Job ID = 5721222 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 16,288,693 reads read : 32,577,386 reads written : 32,577,386 rm: cannot remove ‘[DSE]RR*’: No such file or directory 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: 01:35:00 16288693 reads; of these: 16288693 (100.00%) were paired; of these: 2844319 (17.46%) aligned concordantly 0 times 10047549 (61.68%) aligned concordantly exactly 1 time 3396825 (20.85%) aligned concordantly >1 times ---- 2844319 pairs aligned concordantly 0 times; of these: 522683 (18.38%) aligned discordantly 1 time ---- 2321636 pairs aligned 0 times concordantly or discordantly; of these: 4643272 mates make up the pairs; of these: 2871719 (61.85%) aligned 0 times 285611 (6.15%) aligned exactly 1 time 1485942 (32.00%) aligned >1 times 91.18% overall alignment rate Time searching: 01:35:00 Overall time: 01:35:00 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 16 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] 2128439 / 13918929 = 0.1529 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 @ Thu, 16 Apr 2020 07:58:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6845080/SRX6845080.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6845080/SRX6845080.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6845080/SRX6845080.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6845080/SRX6845080.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 @ Thu, 16 Apr 2020 07:58:24: #1 read tag files... INFO @ Thu, 16 Apr 2020 07:58:24: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 07:58:31: 1000000 INFO @ Thu, 16 Apr 2020 07:58:37: 2000000 INFO @ Thu, 16 Apr 2020 07:58:44: 3000000 INFO @ Thu, 16 Apr 2020 07:58:50: 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 @ Thu, 16 Apr 2020 07:58:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6845080/SRX6845080.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6845080/SRX6845080.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6845080/SRX6845080.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6845080/SRX6845080.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 @ Thu, 16 Apr 2020 07:58:54: #1 read tag files... INFO @ Thu, 16 Apr 2020 07:58:54: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 07:58:57: 5000000 INFO @ Thu, 16 Apr 2020 07:59:01: 1000000 INFO @ Thu, 16 Apr 2020 07:59:04: 6000000 INFO @ Thu, 16 Apr 2020 07:59:09: 2000000 INFO @ Thu, 16 Apr 2020 07:59:12: 7000000 INFO @ Thu, 16 Apr 2020 07:59:16: 3000000 INFO @ Thu, 16 Apr 2020 07:59:19: 8000000 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 @ Thu, 16 Apr 2020 07:59:24: 4000000 INFO @ Thu, 16 Apr 2020 07:59:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6845080/SRX6845080.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6845080/SRX6845080.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6845080/SRX6845080.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6845080/SRX6845080.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 @ Thu, 16 Apr 2020 07:59:24: #1 read tag files... INFO @ Thu, 16 Apr 2020 07:59:24: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 07:59:26: 9000000 INFO @ Thu, 16 Apr 2020 07:59:32: 5000000 INFO @ Thu, 16 Apr 2020 07:59:32: 1000000 INFO @ Thu, 16 Apr 2020 07:59:34: 10000000 INFO @ Thu, 16 Apr 2020 07:59:39: 6000000 INFO @ Thu, 16 Apr 2020 07:59:40: 2000000 INFO @ Thu, 16 Apr 2020 07:59:42: 11000000 INFO @ Thu, 16 Apr 2020 07:59:47: 7000000 INFO @ Thu, 16 Apr 2020 07:59:48: 3000000 INFO @ Thu, 16 Apr 2020 07:59:49: 12000000 INFO @ Thu, 16 Apr 2020 07:59:55: 8000000 INFO @ Thu, 16 Apr 2020 07:59:55: 4000000 INFO @ Thu, 16 Apr 2020 07:59:57: 13000000 INFO @ Thu, 16 Apr 2020 08:00:02: 9000000 INFO @ Thu, 16 Apr 2020 08:00:03: 5000000 INFO @ Thu, 16 Apr 2020 08:00:05: 14000000 INFO @ Thu, 16 Apr 2020 08:00:10: 10000000 INFO @ Thu, 16 Apr 2020 08:00:11: 6000000 INFO @ Thu, 16 Apr 2020 08:00:12: 15000000 INFO @ Thu, 16 Apr 2020 08:00:17: 11000000 INFO @ Thu, 16 Apr 2020 08:00:18: 7000000 INFO @ Thu, 16 Apr 2020 08:00:20: 16000000 INFO @ Thu, 16 Apr 2020 08:00:25: 12000000 INFO @ Thu, 16 Apr 2020 08:00:25: 8000000 INFO @ Thu, 16 Apr 2020 08:00:27: 17000000 INFO @ Thu, 16 Apr 2020 08:00:32: 13000000 INFO @ Thu, 16 Apr 2020 08:00:33: 9000000 INFO @ Thu, 16 Apr 2020 08:00:34: 18000000 INFO @ Thu, 16 Apr 2020 08:00:39: 14000000 INFO @ Thu, 16 Apr 2020 08:00:40: 10000000 INFO @ Thu, 16 Apr 2020 08:00:42: 19000000 INFO @ Thu, 16 Apr 2020 08:00:47: 15000000 INFO @ Thu, 16 Apr 2020 08:00:48: 11000000 INFO @ Thu, 16 Apr 2020 08:00:49: 20000000 INFO @ Thu, 16 Apr 2020 08:00:54: 16000000 INFO @ Thu, 16 Apr 2020 08:00:55: 12000000 INFO @ Thu, 16 Apr 2020 08:00:57: 21000000 INFO @ Thu, 16 Apr 2020 08:01:02: 17000000 INFO @ Thu, 16 Apr 2020 08:01:02: 13000000 INFO @ Thu, 16 Apr 2020 08:01:04: 22000000 INFO @ Thu, 16 Apr 2020 08:01:09: 18000000 INFO @ Thu, 16 Apr 2020 08:01:10: 14000000 INFO @ Thu, 16 Apr 2020 08:01:11: 23000000 INFO @ Thu, 16 Apr 2020 08:01:16: 19000000 INFO @ Thu, 16 Apr 2020 08:01:17: 15000000 INFO @ Thu, 16 Apr 2020 08:01:19: 24000000 INFO @ Thu, 16 Apr 2020 08:01:24: 20000000 INFO @ Thu, 16 Apr 2020 08:01:24: 16000000 INFO @ Thu, 16 Apr 2020 08:01:26: 25000000 INFO @ Thu, 16 Apr 2020 08:01:29: #1 tag size is determined as 101 bps INFO @ Thu, 16 Apr 2020 08:01:29: #1 tag size = 101 INFO @ Thu, 16 Apr 2020 08:01:29: #1 total tags in treatment: 11395918 INFO @ Thu, 16 Apr 2020 08:01:29: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 08:01:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 08:01:29: #1 tags after filtering in treatment: 10722871 INFO @ Thu, 16 Apr 2020 08:01:29: #1 Redundant rate of treatment: 0.06 INFO @ Thu, 16 Apr 2020 08:01:29: #1 finished! INFO @ Thu, 16 Apr 2020 08:01:29: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 08:01:29: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 08:01:30: #2 number of paired peaks: 1099 INFO @ Thu, 16 Apr 2020 08:01:30: start model_add_line... INFO @ Thu, 16 Apr 2020 08:01:30: start X-correlation... INFO @ Thu, 16 Apr 2020 08:01:30: end of X-cor INFO @ Thu, 16 Apr 2020 08:01:30: #2 finished! INFO @ Thu, 16 Apr 2020 08:01:30: #2 predicted fragment length is 205 bps INFO @ Thu, 16 Apr 2020 08:01:30: #2 alternative fragment length(s) may be 205 bps INFO @ Thu, 16 Apr 2020 08:01:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6845080/SRX6845080.05_model.r INFO @ Thu, 16 Apr 2020 08:01:30: #3 Call peaks... INFO @ Thu, 16 Apr 2020 08:01:30: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 08:01:31: 21000000 INFO @ Thu, 16 Apr 2020 08:01:32: 17000000 INFO @ Thu, 16 Apr 2020 08:01:38: 22000000 INFO @ Thu, 16 Apr 2020 08:01:39: 18000000 INFO @ Thu, 16 Apr 2020 08:01:45: 23000000 INFO @ Thu, 16 Apr 2020 08:01:46: 19000000 INFO @ Thu, 16 Apr 2020 08:01:53: 24000000 INFO @ Thu, 16 Apr 2020 08:01:53: 20000000 INFO @ Thu, 16 Apr 2020 08:01:55: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 08:02:00: 25000000 INFO @ Thu, 16 Apr 2020 08:02:01: 21000000 INFO @ Thu, 16 Apr 2020 08:02:03: #1 tag size is determined as 101 bps INFO @ Thu, 16 Apr 2020 08:02:03: #1 tag size = 101 INFO @ Thu, 16 Apr 2020 08:02:03: #1 total tags in treatment: 11395918 INFO @ Thu, 16 Apr 2020 08:02:03: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 08:02:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 08:02:03: #1 tags after filtering in treatment: 10722871 INFO @ Thu, 16 Apr 2020 08:02:03: #1 Redundant rate of treatment: 0.06 INFO @ Thu, 16 Apr 2020 08:02:03: #1 finished! INFO @ Thu, 16 Apr 2020 08:02:03: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 08:02:03: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 08:02:04: #2 number of paired peaks: 1099 INFO @ Thu, 16 Apr 2020 08:02:04: start model_add_line... INFO @ Thu, 16 Apr 2020 08:02:04: start X-correlation... INFO @ Thu, 16 Apr 2020 08:02:04: end of X-cor INFO @ Thu, 16 Apr 2020 08:02:04: #2 finished! INFO @ Thu, 16 Apr 2020 08:02:04: #2 predicted fragment length is 205 bps INFO @ Thu, 16 Apr 2020 08:02:04: #2 alternative fragment length(s) may be 205 bps INFO @ Thu, 16 Apr 2020 08:02:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6845080/SRX6845080.10_model.r INFO @ Thu, 16 Apr 2020 08:02:04: #3 Call peaks... INFO @ Thu, 16 Apr 2020 08:02:04: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 08:02:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6845080/SRX6845080.05_peaks.xls INFO @ Thu, 16 Apr 2020 08:02:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6845080/SRX6845080.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 08:02:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6845080/SRX6845080.05_summits.bed INFO @ Thu, 16 Apr 2020 08:02:07: Done! INFO @ Thu, 16 Apr 2020 08:02:07: 22000000 pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2908 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 08:02:14: 23000000 INFO @ Thu, 16 Apr 2020 08:02:20: 24000000 INFO @ Thu, 16 Apr 2020 08:02:26: 25000000 INFO @ Thu, 16 Apr 2020 08:02:29: #1 tag size is determined as 101 bps INFO @ Thu, 16 Apr 2020 08:02:29: #1 tag size = 101 INFO @ Thu, 16 Apr 2020 08:02:29: #1 total tags in treatment: 11395918 INFO @ Thu, 16 Apr 2020 08:02:29: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 08:02:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 08:02:29: #1 tags after filtering in treatment: 10722871 INFO @ Thu, 16 Apr 2020 08:02:29: #1 Redundant rate of treatment: 0.06 INFO @ Thu, 16 Apr 2020 08:02:29: #1 finished! INFO @ Thu, 16 Apr 2020 08:02:29: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 08:02:29: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 08:02:30: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 08:02:30: #2 number of paired peaks: 1099 INFO @ Thu, 16 Apr 2020 08:02:30: start model_add_line... INFO @ Thu, 16 Apr 2020 08:02:30: start X-correlation... INFO @ Thu, 16 Apr 2020 08:02:30: end of X-cor INFO @ Thu, 16 Apr 2020 08:02:30: #2 finished! INFO @ Thu, 16 Apr 2020 08:02:30: #2 predicted fragment length is 205 bps INFO @ Thu, 16 Apr 2020 08:02:30: #2 alternative fragment length(s) may be 205 bps INFO @ Thu, 16 Apr 2020 08:02:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6845080/SRX6845080.20_model.r INFO @ Thu, 16 Apr 2020 08:02:30: #3 Call peaks... INFO @ Thu, 16 Apr 2020 08:02:30: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 08:02:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6845080/SRX6845080.10_peaks.xls INFO @ Thu, 16 Apr 2020 08:02:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6845080/SRX6845080.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 08:02:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6845080/SRX6845080.10_summits.bed INFO @ Thu, 16 Apr 2020 08:02:42: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1668 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 08:02:53: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 08:03:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6845080/SRX6845080.20_peaks.xls INFO @ Thu, 16 Apr 2020 08:03:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6845080/SRX6845080.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 08:03:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6845080/SRX6845080.20_summits.bed INFO @ Thu, 16 Apr 2020 08:03:04: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (863 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。