Job ID = 16436369 SRX = SRX12440700 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2022-08-02T02:26:14 prefetch.2.10.7: 1) Downloading 'SRR16155881'... 2022-08-02T02:26:14 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T02:30:28 prefetch.2.10.7: HTTPS download succeed 2022-08-02T02:30:28 prefetch.2.10.7: 1) 'SRR16155881' was downloaded successfully 2022-08-02T02:30:28 prefetch.2.10.7: 'SRR16155881' has 0 unresolved dependencies Read 36691105 spots for SRR16155881/SRR16155881.sra Written 36691105 spots for SRR16155881/SRR16155881.sra fastq に変換しました。 bowtie でマッピング中... Your job 16437899 ("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: 01:29:33 36691105 reads; of these: 36691105 (100.00%) were paired; of these: 26635328 (72.59%) aligned concordantly 0 times 8928362 (24.33%) aligned concordantly exactly 1 time 1127415 (3.07%) aligned concordantly >1 times ---- 26635328 pairs aligned concordantly 0 times; of these: 3102702 (11.65%) aligned discordantly 1 time ---- 23532626 pairs aligned 0 times concordantly or discordantly; of these: 47065252 mates make up the pairs; of these: 45592582 (96.87%) aligned 0 times 696045 (1.48%) aligned exactly 1 time 776625 (1.65%) aligned >1 times 37.87% overall alignment rate Time searching: 01:29:34 Overall time: 01:29:34 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 24 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] 2540734 / 13094692 = 0.1940 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 13:21:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12440700/SRX12440700.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12440700/SRX12440700.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12440700/SRX12440700.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12440700/SRX12440700.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 13:21:39: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:21:39: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:21:46: 1000000 INFO @ Tue, 02 Aug 2022 13:21:54: 2000000 INFO @ Tue, 02 Aug 2022 13:22:02: 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 13:22:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12440700/SRX12440700.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12440700/SRX12440700.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12440700/SRX12440700.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12440700/SRX12440700.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 13:22:08: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:22:08: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:22:10: 4000000 INFO @ Tue, 02 Aug 2022 13:22:16: 1000000 INFO @ Tue, 02 Aug 2022 13:22:18: 5000000 INFO @ Tue, 02 Aug 2022 13:22:24: 2000000 INFO @ Tue, 02 Aug 2022 13:22:26: 6000000 INFO @ Tue, 02 Aug 2022 13:22:31: 3000000 INFO @ Tue, 02 Aug 2022 13:22:34: 7000000 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 13:22:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12440700/SRX12440700.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12440700/SRX12440700.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12440700/SRX12440700.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12440700/SRX12440700.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 13:22:38: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:22:38: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:22:39: 4000000 INFO @ Tue, 02 Aug 2022 13:22:43: 8000000 INFO @ Tue, 02 Aug 2022 13:22:46: 1000000 INFO @ Tue, 02 Aug 2022 13:22:47: 5000000 INFO @ Tue, 02 Aug 2022 13:22:52: 9000000 INFO @ Tue, 02 Aug 2022 13:22:55: 6000000 INFO @ Tue, 02 Aug 2022 13:22:55: 2000000 INFO @ Tue, 02 Aug 2022 13:23:01: 10000000 INFO @ Tue, 02 Aug 2022 13:23:03: 7000000 INFO @ Tue, 02 Aug 2022 13:23:04: 3000000 INFO @ Tue, 02 Aug 2022 13:23:10: 11000000 INFO @ Tue, 02 Aug 2022 13:23:10: 8000000 INFO @ Tue, 02 Aug 2022 13:23:12: 4000000 INFO @ Tue, 02 Aug 2022 13:23:18: 9000000 INFO @ Tue, 02 Aug 2022 13:23:19: 12000000 INFO @ Tue, 02 Aug 2022 13:23:21: 5000000 INFO @ Tue, 02 Aug 2022 13:23:27: 10000000 INFO @ Tue, 02 Aug 2022 13:23:28: 13000000 INFO @ Tue, 02 Aug 2022 13:23:29: 6000000 INFO @ Tue, 02 Aug 2022 13:23:35: 11000000 INFO @ Tue, 02 Aug 2022 13:23:36: 14000000 INFO @ Tue, 02 Aug 2022 13:23:37: 7000000 INFO @ Tue, 02 Aug 2022 13:23:43: 12000000 INFO @ Tue, 02 Aug 2022 13:23:45: 15000000 INFO @ Tue, 02 Aug 2022 13:23:46: 8000000 INFO @ Tue, 02 Aug 2022 13:23:51: 13000000 INFO @ Tue, 02 Aug 2022 13:23:54: 16000000 INFO @ Tue, 02 Aug 2022 13:23:54: 9000000 INFO @ Tue, 02 Aug 2022 13:23:59: 14000000 INFO @ Tue, 02 Aug 2022 13:24:04: 17000000 INFO @ Tue, 02 Aug 2022 13:24:04: 10000000 INFO @ Tue, 02 Aug 2022 13:24:08: 15000000 INFO @ Tue, 02 Aug 2022 13:24:13: 18000000 INFO @ Tue, 02 Aug 2022 13:24:13: 11000000 INFO @ Tue, 02 Aug 2022 13:24:16: 16000000 INFO @ Tue, 02 Aug 2022 13:24:22: 19000000 INFO @ Tue, 02 Aug 2022 13:24:22: 12000000 INFO @ Tue, 02 Aug 2022 13:24:24: 17000000 INFO @ Tue, 02 Aug 2022 13:24:30: 20000000 INFO @ Tue, 02 Aug 2022 13:24:30: 13000000 INFO @ Tue, 02 Aug 2022 13:24:32: 18000000 INFO @ Tue, 02 Aug 2022 13:24:39: 21000000 INFO @ Tue, 02 Aug 2022 13:24:39: 14000000 INFO @ Tue, 02 Aug 2022 13:24:40: 19000000 INFO @ Tue, 02 Aug 2022 13:24:48: 22000000 INFO @ Tue, 02 Aug 2022 13:24:48: 15000000 INFO @ Tue, 02 Aug 2022 13:24:48: 20000000 INFO @ Tue, 02 Aug 2022 13:24:55: #1 tag size is determined as 151 bps INFO @ Tue, 02 Aug 2022 13:24:55: #1 tag size = 151 INFO @ Tue, 02 Aug 2022 13:24:55: #1 total tags in treatment: 8110974 INFO @ Tue, 02 Aug 2022 13:24:55: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:24:55: #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 13:24:55: #1 tags after filtering in treatment: 5716072 INFO @ Tue, 02 Aug 2022 13:24:55: #1 Redundant rate of treatment: 0.30 INFO @ Tue, 02 Aug 2022 13:24:55: #1 finished! INFO @ Tue, 02 Aug 2022 13:24:55: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:24:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:24:56: #2 number of paired peaks: 6130 INFO @ Tue, 02 Aug 2022 13:24:56: start model_add_line... INFO @ Tue, 02 Aug 2022 13:24:56: start X-correlation... INFO @ Tue, 02 Aug 2022 13:24:56: end of X-cor INFO @ Tue, 02 Aug 2022 13:24:56: #2 finished! INFO @ Tue, 02 Aug 2022 13:24:56: #2 predicted fragment length is 224 bps INFO @ Tue, 02 Aug 2022 13:24:56: #2 alternative fragment length(s) may be 224 bps INFO @ Tue, 02 Aug 2022 13:24:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12440700/SRX12440700.05_model.r INFO @ Tue, 02 Aug 2022 13:24:56: 21000000 WARNING @ Tue, 02 Aug 2022 13:24:56: #2 Since the d (224) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 13:24:56: #2 You may need to consider one of the other alternative d(s): 224 WARNING @ Tue, 02 Aug 2022 13:24:56: #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 13:24:56: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:24:56: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 13:24:58: 16000000 INFO @ Tue, 02 Aug 2022 13:25:05: 22000000 INFO @ Tue, 02 Aug 2022 13:25:07: 17000000 INFO @ Tue, 02 Aug 2022 13:25:10: #1 tag size is determined as 151 bps INFO @ Tue, 02 Aug 2022 13:25:10: #1 tag size = 151 INFO @ Tue, 02 Aug 2022 13:25:10: #1 total tags in treatment: 8110974 INFO @ Tue, 02 Aug 2022 13:25:10: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:25:10: #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 13:25:11: #1 tags after filtering in treatment: 5716072 INFO @ Tue, 02 Aug 2022 13:25:11: #1 Redundant rate of treatment: 0.30 INFO @ Tue, 02 Aug 2022 13:25:11: #1 finished! INFO @ Tue, 02 Aug 2022 13:25:11: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:25:11: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 13:25:11: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 13:25:11: #2 number of paired peaks: 6130 INFO @ Tue, 02 Aug 2022 13:25:11: start model_add_line... INFO @ Tue, 02 Aug 2022 13:25:12: start X-correlation... INFO @ Tue, 02 Aug 2022 13:25:12: end of X-cor INFO @ Tue, 02 Aug 2022 13:25:12: #2 finished! INFO @ Tue, 02 Aug 2022 13:25:12: #2 predicted fragment length is 224 bps INFO @ Tue, 02 Aug 2022 13:25:12: #2 alternative fragment length(s) may be 224 bps INFO @ Tue, 02 Aug 2022 13:25:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12440700/SRX12440700.10_model.r WARNING @ Tue, 02 Aug 2022 13:25:12: #2 Since the d (224) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 13:25:12: #2 You may need to consider one of the other alternative d(s): 224 WARNING @ Tue, 02 Aug 2022 13:25:12: #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 13:25:12: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:25:12: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 13:25:15: 18000000 INFO @ Tue, 02 Aug 2022 13:25:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12440700/SRX12440700.05_peaks.xls INFO @ Tue, 02 Aug 2022 13:25:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12440700/SRX12440700.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:25:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12440700/SRX12440700.05_summits.bed INFO @ Tue, 02 Aug 2022 13:25:19: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (10316 records, 4 fields): 30 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 13:25:24: 19000000 INFO @ Tue, 02 Aug 2022 13:25:25: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 13:25:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12440700/SRX12440700.10_peaks.xls INFO @ Tue, 02 Aug 2022 13:25:32: 20000000 INFO @ Tue, 02 Aug 2022 13:25:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12440700/SRX12440700.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:25:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12440700/SRX12440700.10_summits.bed INFO @ Tue, 02 Aug 2022 13:25:32: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (7337 records, 4 fields): 36 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 13:25:40: 21000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 13:25:48: 22000000 INFO @ Tue, 02 Aug 2022 13:25:54: #1 tag size is determined as 151 bps INFO @ Tue, 02 Aug 2022 13:25:54: #1 tag size = 151 INFO @ Tue, 02 Aug 2022 13:25:54: #1 total tags in treatment: 8110974 INFO @ Tue, 02 Aug 2022 13:25:54: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:25:54: #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 13:25:54: #1 tags after filtering in treatment: 5716072 INFO @ Tue, 02 Aug 2022 13:25:54: #1 Redundant rate of treatment: 0.30 INFO @ Tue, 02 Aug 2022 13:25:54: #1 finished! INFO @ Tue, 02 Aug 2022 13:25:54: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:25:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:25:55: #2 number of paired peaks: 6130 INFO @ Tue, 02 Aug 2022 13:25:55: start model_add_line... INFO @ Tue, 02 Aug 2022 13:25:55: start X-correlation... INFO @ Tue, 02 Aug 2022 13:25:55: end of X-cor INFO @ Tue, 02 Aug 2022 13:25:55: #2 finished! INFO @ Tue, 02 Aug 2022 13:25:55: #2 predicted fragment length is 224 bps INFO @ Tue, 02 Aug 2022 13:25:55: #2 alternative fragment length(s) may be 224 bps INFO @ Tue, 02 Aug 2022 13:25:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12440700/SRX12440700.20_model.r WARNING @ Tue, 02 Aug 2022 13:25:55: #2 Since the d (224) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 13:25:55: #2 You may need to consider one of the other alternative d(s): 224 WARNING @ Tue, 02 Aug 2022 13:25:55: #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 13:25:55: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:25:55: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 13:26:09: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 13:26:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12440700/SRX12440700.20_peaks.xls INFO @ Tue, 02 Aug 2022 13:26:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12440700/SRX12440700.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:26:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12440700/SRX12440700.20_summits.bed INFO @ Tue, 02 Aug 2022 13:26:17: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (4051 records, 4 fields): 29 millis CompletedMACS2peakCalling