Job ID = 16436986 SRX = SRX12119057 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 28814621 spots for SRR15827095/SRR15827095.sra Written 28814621 spots for SRR15827095/SRR15827095.sra fastq に変換しました。 bowtie でマッピング中... Your job 16437876 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:46:52 28814621 reads; of these: 28814621 (100.00%) were paired; of these: 19986966 (69.36%) aligned concordantly 0 times 7090759 (24.61%) aligned concordantly exactly 1 time 1736896 (6.03%) aligned concordantly >1 times ---- 19986966 pairs aligned concordantly 0 times; of these: 2356342 (11.79%) aligned discordantly 1 time ---- 17630624 pairs aligned 0 times concordantly or discordantly; of these: 35261248 mates make up the pairs; of these: 33110548 (93.90%) aligned 0 times 1057278 (3.00%) aligned exactly 1 time 1093422 (3.10%) aligned >1 times 42.55% overall alignment rate Time searching: 00:46:53 Overall time: 00:46:53 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 20 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] 1847111 / 11124856 = 0.1660 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 13:16:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12119057/SRX12119057.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12119057/SRX12119057.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12119057/SRX12119057.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12119057/SRX12119057.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 13:16:44: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:16:44: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:16:53: 1000000 INFO @ Tue, 02 Aug 2022 13:17:03: 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 13:17:13: 3000000 INFO @ Tue, 02 Aug 2022 13:17:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12119057/SRX12119057.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12119057/SRX12119057.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12119057/SRX12119057.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12119057/SRX12119057.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 13:17:13: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:17:13: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:17:23: 1000000 INFO @ Tue, 02 Aug 2022 13:17:24: 4000000 INFO @ Tue, 02 Aug 2022 13:17:35: 2000000 INFO @ Tue, 02 Aug 2022 13:17:35: 5000000 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 13:17:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12119057/SRX12119057.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12119057/SRX12119057.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12119057/SRX12119057.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12119057/SRX12119057.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 13:17:43: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:17:43: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:17:46: 3000000 INFO @ Tue, 02 Aug 2022 13:17:46: 6000000 INFO @ Tue, 02 Aug 2022 13:17:54: 1000000 INFO @ Tue, 02 Aug 2022 13:17:57: 4000000 INFO @ Tue, 02 Aug 2022 13:17:57: 7000000 INFO @ Tue, 02 Aug 2022 13:18:05: 2000000 INFO @ Tue, 02 Aug 2022 13:18:07: 5000000 INFO @ Tue, 02 Aug 2022 13:18:09: 8000000 INFO @ Tue, 02 Aug 2022 13:18:16: 3000000 INFO @ Tue, 02 Aug 2022 13:18:18: 6000000 INFO @ Tue, 02 Aug 2022 13:18:20: 9000000 INFO @ Tue, 02 Aug 2022 13:18:27: 4000000 INFO @ Tue, 02 Aug 2022 13:18:29: 7000000 INFO @ Tue, 02 Aug 2022 13:18:31: 10000000 INFO @ Tue, 02 Aug 2022 13:18:38: 5000000 INFO @ Tue, 02 Aug 2022 13:18:40: 8000000 INFO @ Tue, 02 Aug 2022 13:18:43: 11000000 INFO @ Tue, 02 Aug 2022 13:18:48: 6000000 INFO @ Tue, 02 Aug 2022 13:18:51: 9000000 INFO @ Tue, 02 Aug 2022 13:18:54: 12000000 INFO @ Tue, 02 Aug 2022 13:18:59: 7000000 INFO @ Tue, 02 Aug 2022 13:19:02: 10000000 INFO @ Tue, 02 Aug 2022 13:19:05: 13000000 INFO @ Tue, 02 Aug 2022 13:19:10: 8000000 INFO @ Tue, 02 Aug 2022 13:19:13: 11000000 INFO @ Tue, 02 Aug 2022 13:19:16: 14000000 INFO @ Tue, 02 Aug 2022 13:19:21: 9000000 INFO @ Tue, 02 Aug 2022 13:19:24: 12000000 INFO @ Tue, 02 Aug 2022 13:19:27: 15000000 INFO @ Tue, 02 Aug 2022 13:19:32: 10000000 INFO @ Tue, 02 Aug 2022 13:19:35: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 13:19:38: 16000000 INFO @ Tue, 02 Aug 2022 13:19:43: 11000000 INFO @ Tue, 02 Aug 2022 13:19:47: 14000000 INFO @ Tue, 02 Aug 2022 13:19:50: 17000000 INFO @ Tue, 02 Aug 2022 13:19:54: 12000000 INFO @ Tue, 02 Aug 2022 13:19:58: 15000000 INFO @ Tue, 02 Aug 2022 13:20:01: 18000000 INFO @ Tue, 02 Aug 2022 13:20:06: 13000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 13:20:09: 16000000 INFO @ Tue, 02 Aug 2022 13:20:12: 19000000 INFO @ Tue, 02 Aug 2022 13:20:18: 14000000 INFO @ Tue, 02 Aug 2022 13:20:20: 17000000 INFO @ Tue, 02 Aug 2022 13:20:24: 20000000 INFO @ Tue, 02 Aug 2022 13:20:29: 15000000 INFO @ Tue, 02 Aug 2022 13:20:31: 18000000 INFO @ Tue, 02 Aug 2022 13:20:33: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 13:20:33: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 13:20:33: #1 total tags in treatment: 7290876 INFO @ Tue, 02 Aug 2022 13:20:33: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:20:33: #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 13:20:33: #1 tags after filtering in treatment: 5598632 INFO @ Tue, 02 Aug 2022 13:20:33: #1 Redundant rate of treatment: 0.23 INFO @ Tue, 02 Aug 2022 13:20:33: #1 finished! INFO @ Tue, 02 Aug 2022 13:20:33: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:20:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:20:34: #2 number of paired peaks: 2881 INFO @ Tue, 02 Aug 2022 13:20:34: start model_add_line... INFO @ Tue, 02 Aug 2022 13:20:34: start X-correlation... INFO @ Tue, 02 Aug 2022 13:20:34: end of X-cor INFO @ Tue, 02 Aug 2022 13:20:34: #2 finished! INFO @ Tue, 02 Aug 2022 13:20:34: #2 predicted fragment length is 239 bps INFO @ Tue, 02 Aug 2022 13:20:34: #2 alternative fragment length(s) may be 239 bps INFO @ Tue, 02 Aug 2022 13:20:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12119057/SRX12119057.05_model.r WARNING @ Tue, 02 Aug 2022 13:20:34: #2 Since the d (239) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 13:20:34: #2 You may need to consider one of the other alternative d(s): 239 WARNING @ Tue, 02 Aug 2022 13:20:34: #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 13:20:34: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:20:34: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 13:20:41: 16000000 INFO @ Tue, 02 Aug 2022 13:20:42: 19000000 INFO @ Tue, 02 Aug 2022 13:20:47: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 13:20:52: 17000000 INFO @ Tue, 02 Aug 2022 13:20:53: 20000000 INFO @ Tue, 02 Aug 2022 13:20:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12119057/SRX12119057.05_peaks.xls INFO @ Tue, 02 Aug 2022 13:20:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12119057/SRX12119057.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:20:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12119057/SRX12119057.05_summits.bed INFO @ Tue, 02 Aug 2022 13:20:54: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (7722 records, 4 fields): 88 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 13:21:01: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 13:21:01: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 13:21:01: #1 total tags in treatment: 7290876 INFO @ Tue, 02 Aug 2022 13:21:01: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:21:01: #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 13:21:02: #1 tags after filtering in treatment: 5598632 INFO @ Tue, 02 Aug 2022 13:21:02: #1 Redundant rate of treatment: 0.23 INFO @ Tue, 02 Aug 2022 13:21:02: #1 finished! INFO @ Tue, 02 Aug 2022 13:21:02: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:21:02: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:21:02: #2 number of paired peaks: 2881 INFO @ Tue, 02 Aug 2022 13:21:02: start model_add_line... INFO @ Tue, 02 Aug 2022 13:21:02: start X-correlation... INFO @ Tue, 02 Aug 2022 13:21:02: end of X-cor INFO @ Tue, 02 Aug 2022 13:21:02: #2 finished! INFO @ Tue, 02 Aug 2022 13:21:02: #2 predicted fragment length is 239 bps INFO @ Tue, 02 Aug 2022 13:21:02: #2 alternative fragment length(s) may be 239 bps INFO @ Tue, 02 Aug 2022 13:21:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12119057/SRX12119057.10_model.r WARNING @ Tue, 02 Aug 2022 13:21:02: #2 Since the d (239) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 13:21:02: #2 You may need to consider one of the other alternative d(s): 239 WARNING @ Tue, 02 Aug 2022 13:21:02: #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 13:21:02: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:21:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 13:21:03: 18000000 INFO @ Tue, 02 Aug 2022 13:21:14: 19000000 INFO @ Tue, 02 Aug 2022 13:21:15: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 13:21:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12119057/SRX12119057.10_peaks.xls INFO @ Tue, 02 Aug 2022 13:21:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12119057/SRX12119057.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:21:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12119057/SRX12119057.10_summits.bed INFO @ Tue, 02 Aug 2022 13:21:22: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (4864 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 13:21:24: 20000000 INFO @ Tue, 02 Aug 2022 13:21:32: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 13:21:32: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 13:21:32: #1 total tags in treatment: 7290876 INFO @ Tue, 02 Aug 2022 13:21:32: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:21:32: #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 13:21:32: #1 tags after filtering in treatment: 5598632 INFO @ Tue, 02 Aug 2022 13:21:32: #1 Redundant rate of treatment: 0.23 INFO @ Tue, 02 Aug 2022 13:21:32: #1 finished! INFO @ Tue, 02 Aug 2022 13:21:32: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:21:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:21:33: #2 number of paired peaks: 2881 INFO @ Tue, 02 Aug 2022 13:21:33: start model_add_line... INFO @ Tue, 02 Aug 2022 13:21:33: start X-correlation... INFO @ Tue, 02 Aug 2022 13:21:33: end of X-cor INFO @ Tue, 02 Aug 2022 13:21:33: #2 finished! INFO @ Tue, 02 Aug 2022 13:21:33: #2 predicted fragment length is 239 bps INFO @ Tue, 02 Aug 2022 13:21:33: #2 alternative fragment length(s) may be 239 bps INFO @ Tue, 02 Aug 2022 13:21:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12119057/SRX12119057.20_model.r WARNING @ Tue, 02 Aug 2022 13:21:33: #2 Since the d (239) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 13:21:33: #2 You may need to consider one of the other alternative d(s): 239 WARNING @ Tue, 02 Aug 2022 13:21:33: #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 13:21:33: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:21:33: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 13:21:46: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 13:21:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12119057/SRX12119057.20_peaks.xls INFO @ Tue, 02 Aug 2022 13:21:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12119057/SRX12119057.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:21:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12119057/SRX12119057.20_summits.bed INFO @ Tue, 02 Aug 2022 13:21:53: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (2137 records, 4 fields): 21 millis CompletedMACS2peakCalling