Job ID = 14169114 SRX = SRX8688996 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: 00:05:39 19783800 reads; of these: 19783800 (100.00%) were unpaired; of these: 1378027 (6.97%) aligned 0 times 14274825 (72.15%) aligned exactly 1 time 4130948 (20.88%) aligned >1 times 93.03% overall alignment rate Time searching: 00:05:39 Overall time: 00:05:39 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] 2321745 / 18405773 = 0.1261 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 @ Fri, 10 Dec 2021 23:58:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8688996/SRX8688996.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8688996/SRX8688996.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8688996/SRX8688996.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8688996/SRX8688996.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 @ Fri, 10 Dec 2021 23:58:38: #1 read tag files... INFO @ Fri, 10 Dec 2021 23:58:38: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 23:58:46: 1000000 INFO @ Fri, 10 Dec 2021 23:58:53: 2000000 INFO @ Fri, 10 Dec 2021 23:59:01: 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 @ Fri, 10 Dec 2021 23:59:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8688996/SRX8688996.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8688996/SRX8688996.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8688996/SRX8688996.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8688996/SRX8688996.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 @ Fri, 10 Dec 2021 23:59:09: #1 read tag files... INFO @ Fri, 10 Dec 2021 23:59:09: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 23:59:09: 4000000 INFO @ Fri, 10 Dec 2021 23:59:16: 1000000 INFO @ Fri, 10 Dec 2021 23:59:16: 5000000 INFO @ Fri, 10 Dec 2021 23:59:23: 2000000 INFO @ Fri, 10 Dec 2021 23:59:24: 6000000 INFO @ Fri, 10 Dec 2021 23:59:30: 3000000 INFO @ Fri, 10 Dec 2021 23:59:32: 7000000 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 @ Fri, 10 Dec 2021 23:59:37: 4000000 INFO @ Fri, 10 Dec 2021 23:59:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8688996/SRX8688996.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8688996/SRX8688996.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8688996/SRX8688996.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8688996/SRX8688996.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 @ Fri, 10 Dec 2021 23:59:39: #1 read tag files... INFO @ Fri, 10 Dec 2021 23:59:39: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 23:59:39: 8000000 INFO @ Fri, 10 Dec 2021 23:59:45: 5000000 INFO @ Fri, 10 Dec 2021 23:59:46: 1000000 INFO @ Fri, 10 Dec 2021 23:59:47: 9000000 INFO @ Fri, 10 Dec 2021 23:59:52: 6000000 INFO @ Fri, 10 Dec 2021 23:59:54: 2000000 INFO @ Fri, 10 Dec 2021 23:59:55: 10000000 INFO @ Sat, 11 Dec 2021 00:00:00: 7000000 INFO @ Sat, 11 Dec 2021 00:00:02: 11000000 INFO @ Sat, 11 Dec 2021 00:00:03: 3000000 INFO @ Sat, 11 Dec 2021 00:00:08: 8000000 INFO @ Sat, 11 Dec 2021 00:00:10: 12000000 INFO @ Sat, 11 Dec 2021 00:00:10: 4000000 INFO @ Sat, 11 Dec 2021 00:00:15: 9000000 INFO @ Sat, 11 Dec 2021 00:00:18: 13000000 INFO @ Sat, 11 Dec 2021 00:00:20: 5000000 INFO @ Sat, 11 Dec 2021 00:00:22: 10000000 INFO @ Sat, 11 Dec 2021 00:00:27: 14000000 INFO @ Sat, 11 Dec 2021 00:00:30: 11000000 INFO @ Sat, 11 Dec 2021 00:00:30: 6000000 INFO @ Sat, 11 Dec 2021 00:00:35: 15000000 INFO @ Sat, 11 Dec 2021 00:00:37: 12000000 INFO @ Sat, 11 Dec 2021 00:00:39: 7000000 INFO @ Sat, 11 Dec 2021 00:00:43: 16000000 INFO @ Sat, 11 Dec 2021 00:00:43: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 00:00:43: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 00:00:43: #1 total tags in treatment: 16084028 INFO @ Sat, 11 Dec 2021 00:00:43: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 00:00:43: #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 00:00:44: #1 tags after filtering in treatment: 16084024 INFO @ Sat, 11 Dec 2021 00:00:44: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 00:00:44: #1 finished! INFO @ Sat, 11 Dec 2021 00:00:44: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 00:00:44: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 00:00:45: 13000000 INFO @ Sat, 11 Dec 2021 00:00:45: #2 number of paired peaks: 168 WARNING @ Sat, 11 Dec 2021 00:00:45: Fewer paired peaks (168) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 168 pairs to build model! INFO @ Sat, 11 Dec 2021 00:00:45: start model_add_line... INFO @ Sat, 11 Dec 2021 00:00:45: start X-correlation... INFO @ Sat, 11 Dec 2021 00:00:45: end of X-cor INFO @ Sat, 11 Dec 2021 00:00:45: #2 finished! INFO @ Sat, 11 Dec 2021 00:00:45: #2 predicted fragment length is 53 bps INFO @ Sat, 11 Dec 2021 00:00:45: #2 alternative fragment length(s) may be 53 bps INFO @ Sat, 11 Dec 2021 00:00:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8688996/SRX8688996.05_model.r WARNING @ Sat, 11 Dec 2021 00:00:45: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 00:00:45: #2 You may need to consider one of the other alternative d(s): 53 WARNING @ Sat, 11 Dec 2021 00:00:45: #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 00:00:45: #3 Call peaks... INFO @ Sat, 11 Dec 2021 00:00:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 00:00:47: 8000000 INFO @ Sat, 11 Dec 2021 00:00:53: 14000000 INFO @ Sat, 11 Dec 2021 00:00:54: 9000000 INFO @ Sat, 11 Dec 2021 00:01:00: 15000000 INFO @ Sat, 11 Dec 2021 00:01:01: 10000000 INFO @ Sat, 11 Dec 2021 00:01:08: 16000000 INFO @ Sat, 11 Dec 2021 00:01:09: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 00:01:09: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 00:01:09: #1 total tags in treatment: 16084028 INFO @ Sat, 11 Dec 2021 00:01:09: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 00:01:09: #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 00:01:09: 11000000 INFO @ Sat, 11 Dec 2021 00:01:09: #1 tags after filtering in treatment: 16084024 INFO @ Sat, 11 Dec 2021 00:01:09: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 00:01:09: #1 finished! INFO @ Sat, 11 Dec 2021 00:01:09: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 00:01:09: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 00:01:11: #2 number of paired peaks: 168 WARNING @ Sat, 11 Dec 2021 00:01:11: Fewer paired peaks (168) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 168 pairs to build model! INFO @ Sat, 11 Dec 2021 00:01:11: start model_add_line... INFO @ Sat, 11 Dec 2021 00:01:11: start X-correlation... INFO @ Sat, 11 Dec 2021 00:01:11: end of X-cor INFO @ Sat, 11 Dec 2021 00:01:11: #2 finished! INFO @ Sat, 11 Dec 2021 00:01:11: #2 predicted fragment length is 53 bps INFO @ Sat, 11 Dec 2021 00:01:11: #2 alternative fragment length(s) may be 53 bps INFO @ Sat, 11 Dec 2021 00:01:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8688996/SRX8688996.10_model.r WARNING @ Sat, 11 Dec 2021 00:01:11: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 00:01:11: #2 You may need to consider one of the other alternative d(s): 53 WARNING @ Sat, 11 Dec 2021 00:01:11: #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 00:01:11: #3 Call peaks... INFO @ Sat, 11 Dec 2021 00:01:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 00:01:16: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 00:01:16: 12000000 INFO @ Sat, 11 Dec 2021 00:01:24: 13000000 INFO @ Sat, 11 Dec 2021 00:01:31: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 00:01:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8688996/SRX8688996.05_peaks.xls INFO @ Sat, 11 Dec 2021 00:01:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8688996/SRX8688996.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 00:01:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8688996/SRX8688996.05_summits.bed INFO @ Sat, 11 Dec 2021 00:01:34: Done! pass1 - making usageList (462 chroms): 2 millis pass2 - checking and writing primary data (3404 records, 4 fields): 33 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 00:01:38: 15000000 INFO @ Sat, 11 Dec 2021 00:01:41: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 00:01:45: 16000000 INFO @ Sat, 11 Dec 2021 00:01:46: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 00:01:46: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 00:01:46: #1 total tags in treatment: 16084028 INFO @ Sat, 11 Dec 2021 00:01:46: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 00:01:46: #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 00:01:47: #1 tags after filtering in treatment: 16084024 INFO @ Sat, 11 Dec 2021 00:01:47: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 00:01:47: #1 finished! INFO @ Sat, 11 Dec 2021 00:01:47: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 00:01:47: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 00:01:48: #2 number of paired peaks: 168 WARNING @ Sat, 11 Dec 2021 00:01:48: Fewer paired peaks (168) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 168 pairs to build model! INFO @ Sat, 11 Dec 2021 00:01:48: start model_add_line... INFO @ Sat, 11 Dec 2021 00:01:48: start X-correlation... INFO @ Sat, 11 Dec 2021 00:01:48: end of X-cor INFO @ Sat, 11 Dec 2021 00:01:48: #2 finished! INFO @ Sat, 11 Dec 2021 00:01:48: #2 predicted fragment length is 53 bps INFO @ Sat, 11 Dec 2021 00:01:48: #2 alternative fragment length(s) may be 53 bps INFO @ Sat, 11 Dec 2021 00:01:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8688996/SRX8688996.20_model.r WARNING @ Sat, 11 Dec 2021 00:01:48: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 00:01:48: #2 You may need to consider one of the other alternative d(s): 53 WARNING @ Sat, 11 Dec 2021 00:01:48: #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 00:01:48: #3 Call peaks... INFO @ Sat, 11 Dec 2021 00:01:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 00:02:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8688996/SRX8688996.10_peaks.xls INFO @ Sat, 11 Dec 2021 00:02:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8688996/SRX8688996.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 00:02:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8688996/SRX8688996.10_summits.bed INFO @ Sat, 11 Dec 2021 00:02:00: Done! pass1 - making usageList (338 chroms): 7 millis pass2 - checking and writing primary data (995 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 00:02:18: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 00:02:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8688996/SRX8688996.20_peaks.xls INFO @ Sat, 11 Dec 2021 00:02:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8688996/SRX8688996.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 00:02:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8688996/SRX8688996.20_summits.bed INFO @ Sat, 11 Dec 2021 00:02:35: Done! pass1 - making usageList (151 chroms): 4 millis pass2 - checking and writing primary data (268 records, 4 fields): 12 millis CompletedMACS2peakCalling