Job ID = 16438057 SRX = SRX12261326 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: 00:09:34 21240024 reads; of these: 21240024 (100.00%) were unpaired; of these: 949923 (4.47%) aligned 0 times 14206855 (66.89%) aligned exactly 1 time 6083246 (28.64%) aligned >1 times 95.53% overall alignment rate Time searching: 00:09:34 Overall time: 00:09:34 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 12 files... [bam_rmdupse_core] 11945836 / 20290101 = 0.5888 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 13:39:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX12261326/SRX12261326.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX12261326/SRX12261326.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX12261326/SRX12261326.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX12261326/SRX12261326.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 13:39:25: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:39:25: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:39:32: 1000000 INFO @ Tue, 02 Aug 2022 13:39:38: 2000000 INFO @ Tue, 02 Aug 2022 13:39:44: 3000000 INFO @ Tue, 02 Aug 2022 13:39:50: 4000000 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 13:39:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX12261326/SRX12261326.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX12261326/SRX12261326.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX12261326/SRX12261326.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX12261326/SRX12261326.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 13:39:55: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:39:55: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:39:57: 5000000 INFO @ Tue, 02 Aug 2022 13:40:01: 1000000 INFO @ Tue, 02 Aug 2022 13:40:03: 6000000 INFO @ Tue, 02 Aug 2022 13:40:07: 2000000 INFO @ Tue, 02 Aug 2022 13:40:09: 7000000 INFO @ Tue, 02 Aug 2022 13:40:13: 3000000 INFO @ Tue, 02 Aug 2022 13:40:15: 8000000 INFO @ Tue, 02 Aug 2022 13:40:17: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 13:40:17: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 13:40:17: #1 total tags in treatment: 8344265 INFO @ Tue, 02 Aug 2022 13:40:17: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:40:17: #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 13:40:18: #1 tags after filtering in treatment: 8344260 INFO @ Tue, 02 Aug 2022 13:40:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 13:40:18: #1 finished! INFO @ Tue, 02 Aug 2022 13:40:18: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:40:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:40:18: #2 number of paired peaks: 1266 INFO @ Tue, 02 Aug 2022 13:40:18: start model_add_line... INFO @ Tue, 02 Aug 2022 13:40:18: start X-correlation... INFO @ Tue, 02 Aug 2022 13:40:18: end of X-cor INFO @ Tue, 02 Aug 2022 13:40:18: #2 finished! INFO @ Tue, 02 Aug 2022 13:40:18: #2 predicted fragment length is 82 bps INFO @ Tue, 02 Aug 2022 13:40:18: #2 alternative fragment length(s) may be 82 bps INFO @ Tue, 02 Aug 2022 13:40:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX12261326/SRX12261326.05_model.r WARNING @ Tue, 02 Aug 2022 13:40:19: #2 Since the d (82) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 13:40:19: #2 You may need to consider one of the other alternative d(s): 82 WARNING @ Tue, 02 Aug 2022 13:40:19: #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 13:40:19: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:40:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 13:40:19: 4000000 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 13:40:24: 5000000 INFO @ Tue, 02 Aug 2022 13:40:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX12261326/SRX12261326.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX12261326/SRX12261326.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX12261326/SRX12261326.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX12261326/SRX12261326.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 13:40:25: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:40:25: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:40:30: 6000000 INFO @ Tue, 02 Aug 2022 13:40:31: 1000000 INFO @ Tue, 02 Aug 2022 13:40:36: 7000000 INFO @ Tue, 02 Aug 2022 13:40:37: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 13:40:38: 2000000 INFO @ Tue, 02 Aug 2022 13:40:41: 8000000 INFO @ Tue, 02 Aug 2022 13:40:44: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 13:40:44: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 13:40:44: #1 total tags in treatment: 8344265 INFO @ Tue, 02 Aug 2022 13:40:44: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:40:44: #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 13:40:44: 3000000 INFO @ Tue, 02 Aug 2022 13:40:44: #1 tags after filtering in treatment: 8344260 INFO @ Tue, 02 Aug 2022 13:40:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 13:40:44: #1 finished! INFO @ Tue, 02 Aug 2022 13:40:44: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:40:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:40:45: #2 number of paired peaks: 1266 INFO @ Tue, 02 Aug 2022 13:40:45: start model_add_line... INFO @ Tue, 02 Aug 2022 13:40:45: start X-correlation... INFO @ Tue, 02 Aug 2022 13:40:45: end of X-cor INFO @ Tue, 02 Aug 2022 13:40:45: #2 finished! INFO @ Tue, 02 Aug 2022 13:40:45: #2 predicted fragment length is 82 bps INFO @ Tue, 02 Aug 2022 13:40:45: #2 alternative fragment length(s) may be 82 bps INFO @ Tue, 02 Aug 2022 13:40:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX12261326/SRX12261326.10_model.r WARNING @ Tue, 02 Aug 2022 13:40:45: #2 Since the d (82) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 13:40:45: #2 You may need to consider one of the other alternative d(s): 82 WARNING @ Tue, 02 Aug 2022 13:40:45: #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 13:40:45: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:40:45: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 13:40:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX12261326/SRX12261326.05_peaks.xls INFO @ Tue, 02 Aug 2022 13:40:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX12261326/SRX12261326.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:40:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX12261326/SRX12261326.05_summits.bed INFO @ Tue, 02 Aug 2022 13:40:46: Done! pass1 - making usageList (699 chroms): 2 millis pass2 - checking and writing primary data (6361 records, 4 fields): 384 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 13:40:50: 4000000 INFO @ Tue, 02 Aug 2022 13:40:55: 5000000 INFO @ Tue, 02 Aug 2022 13:41:01: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 13:41:04: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 13:41:07: 7000000 INFO @ Tue, 02 Aug 2022 13:41:12: 8000000 INFO @ Tue, 02 Aug 2022 13:41:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX12261326/SRX12261326.10_peaks.xls INFO @ Tue, 02 Aug 2022 13:41:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX12261326/SRX12261326.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:41:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX12261326/SRX12261326.10_summits.bed INFO @ Tue, 02 Aug 2022 13:41:13: Done! pass1 - making usageList (558 chroms): 1 millis pass2 - checking and writing primary data (2911 records, 4 fields): 41 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 13:41:14: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 13:41:14: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 13:41:14: #1 total tags in treatment: 8344265 INFO @ Tue, 02 Aug 2022 13:41:14: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:41:14: #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 13:41:15: #1 tags after filtering in treatment: 8344260 INFO @ Tue, 02 Aug 2022 13:41:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 13:41:15: #1 finished! INFO @ Tue, 02 Aug 2022 13:41:15: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:41:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:41:16: #2 number of paired peaks: 1266 INFO @ Tue, 02 Aug 2022 13:41:16: start model_add_line... INFO @ Tue, 02 Aug 2022 13:41:16: start X-correlation... INFO @ Tue, 02 Aug 2022 13:41:16: end of X-cor INFO @ Tue, 02 Aug 2022 13:41:16: #2 finished! INFO @ Tue, 02 Aug 2022 13:41:16: #2 predicted fragment length is 82 bps INFO @ Tue, 02 Aug 2022 13:41:16: #2 alternative fragment length(s) may be 82 bps INFO @ Tue, 02 Aug 2022 13:41:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX12261326/SRX12261326.20_model.r WARNING @ Tue, 02 Aug 2022 13:41:16: #2 Since the d (82) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 13:41:16: #2 You may need to consider one of the other alternative d(s): 82 WARNING @ Tue, 02 Aug 2022 13:41:16: #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 13:41:16: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:41:16: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 13:41:34: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 13:41:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX12261326/SRX12261326.20_peaks.xls INFO @ Tue, 02 Aug 2022 13:41:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX12261326/SRX12261326.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:41:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX12261326/SRX12261326.20_summits.bed INFO @ Tue, 02 Aug 2022 13:41:43: Done! pass1 - making usageList (487 chroms): 2 millis pass2 - checking and writing primary data (1489 records, 4 fields): 29 millis CompletedMACS2peakCalling