Job ID = 16439866 SRX = SRX12175818 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 26582303 spots for SRR15884957/SRR15884957.sra Written 26582303 spots for SRR15884957/SRR15884957.sra fastq に変換しました。 bowtie でマッピング中... Your job 16440193 ("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: 00:55:26 26582303 reads; of these: 26582303 (100.00%) were paired; of these: 15266402 (57.43%) aligned concordantly 0 times 9581854 (36.05%) aligned concordantly exactly 1 time 1734047 (6.52%) aligned concordantly >1 times ---- 15266402 pairs aligned concordantly 0 times; of these: 4221890 (27.65%) aligned discordantly 1 time ---- 11044512 pairs aligned 0 times concordantly or discordantly; of these: 22089024 mates make up the pairs; of these: 19627321 (88.86%) aligned 0 times 1272446 (5.76%) aligned exactly 1 time 1189257 (5.38%) aligned >1 times 63.08% overall alignment rate Time searching: 00:55:26 Overall time: 00:55:26 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 28 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] 2881036 / 15474854 = 0.1862 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 17:39:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12175818/SRX12175818.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12175818/SRX12175818.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12175818/SRX12175818.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12175818/SRX12175818.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 17:39:34: #1 read tag files... INFO @ Tue, 02 Aug 2022 17:39:34: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 17:39:42: 1000000 INFO @ Tue, 02 Aug 2022 17:39:50: 2000000 INFO @ Tue, 02 Aug 2022 17:39:58: 3000000 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 17:40:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12175818/SRX12175818.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12175818/SRX12175818.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12175818/SRX12175818.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12175818/SRX12175818.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 17:40:03: #1 read tag files... INFO @ Tue, 02 Aug 2022 17:40:03: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 17:40:06: 4000000 INFO @ Tue, 02 Aug 2022 17:40:11: 1000000 INFO @ Tue, 02 Aug 2022 17:40:15: 5000000 INFO @ Tue, 02 Aug 2022 17:40:19: 2000000 INFO @ Tue, 02 Aug 2022 17:40:23: 6000000 INFO @ Tue, 02 Aug 2022 17:40:27: 3000000 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 17:40:32: 7000000 INFO @ Tue, 02 Aug 2022 17:40:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12175818/SRX12175818.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12175818/SRX12175818.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12175818/SRX12175818.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12175818/SRX12175818.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 17:40:33: #1 read tag files... INFO @ Tue, 02 Aug 2022 17:40:33: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 17:40:34: 4000000 INFO @ Tue, 02 Aug 2022 17:40:41: 8000000 INFO @ Tue, 02 Aug 2022 17:40:42: 5000000 INFO @ Tue, 02 Aug 2022 17:40:42: 1000000 INFO @ Tue, 02 Aug 2022 17:40:49: 6000000 INFO @ Tue, 02 Aug 2022 17:40:50: 9000000 INFO @ Tue, 02 Aug 2022 17:40:50: 2000000 INFO @ Tue, 02 Aug 2022 17:40:57: 7000000 INFO @ Tue, 02 Aug 2022 17:40:59: 10000000 INFO @ Tue, 02 Aug 2022 17:40:59: 3000000 INFO @ Tue, 02 Aug 2022 17:41:04: 8000000 INFO @ Tue, 02 Aug 2022 17:41:07: 4000000 INFO @ Tue, 02 Aug 2022 17:41:07: 11000000 INFO @ Tue, 02 Aug 2022 17:41:12: 9000000 INFO @ Tue, 02 Aug 2022 17:41:16: 5000000 INFO @ Tue, 02 Aug 2022 17:41:16: 12000000 INFO @ Tue, 02 Aug 2022 17:41:19: 10000000 INFO @ Tue, 02 Aug 2022 17:41:24: 6000000 INFO @ Tue, 02 Aug 2022 17:41:25: 13000000 INFO @ Tue, 02 Aug 2022 17:41:27: 11000000 INFO @ Tue, 02 Aug 2022 17:41:32: 7000000 INFO @ Tue, 02 Aug 2022 17:41:34: 12000000 INFO @ Tue, 02 Aug 2022 17:41:34: 14000000 INFO @ Tue, 02 Aug 2022 17:41:40: 8000000 INFO @ Tue, 02 Aug 2022 17:41:42: 13000000 INFO @ Tue, 02 Aug 2022 17:41:43: 15000000 INFO @ Tue, 02 Aug 2022 17:41:48: 9000000 INFO @ Tue, 02 Aug 2022 17:41:50: 14000000 INFO @ Tue, 02 Aug 2022 17:41:52: 16000000 INFO @ Tue, 02 Aug 2022 17:41:56: 10000000 INFO @ Tue, 02 Aug 2022 17:41:58: 15000000 INFO @ Tue, 02 Aug 2022 17:42:01: 17000000 INFO @ Tue, 02 Aug 2022 17:42:04: 11000000 INFO @ Tue, 02 Aug 2022 17:42:06: 16000000 INFO @ Tue, 02 Aug 2022 17:42:10: 18000000 INFO @ Tue, 02 Aug 2022 17:42:12: 12000000 INFO @ Tue, 02 Aug 2022 17:42:13: 17000000 INFO @ Tue, 02 Aug 2022 17:42:19: 19000000 INFO @ Tue, 02 Aug 2022 17:42:20: 13000000 INFO @ Tue, 02 Aug 2022 17:42:21: 18000000 INFO @ Tue, 02 Aug 2022 17:42:27: 20000000 INFO @ Tue, 02 Aug 2022 17:42:28: 14000000 INFO @ Tue, 02 Aug 2022 17:42:29: 19000000 INFO @ Tue, 02 Aug 2022 17:42:36: 21000000 INFO @ Tue, 02 Aug 2022 17:42:36: 20000000 INFO @ Tue, 02 Aug 2022 17:42:36: 15000000 INFO @ Tue, 02 Aug 2022 17:42:44: 21000000 INFO @ Tue, 02 Aug 2022 17:42:44: 16000000 INFO @ Tue, 02 Aug 2022 17:42:44: 22000000 INFO @ Tue, 02 Aug 2022 17:42:52: 17000000 INFO @ Tue, 02 Aug 2022 17:42:52: 22000000 INFO @ Tue, 02 Aug 2022 17:42:53: 23000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 17:42:59: 18000000 INFO @ Tue, 02 Aug 2022 17:43:00: 23000000 INFO @ Tue, 02 Aug 2022 17:43:01: 24000000 INFO @ Tue, 02 Aug 2022 17:43:07: 19000000 INFO @ Tue, 02 Aug 2022 17:43:08: 24000000 INFO @ Tue, 02 Aug 2022 17:43:09: 25000000 INFO @ Tue, 02 Aug 2022 17:43:14: 20000000 INFO @ Tue, 02 Aug 2022 17:43:15: 25000000 INFO @ Tue, 02 Aug 2022 17:43:17: 26000000 INFO @ Tue, 02 Aug 2022 17:43:22: 21000000 INFO @ Tue, 02 Aug 2022 17:43:24: 26000000 INFO @ Tue, 02 Aug 2022 17:43:25: 27000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 17:43:29: 22000000 INFO @ Tue, 02 Aug 2022 17:43:31: 27000000 INFO @ Tue, 02 Aug 2022 17:43:32: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 17:43:32: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 17:43:32: #1 total tags in treatment: 9045785 INFO @ Tue, 02 Aug 2022 17:43:32: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 17:43:32: #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 17:43:32: #1 tags after filtering in treatment: 5937179 INFO @ Tue, 02 Aug 2022 17:43:32: #1 Redundant rate of treatment: 0.34 INFO @ Tue, 02 Aug 2022 17:43:32: #1 finished! INFO @ Tue, 02 Aug 2022 17:43:32: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 17:43:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 17:43:32: #2 number of paired peaks: 4838 INFO @ Tue, 02 Aug 2022 17:43:32: start model_add_line... INFO @ Tue, 02 Aug 2022 17:43:33: start X-correlation... INFO @ Tue, 02 Aug 2022 17:43:33: end of X-cor INFO @ Tue, 02 Aug 2022 17:43:33: #2 finished! INFO @ Tue, 02 Aug 2022 17:43:33: #2 predicted fragment length is 259 bps INFO @ Tue, 02 Aug 2022 17:43:33: #2 alternative fragment length(s) may be 259 bps INFO @ Tue, 02 Aug 2022 17:43:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12175818/SRX12175818.05_model.r WARNING @ Tue, 02 Aug 2022 17:43:33: #2 Since the d (259) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 17:43:33: #2 You may need to consider one of the other alternative d(s): 259 WARNING @ Tue, 02 Aug 2022 17:43:33: #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 17:43:33: #3 Call peaks... INFO @ Tue, 02 Aug 2022 17:43:33: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 17:43:37: 23000000 INFO @ Tue, 02 Aug 2022 17:43:38: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 17:43:38: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 17:43:38: #1 total tags in treatment: 9045785 INFO @ Tue, 02 Aug 2022 17:43:38: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 17:43:38: #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 17:43:38: #1 tags after filtering in treatment: 5937179 INFO @ Tue, 02 Aug 2022 17:43:38: #1 Redundant rate of treatment: 0.34 INFO @ Tue, 02 Aug 2022 17:43:38: #1 finished! INFO @ Tue, 02 Aug 2022 17:43:38: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 17:43:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 17:43:39: #2 number of paired peaks: 4838 INFO @ Tue, 02 Aug 2022 17:43:39: start model_add_line... INFO @ Tue, 02 Aug 2022 17:43:39: start X-correlation... INFO @ Tue, 02 Aug 2022 17:43:39: end of X-cor INFO @ Tue, 02 Aug 2022 17:43:39: #2 finished! INFO @ Tue, 02 Aug 2022 17:43:39: #2 predicted fragment length is 259 bps INFO @ Tue, 02 Aug 2022 17:43:39: #2 alternative fragment length(s) may be 259 bps INFO @ Tue, 02 Aug 2022 17:43:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12175818/SRX12175818.10_model.r WARNING @ Tue, 02 Aug 2022 17:43:39: #2 Since the d (259) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 17:43:39: #2 You may need to consider one of the other alternative d(s): 259 WARNING @ Tue, 02 Aug 2022 17:43:39: #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 17:43:39: #3 Call peaks... INFO @ Tue, 02 Aug 2022 17:43:39: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 17:43:45: 24000000 INFO @ Tue, 02 Aug 2022 17:43:48: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 17:43:52: 25000000 INFO @ Tue, 02 Aug 2022 17:43:53: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 17:43:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12175818/SRX12175818.05_peaks.xls INFO @ Tue, 02 Aug 2022 17:43:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12175818/SRX12175818.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 17:43:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12175818/SRX12175818.05_summits.bed INFO @ Tue, 02 Aug 2022 17:43:57: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (8880 records, 4 fields): 75 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 17:44:00: 26000000 INFO @ Tue, 02 Aug 2022 17:44:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12175818/SRX12175818.10_peaks.xls INFO @ Tue, 02 Aug 2022 17:44:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12175818/SRX12175818.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 17:44:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12175818/SRX12175818.10_summits.bed INFO @ Tue, 02 Aug 2022 17:44:01: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6315 records, 4 fields): 41 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 17:44:07: 27000000 INFO @ Tue, 02 Aug 2022 17:44:13: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 17:44:13: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 17:44:13: #1 total tags in treatment: 9045785 INFO @ Tue, 02 Aug 2022 17:44:13: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 17:44:13: #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 17:44:13: #1 tags after filtering in treatment: 5937179 INFO @ Tue, 02 Aug 2022 17:44:13: #1 Redundant rate of treatment: 0.34 INFO @ Tue, 02 Aug 2022 17:44:13: #1 finished! INFO @ Tue, 02 Aug 2022 17:44:13: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 17:44:13: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 17:44:14: #2 number of paired peaks: 4838 INFO @ Tue, 02 Aug 2022 17:44:14: start model_add_line... INFO @ Tue, 02 Aug 2022 17:44:14: start X-correlation... INFO @ Tue, 02 Aug 2022 17:44:14: end of X-cor INFO @ Tue, 02 Aug 2022 17:44:14: #2 finished! INFO @ Tue, 02 Aug 2022 17:44:14: #2 predicted fragment length is 259 bps INFO @ Tue, 02 Aug 2022 17:44:14: #2 alternative fragment length(s) may be 259 bps INFO @ Tue, 02 Aug 2022 17:44:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12175818/SRX12175818.20_model.r WARNING @ Tue, 02 Aug 2022 17:44:14: #2 Since the d (259) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 17:44:14: #2 You may need to consider one of the other alternative d(s): 259 WARNING @ Tue, 02 Aug 2022 17:44:14: #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 17:44:14: #3 Call peaks... INFO @ Tue, 02 Aug 2022 17:44:14: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 17:44:29: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 17:44:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12175818/SRX12175818.20_peaks.xls INFO @ Tue, 02 Aug 2022 17:44:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12175818/SRX12175818.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 17:44:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12175818/SRX12175818.20_summits.bed INFO @ Tue, 02 Aug 2022 17:44:37: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (3466 records, 4 fields): 58 millis CompletedMACS2peakCalling