Job ID = 14168959 SRX = SRX8688982 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: 00:02:21 7017424 reads; of these: 7017424 (100.00%) were unpaired; of these: 687859 (9.80%) aligned 0 times 4657115 (66.37%) aligned exactly 1 time 1672450 (23.83%) aligned >1 times 90.20% overall alignment rate Time searching: 00:02:22 Overall time: 00:02:22 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_rmdupse_core] 412100 / 6329565 = 0.0651 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 22:28:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8688982/SRX8688982.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8688982/SRX8688982.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8688982/SRX8688982.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8688982/SRX8688982.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 22:28:33: #1 read tag files... INFO @ Fri, 10 Dec 2021 22:28:33: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 22:28:42: 1000000 INFO @ Fri, 10 Dec 2021 22:28:52: 2000000 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 22:29:01: 3000000 INFO @ Fri, 10 Dec 2021 22:29:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8688982/SRX8688982.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8688982/SRX8688982.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8688982/SRX8688982.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8688982/SRX8688982.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 22:29:03: #1 read tag files... INFO @ Fri, 10 Dec 2021 22:29:03: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 22:29:10: 4000000 INFO @ Fri, 10 Dec 2021 22:29:13: 1000000 INFO @ Fri, 10 Dec 2021 22:29:20: 5000000 INFO @ Fri, 10 Dec 2021 22:29:22: 2000000 INFO @ Fri, 10 Dec 2021 22:29:29: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 22:29:29: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 22:29:29: #1 total tags in treatment: 5917465 INFO @ Fri, 10 Dec 2021 22:29:29: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 22:29:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 22:29:30: #1 tags after filtering in treatment: 5917451 INFO @ Fri, 10 Dec 2021 22:29:30: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 22:29:30: #1 finished! INFO @ Fri, 10 Dec 2021 22:29:30: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 22:29:30: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 22:29:30: #2 number of paired peaks: 585 WARNING @ Fri, 10 Dec 2021 22:29:30: Fewer paired peaks (585) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 585 pairs to build model! INFO @ Fri, 10 Dec 2021 22:29:30: start model_add_line... BedGraph に変換中... INFO @ Fri, 10 Dec 2021 22:29:31: start X-correlation... 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 22:29:31: end of X-cor INFO @ Fri, 10 Dec 2021 22:29:31: #2 finished! INFO @ Fri, 10 Dec 2021 22:29:31: #2 predicted fragment length is 67 bps INFO @ Fri, 10 Dec 2021 22:29:31: #2 alternative fragment length(s) may be 67,560 bps INFO @ Fri, 10 Dec 2021 22:29:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8688982/SRX8688982.05_model.r WARNING @ Fri, 10 Dec 2021 22:29:31: #2 Since the d (67) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 22:29:31: #2 You may need to consider one of the other alternative d(s): 67,560 WARNING @ Fri, 10 Dec 2021 22:29:31: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 22:29:31: #3 Call peaks... INFO @ Fri, 10 Dec 2021 22:29:31: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 22:29:31: 3000000 INFO @ Fri, 10 Dec 2021 22:29:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8688982/SRX8688982.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8688982/SRX8688982.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8688982/SRX8688982.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8688982/SRX8688982.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 22:29:33: #1 read tag files... INFO @ Fri, 10 Dec 2021 22:29:33: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 22:29:40: 1000000 INFO @ Fri, 10 Dec 2021 22:29:41: 4000000 INFO @ Fri, 10 Dec 2021 22:29:43: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 22:29:48: 2000000 INFO @ Fri, 10 Dec 2021 22:29:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8688982/SRX8688982.05_peaks.xls INFO @ Fri, 10 Dec 2021 22:29:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8688982/SRX8688982.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 22:29:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8688982/SRX8688982.05_summits.bed INFO @ Fri, 10 Dec 2021 22:29:50: Done! pass1 - making usageList (464 chroms): 1 millis pass2 - checking and writing primary data (1483 records, 4 fields): 32 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 22:29:51: 5000000 INFO @ Fri, 10 Dec 2021 22:29:55: 3000000 INFO @ Fri, 10 Dec 2021 22:30:00: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 22:30:00: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 22:30:00: #1 total tags in treatment: 5917465 INFO @ Fri, 10 Dec 2021 22:30:00: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 22:30:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 22:30:01: #1 tags after filtering in treatment: 5917451 INFO @ Fri, 10 Dec 2021 22:30:01: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 22:30:01: #1 finished! INFO @ Fri, 10 Dec 2021 22:30:01: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 22:30:01: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 22:30:01: #2 number of paired peaks: 585 WARNING @ Fri, 10 Dec 2021 22:30:01: Fewer paired peaks (585) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 585 pairs to build model! INFO @ Fri, 10 Dec 2021 22:30:01: start model_add_line... INFO @ Fri, 10 Dec 2021 22:30:01: start X-correlation... INFO @ Fri, 10 Dec 2021 22:30:01: end of X-cor INFO @ Fri, 10 Dec 2021 22:30:01: #2 finished! INFO @ Fri, 10 Dec 2021 22:30:01: #2 predicted fragment length is 67 bps INFO @ Fri, 10 Dec 2021 22:30:01: #2 alternative fragment length(s) may be 67,560 bps INFO @ Fri, 10 Dec 2021 22:30:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8688982/SRX8688982.10_model.r WARNING @ Fri, 10 Dec 2021 22:30:01: #2 Since the d (67) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 22:30:01: #2 You may need to consider one of the other alternative d(s): 67,560 WARNING @ Fri, 10 Dec 2021 22:30:01: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 22:30:01: #3 Call peaks... INFO @ Fri, 10 Dec 2021 22:30:01: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 22:30:02: 4000000 INFO @ Fri, 10 Dec 2021 22:30:10: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 22:30:14: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 22:30:17: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 22:30:17: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 22:30:17: #1 total tags in treatment: 5917465 INFO @ Fri, 10 Dec 2021 22:30:17: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 22:30:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 22:30:17: #1 tags after filtering in treatment: 5917451 INFO @ Fri, 10 Dec 2021 22:30:17: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 22:30:17: #1 finished! INFO @ Fri, 10 Dec 2021 22:30:17: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 22:30:17: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 22:30:18: #2 number of paired peaks: 585 WARNING @ Fri, 10 Dec 2021 22:30:18: Fewer paired peaks (585) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 585 pairs to build model! INFO @ Fri, 10 Dec 2021 22:30:18: start model_add_line... INFO @ Fri, 10 Dec 2021 22:30:18: start X-correlation... INFO @ Fri, 10 Dec 2021 22:30:18: end of X-cor INFO @ Fri, 10 Dec 2021 22:30:18: #2 finished! INFO @ Fri, 10 Dec 2021 22:30:18: #2 predicted fragment length is 67 bps INFO @ Fri, 10 Dec 2021 22:30:18: #2 alternative fragment length(s) may be 67,560 bps INFO @ Fri, 10 Dec 2021 22:30:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8688982/SRX8688982.20_model.r WARNING @ Fri, 10 Dec 2021 22:30:18: #2 Since the d (67) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 22:30:18: #2 You may need to consider one of the other alternative d(s): 67,560 WARNING @ Fri, 10 Dec 2021 22:30:18: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 22:30:18: #3 Call peaks... INFO @ Fri, 10 Dec 2021 22:30:18: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 22:30:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8688982/SRX8688982.10_peaks.xls INFO @ Fri, 10 Dec 2021 22:30:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8688982/SRX8688982.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 22:30:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8688982/SRX8688982.10_summits.bed INFO @ Fri, 10 Dec 2021 22:30:21: Done! pass1 - making usageList (283 chroms): 1 millis pass2 - checking and writing primary data (594 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 22:30:30: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 22:30:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8688982/SRX8688982.20_peaks.xls INFO @ Fri, 10 Dec 2021 22:30:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8688982/SRX8688982.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 22:30:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8688982/SRX8688982.20_summits.bed INFO @ Fri, 10 Dec 2021 22:30:36: Done! pass1 - making usageList (125 chroms): 1 millis pass2 - checking and writing primary data (214 records, 4 fields): 10 millis CompletedMACS2peakCalling