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:18:52: #2 You may need to consider one of the other alternative d(s): 4,86 WARNING @ Tue, 02 Aug 2022 14:18:52: #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 14:18:52: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:18:52: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:18:54: 5000000 INFO @ Tue, 02 Aug 2022 14:19:00: 6000000 INFO @ Tue, 02 Aug 2022 14:19:05: 7000000 INFO @ Tue, 02 Aug 2022 14:19:10: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:19:11: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 14:19:16: 9000000 INFO @ Tue, 02 Aug 2022 14:19:19: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 14:19:19: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 14:19:19: #1 total tags in treatment: 9532870 INFO @ Tue, 02 Aug 2022 14:19:19: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:19:19: #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 14:19:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX15206501/SRX15206501.10_peaks.xls INFO @ Tue, 02 Aug 2022 14:19:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX15206501/SRX15206501.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:19:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX15206501/SRX15206501.10_summits.bed INFO @ Tue, 02 Aug 2022 14:19:20: Done! INFO @ Tue, 02 Aug 2022 14:19:20: #1 tags after filtering in treatment: 9532690 INFO @ Tue, 02 Aug 2022 14:19:20: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:19:20: #1 finished! INFO @ Tue, 02 Aug 2022 14:19:20: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:19:20: #2 looking for paired plus/minus strand peaks... pass1 - making usageList (139 chroms): 1 millis pass2 - checking and writing primary data (297 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:19:20: #2 number of paired peaks: 260 WARNING @ Tue, 02 Aug 2022 14:19:20: Fewer paired peaks (260) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 260 pairs to build model! INFO @ Tue, 02 Aug 2022 14:19:20: start model_add_line... INFO @ Tue, 02 Aug 2022 14:19:20: start X-correlation... INFO @ Tue, 02 Aug 2022 14:19:20: end of X-cor INFO @ Tue, 02 Aug 2022 14:19:20: #2 finished! INFO @ Tue, 02 Aug 2022 14:19:20: #2 predicted fragment length is 86 bps INFO @ Tue, 02 Aug 2022 14:19:20: #2 alternative fragment length(s) may be 4,86 bps INFO @ Tue, 02 Aug 2022 14:19:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX15206501/SRX15206501.20_model.r WARNING @ Tue, 02 Aug 2022 14:19:20: #2 Since the d (86) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:19:20: #2 You may need to consider one of the other alternative d(s): 4,86 WARNING @ Tue, 02 Aug 2022 14:19:20: #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 14:19:20: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:19:20: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 14:19:40: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:19:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX15206501/SRX15206501.20_peaks.xls INFO @ Tue, 02 Aug 2022 14:19:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX15206501/SRX15206501.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:19:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX15206501/SRX15206501.20_summits.bed INFO @ Tue, 02 Aug 2022 14:19:49: Done! pass1 - making usageList (88 chroms): 1 millis pass2 - checking and writing primary data (169 records, 4 fields): 129 millis CompletedMACS2peakCalling