Job ID = 16437306 SRX = SRX12119066 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 34034050 spots for SRR15827104/SRR15827104.sra Written 34034050 spots for SRR15827104/SRR15827104.sra fastq に変換しました。 bowtie でマッピング中... Your job 16438507 ("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: 01:25:20 34034050 reads; of these: 34034050 (100.00%) were paired; of these: 21127824 (62.08%) aligned concordantly 0 times 10819879 (31.79%) aligned concordantly exactly 1 time 2086347 (6.13%) aligned concordantly >1 times ---- 21127824 pairs aligned concordantly 0 times; of these: 2988178 (14.14%) aligned discordantly 1 time ---- 18139646 pairs aligned 0 times concordantly or discordantly; of these: 36279292 mates make up the pairs; of these: 33406770 (92.08%) aligned 0 times 1755121 (4.84%) aligned exactly 1 time 1117401 (3.08%) aligned >1 times 50.92% overall alignment rate Time searching: 01:25:20 Overall time: 01:25:20 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] 3166416 / 15811632 = 0.2003 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 14:11:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12119066/SRX12119066.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12119066/SRX12119066.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12119066/SRX12119066.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12119066/SRX12119066.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 14:11:44: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:11:44: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:11:54: 1000000 INFO @ Tue, 02 Aug 2022 14:12:04: 2000000 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 14:12:14: 3000000 INFO @ Tue, 02 Aug 2022 14:12:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12119066/SRX12119066.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12119066/SRX12119066.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12119066/SRX12119066.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12119066/SRX12119066.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 14:12:14: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:12:14: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:12:24: 4000000 INFO @ Tue, 02 Aug 2022 14:12:27: 1000000 INFO @ Tue, 02 Aug 2022 14:12:34: 5000000 INFO @ Tue, 02 Aug 2022 14:12:39: 2000000 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 14:12:44: 6000000 INFO @ Tue, 02 Aug 2022 14:12:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12119066/SRX12119066.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12119066/SRX12119066.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12119066/SRX12119066.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12119066/SRX12119066.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 14:12:44: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:12:44: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:12:51: 3000000 INFO @ Tue, 02 Aug 2022 14:12:55: 7000000 INFO @ Tue, 02 Aug 2022 14:12:56: 1000000 INFO @ Tue, 02 Aug 2022 14:13:02: 4000000 INFO @ Tue, 02 Aug 2022 14:13:07: 8000000 INFO @ Tue, 02 Aug 2022 14:13:08: 2000000 INFO @ Tue, 02 Aug 2022 14:13:13: 5000000 INFO @ Tue, 02 Aug 2022 14:13:18: 9000000 INFO @ Tue, 02 Aug 2022 14:13:19: 3000000 INFO @ Tue, 02 Aug 2022 14:13:25: 6000000 INFO @ Tue, 02 Aug 2022 14:13:29: 10000000 INFO @ Tue, 02 Aug 2022 14:13:30: 4000000 INFO @ Tue, 02 Aug 2022 14:13:37: 7000000 INFO @ Tue, 02 Aug 2022 14:13:40: 11000000 INFO @ Tue, 02 Aug 2022 14:13:41: 5000000 INFO @ Tue, 02 Aug 2022 14:13:48: 8000000 INFO @ Tue, 02 Aug 2022 14:13:51: 12000000 INFO @ Tue, 02 Aug 2022 14:13:52: 6000000 INFO @ Tue, 02 Aug 2022 14:14:00: 9000000 INFO @ Tue, 02 Aug 2022 14:14:02: 13000000 INFO @ Tue, 02 Aug 2022 14:14:03: 7000000 INFO @ Tue, 02 Aug 2022 14:14:11: 10000000 INFO @ Tue, 02 Aug 2022 14:14:13: 14000000 INFO @ Tue, 02 Aug 2022 14:14:14: 8000000 INFO @ Tue, 02 Aug 2022 14:14:22: 11000000 INFO @ Tue, 02 Aug 2022 14:14:24: 15000000 INFO @ Tue, 02 Aug 2022 14:14:25: 9000000 INFO @ Tue, 02 Aug 2022 14:14:34: 12000000 INFO @ Tue, 02 Aug 2022 14:14:34: 16000000 INFO @ Tue, 02 Aug 2022 14:14:36: 10000000 INFO @ Tue, 02 Aug 2022 14:14:45: 13000000 INFO @ Tue, 02 Aug 2022 14:14:45: 17000000 INFO @ Tue, 02 Aug 2022 14:14:47: 11000000 INFO @ Tue, 02 Aug 2022 14:14:57: 14000000 INFO @ Tue, 02 Aug 2022 14:14:57: 18000000 INFO @ Tue, 02 Aug 2022 14:14:59: 12000000 INFO @ Tue, 02 Aug 2022 14:15:08: 15000000 INFO @ Tue, 02 Aug 2022 14:15:09: 19000000 INFO @ Tue, 02 Aug 2022 14:15:11: 13000000 INFO @ Tue, 02 Aug 2022 14:15:19: 16000000 INFO @ Tue, 02 Aug 2022 14:15:21: 20000000 INFO @ Tue, 02 Aug 2022 14:15:23: 14000000 INFO @ Tue, 02 Aug 2022 14:15:32: 17000000 INFO @ Tue, 02 Aug 2022 14:15:33: 21000000 INFO @ Tue, 02 Aug 2022 14:15:35: 15000000 INFO @ Tue, 02 Aug 2022 14:15:44: 18000000 INFO @ Tue, 02 Aug 2022 14:15:46: 22000000 INFO @ Tue, 02 Aug 2022 14:15:47: 16000000 INFO @ Tue, 02 Aug 2022 14:15:57: 19000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 14:15:59: 23000000 INFO @ Tue, 02 Aug 2022 14:16:00: 17000000 INFO @ Tue, 02 Aug 2022 14:16:10: 20000000 INFO @ Tue, 02 Aug 2022 14:16:11: 24000000 INFO @ Tue, 02 Aug 2022 14:16:13: 18000000 INFO @ Tue, 02 Aug 2022 14:16:23: 21000000 INFO @ Tue, 02 Aug 2022 14:16:24: 25000000 INFO @ Tue, 02 Aug 2022 14:16:26: 19000000 INFO @ Tue, 02 Aug 2022 14:16:35: 26000000 INFO @ Tue, 02 Aug 2022 14:16:36: 22000000 INFO @ Tue, 02 Aug 2022 14:16:38: 20000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 14:16:47: 27000000 INFO @ Tue, 02 Aug 2022 14:16:49: 23000000 INFO @ Tue, 02 Aug 2022 14:16:50: 21000000 INFO @ Tue, 02 Aug 2022 14:16:59: 28000000 INFO @ Tue, 02 Aug 2022 14:17:02: 22000000 INFO @ Tue, 02 Aug 2022 14:17:02: 24000000 INFO @ Tue, 02 Aug 2022 14:17:03: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 14:17:03: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 14:17:03: #1 total tags in treatment: 10282012 INFO @ Tue, 02 Aug 2022 14:17:03: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:17:03: #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 14:17:03: #1 tags after filtering in treatment: 7016445 INFO @ Tue, 02 Aug 2022 14:17:03: #1 Redundant rate of treatment: 0.32 INFO @ Tue, 02 Aug 2022 14:17:03: #1 finished! INFO @ Tue, 02 Aug 2022 14:17:03: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:17:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:17:04: #2 number of paired peaks: 4230 INFO @ Tue, 02 Aug 2022 14:17:04: start model_add_line... INFO @ Tue, 02 Aug 2022 14:17:04: start X-correlation... INFO @ Tue, 02 Aug 2022 14:17:04: end of X-cor INFO @ Tue, 02 Aug 2022 14:17:04: #2 finished! INFO @ Tue, 02 Aug 2022 14:17:04: #2 predicted fragment length is 221 bps INFO @ Tue, 02 Aug 2022 14:17:04: #2 alternative fragment length(s) may be 221 bps INFO @ Tue, 02 Aug 2022 14:17:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12119066/SRX12119066.05_model.r WARNING @ Tue, 02 Aug 2022 14:17:04: #2 Since the d (221) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:17:04: #2 You may need to consider one of the other alternative d(s): 221 WARNING @ Tue, 02 Aug 2022 14:17:04: #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 14:17:04: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:17:04: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:17:12: 23000000 INFO @ Tue, 02 Aug 2022 14:17:16: 25000000 INFO @ Tue, 02 Aug 2022 14:17:22: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:17:23: 24000000 INFO @ Tue, 02 Aug 2022 14:17:29: 26000000 INFO @ Tue, 02 Aug 2022 14:17:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12119066/SRX12119066.05_peaks.xls INFO @ Tue, 02 Aug 2022 14:17:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12119066/SRX12119066.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:17:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12119066/SRX12119066.05_summits.bed INFO @ Tue, 02 Aug 2022 14:17:31: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (8034 records, 4 fields): 57 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:17:33: 25000000 INFO @ Tue, 02 Aug 2022 14:17:42: 27000000 INFO @ Tue, 02 Aug 2022 14:17:44: 26000000 INFO @ Tue, 02 Aug 2022 14:17:54: 27000000 INFO @ Tue, 02 Aug 2022 14:17:55: 28000000 INFO @ Tue, 02 Aug 2022 14:17:59: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 14:17:59: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 14:17:59: #1 total tags in treatment: 10282012 INFO @ Tue, 02 Aug 2022 14:17:59: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:17:59: #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 14:18:00: #1 tags after filtering in treatment: 7016445 INFO @ Tue, 02 Aug 2022 14:18:00: #1 Redundant rate of treatment: 0.32 INFO @ Tue, 02 Aug 2022 14:18:00: #1 finished! INFO @ Tue, 02 Aug 2022 14:18:00: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:18:00: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:18:00: #2 number of paired peaks: 4230 INFO @ Tue, 02 Aug 2022 14:18:00: start model_add_line... INFO @ Tue, 02 Aug 2022 14:18:00: start X-correlation... INFO @ Tue, 02 Aug 2022 14:18:01: end of X-cor INFO @ Tue, 02 Aug 2022 14:18:01: #2 finished! INFO @ Tue, 02 Aug 2022 14:18:01: #2 predicted fragment length is 221 bps INFO @ Tue, 02 Aug 2022 14:18:01: #2 alternative fragment length(s) may be 221 bps INFO @ Tue, 02 Aug 2022 14:18:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12119066/SRX12119066.10_model.r WARNING @ Tue, 02 Aug 2022 14:18:01: #2 Since the d (221) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:18:01: #2 You may need to consider one of the other alternative d(s): 221 WARNING @ Tue, 02 Aug 2022 14:18:01: #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 14:18:01: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:18:01: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:18:05: 28000000 INFO @ Tue, 02 Aug 2022 14:18:08: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 14:18:08: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 14:18:08: #1 total tags in treatment: 10282012 INFO @ Tue, 02 Aug 2022 14:18:08: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:18:08: #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 14:18:08: #1 tags after filtering in treatment: 7016445 INFO @ Tue, 02 Aug 2022 14:18:08: #1 Redundant rate of treatment: 0.32 INFO @ Tue, 02 Aug 2022 14:18:08: #1 finished! INFO @ Tue, 02 Aug 2022 14:18:08: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:18:08: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:18:09: #2 number of paired peaks: 4230 INFO @ Tue, 02 Aug 2022 14:18:09: start model_add_line... INFO @ Tue, 02 Aug 2022 14:18:09: start X-correlation... INFO @ Tue, 02 Aug 2022 14:18:09: end of X-cor INFO @ Tue, 02 Aug 2022 14:18:09: #2 finished! INFO @ Tue, 02 Aug 2022 14:18:09: #2 predicted fragment length is 221 bps INFO @ Tue, 02 Aug 2022 14:18:09: #2 alternative fragment length(s) may be 221 bps INFO @ Tue, 02 Aug 2022 14:18:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12119066/SRX12119066.20_model.r WARNING @ Tue, 02 Aug 2022 14:18:09: #2 Since the d (221) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:18:09: #2 You may need to consider one of the other alternative d(s): 221 WARNING @ Tue, 02 Aug 2022 14:18:09: #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 14:18:09: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:18:09: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:18:19: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:18:27: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:18:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12119066/SRX12119066.10_peaks.xls INFO @ Tue, 02 Aug 2022 14:18:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12119066/SRX12119066.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:18:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12119066/SRX12119066.10_summits.bed INFO @ Tue, 02 Aug 2022 14:18:27: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (5812 records, 4 fields): 28 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:18:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12119066/SRX12119066.20_peaks.xls INFO @ Tue, 02 Aug 2022 14:18:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12119066/SRX12119066.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:18:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12119066/SRX12119066.20_summits.bed INFO @ Tue, 02 Aug 2022 14:18:35: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3505 records, 4 fields): 40 millis CompletedMACS2peakCalling