Job ID = 16436379 SRX = SRX12440703 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2022-08-02T02:29:01 prefetch.2.10.7: 1) Downloading 'SRR16155884'... 2022-08-02T02:29:01 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T02:32:39 prefetch.2.10.7: HTTPS download succeed 2022-08-02T02:32:39 prefetch.2.10.7: 1) 'SRR16155884' was downloaded successfully 2022-08-02T02:32:39 prefetch.2.10.7: 'SRR16155884' has 0 unresolved dependencies Read 31011941 spots for SRR16155884/SRR16155884.sra Written 31011941 spots for SRR16155884/SRR16155884.sra fastq に変換しました。 bowtie でマッピング中... Your job 16437879 ("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: 01:25:53 31011941 reads; of these: 31011941 (100.00%) were paired; of these: 23136521 (74.61%) aligned concordantly 0 times 7140544 (23.03%) aligned concordantly exactly 1 time 734876 (2.37%) aligned concordantly >1 times ---- 23136521 pairs aligned concordantly 0 times; of these: 2739971 (11.84%) aligned discordantly 1 time ---- 20396550 pairs aligned 0 times concordantly or discordantly; of these: 40793100 mates make up the pairs; of these: 39513137 (96.86%) aligned 0 times 702815 (1.72%) aligned exactly 1 time 577148 (1.41%) aligned >1 times 36.29% overall alignment rate Time searching: 01:25:54 Overall time: 01:25:54 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] 1968944 / 10563402 = 0.1864 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 13:19:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12440703/SRX12440703.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12440703/SRX12440703.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12440703/SRX12440703.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12440703/SRX12440703.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 13:19:57: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:19:57: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:20:05: 1000000 INFO @ Tue, 02 Aug 2022 13:20:14: 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 13:20:22: 3000000 INFO @ Tue, 02 Aug 2022 13:20:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12440703/SRX12440703.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12440703/SRX12440703.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12440703/SRX12440703.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12440703/SRX12440703.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 13:20:26: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:20:26: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:20:31: 4000000 INFO @ Tue, 02 Aug 2022 13:20:35: 1000000 INFO @ Tue, 02 Aug 2022 13:20:41: 5000000 INFO @ Tue, 02 Aug 2022 13:20:44: 2000000 INFO @ Tue, 02 Aug 2022 13:20:50: 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 13:20:54: 3000000 INFO @ Tue, 02 Aug 2022 13:20:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12440703/SRX12440703.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12440703/SRX12440703.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12440703/SRX12440703.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12440703/SRX12440703.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 13:20:57: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:20:57: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:21:00: 7000000 INFO @ Tue, 02 Aug 2022 13:21:03: 4000000 INFO @ Tue, 02 Aug 2022 13:21:07: 1000000 INFO @ Tue, 02 Aug 2022 13:21:10: 8000000 INFO @ Tue, 02 Aug 2022 13:21:14: 5000000 INFO @ Tue, 02 Aug 2022 13:21:17: 2000000 INFO @ Tue, 02 Aug 2022 13:21:21: 9000000 INFO @ Tue, 02 Aug 2022 13:21:24: 6000000 INFO @ Tue, 02 Aug 2022 13:21:28: 3000000 INFO @ Tue, 02 Aug 2022 13:21:31: 10000000 INFO @ Tue, 02 Aug 2022 13:21:34: 7000000 INFO @ Tue, 02 Aug 2022 13:21:38: 4000000 INFO @ Tue, 02 Aug 2022 13:21:41: 11000000 INFO @ Tue, 02 Aug 2022 13:21:45: 8000000 INFO @ Tue, 02 Aug 2022 13:21:49: 5000000 INFO @ Tue, 02 Aug 2022 13:21:51: 12000000 INFO @ Tue, 02 Aug 2022 13:21:55: 9000000 INFO @ Tue, 02 Aug 2022 13:22:00: 6000000 INFO @ Tue, 02 Aug 2022 13:22:02: 13000000 INFO @ Tue, 02 Aug 2022 13:22:06: 10000000 INFO @ Tue, 02 Aug 2022 13:22:10: 7000000 INFO @ Tue, 02 Aug 2022 13:22:13: 14000000 INFO @ Tue, 02 Aug 2022 13:22:16: 11000000 INFO @ Tue, 02 Aug 2022 13:22:21: 8000000 INFO @ Tue, 02 Aug 2022 13:22:23: 15000000 INFO @ Tue, 02 Aug 2022 13:22:26: 12000000 INFO @ Tue, 02 Aug 2022 13:22:32: 9000000 INFO @ Tue, 02 Aug 2022 13:22:34: 16000000 INFO @ Tue, 02 Aug 2022 13:22:36: 13000000 INFO @ Tue, 02 Aug 2022 13:22:42: 10000000 INFO @ Tue, 02 Aug 2022 13:22:44: 17000000 INFO @ Tue, 02 Aug 2022 13:22:46: 14000000 INFO @ Tue, 02 Aug 2022 13:22:52: 11000000 INFO @ Tue, 02 Aug 2022 13:22:55: 18000000 INFO @ Tue, 02 Aug 2022 13:22:57: 15000000 INFO @ Tue, 02 Aug 2022 13:23:01: #1 tag size is determined as 151 bps INFO @ Tue, 02 Aug 2022 13:23:01: #1 tag size = 151 INFO @ Tue, 02 Aug 2022 13:23:01: #1 total tags in treatment: 6422047 INFO @ Tue, 02 Aug 2022 13:23:01: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:23:01: #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 13:23:02: #1 tags after filtering in treatment: 4640516 INFO @ Tue, 02 Aug 2022 13:23:02: #1 Redundant rate of treatment: 0.28 INFO @ Tue, 02 Aug 2022 13:23:02: #1 finished! INFO @ Tue, 02 Aug 2022 13:23:02: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:23:02: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:23:02: 12000000 INFO @ Tue, 02 Aug 2022 13:23:02: #2 number of paired peaks: 6712 INFO @ Tue, 02 Aug 2022 13:23:02: start model_add_line... INFO @ Tue, 02 Aug 2022 13:23:02: start X-correlation... INFO @ Tue, 02 Aug 2022 13:23:03: end of X-cor INFO @ Tue, 02 Aug 2022 13:23:03: #2 finished! INFO @ Tue, 02 Aug 2022 13:23:03: #2 predicted fragment length is 219 bps INFO @ Tue, 02 Aug 2022 13:23:03: #2 alternative fragment length(s) may be 219 bps INFO @ Tue, 02 Aug 2022 13:23:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12440703/SRX12440703.05_model.r WARNING @ Tue, 02 Aug 2022 13:23:03: #2 Since the d (219) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 13:23:03: #2 You may need to consider one of the other alternative d(s): 219 WARNING @ Tue, 02 Aug 2022 13:23:03: #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 13:23:03: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:23:03: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 13:23:07: 16000000 INFO @ Tue, 02 Aug 2022 13:23:11: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 13:23:16: 17000000 INFO @ Tue, 02 Aug 2022 13:23:17: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 13:23:21: 14000000 INFO @ Tue, 02 Aug 2022 13:23:26: 18000000 INFO @ Tue, 02 Aug 2022 13:23:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12440703/SRX12440703.05_peaks.xls INFO @ Tue, 02 Aug 2022 13:23:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12440703/SRX12440703.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:23:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12440703/SRX12440703.05_summits.bed INFO @ Tue, 02 Aug 2022 13:23:27: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (9937 records, 4 fields): 113 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 13:23:30: 15000000 INFO @ Tue, 02 Aug 2022 13:23:32: #1 tag size is determined as 151 bps INFO @ Tue, 02 Aug 2022 13:23:32: #1 tag size = 151 INFO @ Tue, 02 Aug 2022 13:23:32: #1 total tags in treatment: 6422047 INFO @ Tue, 02 Aug 2022 13:23:32: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:23:32: #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 13:23:32: #1 tags after filtering in treatment: 4640516 INFO @ Tue, 02 Aug 2022 13:23:32: #1 Redundant rate of treatment: 0.28 INFO @ Tue, 02 Aug 2022 13:23:32: #1 finished! INFO @ Tue, 02 Aug 2022 13:23:32: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:23:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:23:33: #2 number of paired peaks: 6712 INFO @ Tue, 02 Aug 2022 13:23:33: start model_add_line... INFO @ Tue, 02 Aug 2022 13:23:33: start X-correlation... INFO @ Tue, 02 Aug 2022 13:23:34: end of X-cor INFO @ Tue, 02 Aug 2022 13:23:34: #2 finished! INFO @ Tue, 02 Aug 2022 13:23:34: #2 predicted fragment length is 219 bps INFO @ Tue, 02 Aug 2022 13:23:34: #2 alternative fragment length(s) may be 219 bps INFO @ Tue, 02 Aug 2022 13:23:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12440703/SRX12440703.10_model.r WARNING @ Tue, 02 Aug 2022 13:23:34: #2 Since the d (219) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 13:23:34: #2 You may need to consider one of the other alternative d(s): 219 WARNING @ Tue, 02 Aug 2022 13:23:34: #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 13:23:34: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:23:34: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 13:23:38: 16000000 INFO @ Tue, 02 Aug 2022 13:23:47: 17000000 INFO @ Tue, 02 Aug 2022 13:23:48: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 13:23:55: 18000000 INFO @ Tue, 02 Aug 2022 13:23:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12440703/SRX12440703.10_peaks.xls INFO @ Tue, 02 Aug 2022 13:23:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12440703/SRX12440703.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:23:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12440703/SRX12440703.10_summits.bed INFO @ Tue, 02 Aug 2022 13:23:57: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (6854 records, 4 fields): 79 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 13:24:01: #1 tag size is determined as 151 bps INFO @ Tue, 02 Aug 2022 13:24:01: #1 tag size = 151 INFO @ Tue, 02 Aug 2022 13:24:01: #1 total tags in treatment: 6422047 INFO @ Tue, 02 Aug 2022 13:24:01: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:24:01: #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 13:24:01: #1 tags after filtering in treatment: 4640516 INFO @ Tue, 02 Aug 2022 13:24:01: #1 Redundant rate of treatment: 0.28 INFO @ Tue, 02 Aug 2022 13:24:01: #1 finished! INFO @ Tue, 02 Aug 2022 13:24:01: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:24:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:24:02: #2 number of paired peaks: 6712 INFO @ Tue, 02 Aug 2022 13:24:02: start model_add_line... INFO @ Tue, 02 Aug 2022 13:24:02: start X-correlation... INFO @ Tue, 02 Aug 2022 13:24:03: end of X-cor INFO @ Tue, 02 Aug 2022 13:24:03: #2 finished! INFO @ Tue, 02 Aug 2022 13:24:03: #2 predicted fragment length is 219 bps INFO @ Tue, 02 Aug 2022 13:24:03: #2 alternative fragment length(s) may be 219 bps INFO @ Tue, 02 Aug 2022 13:24:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12440703/SRX12440703.20_model.r WARNING @ Tue, 02 Aug 2022 13:24:03: #2 Since the d (219) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 13:24:03: #2 You may need to consider one of the other alternative d(s): 219 WARNING @ Tue, 02 Aug 2022 13:24:03: #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 13:24:03: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:24:03: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 13:24:19: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 13:24:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12440703/SRX12440703.20_peaks.xls INFO @ Tue, 02 Aug 2022 13:24:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12440703/SRX12440703.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:24:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12440703/SRX12440703.20_summits.bed INFO @ Tue, 02 Aug 2022 13:24:29: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (3681 records, 4 fields): 91 millis CompletedMACS2peakCalling