Job ID = 16436378 SRX = SRX12440702 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2022-08-02T02:28:44 prefetch.2.10.7: 1) Downloading 'SRR16155883'... 2022-08-02T02:28:44 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T02:34:41 prefetch.2.10.7: HTTPS download succeed 2022-08-02T02:34:41 prefetch.2.10.7: 1) 'SRR16155883' was downloaded successfully 2022-08-02T02:34:41 prefetch.2.10.7: 'SRR16155883' has 0 unresolved dependencies Read 45491764 spots for SRR16155883/SRR16155883.sra Written 45491764 spots for SRR16155883/SRR16155883.sra fastq に変換しました。 bowtie でマッピング中... Your job 16437624 ("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: 01:14:16 45491764 reads; of these: 45491764 (100.00%) were paired; of these: 34218148 (75.22%) aligned concordantly 0 times 10118284 (22.24%) aligned concordantly exactly 1 time 1155332 (2.54%) aligned concordantly >1 times ---- 34218148 pairs aligned concordantly 0 times; of these: 3792322 (11.08%) aligned discordantly 1 time ---- 30425826 pairs aligned 0 times concordantly or discordantly; of these: 60851652 mates make up the pairs; of these: 59012438 (96.98%) aligned 0 times 951449 (1.56%) aligned exactly 1 time 887765 (1.46%) aligned >1 times 35.14% overall alignment rate Time searching: 01:14:17 Overall time: 01:14:17 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] 3149443 / 14989830 = 0.2101 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 13:08:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12440702/SRX12440702.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12440702/SRX12440702.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12440702/SRX12440702.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12440702/SRX12440702.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 13:08:02: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:08:02: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:08:09: 1000000 INFO @ Tue, 02 Aug 2022 13:08:17: 2000000 INFO @ Tue, 02 Aug 2022 13:08:24: 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 13:08:31: 4000000 INFO @ Tue, 02 Aug 2022 13:08:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12440702/SRX12440702.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12440702/SRX12440702.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12440702/SRX12440702.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12440702/SRX12440702.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 13:08:32: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:08:32: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:08:39: 5000000 INFO @ Tue, 02 Aug 2022 13:08:39: 1000000 INFO @ Tue, 02 Aug 2022 13:08:46: 2000000 INFO @ Tue, 02 Aug 2022 13:08:46: 6000000 INFO @ Tue, 02 Aug 2022 13:08:53: 3000000 INFO @ Tue, 02 Aug 2022 13:08:53: 7000000 INFO @ Tue, 02 Aug 2022 13:09:00: 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 13:09:01: 8000000 INFO @ Tue, 02 Aug 2022 13:09:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12440702/SRX12440702.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12440702/SRX12440702.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12440702/SRX12440702.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12440702/SRX12440702.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 13:09:02: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:09:02: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:09:07: 5000000 INFO @ Tue, 02 Aug 2022 13:09:09: 9000000 INFO @ Tue, 02 Aug 2022 13:09:09: 1000000 INFO @ Tue, 02 Aug 2022 13:09:14: 6000000 INFO @ Tue, 02 Aug 2022 13:09:16: 2000000 INFO @ Tue, 02 Aug 2022 13:09:17: 10000000 INFO @ Tue, 02 Aug 2022 13:09:21: 7000000 INFO @ Tue, 02 Aug 2022 13:09:23: 3000000 INFO @ Tue, 02 Aug 2022 13:09:25: 11000000 INFO @ Tue, 02 Aug 2022 13:09:28: 8000000 INFO @ Tue, 02 Aug 2022 13:09:30: 4000000 INFO @ Tue, 02 Aug 2022 13:09:33: 12000000 INFO @ Tue, 02 Aug 2022 13:09:35: 9000000 INFO @ Tue, 02 Aug 2022 13:09:37: 5000000 INFO @ Tue, 02 Aug 2022 13:09:41: 13000000 INFO @ Tue, 02 Aug 2022 13:09:42: 10000000 INFO @ Tue, 02 Aug 2022 13:09:43: 6000000 INFO @ Tue, 02 Aug 2022 13:09:49: 14000000 INFO @ Tue, 02 Aug 2022 13:09:50: 11000000 INFO @ Tue, 02 Aug 2022 13:09:51: 7000000 INFO @ Tue, 02 Aug 2022 13:09:57: 15000000 INFO @ Tue, 02 Aug 2022 13:09:57: 12000000 INFO @ Tue, 02 Aug 2022 13:09:58: 8000000 INFO @ Tue, 02 Aug 2022 13:10:05: 9000000 INFO @ Tue, 02 Aug 2022 13:10:05: 13000000 INFO @ Tue, 02 Aug 2022 13:10:06: 16000000 INFO @ Tue, 02 Aug 2022 13:10:12: 10000000 INFO @ Tue, 02 Aug 2022 13:10:12: 14000000 INFO @ Tue, 02 Aug 2022 13:10:13: 17000000 INFO @ Tue, 02 Aug 2022 13:10:20: 11000000 INFO @ Tue, 02 Aug 2022 13:10:20: 15000000 INFO @ Tue, 02 Aug 2022 13:10:22: 18000000 INFO @ Tue, 02 Aug 2022 13:10:27: 16000000 INFO @ Tue, 02 Aug 2022 13:10:27: 12000000 INFO @ Tue, 02 Aug 2022 13:10:30: 19000000 INFO @ Tue, 02 Aug 2022 13:10:35: 17000000 INFO @ Tue, 02 Aug 2022 13:10:35: 13000000 INFO @ Tue, 02 Aug 2022 13:10:38: 20000000 INFO @ Tue, 02 Aug 2022 13:10:42: 14000000 INFO @ Tue, 02 Aug 2022 13:10:42: 18000000 INFO @ Tue, 02 Aug 2022 13:10:45: 21000000 INFO @ Tue, 02 Aug 2022 13:10:49: 15000000 INFO @ Tue, 02 Aug 2022 13:10:49: 19000000 INFO @ Tue, 02 Aug 2022 13:10:53: 22000000 INFO @ Tue, 02 Aug 2022 13:10:57: 16000000 INFO @ Tue, 02 Aug 2022 13:10:57: 20000000 INFO @ Tue, 02 Aug 2022 13:11:00: 23000000 INFO @ Tue, 02 Aug 2022 13:11:04: 17000000 INFO @ Tue, 02 Aug 2022 13:11:04: 21000000 INFO @ Tue, 02 Aug 2022 13:11:07: 24000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 13:11:11: 18000000 INFO @ Tue, 02 Aug 2022 13:11:12: 22000000 INFO @ Tue, 02 Aug 2022 13:11:15: 25000000 INFO @ Tue, 02 Aug 2022 13:11:19: 19000000 INFO @ Tue, 02 Aug 2022 13:11:20: 23000000 INFO @ Tue, 02 Aug 2022 13:11:20: #1 tag size is determined as 151 bps INFO @ Tue, 02 Aug 2022 13:11:20: #1 tag size = 151 INFO @ Tue, 02 Aug 2022 13:11:20: #1 total tags in treatment: 8913922 INFO @ Tue, 02 Aug 2022 13:11:20: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:11:20: #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 13:11:20: #1 tags after filtering in treatment: 6267684 INFO @ Tue, 02 Aug 2022 13:11:20: #1 Redundant rate of treatment: 0.30 INFO @ Tue, 02 Aug 2022 13:11:20: #1 finished! INFO @ Tue, 02 Aug 2022 13:11:20: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:11:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:11:21: #2 number of paired peaks: 5779 INFO @ Tue, 02 Aug 2022 13:11:21: start model_add_line... INFO @ Tue, 02 Aug 2022 13:11:21: start X-correlation... INFO @ Tue, 02 Aug 2022 13:11:21: end of X-cor INFO @ Tue, 02 Aug 2022 13:11:21: #2 finished! INFO @ Tue, 02 Aug 2022 13:11:21: #2 predicted fragment length is 218 bps INFO @ Tue, 02 Aug 2022 13:11:21: #2 alternative fragment length(s) may be 218 bps INFO @ Tue, 02 Aug 2022 13:11:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12440702/SRX12440702.05_model.r WARNING @ Tue, 02 Aug 2022 13:11:21: #2 Since the d (218) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 13:11:21: #2 You may need to consider one of the other alternative d(s): 218 WARNING @ Tue, 02 Aug 2022 13:11:21: #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 13:11:21: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:11:21: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 13:11:26: 20000000 INFO @ Tue, 02 Aug 2022 13:11:27: 24000000 INFO @ Tue, 02 Aug 2022 13:11:34: 21000000 INFO @ Tue, 02 Aug 2022 13:11:34: 25000000 INFO @ Tue, 02 Aug 2022 13:11:35: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 13:11:39: #1 tag size is determined as 151 bps INFO @ Tue, 02 Aug 2022 13:11:39: #1 tag size = 151 INFO @ Tue, 02 Aug 2022 13:11:39: #1 total tags in treatment: 8913922 INFO @ Tue, 02 Aug 2022 13:11:39: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:11:39: #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 13:11:40: #1 tags after filtering in treatment: 6267684 INFO @ Tue, 02 Aug 2022 13:11:40: #1 Redundant rate of treatment: 0.30 INFO @ Tue, 02 Aug 2022 13:11:40: #1 finished! INFO @ Tue, 02 Aug 2022 13:11:40: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:11:40: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:11:40: #2 number of paired peaks: 5779 INFO @ Tue, 02 Aug 2022 13:11:40: start model_add_line... INFO @ Tue, 02 Aug 2022 13:11:40: start X-correlation... INFO @ Tue, 02 Aug 2022 13:11:40: end of X-cor INFO @ Tue, 02 Aug 2022 13:11:40: #2 finished! INFO @ Tue, 02 Aug 2022 13:11:40: #2 predicted fragment length is 218 bps INFO @ Tue, 02 Aug 2022 13:11:40: #2 alternative fragment length(s) may be 218 bps INFO @ Tue, 02 Aug 2022 13:11:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12440702/SRX12440702.10_model.r WARNING @ Tue, 02 Aug 2022 13:11:40: #2 Since the d (218) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 13:11:40: #2 You may need to consider one of the other alternative d(s): 218 WARNING @ Tue, 02 Aug 2022 13:11:40: #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 13:11:40: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:11:40: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 13:11:41: 22000000 INFO @ Tue, 02 Aug 2022 13:11:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12440702/SRX12440702.05_peaks.xls INFO @ Tue, 02 Aug 2022 13:11:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12440702/SRX12440702.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:11:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12440702/SRX12440702.05_summits.bed INFO @ Tue, 02 Aug 2022 13:11:43: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (10437 records, 4 fields): 29 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 13:11:48: 23000000 INFO @ Tue, 02 Aug 2022 13:11:55: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 13:11:55: 24000000 INFO @ Tue, 02 Aug 2022 13:12:02: 25000000 INFO @ Tue, 02 Aug 2022 13:12:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12440702/SRX12440702.10_peaks.xls INFO @ Tue, 02 Aug 2022 13:12:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12440702/SRX12440702.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:12:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12440702/SRX12440702.10_summits.bed INFO @ Tue, 02 Aug 2022 13:12:03: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (7421 records, 4 fields): 55 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 13:12:07: #1 tag size is determined as 151 bps INFO @ Tue, 02 Aug 2022 13:12:07: #1 tag size = 151 INFO @ Tue, 02 Aug 2022 13:12:07: #1 total tags in treatment: 8913922 INFO @ Tue, 02 Aug 2022 13:12:07: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:12:07: #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 13:12:07: #1 tags after filtering in treatment: 6267684 INFO @ Tue, 02 Aug 2022 13:12:07: #1 Redundant rate of treatment: 0.30 INFO @ Tue, 02 Aug 2022 13:12:07: #1 finished! INFO @ Tue, 02 Aug 2022 13:12:07: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:12:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:12:08: #2 number of paired peaks: 5779 INFO @ Tue, 02 Aug 2022 13:12:08: start model_add_line... INFO @ Tue, 02 Aug 2022 13:12:08: start X-correlation... INFO @ Tue, 02 Aug 2022 13:12:08: end of X-cor INFO @ Tue, 02 Aug 2022 13:12:08: #2 finished! INFO @ Tue, 02 Aug 2022 13:12:08: #2 predicted fragment length is 218 bps INFO @ Tue, 02 Aug 2022 13:12:08: #2 alternative fragment length(s) may be 218 bps INFO @ Tue, 02 Aug 2022 13:12:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12440702/SRX12440702.20_model.r WARNING @ Tue, 02 Aug 2022 13:12:08: #2 Since the d (218) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 13:12:08: #2 You may need to consider one of the other alternative d(s): 218 WARNING @ Tue, 02 Aug 2022 13:12:08: #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 13:12:08: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:12:08: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 13:12:23: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 13:12:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12440702/SRX12440702.20_peaks.xls INFO @ Tue, 02 Aug 2022 13:12:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12440702/SRX12440702.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:12:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12440702/SRX12440702.20_summits.bed INFO @ Tue, 02 Aug 2022 13:12:30: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4208 records, 4 fields): 21 millis CompletedMACS2peakCalling