Job ID = 16439868 SRX = SRX12175819 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 23676102 spots for SRR15884958/SRR15884958.sra Written 23676102 spots for SRR15884958/SRR15884958.sra fastq に変換しました。 bowtie でマッピング中... Your job 16440123 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:43:05 23676102 reads; of these: 23676102 (100.00%) were paired; of these: 13177444 (55.66%) aligned concordantly 0 times 9197369 (38.85%) aligned concordantly exactly 1 time 1301289 (5.50%) aligned concordantly >1 times ---- 13177444 pairs aligned concordantly 0 times; of these: 3459793 (26.26%) aligned discordantly 1 time ---- 9717651 pairs aligned 0 times concordantly or discordantly; of these: 19435302 mates make up the pairs; of these: 17732458 (91.24%) aligned 0 times 873640 (4.50%) aligned exactly 1 time 829204 (4.27%) aligned >1 times 62.55% overall alignment rate Time searching: 00:43:05 Overall time: 00:43:05 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 24 files... [bam_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 2876031 / 13901150 = 0.2069 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 17:25:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12175819/SRX12175819.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12175819/SRX12175819.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12175819/SRX12175819.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12175819/SRX12175819.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 17:25:20: #1 read tag files... INFO @ Tue, 02 Aug 2022 17:25:20: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 17:25:28: 1000000 INFO @ Tue, 02 Aug 2022 17:25:34: 2000000 INFO @ Tue, 02 Aug 2022 17:25:42: 3000000 INFO @ Tue, 02 Aug 2022 17:25:48: 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 17:25:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12175819/SRX12175819.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12175819/SRX12175819.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12175819/SRX12175819.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12175819/SRX12175819.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 17:25:50: #1 read tag files... INFO @ Tue, 02 Aug 2022 17:25:50: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 17:25:56: 5000000 INFO @ Tue, 02 Aug 2022 17:25:58: 1000000 INFO @ Tue, 02 Aug 2022 17:26:03: 6000000 INFO @ Tue, 02 Aug 2022 17:26:05: 2000000 INFO @ Tue, 02 Aug 2022 17:26:11: 7000000 INFO @ Tue, 02 Aug 2022 17:26:12: 3000000 INFO @ Tue, 02 Aug 2022 17:26:18: 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 17:26:18: 4000000 INFO @ Tue, 02 Aug 2022 17:26:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12175819/SRX12175819.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12175819/SRX12175819.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12175819/SRX12175819.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12175819/SRX12175819.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 17:26:20: #1 read tag files... INFO @ Tue, 02 Aug 2022 17:26:20: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 17:26:26: 5000000 INFO @ Tue, 02 Aug 2022 17:26:26: 9000000 INFO @ Tue, 02 Aug 2022 17:26:29: 1000000 INFO @ Tue, 02 Aug 2022 17:26:33: 6000000 INFO @ Tue, 02 Aug 2022 17:26:34: 10000000 INFO @ Tue, 02 Aug 2022 17:26:38: 2000000 INFO @ Tue, 02 Aug 2022 17:26:41: 7000000 INFO @ Tue, 02 Aug 2022 17:26:41: 11000000 INFO @ Tue, 02 Aug 2022 17:26:46: 3000000 INFO @ Tue, 02 Aug 2022 17:26:48: 8000000 INFO @ Tue, 02 Aug 2022 17:26:49: 12000000 INFO @ Tue, 02 Aug 2022 17:26:55: 4000000 INFO @ Tue, 02 Aug 2022 17:26:56: 9000000 INFO @ Tue, 02 Aug 2022 17:26:57: 13000000 INFO @ Tue, 02 Aug 2022 17:27:03: 10000000 INFO @ Tue, 02 Aug 2022 17:27:04: 5000000 INFO @ Tue, 02 Aug 2022 17:27:05: 14000000 INFO @ Tue, 02 Aug 2022 17:27:10: 11000000 INFO @ Tue, 02 Aug 2022 17:27:12: 6000000 INFO @ Tue, 02 Aug 2022 17:27:13: 15000000 INFO @ Tue, 02 Aug 2022 17:27:18: 12000000 INFO @ Tue, 02 Aug 2022 17:27:21: 16000000 INFO @ Tue, 02 Aug 2022 17:27:21: 7000000 INFO @ Tue, 02 Aug 2022 17:27:26: 13000000 INFO @ Tue, 02 Aug 2022 17:27:28: 17000000 INFO @ Tue, 02 Aug 2022 17:27:29: 8000000 INFO @ Tue, 02 Aug 2022 17:27:33: 14000000 INFO @ Tue, 02 Aug 2022 17:27:36: 18000000 INFO @ Tue, 02 Aug 2022 17:27:38: 9000000 INFO @ Tue, 02 Aug 2022 17:27:41: 15000000 INFO @ Tue, 02 Aug 2022 17:27:44: 19000000 INFO @ Tue, 02 Aug 2022 17:27:47: 10000000 INFO @ Tue, 02 Aug 2022 17:27:48: 16000000 INFO @ Tue, 02 Aug 2022 17:27:52: 20000000 INFO @ Tue, 02 Aug 2022 17:27:55: 11000000 INFO @ Tue, 02 Aug 2022 17:27:55: 17000000 INFO @ Tue, 02 Aug 2022 17:28:00: 21000000 INFO @ Tue, 02 Aug 2022 17:28:03: 18000000 INFO @ Tue, 02 Aug 2022 17:28:03: 12000000 INFO @ Tue, 02 Aug 2022 17:28:07: 22000000 INFO @ Tue, 02 Aug 2022 17:28:10: 19000000 INFO @ Tue, 02 Aug 2022 17:28:12: 13000000 INFO @ Tue, 02 Aug 2022 17:28:16: 23000000 INFO @ Tue, 02 Aug 2022 17:28:17: 20000000 INFO @ Tue, 02 Aug 2022 17:28:20: 14000000 INFO @ Tue, 02 Aug 2022 17:28:22: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 17:28:22: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 17:28:22: #1 total tags in treatment: 8181066 INFO @ Tue, 02 Aug 2022 17:28:22: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 17:28:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 17:28:22: #1 tags after filtering in treatment: 5184007 INFO @ Tue, 02 Aug 2022 17:28:22: #1 Redundant rate of treatment: 0.37 INFO @ Tue, 02 Aug 2022 17:28:22: #1 finished! INFO @ Tue, 02 Aug 2022 17:28:22: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 17:28:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 17:28:23: #2 number of paired peaks: 6589 INFO @ Tue, 02 Aug 2022 17:28:23: start model_add_line... INFO @ Tue, 02 Aug 2022 17:28:23: start X-correlation... INFO @ Tue, 02 Aug 2022 17:28:23: end of X-cor INFO @ Tue, 02 Aug 2022 17:28:23: #2 finished! INFO @ Tue, 02 Aug 2022 17:28:23: #2 predicted fragment length is 264 bps INFO @ Tue, 02 Aug 2022 17:28:23: #2 alternative fragment length(s) may be 264 bps INFO @ Tue, 02 Aug 2022 17:28:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12175819/SRX12175819.05_model.r WARNING @ Tue, 02 Aug 2022 17:28:23: #2 Since the d (264) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 17:28:23: #2 You may need to consider one of the other alternative d(s): 264 WARNING @ Tue, 02 Aug 2022 17:28:23: #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 17:28:23: #3 Call peaks... INFO @ Tue, 02 Aug 2022 17:28:23: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 17:28:24: 21000000 INFO @ Tue, 02 Aug 2022 17:28:29: 15000000 INFO @ Tue, 02 Aug 2022 17:28:32: 22000000 INFO @ Tue, 02 Aug 2022 17:28:37: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 17:28:37: 16000000 INFO @ Tue, 02 Aug 2022 17:28:39: 23000000 INFO @ Tue, 02 Aug 2022 17:28:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12175819/SRX12175819.05_peaks.xls INFO @ Tue, 02 Aug 2022 17:28:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12175819/SRX12175819.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 17:28:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12175819/SRX12175819.05_summits.bed INFO @ Tue, 02 Aug 2022 17:28:44: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (8779 records, 4 fields): 80 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 17:28:46: 17000000 INFO @ Tue, 02 Aug 2022 17:28:46: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 17:28:46: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 17:28:46: #1 total tags in treatment: 8181066 INFO @ Tue, 02 Aug 2022 17:28:46: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 17:28:46: #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 17:28:46: #1 tags after filtering in treatment: 5184007 INFO @ Tue, 02 Aug 2022 17:28:46: #1 Redundant rate of treatment: 0.37 INFO @ Tue, 02 Aug 2022 17:28:46: #1 finished! INFO @ Tue, 02 Aug 2022 17:28:46: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 17:28:46: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 17:28:47: #2 number of paired peaks: 6589 INFO @ Tue, 02 Aug 2022 17:28:47: start model_add_line... INFO @ Tue, 02 Aug 2022 17:28:47: start X-correlation... INFO @ Tue, 02 Aug 2022 17:28:47: end of X-cor INFO @ Tue, 02 Aug 2022 17:28:47: #2 finished! INFO @ Tue, 02 Aug 2022 17:28:47: #2 predicted fragment length is 264 bps INFO @ Tue, 02 Aug 2022 17:28:47: #2 alternative fragment length(s) may be 264 bps INFO @ Tue, 02 Aug 2022 17:28:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12175819/SRX12175819.10_model.r WARNING @ Tue, 02 Aug 2022 17:28:47: #2 Since the d (264) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 17:28:47: #2 You may need to consider one of the other alternative d(s): 264 WARNING @ Tue, 02 Aug 2022 17:28:47: #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 17:28:47: #3 Call peaks... INFO @ Tue, 02 Aug 2022 17:28:47: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 17:28:55: 18000000 INFO @ Tue, 02 Aug 2022 17:29:00: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 17:29:03: 19000000 INFO @ Tue, 02 Aug 2022 17:29:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12175819/SRX12175819.10_peaks.xls INFO @ Tue, 02 Aug 2022 17:29:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12175819/SRX12175819.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 17:29:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12175819/SRX12175819.10_summits.bed INFO @ Tue, 02 Aug 2022 17:29:07: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (6456 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 17:29:12: 20000000 INFO @ Tue, 02 Aug 2022 17:29:20: 21000000 INFO @ Tue, 02 Aug 2022 17:29:28: 22000000 INFO @ Tue, 02 Aug 2022 17:29:36: 23000000 INFO @ Tue, 02 Aug 2022 17:29:44: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 17:29:44: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 17:29:44: #1 total tags in treatment: 8181066 INFO @ Tue, 02 Aug 2022 17:29:44: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 17:29:44: #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 17:29:44: #1 tags after filtering in treatment: 5184007 INFO @ Tue, 02 Aug 2022 17:29:44: #1 Redundant rate of treatment: 0.37 INFO @ Tue, 02 Aug 2022 17:29:44: #1 finished! INFO @ Tue, 02 Aug 2022 17:29:44: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 17:29:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 17:29:45: #2 number of paired peaks: 6589 INFO @ Tue, 02 Aug 2022 17:29:45: start model_add_line... INFO @ Tue, 02 Aug 2022 17:29:45: start X-correlation... INFO @ Tue, 02 Aug 2022 17:29:45: end of X-cor INFO @ Tue, 02 Aug 2022 17:29:45: #2 finished! INFO @ Tue, 02 Aug 2022 17:29:45: #2 predicted fragment length is 264 bps INFO @ Tue, 02 Aug 2022 17:29:45: #2 alternative fragment length(s) may be 264 bps INFO @ Tue, 02 Aug 2022 17:29:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12175819/SRX12175819.20_model.r WARNING @ Tue, 02 Aug 2022 17:29:45: #2 Since the d (264) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 17:29:45: #2 You may need to consider one of the other alternative d(s): 264 WARNING @ Tue, 02 Aug 2022 17:29:45: #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 17:29:45: #3 Call peaks... INFO @ Tue, 02 Aug 2022 17:29:45: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 17:29:59: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 17:30:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12175819/SRX12175819.20_peaks.xls INFO @ Tue, 02 Aug 2022 17:30:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12175819/SRX12175819.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 17:30:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12175819/SRX12175819.20_summits.bed INFO @ Tue, 02 Aug 2022 17:30:05: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3999 records, 4 fields): 32 millis CompletedMACS2peakCalling