Job ID = 16439862 SRX = SRX12175816 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 32067076 spots for SRR15884955/SRR15884955.sra Written 32067076 spots for SRR15884955/SRR15884955.sra fastq に変換しました。 bowtie でマッピング中... Your job 16440793 ("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: 01:22:01 32067076 reads; of these: 32067076 (100.00%) were paired; of these: 16102630 (50.22%) aligned concordantly 0 times 14465603 (45.11%) aligned concordantly exactly 1 time 1498843 (4.67%) aligned concordantly >1 times ---- 16102630 pairs aligned concordantly 0 times; of these: 5531548 (34.35%) aligned discordantly 1 time ---- 10571082 pairs aligned 0 times concordantly or discordantly; of these: 21142164 mates make up the pairs; of these: 18729889 (88.59%) aligned 0 times 1417107 (6.70%) aligned exactly 1 time 995168 (4.71%) aligned >1 times 70.80% overall alignment rate Time searching: 01:22:01 Overall time: 01:22:01 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 36 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] 4576070 / 21410452 = 0.2137 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 18:17:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12175816/SRX12175816.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12175816/SRX12175816.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12175816/SRX12175816.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12175816/SRX12175816.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 18:17:46: #1 read tag files... INFO @ Tue, 02 Aug 2022 18:17:46: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 18:17:55: 1000000 INFO @ Tue, 02 Aug 2022 18:18:04: 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 18:18:13: 3000000 INFO @ Tue, 02 Aug 2022 18:18:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12175816/SRX12175816.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12175816/SRX12175816.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12175816/SRX12175816.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12175816/SRX12175816.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 18:18:15: #1 read tag files... INFO @ Tue, 02 Aug 2022 18:18:15: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 18:18:22: 4000000 INFO @ Tue, 02 Aug 2022 18:18:23: 1000000 INFO @ Tue, 02 Aug 2022 18:18:30: 2000000 INFO @ Tue, 02 Aug 2022 18:18:31: 5000000 INFO @ Tue, 02 Aug 2022 18:18:38: 3000000 INFO @ Tue, 02 Aug 2022 18:18:41: 6000000 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 18:18:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12175816/SRX12175816.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12175816/SRX12175816.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12175816/SRX12175816.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12175816/SRX12175816.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 18:18:45: #1 read tag files... INFO @ Tue, 02 Aug 2022 18:18:45: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 18:18:45: 4000000 INFO @ Tue, 02 Aug 2022 18:18:50: 7000000 INFO @ Tue, 02 Aug 2022 18:18:53: 5000000 INFO @ Tue, 02 Aug 2022 18:18:57: 1000000 INFO @ Tue, 02 Aug 2022 18:19:00: 8000000 INFO @ Tue, 02 Aug 2022 18:19:01: 6000000 INFO @ Tue, 02 Aug 2022 18:19:07: 2000000 INFO @ Tue, 02 Aug 2022 18:19:09: 7000000 INFO @ Tue, 02 Aug 2022 18:19:11: 9000000 INFO @ Tue, 02 Aug 2022 18:19:16: 8000000 INFO @ Tue, 02 Aug 2022 18:19:18: 3000000 INFO @ Tue, 02 Aug 2022 18:19:22: 10000000 INFO @ Tue, 02 Aug 2022 18:19:24: 9000000 INFO @ Tue, 02 Aug 2022 18:19:28: 4000000 INFO @ Tue, 02 Aug 2022 18:19:32: 10000000 INFO @ Tue, 02 Aug 2022 18:19:33: 11000000 INFO @ Tue, 02 Aug 2022 18:19:38: 5000000 INFO @ Tue, 02 Aug 2022 18:19:39: 11000000 INFO @ Tue, 02 Aug 2022 18:19:44: 12000000 INFO @ Tue, 02 Aug 2022 18:19:47: 12000000 INFO @ Tue, 02 Aug 2022 18:19:48: 6000000 INFO @ Tue, 02 Aug 2022 18:19:54: 13000000 INFO @ Tue, 02 Aug 2022 18:19:55: 13000000 INFO @ Tue, 02 Aug 2022 18:19:58: 7000000 INFO @ Tue, 02 Aug 2022 18:20:03: 14000000 INFO @ Tue, 02 Aug 2022 18:20:05: 14000000 INFO @ Tue, 02 Aug 2022 18:20:10: 8000000 INFO @ Tue, 02 Aug 2022 18:20:12: 15000000 INFO @ Tue, 02 Aug 2022 18:20:15: 15000000 INFO @ Tue, 02 Aug 2022 18:20:20: 16000000 INFO @ Tue, 02 Aug 2022 18:20:21: 9000000 INFO @ Tue, 02 Aug 2022 18:20:24: 16000000 INFO @ Tue, 02 Aug 2022 18:20:28: 17000000 INFO @ Tue, 02 Aug 2022 18:20:33: 10000000 INFO @ Tue, 02 Aug 2022 18:20:34: 17000000 INFO @ Tue, 02 Aug 2022 18:20:35: 18000000 INFO @ Tue, 02 Aug 2022 18:20:43: 19000000 INFO @ Tue, 02 Aug 2022 18:20:44: 18000000 INFO @ Tue, 02 Aug 2022 18:20:44: 11000000 INFO @ Tue, 02 Aug 2022 18:20:51: 20000000 INFO @ Tue, 02 Aug 2022 18:20:54: 19000000 INFO @ Tue, 02 Aug 2022 18:20:56: 12000000 INFO @ Tue, 02 Aug 2022 18:20:58: 21000000 INFO @ Tue, 02 Aug 2022 18:21:04: 20000000 INFO @ Tue, 02 Aug 2022 18:21:06: 22000000 INFO @ Tue, 02 Aug 2022 18:21:07: 13000000 INFO @ Tue, 02 Aug 2022 18:21:13: 23000000 INFO @ Tue, 02 Aug 2022 18:21:13: 21000000 INFO @ Tue, 02 Aug 2022 18:21:18: 14000000 INFO @ Tue, 02 Aug 2022 18:21:21: 24000000 INFO @ Tue, 02 Aug 2022 18:21:23: 22000000 INFO @ Tue, 02 Aug 2022 18:21:29: 25000000 INFO @ Tue, 02 Aug 2022 18:21:29: 15000000 INFO @ Tue, 02 Aug 2022 18:21:32: 23000000 INFO @ Tue, 02 Aug 2022 18:21:36: 26000000 INFO @ Tue, 02 Aug 2022 18:21:40: 16000000 INFO @ Tue, 02 Aug 2022 18:21:42: 24000000 INFO @ Tue, 02 Aug 2022 18:21:44: 27000000 INFO @ Tue, 02 Aug 2022 18:21:51: 28000000 INFO @ Tue, 02 Aug 2022 18:21:51: 17000000 INFO @ Tue, 02 Aug 2022 18:21:52: 25000000 INFO @ Tue, 02 Aug 2022 18:21:59: 29000000 INFO @ Tue, 02 Aug 2022 18:22:02: 26000000 INFO @ Tue, 02 Aug 2022 18:22:02: 18000000 INFO @ Tue, 02 Aug 2022 18:22:07: 30000000 INFO @ Tue, 02 Aug 2022 18:22:12: 27000000 INFO @ Tue, 02 Aug 2022 18:22:13: 19000000 INFO @ Tue, 02 Aug 2022 18:22:14: 31000000 INFO @ Tue, 02 Aug 2022 18:22:22: 28000000 INFO @ Tue, 02 Aug 2022 18:22:22: 32000000 INFO @ Tue, 02 Aug 2022 18:22:24: 20000000 INFO @ Tue, 02 Aug 2022 18:22:30: 33000000 INFO @ Tue, 02 Aug 2022 18:22:31: 29000000 INFO @ Tue, 02 Aug 2022 18:22:35: 21000000 INFO @ Tue, 02 Aug 2022 18:22:37: 34000000 INFO @ Tue, 02 Aug 2022 18:22:42: 30000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 18:22:45: 35000000 INFO @ Tue, 02 Aug 2022 18:22:46: 22000000 INFO @ Tue, 02 Aug 2022 18:22:52: 31000000 INFO @ Tue, 02 Aug 2022 18:22:52: 36000000 INFO @ Tue, 02 Aug 2022 18:22:54: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 18:22:54: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 18:22:54: #1 total tags in treatment: 12327606 INFO @ Tue, 02 Aug 2022 18:22:54: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 18:22:54: #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 18:22:55: #1 tags after filtering in treatment: 7045621 INFO @ Tue, 02 Aug 2022 18:22:55: #1 Redundant rate of treatment: 0.43 INFO @ Tue, 02 Aug 2022 18:22:55: #1 finished! INFO @ Tue, 02 Aug 2022 18:22:55: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 18:22:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 18:22:56: #2 number of paired peaks: 7131 INFO @ Tue, 02 Aug 2022 18:22:56: start model_add_line... INFO @ Tue, 02 Aug 2022 18:22:56: start X-correlation... INFO @ Tue, 02 Aug 2022 18:22:56: end of X-cor INFO @ Tue, 02 Aug 2022 18:22:56: #2 finished! INFO @ Tue, 02 Aug 2022 18:22:56: #2 predicted fragment length is 253 bps INFO @ Tue, 02 Aug 2022 18:22:56: #2 alternative fragment length(s) may be 253 bps INFO @ Tue, 02 Aug 2022 18:22:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12175816/SRX12175816.10_model.r WARNING @ Tue, 02 Aug 2022 18:22:56: #2 Since the d (253) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 18:22:56: #2 You may need to consider one of the other alternative d(s): 253 WARNING @ Tue, 02 Aug 2022 18:22:56: #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 18:22:56: #3 Call peaks... INFO @ Tue, 02 Aug 2022 18:22:56: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 18:22:57: 23000000 INFO @ Tue, 02 Aug 2022 18:23:01: 32000000 INFO @ Tue, 02 Aug 2022 18:23:07: 24000000 INFO @ Tue, 02 Aug 2022 18:23:11: 33000000 INFO @ Tue, 02 Aug 2022 18:23:15: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 18:23:18: 25000000 INFO @ Tue, 02 Aug 2022 18:23:21: 34000000 INFO @ Tue, 02 Aug 2022 18:23:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12175816/SRX12175816.10_peaks.xls INFO @ Tue, 02 Aug 2022 18:23:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12175816/SRX12175816.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 18:23:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12175816/SRX12175816.10_summits.bed INFO @ Tue, 02 Aug 2022 18:23:24: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (7104 records, 4 fields): 20 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 18:23:28: 26000000 INFO @ Tue, 02 Aug 2022 18:23:30: 35000000 INFO @ Tue, 02 Aug 2022 18:23:38: 27000000 INFO @ Tue, 02 Aug 2022 18:23:40: 36000000 INFO @ Tue, 02 Aug 2022 18:23:43: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 18:23:43: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 18:23:43: #1 total tags in treatment: 12327606 INFO @ Tue, 02 Aug 2022 18:23:43: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 18:23:43: #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 18:23:43: #1 tags after filtering in treatment: 7045621 INFO @ Tue, 02 Aug 2022 18:23:43: #1 Redundant rate of treatment: 0.43 INFO @ Tue, 02 Aug 2022 18:23:43: #1 finished! INFO @ Tue, 02 Aug 2022 18:23:43: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 18:23:43: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 18:23:44: #2 number of paired peaks: 7131 INFO @ Tue, 02 Aug 2022 18:23:44: start model_add_line... INFO @ Tue, 02 Aug 2022 18:23:44: start X-correlation... INFO @ Tue, 02 Aug 2022 18:23:44: end of X-cor INFO @ Tue, 02 Aug 2022 18:23:44: #2 finished! INFO @ Tue, 02 Aug 2022 18:23:44: #2 predicted fragment length is 253 bps INFO @ Tue, 02 Aug 2022 18:23:44: #2 alternative fragment length(s) may be 253 bps INFO @ Tue, 02 Aug 2022 18:23:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12175816/SRX12175816.05_model.r WARNING @ Tue, 02 Aug 2022 18:23:44: #2 Since the d (253) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 18:23:44: #2 You may need to consider one of the other alternative d(s): 253 WARNING @ Tue, 02 Aug 2022 18:23:44: #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 18:23:44: #3 Call peaks... INFO @ Tue, 02 Aug 2022 18:23:44: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 18:23:49: 28000000 INFO @ Tue, 02 Aug 2022 18:23:59: 29000000 INFO @ Tue, 02 Aug 2022 18:24:05: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 18:24:09: 30000000 INFO @ Tue, 02 Aug 2022 18:24:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12175816/SRX12175816.05_peaks.xls INFO @ Tue, 02 Aug 2022 18:24:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12175816/SRX12175816.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 18:24:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12175816/SRX12175816.05_summits.bed INFO @ Tue, 02 Aug 2022 18:24:14: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (9333 records, 4 fields): 54 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 18:24:20: 31000000 INFO @ Tue, 02 Aug 2022 18:24:29: 32000000 INFO @ Tue, 02 Aug 2022 18:24:40: 33000000 INFO @ Tue, 02 Aug 2022 18:24:50: 34000000 INFO @ Tue, 02 Aug 2022 18:25:00: 35000000 INFO @ Tue, 02 Aug 2022 18:25:10: 36000000 INFO @ Tue, 02 Aug 2022 18:25:12: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 18:25:12: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 18:25:12: #1 total tags in treatment: 12327606 INFO @ Tue, 02 Aug 2022 18:25:12: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 18:25:12: #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 18:25:13: #1 tags after filtering in treatment: 7045621 INFO @ Tue, 02 Aug 2022 18:25:13: #1 Redundant rate of treatment: 0.43 INFO @ Tue, 02 Aug 2022 18:25:13: #1 finished! INFO @ Tue, 02 Aug 2022 18:25:13: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 18:25:13: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 18:25:14: #2 number of paired peaks: 7131 INFO @ Tue, 02 Aug 2022 18:25:14: start model_add_line... INFO @ Tue, 02 Aug 2022 18:25:14: start X-correlation... INFO @ Tue, 02 Aug 2022 18:25:14: end of X-cor INFO @ Tue, 02 Aug 2022 18:25:14: #2 finished! INFO @ Tue, 02 Aug 2022 18:25:14: #2 predicted fragment length is 253 bps INFO @ Tue, 02 Aug 2022 18:25:14: #2 alternative fragment length(s) may be 253 bps INFO @ Tue, 02 Aug 2022 18:25:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12175816/SRX12175816.20_model.r WARNING @ Tue, 02 Aug 2022 18:25:14: #2 Since the d (253) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 18:25:14: #2 You may need to consider one of the other alternative d(s): 253 WARNING @ Tue, 02 Aug 2022 18:25:14: #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 18:25:14: #3 Call peaks... INFO @ Tue, 02 Aug 2022 18:25:14: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 18:25:35: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 18:25:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12175816/SRX12175816.20_peaks.xls INFO @ Tue, 02 Aug 2022 18:25:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12175816/SRX12175816.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 18:25:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12175816/SRX12175816.20_summits.bed INFO @ Tue, 02 Aug 2022 18:25:44: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (4663 records, 4 fields): 17 millis CompletedMACS2peakCalling