Job ID = 6498446 SRX = SRX511344 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-25T23:43:52 prefetch.2.10.7: 1) Downloading 'SRR1217606'... 2020-06-25T23:43:52 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T23:45:53 prefetch.2.10.7: HTTPS download succeed 2020-06-25T23:45:53 prefetch.2.10.7: 1) 'SRR1217606' was downloaded successfully Read 12450579 spots for SRR1217606/SRR1217606.sra Written 12450579 spots for SRR1217606/SRR1217606.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:20:10 12450579 reads; of these: 12450579 (100.00%) were paired; of these: 2352940 (18.90%) aligned concordantly 0 times 7649180 (61.44%) aligned concordantly exactly 1 time 2448459 (19.67%) aligned concordantly >1 times ---- 2352940 pairs aligned concordantly 0 times; of these: 6780 (0.29%) aligned discordantly 1 time ---- 2346160 pairs aligned 0 times concordantly or discordantly; of these: 4692320 mates make up the pairs; of these: 4439317 (94.61%) aligned 0 times 181763 (3.87%) aligned exactly 1 time 71240 (1.52%) aligned >1 times 82.17% overall alignment rate Time searching: 00:20:10 Overall time: 00:20:10 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 12 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] 1636146 / 10097389 = 0.1620 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 26 Jun 2020 09:13:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX511344/SRX511344.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX511344/SRX511344.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX511344/SRX511344.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX511344/SRX511344.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 @ Fri, 26 Jun 2020 09:13:02: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:13:02: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:13:08: 1000000 INFO @ Fri, 26 Jun 2020 09:13:14: 2000000 INFO @ Fri, 26 Jun 2020 09:13:19: 3000000 INFO @ Fri, 26 Jun 2020 09:13:25: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 26 Jun 2020 09:13:31: 5000000 INFO @ Fri, 26 Jun 2020 09:13:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX511344/SRX511344.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX511344/SRX511344.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX511344/SRX511344.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX511344/SRX511344.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 @ Fri, 26 Jun 2020 09:13:32: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:13:32: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:13:37: 6000000 INFO @ Fri, 26 Jun 2020 09:13:39: 1000000 INFO @ Fri, 26 Jun 2020 09:13:44: 7000000 INFO @ Fri, 26 Jun 2020 09:13:45: 2000000 INFO @ Fri, 26 Jun 2020 09:13:51: 8000000 INFO @ Fri, 26 Jun 2020 09:13:51: 3000000 INFO @ Fri, 26 Jun 2020 09:13:57: 4000000 INFO @ Fri, 26 Jun 2020 09:13:57: 9000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 26 Jun 2020 09:14:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX511344/SRX511344.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX511344/SRX511344.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX511344/SRX511344.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX511344/SRX511344.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 @ Fri, 26 Jun 2020 09:14:02: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:14:02: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:14:04: 5000000 INFO @ Fri, 26 Jun 2020 09:14:04: 10000000 INFO @ Fri, 26 Jun 2020 09:14:09: 1000000 INFO @ Fri, 26 Jun 2020 09:14:10: 6000000 INFO @ Fri, 26 Jun 2020 09:14:11: 11000000 INFO @ Fri, 26 Jun 2020 09:14:15: 2000000 INFO @ Fri, 26 Jun 2020 09:14:17: 7000000 INFO @ Fri, 26 Jun 2020 09:14:17: 12000000 INFO @ Fri, 26 Jun 2020 09:14:21: 3000000 INFO @ Fri, 26 Jun 2020 09:14:24: 8000000 INFO @ Fri, 26 Jun 2020 09:14:24: 13000000 INFO @ Fri, 26 Jun 2020 09:14:28: 4000000 INFO @ Fri, 26 Jun 2020 09:14:31: 9000000 INFO @ Fri, 26 Jun 2020 09:14:31: 14000000 INFO @ Fri, 26 Jun 2020 09:14:35: 5000000 INFO @ Fri, 26 Jun 2020 09:14:37: 10000000 INFO @ Fri, 26 Jun 2020 09:14:38: 15000000 INFO @ Fri, 26 Jun 2020 09:14:41: 6000000 INFO @ Fri, 26 Jun 2020 09:14:44: 11000000 INFO @ Fri, 26 Jun 2020 09:14:45: 16000000 INFO @ Fri, 26 Jun 2020 09:14:48: 7000000 INFO @ Fri, 26 Jun 2020 09:14:51: 12000000 INFO @ Fri, 26 Jun 2020 09:14:51: 17000000 INFO @ Fri, 26 Jun 2020 09:14:53: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 09:14:53: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 09:14:53: #1 total tags in treatment: 8462235 INFO @ Fri, 26 Jun 2020 09:14:53: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:14:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 09:14:53: #1 tags after filtering in treatment: 7820732 INFO @ Fri, 26 Jun 2020 09:14:53: #1 Redundant rate of treatment: 0.08 INFO @ Fri, 26 Jun 2020 09:14:53: #1 finished! INFO @ Fri, 26 Jun 2020 09:14:53: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:14:53: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:14:53: #2 number of paired peaks: 1142 INFO @ Fri, 26 Jun 2020 09:14:53: start model_add_line... INFO @ Fri, 26 Jun 2020 09:14:53: start X-correlation... INFO @ Fri, 26 Jun 2020 09:14:53: end of X-cor INFO @ Fri, 26 Jun 2020 09:14:53: #2 finished! INFO @ Fri, 26 Jun 2020 09:14:53: #2 predicted fragment length is 150 bps INFO @ Fri, 26 Jun 2020 09:14:53: #2 alternative fragment length(s) may be 150 bps INFO @ Fri, 26 Jun 2020 09:14:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX511344/SRX511344.05_model.r INFO @ Fri, 26 Jun 2020 09:14:53: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:14:53: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:14:55: 8000000 INFO @ Fri, 26 Jun 2020 09:14:58: 13000000 INFO @ Fri, 26 Jun 2020 09:15:02: 9000000 INFO @ Fri, 26 Jun 2020 09:15:05: 14000000 INFO @ Fri, 26 Jun 2020 09:15:08: 10000000 INFO @ Fri, 26 Jun 2020 09:15:11: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:15:12: 15000000 INFO @ Fri, 26 Jun 2020 09:15:15: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 09:15:18: 16000000 INFO @ Fri, 26 Jun 2020 09:15:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX511344/SRX511344.05_peaks.xls INFO @ Fri, 26 Jun 2020 09:15:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX511344/SRX511344.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:15:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX511344/SRX511344.05_summits.bed INFO @ Fri, 26 Jun 2020 09:15:20: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (8079 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 09:15:22: 12000000 INFO @ Fri, 26 Jun 2020 09:15:25: 17000000 INFO @ Fri, 26 Jun 2020 09:15:26: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 09:15:26: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 09:15:26: #1 total tags in treatment: 8462235 INFO @ Fri, 26 Jun 2020 09:15:26: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:15:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 09:15:26: #1 tags after filtering in treatment: 7820732 INFO @ Fri, 26 Jun 2020 09:15:26: #1 Redundant rate of treatment: 0.08 INFO @ Fri, 26 Jun 2020 09:15:26: #1 finished! INFO @ Fri, 26 Jun 2020 09:15:26: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:15:26: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:15:27: #2 number of paired peaks: 1142 INFO @ Fri, 26 Jun 2020 09:15:27: start model_add_line... INFO @ Fri, 26 Jun 2020 09:15:27: start X-correlation... INFO @ Fri, 26 Jun 2020 09:15:27: end of X-cor INFO @ Fri, 26 Jun 2020 09:15:27: #2 finished! INFO @ Fri, 26 Jun 2020 09:15:27: #2 predicted fragment length is 150 bps INFO @ Fri, 26 Jun 2020 09:15:27: #2 alternative fragment length(s) may be 150 bps INFO @ Fri, 26 Jun 2020 09:15:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX511344/SRX511344.10_model.r INFO @ Fri, 26 Jun 2020 09:15:27: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:15:27: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:15:28: 13000000 INFO @ Fri, 26 Jun 2020 09:15:35: 14000000 INFO @ Fri, 26 Jun 2020 09:15:41: 15000000 INFO @ Fri, 26 Jun 2020 09:15:44: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:15:47: 16000000 BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 09:15:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX511344/SRX511344.10_peaks.xls INFO @ Fri, 26 Jun 2020 09:15:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX511344/SRX511344.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:15:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX511344/SRX511344.10_summits.bed INFO @ Fri, 26 Jun 2020 09:15:53: Done! pass1 - making usageList (15 chroms): 1 millis INFO @ Fri, 26 Jun 2020 09:15:53: 17000000 pass2 - checking and writing primary data (4802 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 09:15:54: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 09:15:54: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 09:15:54: #1 total tags in treatment: 8462235 INFO @ Fri, 26 Jun 2020 09:15:54: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:15:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 09:15:55: #1 tags after filtering in treatment: 7820732 INFO @ Fri, 26 Jun 2020 09:15:55: #1 Redundant rate of treatment: 0.08 INFO @ Fri, 26 Jun 2020 09:15:55: #1 finished! INFO @ Fri, 26 Jun 2020 09:15:55: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:15:55: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:15:55: #2 number of paired peaks: 1142 INFO @ Fri, 26 Jun 2020 09:15:55: start model_add_line... INFO @ Fri, 26 Jun 2020 09:15:55: start X-correlation... INFO @ Fri, 26 Jun 2020 09:15:55: end of X-cor INFO @ Fri, 26 Jun 2020 09:15:55: #2 finished! INFO @ Fri, 26 Jun 2020 09:15:55: #2 predicted fragment length is 150 bps INFO @ Fri, 26 Jun 2020 09:15:55: #2 alternative fragment length(s) may be 150 bps INFO @ Fri, 26 Jun 2020 09:15:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX511344/SRX511344.20_model.r INFO @ Fri, 26 Jun 2020 09:15:55: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:15:55: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:16:13: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:16:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX511344/SRX511344.20_peaks.xls INFO @ Fri, 26 Jun 2020 09:16:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX511344/SRX511344.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:16:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX511344/SRX511344.20_summits.bed INFO @ Fri, 26 Jun 2020 09:16:22: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2351 records, 4 fields): 4 millis CompletedMACS2peakCalling