Job ID = 14167753 SRX = SRX6407576 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:04:56 8024682 reads; of these: 8024682 (100.00%) were unpaired; of these: 441138 (5.50%) aligned 0 times 6134123 (76.44%) aligned exactly 1 time 1449421 (18.06%) aligned >1 times 94.50% overall alignment rate Time searching: 00:04:57 Overall time: 00:04:57 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] 688027 / 7583544 = 0.0907 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 13:27:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6407576/SRX6407576.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6407576/SRX6407576.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6407576/SRX6407576.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6407576/SRX6407576.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 13:27:55: #1 read tag files... INFO @ Fri, 10 Dec 2021 13:27:55: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 13:28:03: 1000000 INFO @ Fri, 10 Dec 2021 13:28:10: 2000000 INFO @ Fri, 10 Dec 2021 13:28:17: 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 13:28:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6407576/SRX6407576.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6407576/SRX6407576.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6407576/SRX6407576.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6407576/SRX6407576.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 13:28:26: #1 read tag files... INFO @ Fri, 10 Dec 2021 13:28:26: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 13:28:26: 4000000 INFO @ Fri, 10 Dec 2021 13:28:36: 1000000 INFO @ Fri, 10 Dec 2021 13:28:37: 5000000 INFO @ Fri, 10 Dec 2021 13:28:45: 2000000 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 13:28:53: 3000000 INFO @ Fri, 10 Dec 2021 13:28:54: 6000000 INFO @ Fri, 10 Dec 2021 13:28:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6407576/SRX6407576.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6407576/SRX6407576.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6407576/SRX6407576.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6407576/SRX6407576.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 13:28:56: #1 read tag files... INFO @ Fri, 10 Dec 2021 13:28:56: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 13:29:02: 4000000 INFO @ Fri, 10 Dec 2021 13:29:03: #1 tag size is determined as 100 bps INFO @ Fri, 10 Dec 2021 13:29:03: #1 tag size = 100 INFO @ Fri, 10 Dec 2021 13:29:03: #1 total tags in treatment: 6895517 INFO @ Fri, 10 Dec 2021 13:29:03: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 13:29:03: #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 13:29:04: #1 tags after filtering in treatment: 6895310 INFO @ Fri, 10 Dec 2021 13:29:06: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 13:29:06: #1 finished! INFO @ Fri, 10 Dec 2021 13:29:06: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 13:29:06: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 13:29:06: #2 number of paired peaks: 929 WARNING @ Fri, 10 Dec 2021 13:29:06: Fewer paired peaks (929) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 929 pairs to build model! INFO @ Fri, 10 Dec 2021 13:29:06: start model_add_line... INFO @ Fri, 10 Dec 2021 13:29:06: start X-correlation... INFO @ Fri, 10 Dec 2021 13:29:07: end of X-cor INFO @ Fri, 10 Dec 2021 13:29:07: #2 finished! INFO @ Fri, 10 Dec 2021 13:29:07: #2 predicted fragment length is 155 bps INFO @ Fri, 10 Dec 2021 13:29:07: #2 alternative fragment length(s) may be 155 bps INFO @ Fri, 10 Dec 2021 13:29:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6407576/SRX6407576.05_model.r WARNING @ Fri, 10 Dec 2021 13:29:07: #2 Since the d (155) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 13:29:07: #2 You may need to consider one of the other alternative d(s): 155 WARNING @ Fri, 10 Dec 2021 13:29:07: #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 13:29:07: #3 Call peaks... INFO @ Fri, 10 Dec 2021 13:29:07: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 13:29:07: 1000000 INFO @ Fri, 10 Dec 2021 13:29:11: 5000000 INFO @ Fri, 10 Dec 2021 13:29:29: 2000000 INFO @ Fri, 10 Dec 2021 13:29:32: 6000000 INFO @ Fri, 10 Dec 2021 13:29:36: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 13:29:38: 3000000 INFO @ Fri, 10 Dec 2021 13:29:40: #1 tag size is determined as 100 bps INFO @ Fri, 10 Dec 2021 13:29:40: #1 tag size = 100 INFO @ Fri, 10 Dec 2021 13:29:40: #1 total tags in treatment: 6895517 INFO @ Fri, 10 Dec 2021 13:29:40: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 13:29:40: #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 13:29:41: #1 tags after filtering in treatment: 6895310 INFO @ Fri, 10 Dec 2021 13:29:41: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 13:29:41: #1 finished! INFO @ Fri, 10 Dec 2021 13:29:41: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 13:29:41: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 13:29:41: #2 number of paired peaks: 929 WARNING @ Fri, 10 Dec 2021 13:29:41: Fewer paired peaks (929) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 929 pairs to build model! INFO @ Fri, 10 Dec 2021 13:29:41: start model_add_line... INFO @ Fri, 10 Dec 2021 13:29:41: start X-correlation... INFO @ Fri, 10 Dec 2021 13:29:42: end of X-cor INFO @ Fri, 10 Dec 2021 13:29:42: #2 finished! INFO @ Fri, 10 Dec 2021 13:29:42: #2 predicted fragment length is 155 bps INFO @ Fri, 10 Dec 2021 13:29:42: #2 alternative fragment length(s) may be 155 bps INFO @ Fri, 10 Dec 2021 13:29:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6407576/SRX6407576.10_model.r WARNING @ Fri, 10 Dec 2021 13:29:42: #2 Since the d (155) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 13:29:42: #2 You may need to consider one of the other alternative d(s): 155 WARNING @ Fri, 10 Dec 2021 13:29:42: #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 13:29:42: #3 Call peaks... INFO @ Fri, 10 Dec 2021 13:29:42: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 13:29:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6407576/SRX6407576.05_peaks.xls INFO @ Fri, 10 Dec 2021 13:29:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6407576/SRX6407576.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 13:29:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6407576/SRX6407576.05_summits.bed INFO @ Fri, 10 Dec 2021 13:29:48: Done! INFO @ Fri, 10 Dec 2021 13:29:48: 4000000 pass1 - making usageList (350 chroms): 2 millis pass2 - checking and writing primary data (1454 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 13:29:55: 5000000 INFO @ Fri, 10 Dec 2021 13:30:02: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 13:30:05: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 13:30:12: #1 tag size is determined as 100 bps INFO @ Fri, 10 Dec 2021 13:30:12: #1 tag size = 100 INFO @ Fri, 10 Dec 2021 13:30:12: #1 total tags in treatment: 6895517 INFO @ Fri, 10 Dec 2021 13:30:12: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 13:30:12: #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 13:30:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6407576/SRX6407576.10_peaks.xls INFO @ Fri, 10 Dec 2021 13:30:13: #1 tags after filtering in treatment: 6895310 INFO @ Fri, 10 Dec 2021 13:30:13: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 13:30:13: #1 finished! INFO @ Fri, 10 Dec 2021 13:30:13: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 13:30:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6407576/SRX6407576.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 13:30:13: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 13:30:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6407576/SRX6407576.10_summits.bed INFO @ Fri, 10 Dec 2021 13:30:13: Done! INFO @ Fri, 10 Dec 2021 13:30:13: #2 number of paired peaks: 929 WARNING @ Fri, 10 Dec 2021 13:30:13: Fewer paired peaks (929) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 929 pairs to build model! INFO @ Fri, 10 Dec 2021 13:30:13: start model_add_line... INFO @ Fri, 10 Dec 2021 13:30:13: start X-correlation... INFO @ Fri, 10 Dec 2021 13:30:14: end of X-cor INFO @ Fri, 10 Dec 2021 13:30:14: #2 finished! INFO @ Fri, 10 Dec 2021 13:30:14: #2 predicted fragment length is 155 bps INFO @ Fri, 10 Dec 2021 13:30:14: #2 alternative fragment length(s) may be 155 bps INFO @ Fri, 10 Dec 2021 13:30:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6407576/SRX6407576.20_model.r WARNING @ Fri, 10 Dec 2021 13:30:14: #2 Since the d (155) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 13:30:14: #2 You may need to consider one of the other alternative d(s): 155 WARNING @ Fri, 10 Dec 2021 13:30:14: #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 13:30:14: #3 Call peaks... INFO @ Fri, 10 Dec 2021 13:30:14: #3 Pre-compute pvalue-qvalue table... pass1 - making usageList (260 chroms): 1 millis pass2 - checking and writing primary data (782 records, 4 fields): 18 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 13:30:31: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 13:30:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6407576/SRX6407576.20_peaks.xls INFO @ Fri, 10 Dec 2021 13:30:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6407576/SRX6407576.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 13:30:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6407576/SRX6407576.20_summits.bed INFO @ Fri, 10 Dec 2021 13:30:41: Done! pass1 - making usageList (171 chroms): 1 millis pass2 - checking and writing primary data (372 records, 4 fields): 14 millis CompletedMACS2peakCalling