Job ID = 14170950 SRX = SRX9720889 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: 00:03:10 9619195 reads; of these: 9619195 (100.00%) were unpaired; of these: 547860 (5.70%) aligned 0 times 6110292 (63.52%) aligned exactly 1 time 2961043 (30.78%) aligned >1 times 94.30% overall alignment rate Time searching: 00:03:10 Overall time: 00:03:10 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] 997540 / 9071335 = 0.1100 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 09:09:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX9720889/SRX9720889.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX9720889/SRX9720889.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX9720889/SRX9720889.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX9720889/SRX9720889.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 09:09:22: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:09:22: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:09:28: 1000000 INFO @ Sat, 11 Dec 2021 09:09:34: 2000000 INFO @ Sat, 11 Dec 2021 09:09:40: 3000000 INFO @ Sat, 11 Dec 2021 09:09:46: 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 09:09:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX9720889/SRX9720889.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX9720889/SRX9720889.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX9720889/SRX9720889.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX9720889/SRX9720889.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 09:09:52: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:09:52: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:09:52: 5000000 INFO @ Sat, 11 Dec 2021 09:09:58: 1000000 INFO @ Sat, 11 Dec 2021 09:09:58: 6000000 INFO @ Sat, 11 Dec 2021 09:10:04: 2000000 INFO @ Sat, 11 Dec 2021 09:10:06: 7000000 INFO @ Sat, 11 Dec 2021 09:10:11: 3000000 INFO @ Sat, 11 Dec 2021 09:10:12: 8000000 INFO @ Sat, 11 Dec 2021 09:10:13: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 09:10:13: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 09:10:13: #1 total tags in treatment: 8073795 INFO @ Sat, 11 Dec 2021 09:10:13: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:10:13: #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 09:10:14: #1 tags after filtering in treatment: 8073682 INFO @ Sat, 11 Dec 2021 09:10:14: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 09:10:14: #1 finished! INFO @ Sat, 11 Dec 2021 09:10:14: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:10:14: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:10:14: #2 number of paired peaks: 1470 INFO @ Sat, 11 Dec 2021 09:10:14: start model_add_line... INFO @ Sat, 11 Dec 2021 09:10:14: start X-correlation... INFO @ Sat, 11 Dec 2021 09:10:14: end of X-cor INFO @ Sat, 11 Dec 2021 09:10:14: #2 finished! INFO @ Sat, 11 Dec 2021 09:10:14: #2 predicted fragment length is 49 bps INFO @ Sat, 11 Dec 2021 09:10:14: #2 alternative fragment length(s) may be 4,49 bps INFO @ Sat, 11 Dec 2021 09:10:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX9720889/SRX9720889.05_model.r WARNING @ Sat, 11 Dec 2021 09:10:14: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 09:10:14: #2 You may need to consider one of the other alternative d(s): 4,49 WARNING @ Sat, 11 Dec 2021 09:10:14: #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 09:10:14: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:10:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:10:17: 4000000 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 09:10:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX9720889/SRX9720889.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX9720889/SRX9720889.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX9720889/SRX9720889.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX9720889/SRX9720889.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 09:10:22: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:10:22: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:10:23: 5000000 INFO @ Sat, 11 Dec 2021 09:10:28: 1000000 INFO @ Sat, 11 Dec 2021 09:10:30: 6000000 INFO @ Sat, 11 Dec 2021 09:10:31: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:10:35: 2000000 INFO @ Sat, 11 Dec 2021 09:10:37: 7000000 INFO @ Sat, 11 Dec 2021 09:10:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX9720889/SRX9720889.05_peaks.xls INFO @ Sat, 11 Dec 2021 09:10:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX9720889/SRX9720889.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:10:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX9720889/SRX9720889.05_summits.bed INFO @ Sat, 11 Dec 2021 09:10:41: Done! pass1 - making usageList (579 chroms): 2 millis pass2 - checking and writing primary data (2512 records, 4 fields): 46 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 09:10:42: 3000000 INFO @ Sat, 11 Dec 2021 09:10:44: 8000000 INFO @ Sat, 11 Dec 2021 09:10:45: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 09:10:45: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 09:10:45: #1 total tags in treatment: 8073795 INFO @ Sat, 11 Dec 2021 09:10:45: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:10:45: #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 09:10:46: #1 tags after filtering in treatment: 8073682 INFO @ Sat, 11 Dec 2021 09:10:46: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 09:10:46: #1 finished! INFO @ Sat, 11 Dec 2021 09:10:46: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:10:46: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:10:46: #2 number of paired peaks: 1470 INFO @ Sat, 11 Dec 2021 09:10:46: start model_add_line... INFO @ Sat, 11 Dec 2021 09:10:46: start X-correlation... INFO @ Sat, 11 Dec 2021 09:10:46: end of X-cor INFO @ Sat, 11 Dec 2021 09:10:46: #2 finished! INFO @ Sat, 11 Dec 2021 09:10:46: #2 predicted fragment length is 49 bps INFO @ Sat, 11 Dec 2021 09:10:46: #2 alternative fragment length(s) may be 4,49 bps INFO @ Sat, 11 Dec 2021 09:10:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX9720889/SRX9720889.10_model.r WARNING @ Sat, 11 Dec 2021 09:10:47: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 09:10:47: #2 You may need to consider one of the other alternative d(s): 4,49 WARNING @ Sat, 11 Dec 2021 09:10:47: #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 09:10:47: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:10:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:10:48: 4000000 INFO @ Sat, 11 Dec 2021 09:10:54: 5000000 INFO @ Sat, 11 Dec 2021 09:11:00: 6000000 INFO @ Sat, 11 Dec 2021 09:11:03: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:11:06: 7000000 INFO @ Sat, 11 Dec 2021 09:11:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX9720889/SRX9720889.10_peaks.xls INFO @ Sat, 11 Dec 2021 09:11:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX9720889/SRX9720889.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:11:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX9720889/SRX9720889.10_summits.bed INFO @ Sat, 11 Dec 2021 09:11:12: Done! INFO @ Sat, 11 Dec 2021 09:11:13: 8000000 pass1 - making usageList (450 chroms): 1 millis pass2 - checking and writing primary data (1319 records, 4 fields): 30 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 09:11:13: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 09:11:13: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 09:11:13: #1 total tags in treatment: 8073795 INFO @ Sat, 11 Dec 2021 09:11:13: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:11:13: #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 09:11:14: #1 tags after filtering in treatment: 8073682 INFO @ Sat, 11 Dec 2021 09:11:14: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 09:11:14: #1 finished! INFO @ Sat, 11 Dec 2021 09:11:14: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:11:14: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 09:11:14: #2 number of paired peaks: 1470 INFO @ Sat, 11 Dec 2021 09:11:14: start model_add_line... INFO @ Sat, 11 Dec 2021 09:11:15: start X-correlation... INFO @ Sat, 11 Dec 2021 09:11:15: end of X-cor INFO @ Sat, 11 Dec 2021 09:11:15: #2 finished! INFO @ Sat, 11 Dec 2021 09:11:15: #2 predicted fragment length is 49 bps INFO @ Sat, 11 Dec 2021 09:11:15: #2 alternative fragment length(s) may be 4,49 bps INFO @ Sat, 11 Dec 2021 09:11:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX9720889/SRX9720889.20_model.r WARNING @ Sat, 11 Dec 2021 09:11:15: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 09:11:15: #2 You may need to consider one of the other alternative d(s): 4,49 WARNING @ Sat, 11 Dec 2021 09:11:15: #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 09:11:15: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:11:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:11:31: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 09:11:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX9720889/SRX9720889.20_peaks.xls INFO @ Sat, 11 Dec 2021 09:11:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX9720889/SRX9720889.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:11:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX9720889/SRX9720889.20_summits.bed INFO @ Sat, 11 Dec 2021 09:11:40: Done! pass1 - making usageList (233 chroms): 1 millis pass2 - checking and writing primary data (497 records, 4 fields): 16 millis CompletedMACS2peakCalling