Job ID = 16437217 SRX = SRX12119062 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 36722255 spots for SRR15827100/SRR15827100.sra Written 36722255 spots for SRR15827100/SRR15827100.sra fastq に変換しました。 bowtie でマッピング中... Your job 16438589 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:01 Multiseed full-index search: 01:30:59 36722255 reads; of these: 36722255 (100.00%) were paired; of these: 22994781 (62.62%) aligned concordantly 0 times 11743560 (31.98%) aligned concordantly exactly 1 time 1983914 (5.40%) aligned concordantly >1 times ---- 22994781 pairs aligned concordantly 0 times; of these: 3930197 (17.09%) aligned discordantly 1 time ---- 19064584 pairs aligned 0 times concordantly or discordantly; of these: 38129168 mates make up the pairs; of these: 35256771 (92.47%) aligned 0 times 1649331 (4.33%) aligned exactly 1 time 1223066 (3.21%) aligned >1 times 52.00% overall alignment rate Time searching: 01:31:00 Overall time: 01:31:00 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] 3740324 / 17563298 = 0.2130 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 14:20:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12119062/SRX12119062.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12119062/SRX12119062.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12119062/SRX12119062.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12119062/SRX12119062.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 14:20:46: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:20:46: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:20:59: 1000000 INFO @ Tue, 02 Aug 2022 14:21:11: 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 14:21:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12119062/SRX12119062.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12119062/SRX12119062.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12119062/SRX12119062.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12119062/SRX12119062.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 14:21:16: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:21:16: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:21:25: 3000000 INFO @ Tue, 02 Aug 2022 14:21:27: 1000000 INFO @ Tue, 02 Aug 2022 14:21:38: 2000000 INFO @ Tue, 02 Aug 2022 14:21:38: 4000000 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 14:21:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12119062/SRX12119062.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12119062/SRX12119062.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12119062/SRX12119062.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12119062/SRX12119062.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 14:21:47: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:21:47: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:21:50: 3000000 INFO @ Tue, 02 Aug 2022 14:21:53: 5000000 INFO @ Tue, 02 Aug 2022 14:22:01: 1000000 INFO @ Tue, 02 Aug 2022 14:22:02: 4000000 INFO @ Tue, 02 Aug 2022 14:22:07: 6000000 INFO @ Tue, 02 Aug 2022 14:22:15: 5000000 INFO @ Tue, 02 Aug 2022 14:22:15: 2000000 INFO @ Tue, 02 Aug 2022 14:22:19: 7000000 INFO @ Tue, 02 Aug 2022 14:22:27: 6000000 INFO @ Tue, 02 Aug 2022 14:22:30: 3000000 INFO @ Tue, 02 Aug 2022 14:22:30: 8000000 INFO @ Tue, 02 Aug 2022 14:22:38: 7000000 INFO @ Tue, 02 Aug 2022 14:22:42: 9000000 INFO @ Tue, 02 Aug 2022 14:22:45: 4000000 INFO @ Tue, 02 Aug 2022 14:22:50: 8000000 INFO @ Tue, 02 Aug 2022 14:22:53: 10000000 INFO @ Tue, 02 Aug 2022 14:22:59: 5000000 INFO @ Tue, 02 Aug 2022 14:23:01: 9000000 INFO @ Tue, 02 Aug 2022 14:23:05: 11000000 INFO @ Tue, 02 Aug 2022 14:23:12: 10000000 INFO @ Tue, 02 Aug 2022 14:23:14: 6000000 INFO @ Tue, 02 Aug 2022 14:23:16: 12000000 INFO @ Tue, 02 Aug 2022 14:23:24: 11000000 INFO @ Tue, 02 Aug 2022 14:23:28: 7000000 INFO @ Tue, 02 Aug 2022 14:23:28: 13000000 INFO @ Tue, 02 Aug 2022 14:23:35: 12000000 INFO @ Tue, 02 Aug 2022 14:23:40: 14000000 INFO @ Tue, 02 Aug 2022 14:23:42: 8000000 INFO @ Tue, 02 Aug 2022 14:23:48: 13000000 INFO @ Tue, 02 Aug 2022 14:23:51: 15000000 INFO @ Tue, 02 Aug 2022 14:23:56: 9000000 INFO @ Tue, 02 Aug 2022 14:23:59: 14000000 INFO @ Tue, 02 Aug 2022 14:24:03: 16000000 INFO @ Tue, 02 Aug 2022 14:24:10: 10000000 INFO @ Tue, 02 Aug 2022 14:24:10: 15000000 INFO @ Tue, 02 Aug 2022 14:24:15: 17000000 INFO @ Tue, 02 Aug 2022 14:24:22: 16000000 INFO @ Tue, 02 Aug 2022 14:24:24: 11000000 INFO @ Tue, 02 Aug 2022 14:24:26: 18000000 INFO @ Tue, 02 Aug 2022 14:24:33: 17000000 INFO @ Tue, 02 Aug 2022 14:24:37: 19000000 INFO @ Tue, 02 Aug 2022 14:24:38: 12000000 INFO @ Tue, 02 Aug 2022 14:24:44: 18000000 INFO @ Tue, 02 Aug 2022 14:24:49: 20000000 INFO @ Tue, 02 Aug 2022 14:24:51: 13000000 INFO @ Tue, 02 Aug 2022 14:24:56: 19000000 INFO @ Tue, 02 Aug 2022 14:25:01: 21000000 INFO @ Tue, 02 Aug 2022 14:25:05: 14000000 INFO @ Tue, 02 Aug 2022 14:25:07: 20000000 INFO @ Tue, 02 Aug 2022 14:25:13: 22000000 INFO @ Tue, 02 Aug 2022 14:25:18: 15000000 INFO @ Tue, 02 Aug 2022 14:25:19: 21000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 14:25:24: 23000000 INFO @ Tue, 02 Aug 2022 14:25:31: 22000000 INFO @ Tue, 02 Aug 2022 14:25:32: 16000000 INFO @ Tue, 02 Aug 2022 14:25:36: 24000000 INFO @ Tue, 02 Aug 2022 14:25:42: 23000000 INFO @ Tue, 02 Aug 2022 14:25:45: 17000000 INFO @ Tue, 02 Aug 2022 14:25:48: 25000000 INFO @ Tue, 02 Aug 2022 14:25:54: 24000000 INFO @ Tue, 02 Aug 2022 14:25:58: 18000000 INFO @ Tue, 02 Aug 2022 14:26:00: 26000000 INFO @ Tue, 02 Aug 2022 14:26:06: 25000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 14:26:12: 27000000 INFO @ Tue, 02 Aug 2022 14:26:12: 19000000 INFO @ Tue, 02 Aug 2022 14:26:17: 26000000 INFO @ Tue, 02 Aug 2022 14:26:23: 28000000 INFO @ Tue, 02 Aug 2022 14:26:26: 20000000 INFO @ Tue, 02 Aug 2022 14:26:29: 27000000 INFO @ Tue, 02 Aug 2022 14:26:34: 29000000 INFO @ Tue, 02 Aug 2022 14:26:40: 28000000 INFO @ Tue, 02 Aug 2022 14:26:41: 21000000 INFO @ Tue, 02 Aug 2022 14:26:46: 30000000 INFO @ Tue, 02 Aug 2022 14:26:51: 29000000 INFO @ Tue, 02 Aug 2022 14:26:54: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 14:26:54: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 14:26:54: #1 total tags in treatment: 10703678 INFO @ Tue, 02 Aug 2022 14:26:54: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:26:54: #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 14:26:54: #1 tags after filtering in treatment: 6941625 INFO @ Tue, 02 Aug 2022 14:26:54: #1 Redundant rate of treatment: 0.35 INFO @ Tue, 02 Aug 2022 14:26:54: #1 finished! INFO @ Tue, 02 Aug 2022 14:26:54: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:26:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:26:54: 22000000 INFO @ Tue, 02 Aug 2022 14:26:55: #2 number of paired peaks: 4597 INFO @ Tue, 02 Aug 2022 14:26:55: start model_add_line... INFO @ Tue, 02 Aug 2022 14:26:55: start X-correlation... INFO @ Tue, 02 Aug 2022 14:26:55: end of X-cor INFO @ Tue, 02 Aug 2022 14:26:55: #2 finished! INFO @ Tue, 02 Aug 2022 14:26:55: #2 predicted fragment length is 227 bps INFO @ Tue, 02 Aug 2022 14:26:55: #2 alternative fragment length(s) may be 227 bps INFO @ Tue, 02 Aug 2022 14:26:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12119062/SRX12119062.05_model.r WARNING @ Tue, 02 Aug 2022 14:26:55: #2 Since the d (227) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:26:55: #2 You may need to consider one of the other alternative d(s): 227 WARNING @ Tue, 02 Aug 2022 14:26:55: #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 14:26:55: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:26:55: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:27:02: 30000000 INFO @ Tue, 02 Aug 2022 14:27:07: 23000000 INFO @ Tue, 02 Aug 2022 14:27:10: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 14:27:10: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 14:27:10: #1 total tags in treatment: 10703678 INFO @ Tue, 02 Aug 2022 14:27:10: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:27:10: #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 14:27:10: #1 tags after filtering in treatment: 6941625 INFO @ Tue, 02 Aug 2022 14:27:10: #1 Redundant rate of treatment: 0.35 INFO @ Tue, 02 Aug 2022 14:27:10: #1 finished! INFO @ Tue, 02 Aug 2022 14:27:10: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:27:10: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:27:11: #2 number of paired peaks: 4597 INFO @ Tue, 02 Aug 2022 14:27:11: start model_add_line... INFO @ Tue, 02 Aug 2022 14:27:11: start X-correlation... INFO @ Tue, 02 Aug 2022 14:27:11: end of X-cor INFO @ Tue, 02 Aug 2022 14:27:11: #2 finished! INFO @ Tue, 02 Aug 2022 14:27:11: #2 predicted fragment length is 227 bps INFO @ Tue, 02 Aug 2022 14:27:11: #2 alternative fragment length(s) may be 227 bps INFO @ Tue, 02 Aug 2022 14:27:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12119062/SRX12119062.10_model.r WARNING @ Tue, 02 Aug 2022 14:27:11: #2 Since the d (227) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:27:11: #2 You may need to consider one of the other alternative d(s): 227 WARNING @ Tue, 02 Aug 2022 14:27:11: #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 14:27:11: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:27:11: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:27:14: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:27:19: 24000000 INFO @ Tue, 02 Aug 2022 14:27:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12119062/SRX12119062.05_peaks.xls INFO @ Tue, 02 Aug 2022 14:27:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12119062/SRX12119062.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:27:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12119062/SRX12119062.05_summits.bed INFO @ Tue, 02 Aug 2022 14:27:23: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (8683 records, 4 fields): 49 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:27:29: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:27:31: 25000000 INFO @ Tue, 02 Aug 2022 14:27:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12119062/SRX12119062.10_peaks.xls INFO @ Tue, 02 Aug 2022 14:27:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12119062/SRX12119062.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:27:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12119062/SRX12119062.10_summits.bed INFO @ Tue, 02 Aug 2022 14:27:39: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (6366 records, 4 fields): 29 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:27:42: 26000000 INFO @ Tue, 02 Aug 2022 14:27:55: 27000000 INFO @ Tue, 02 Aug 2022 14:28:05: 28000000 INFO @ Tue, 02 Aug 2022 14:28:15: 29000000 INFO @ Tue, 02 Aug 2022 14:28:25: 30000000 INFO @ Tue, 02 Aug 2022 14:28:33: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 14:28:33: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 14:28:33: #1 total tags in treatment: 10703678 INFO @ Tue, 02 Aug 2022 14:28:33: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:28:33: #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 14:28:33: #1 tags after filtering in treatment: 6941625 INFO @ Tue, 02 Aug 2022 14:28:33: #1 Redundant rate of treatment: 0.35 INFO @ Tue, 02 Aug 2022 14:28:33: #1 finished! INFO @ Tue, 02 Aug 2022 14:28:33: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:28:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:28:34: #2 number of paired peaks: 4597 INFO @ Tue, 02 Aug 2022 14:28:34: start model_add_line... INFO @ Tue, 02 Aug 2022 14:28:34: start X-correlation... INFO @ Tue, 02 Aug 2022 14:28:34: end of X-cor INFO @ Tue, 02 Aug 2022 14:28:34: #2 finished! INFO @ Tue, 02 Aug 2022 14:28:34: #2 predicted fragment length is 227 bps INFO @ Tue, 02 Aug 2022 14:28:34: #2 alternative fragment length(s) may be 227 bps INFO @ Tue, 02 Aug 2022 14:28:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12119062/SRX12119062.20_model.r WARNING @ Tue, 02 Aug 2022 14:28:34: #2 Since the d (227) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:28:34: #2 You may need to consider one of the other alternative d(s): 227 WARNING @ Tue, 02 Aug 2022 14:28:34: #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 14:28:34: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:28:34: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:28:52: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:29:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12119062/SRX12119062.20_peaks.xls INFO @ Tue, 02 Aug 2022 14:29:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12119062/SRX12119062.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:29:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12119062/SRX12119062.20_summits.bed INFO @ Tue, 02 Aug 2022 14:29:00: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (3758 records, 4 fields): 22 millis CompletedMACS2peakCalling