Job ID = 16438144 SRX = SRX12261349 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: 00:09:16 21879036 reads; of these: 21879036 (100.00%) were unpaired; of these: 998963 (4.57%) aligned 0 times 13060538 (59.69%) aligned exactly 1 time 7819535 (35.74%) aligned >1 times 95.43% overall alignment rate Time searching: 00:09:16 Overall time: 00:09:16 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] 10430960 / 20880073 = 0.4996 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 13:59:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX12261349/SRX12261349.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX12261349/SRX12261349.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX12261349/SRX12261349.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX12261349/SRX12261349.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 13:59:01: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:59:01: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:59:07: 1000000 INFO @ Tue, 02 Aug 2022 13:59:14: 2000000 INFO @ Tue, 02 Aug 2022 13:59:20: 3000000 INFO @ Tue, 02 Aug 2022 13:59:27: 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 13:59:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX12261349/SRX12261349.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX12261349/SRX12261349.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX12261349/SRX12261349.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX12261349/SRX12261349.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 13:59:31: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:59:31: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:59:34: 5000000 INFO @ Tue, 02 Aug 2022 13:59:38: 1000000 INFO @ Tue, 02 Aug 2022 13:59:41: 6000000 INFO @ Tue, 02 Aug 2022 13:59:45: 2000000 INFO @ Tue, 02 Aug 2022 13:59:48: 7000000 INFO @ Tue, 02 Aug 2022 13:59:52: 3000000 INFO @ Tue, 02 Aug 2022 13:59:55: 8000000 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 14:00:00: 4000000 INFO @ Tue, 02 Aug 2022 14:00:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX12261349/SRX12261349.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX12261349/SRX12261349.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX12261349/SRX12261349.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX12261349/SRX12261349.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 14:00:01: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:00:01: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:00:02: 9000000 INFO @ Tue, 02 Aug 2022 14:00:07: 5000000 INFO @ Tue, 02 Aug 2022 14:00:08: 1000000 INFO @ Tue, 02 Aug 2022 14:00:09: 10000000 INFO @ Tue, 02 Aug 2022 14:00:13: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 14:00:13: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 14:00:13: #1 total tags in treatment: 10449113 INFO @ Tue, 02 Aug 2022 14:00:13: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:00:13: #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 14:00:13: #1 tags after filtering in treatment: 10449101 INFO @ Tue, 02 Aug 2022 14:00:13: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:00:13: #1 finished! INFO @ Tue, 02 Aug 2022 14:00:13: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:00:13: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:00:14: #2 number of paired peaks: 1096 INFO @ Tue, 02 Aug 2022 14:00:14: start model_add_line... INFO @ Tue, 02 Aug 2022 14:00:14: start X-correlation... INFO @ Tue, 02 Aug 2022 14:00:14: end of X-cor INFO @ Tue, 02 Aug 2022 14:00:14: #2 finished! INFO @ Tue, 02 Aug 2022 14:00:14: #2 predicted fragment length is 73 bps INFO @ Tue, 02 Aug 2022 14:00:14: #2 alternative fragment length(s) may be 73 bps INFO @ Tue, 02 Aug 2022 14:00:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX12261349/SRX12261349.05_model.r WARNING @ Tue, 02 Aug 2022 14:00:14: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:00:14: #2 You may need to consider one of the other alternative d(s): 73 WARNING @ Tue, 02 Aug 2022 14:00:14: #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 14:00:14: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:00:14: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:00:15: 6000000 INFO @ Tue, 02 Aug 2022 14:00:15: 2000000 INFO @ Tue, 02 Aug 2022 14:00:22: 3000000 INFO @ Tue, 02 Aug 2022 14:00:22: 7000000 INFO @ Tue, 02 Aug 2022 14:00:30: 4000000 INFO @ Tue, 02 Aug 2022 14:00:30: 8000000 INFO @ Tue, 02 Aug 2022 14:00:35: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:00:37: 5000000 INFO @ Tue, 02 Aug 2022 14:00:38: 9000000 INFO @ Tue, 02 Aug 2022 14:00:44: 6000000 INFO @ Tue, 02 Aug 2022 14:00:45: 10000000 INFO @ Tue, 02 Aug 2022 14:00:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX12261349/SRX12261349.05_peaks.xls INFO @ Tue, 02 Aug 2022 14:00:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX12261349/SRX12261349.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:00:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX12261349/SRX12261349.05_summits.bed INFO @ Tue, 02 Aug 2022 14:00:45: Done! pass1 - making usageList (703 chroms): 1 millis pass2 - checking and writing primary data (2842 records, 4 fields): 77 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 14:00:49: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 14:00:49: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 14:00:49: #1 total tags in treatment: 10449113 INFO @ Tue, 02 Aug 2022 14:00:49: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:00:49: #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 14:00:49: #1 tags after filtering in treatment: 10449101 INFO @ Tue, 02 Aug 2022 14:00:49: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:00:49: #1 finished! INFO @ Tue, 02 Aug 2022 14:00:49: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:00:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:00:50: #2 number of paired peaks: 1096 INFO @ Tue, 02 Aug 2022 14:00:50: start model_add_line... INFO @ Tue, 02 Aug 2022 14:00:50: start X-correlation... INFO @ Tue, 02 Aug 2022 14:00:50: end of X-cor INFO @ Tue, 02 Aug 2022 14:00:50: #2 finished! INFO @ Tue, 02 Aug 2022 14:00:50: #2 predicted fragment length is 73 bps INFO @ Tue, 02 Aug 2022 14:00:50: #2 alternative fragment length(s) may be 73 bps INFO @ Tue, 02 Aug 2022 14:00:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX12261349/SRX12261349.10_model.r WARNING @ Tue, 02 Aug 2022 14:00:50: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:00:50: #2 You may need to consider one of the other alternative d(s): 73 WARNING @ Tue, 02 Aug 2022 14:00:50: #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 14:00:50: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:00:50: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:00:52: 7000000 INFO @ Tue, 02 Aug 2022 14:00:59: 8000000 INFO @ Tue, 02 Aug 2022 14:01:06: 9000000 INFO @ Tue, 02 Aug 2022 14:01:11: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 14:01:13: 10000000 INFO @ Tue, 02 Aug 2022 14:01:16: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 14:01:16: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 14:01:16: #1 total tags in treatment: 10449113 INFO @ Tue, 02 Aug 2022 14:01:16: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:01:16: #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 14:01:16: #1 tags after filtering in treatment: 10449101 INFO @ Tue, 02 Aug 2022 14:01:16: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:01:16: #1 finished! INFO @ Tue, 02 Aug 2022 14:01:16: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:01:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:01:17: #2 number of paired peaks: 1096 INFO @ Tue, 02 Aug 2022 14:01:17: start model_add_line... INFO @ Tue, 02 Aug 2022 14:01:17: start X-correlation... INFO @ Tue, 02 Aug 2022 14:01:17: end of X-cor INFO @ Tue, 02 Aug 2022 14:01:17: #2 finished! INFO @ Tue, 02 Aug 2022 14:01:17: #2 predicted fragment length is 73 bps INFO @ Tue, 02 Aug 2022 14:01:17: #2 alternative fragment length(s) may be 73 bps INFO @ Tue, 02 Aug 2022 14:01:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX12261349/SRX12261349.20_model.r WARNING @ Tue, 02 Aug 2022 14:01:17: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:01:17: #2 You may need to consider one of the other alternative d(s): 73 WARNING @ Tue, 02 Aug 2022 14:01:17: #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 14:01:17: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:01:17: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:01:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX12261349/SRX12261349.10_peaks.xls INFO @ Tue, 02 Aug 2022 14:01:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX12261349/SRX12261349.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:01:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX12261349/SRX12261349.10_summits.bed INFO @ Tue, 02 Aug 2022 14:01:21: Done! pass1 - making usageList (581 chroms): 1 millis pass2 - checking and writing primary data (1744 records, 4 fields): 100 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:01:37: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:01:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX12261349/SRX12261349.20_peaks.xls INFO @ Tue, 02 Aug 2022 14:01:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX12261349/SRX12261349.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:01:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX12261349/SRX12261349.20_summits.bed INFO @ Tue, 02 Aug 2022 14:01:47: Done! pass1 - making usageList (509 chroms): 2 millis pass2 - checking and writing primary data (1423 records, 4 fields): 55 millis CompletedMACS2peakCalling