Job ID = 5721119 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 7,488,686 reads read : 14,977,372 reads written : 14,977,372 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: 00:12:07 7488686 reads; of these: 7488686 (100.00%) were paired; of these: 1577007 (21.06%) aligned concordantly 0 times 4574621 (61.09%) aligned concordantly exactly 1 time 1337058 (17.85%) aligned concordantly >1 times ---- 1577007 pairs aligned concordantly 0 times; of these: 227362 (14.42%) aligned discordantly 1 time ---- 1349645 pairs aligned 0 times concordantly or discordantly; of these: 2699290 mates make up the pairs; of these: 2204247 (81.66%) aligned 0 times 268053 (9.93%) aligned exactly 1 time 226990 (8.41%) aligned >1 times 85.28% overall alignment rate Time searching: 00:12:07 Overall time: 00:12:07 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 8 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] 680036 / 6118830 = 0.1111 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 05:15:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6708262/SRX6708262.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6708262/SRX6708262.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6708262/SRX6708262.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6708262/SRX6708262.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 05:15:32: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:15:32: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:15:38: 1000000 INFO @ Thu, 16 Apr 2020 05:15:44: 2000000 INFO @ Thu, 16 Apr 2020 05:15:50: 3000000 INFO @ Thu, 16 Apr 2020 05:15:56: 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 05:16:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6708262/SRX6708262.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6708262/SRX6708262.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6708262/SRX6708262.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6708262/SRX6708262.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 05:16:01: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:16:01: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:16:02: 5000000 INFO @ Thu, 16 Apr 2020 05:16:07: 1000000 INFO @ Thu, 16 Apr 2020 05:16:08: 6000000 INFO @ Thu, 16 Apr 2020 05:16:14: 2000000 INFO @ Thu, 16 Apr 2020 05:16:15: 7000000 INFO @ Thu, 16 Apr 2020 05:16:20: 3000000 INFO @ Thu, 16 Apr 2020 05:16:21: 8000000 INFO @ Thu, 16 Apr 2020 05:16:27: 4000000 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 05:16:28: 9000000 INFO @ Thu, 16 Apr 2020 05:16:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6708262/SRX6708262.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6708262/SRX6708262.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6708262/SRX6708262.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6708262/SRX6708262.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 05:16:30: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:16:30: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:16:33: 5000000 INFO @ Thu, 16 Apr 2020 05:16:34: 10000000 INFO @ Thu, 16 Apr 2020 05:16:36: 1000000 INFO @ Thu, 16 Apr 2020 05:16:40: 6000000 INFO @ Thu, 16 Apr 2020 05:16:41: 11000000 INFO @ Thu, 16 Apr 2020 05:16:43: 2000000 INFO @ Thu, 16 Apr 2020 05:16:43: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 05:16:43: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 05:16:43: #1 total tags in treatment: 5248146 INFO @ Thu, 16 Apr 2020 05:16:43: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:16:43: #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 05:16:44: #1 tags after filtering in treatment: 4925771 INFO @ Thu, 16 Apr 2020 05:16:44: #1 Redundant rate of treatment: 0.06 INFO @ Thu, 16 Apr 2020 05:16:44: #1 finished! INFO @ Thu, 16 Apr 2020 05:16:44: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:16:44: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:16:44: #2 number of paired peaks: 1780 INFO @ Thu, 16 Apr 2020 05:16:44: start model_add_line... INFO @ Thu, 16 Apr 2020 05:16:44: start X-correlation... INFO @ Thu, 16 Apr 2020 05:16:44: end of X-cor INFO @ Thu, 16 Apr 2020 05:16:44: #2 finished! INFO @ Thu, 16 Apr 2020 05:16:44: #2 predicted fragment length is 174 bps INFO @ Thu, 16 Apr 2020 05:16:44: #2 alternative fragment length(s) may be 174 bps INFO @ Thu, 16 Apr 2020 05:16:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6708262/SRX6708262.05_model.r INFO @ Thu, 16 Apr 2020 05:16:44: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:16:44: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:16:46: 7000000 INFO @ Thu, 16 Apr 2020 05:16:49: 3000000 INFO @ Thu, 16 Apr 2020 05:16:53: 8000000 INFO @ Thu, 16 Apr 2020 05:16:55: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:16:56: 4000000 INFO @ Thu, 16 Apr 2020 05:16:59: 9000000 INFO @ Thu, 16 Apr 2020 05:17:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6708262/SRX6708262.05_peaks.xls INFO @ Thu, 16 Apr 2020 05:17:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6708262/SRX6708262.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:17:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6708262/SRX6708262.05_summits.bed INFO @ Thu, 16 Apr 2020 05:17:01: Done! INFO @ Thu, 16 Apr 2020 05:17:02: 5000000 INFO @ Thu, 16 Apr 2020 05:17:06: 10000000 pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (4832 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 05:17:09: 6000000 INFO @ Thu, 16 Apr 2020 05:17:12: 11000000 INFO @ Thu, 16 Apr 2020 05:17:15: 7000000 INFO @ Thu, 16 Apr 2020 05:17:15: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 05:17:15: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 05:17:15: #1 total tags in treatment: 5248146 INFO @ Thu, 16 Apr 2020 05:17:15: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:17:15: #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 05:17:15: #1 tags after filtering in treatment: 4925771 INFO @ Thu, 16 Apr 2020 05:17:15: #1 Redundant rate of treatment: 0.06 INFO @ Thu, 16 Apr 2020 05:17:15: #1 finished! INFO @ Thu, 16 Apr 2020 05:17:15: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:17:15: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:17:16: #2 number of paired peaks: 1780 INFO @ Thu, 16 Apr 2020 05:17:16: start model_add_line... INFO @ Thu, 16 Apr 2020 05:17:16: start X-correlation... INFO @ Thu, 16 Apr 2020 05:17:16: end of X-cor INFO @ Thu, 16 Apr 2020 05:17:16: #2 finished! INFO @ Thu, 16 Apr 2020 05:17:16: #2 predicted fragment length is 174 bps INFO @ Thu, 16 Apr 2020 05:17:16: #2 alternative fragment length(s) may be 174 bps INFO @ Thu, 16 Apr 2020 05:17:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6708262/SRX6708262.10_model.r INFO @ Thu, 16 Apr 2020 05:17:16: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:17:16: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:17:21: 8000000 INFO @ Thu, 16 Apr 2020 05:17:27: 9000000 INFO @ Thu, 16 Apr 2020 05:17:27: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:17:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6708262/SRX6708262.10_peaks.xls INFO @ Thu, 16 Apr 2020 05:17:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6708262/SRX6708262.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:17:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6708262/SRX6708262.10_summits.bed INFO @ Thu, 16 Apr 2020 05:17:32: Done! INFO @ Thu, 16 Apr 2020 05:17:33: 10000000 pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2504 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 05:17:39: 11000000 INFO @ Thu, 16 Apr 2020 05:17:41: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 05:17:41: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 05:17:41: #1 total tags in treatment: 5248146 INFO @ Thu, 16 Apr 2020 05:17:41: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:17:41: #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 05:17:41: #1 tags after filtering in treatment: 4925771 INFO @ Thu, 16 Apr 2020 05:17:41: #1 Redundant rate of treatment: 0.06 INFO @ Thu, 16 Apr 2020 05:17:41: #1 finished! INFO @ Thu, 16 Apr 2020 05:17:41: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:17:41: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:17:42: #2 number of paired peaks: 1780 INFO @ Thu, 16 Apr 2020 05:17:42: start model_add_line... INFO @ Thu, 16 Apr 2020 05:17:42: start X-correlation... INFO @ Thu, 16 Apr 2020 05:17:42: end of X-cor INFO @ Thu, 16 Apr 2020 05:17:42: #2 finished! INFO @ Thu, 16 Apr 2020 05:17:42: #2 predicted fragment length is 174 bps INFO @ Thu, 16 Apr 2020 05:17:42: #2 alternative fragment length(s) may be 174 bps INFO @ Thu, 16 Apr 2020 05:17:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6708262/SRX6708262.20_model.r INFO @ Thu, 16 Apr 2020 05:17:42: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:17:42: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:17:53: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:17:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6708262/SRX6708262.20_peaks.xls INFO @ Thu, 16 Apr 2020 05:17:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6708262/SRX6708262.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:17:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6708262/SRX6708262.20_summits.bed INFO @ Thu, 16 Apr 2020 05:17:59: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (963 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。