Job ID = 5721152 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 11,782,644 reads read : 23,565,288 reads written : 23,565,288 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: 00:20:09 11782644 reads; of these: 11782644 (100.00%) were paired; of these: 2338833 (19.85%) aligned concordantly 0 times 7735626 (65.65%) aligned concordantly exactly 1 time 1708185 (14.50%) aligned concordantly >1 times ---- 2338833 pairs aligned concordantly 0 times; of these: 181620 (7.77%) aligned discordantly 1 time ---- 2157213 pairs aligned 0 times concordantly or discordantly; of these: 4314426 mates make up the pairs; of these: 3862342 (89.52%) aligned 0 times 231455 (5.36%) aligned exactly 1 time 220629 (5.11%) aligned >1 times 83.61% overall alignment rate Time searching: 00:20:09 Overall time: 00:20:09 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] 432657 / 9619464 = 0.0450 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 05:53:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6708290/SRX6708290.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6708290/SRX6708290.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6708290/SRX6708290.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6708290/SRX6708290.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 05:53:27: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:53:27: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:53:34: 1000000 INFO @ Thu, 16 Apr 2020 05:53:41: 2000000 INFO @ Thu, 16 Apr 2020 05:53:48: 3000000 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 05:53:55: 4000000 INFO @ Thu, 16 Apr 2020 05:53:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6708290/SRX6708290.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6708290/SRX6708290.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6708290/SRX6708290.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6708290/SRX6708290.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 05:53:57: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:53:57: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:54:03: 5000000 INFO @ Thu, 16 Apr 2020 05:54:05: 1000000 INFO @ Thu, 16 Apr 2020 05:54:11: 6000000 INFO @ Thu, 16 Apr 2020 05:54:12: 2000000 INFO @ Thu, 16 Apr 2020 05:54:20: 3000000 INFO @ Thu, 16 Apr 2020 05:54:20: 7000000 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 05:54:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6708290/SRX6708290.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6708290/SRX6708290.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6708290/SRX6708290.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6708290/SRX6708290.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 05:54:27: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:54:27: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:54:27: 4000000 INFO @ Thu, 16 Apr 2020 05:54:28: 8000000 INFO @ Thu, 16 Apr 2020 05:54:35: 5000000 INFO @ Thu, 16 Apr 2020 05:54:36: 1000000 INFO @ Thu, 16 Apr 2020 05:54:37: 9000000 INFO @ Thu, 16 Apr 2020 05:54:43: 6000000 INFO @ Thu, 16 Apr 2020 05:54:45: 2000000 INFO @ Thu, 16 Apr 2020 05:54:46: 10000000 INFO @ Thu, 16 Apr 2020 05:54:50: 7000000 INFO @ Thu, 16 Apr 2020 05:54:53: 3000000 INFO @ Thu, 16 Apr 2020 05:54:54: 11000000 INFO @ Thu, 16 Apr 2020 05:54:58: 8000000 INFO @ Thu, 16 Apr 2020 05:55:02: 4000000 INFO @ Thu, 16 Apr 2020 05:55:03: 12000000 INFO @ Thu, 16 Apr 2020 05:55:06: 9000000 INFO @ Thu, 16 Apr 2020 05:55:11: 5000000 INFO @ Thu, 16 Apr 2020 05:55:11: 13000000 INFO @ Thu, 16 Apr 2020 05:55:13: 10000000 INFO @ Thu, 16 Apr 2020 05:55:20: 14000000 INFO @ Thu, 16 Apr 2020 05:55:20: 6000000 INFO @ Thu, 16 Apr 2020 05:55:21: 11000000 INFO @ Thu, 16 Apr 2020 05:55:29: 12000000 INFO @ Thu, 16 Apr 2020 05:55:29: 15000000 INFO @ Thu, 16 Apr 2020 05:55:29: 7000000 INFO @ Thu, 16 Apr 2020 05:55:36: 13000000 INFO @ Thu, 16 Apr 2020 05:55:37: 16000000 INFO @ Thu, 16 Apr 2020 05:55:38: 8000000 INFO @ Thu, 16 Apr 2020 05:55:44: 14000000 INFO @ Thu, 16 Apr 2020 05:55:46: 17000000 INFO @ Thu, 16 Apr 2020 05:55:47: 9000000 INFO @ Thu, 16 Apr 2020 05:55:52: 15000000 INFO @ Thu, 16 Apr 2020 05:55:55: 18000000 INFO @ Thu, 16 Apr 2020 05:55:55: 10000000 INFO @ Thu, 16 Apr 2020 05:55:59: 16000000 INFO @ Thu, 16 Apr 2020 05:56:02: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 05:56:02: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 05:56:02: #1 total tags in treatment: 9015172 INFO @ Thu, 16 Apr 2020 05:56:02: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:56:02: #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 05:56:02: #1 tags after filtering in treatment: 7678194 INFO @ Thu, 16 Apr 2020 05:56:02: #1 Redundant rate of treatment: 0.15 INFO @ Thu, 16 Apr 2020 05:56:02: #1 finished! INFO @ Thu, 16 Apr 2020 05:56:02: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:56:02: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:56:03: #2 number of paired peaks: 5193 INFO @ Thu, 16 Apr 2020 05:56:03: start model_add_line... INFO @ Thu, 16 Apr 2020 05:56:03: start X-correlation... INFO @ Thu, 16 Apr 2020 05:56:03: end of X-cor INFO @ Thu, 16 Apr 2020 05:56:03: #2 finished! INFO @ Thu, 16 Apr 2020 05:56:03: #2 predicted fragment length is 183 bps INFO @ Thu, 16 Apr 2020 05:56:03: #2 alternative fragment length(s) may be 183 bps INFO @ Thu, 16 Apr 2020 05:56:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6708290/SRX6708290.05_model.r INFO @ Thu, 16 Apr 2020 05:56:03: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:56:03: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:56:04: 11000000 INFO @ Thu, 16 Apr 2020 05:56:07: 17000000 INFO @ Thu, 16 Apr 2020 05:56:13: 12000000 INFO @ Thu, 16 Apr 2020 05:56:14: 18000000 INFO @ Thu, 16 Apr 2020 05:56:21: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 05:56:21: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 05:56:21: #1 total tags in treatment: 9015172 INFO @ Thu, 16 Apr 2020 05:56:21: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:56:21: #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 05:56:21: #1 tags after filtering in treatment: 7678194 INFO @ Thu, 16 Apr 2020 05:56:21: #1 Redundant rate of treatment: 0.15 INFO @ Thu, 16 Apr 2020 05:56:21: #1 finished! INFO @ Thu, 16 Apr 2020 05:56:21: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:56:21: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:56:21: 13000000 INFO @ Thu, 16 Apr 2020 05:56:22: #2 number of paired peaks: 5193 INFO @ Thu, 16 Apr 2020 05:56:22: start model_add_line... INFO @ Thu, 16 Apr 2020 05:56:22: start X-correlation... INFO @ Thu, 16 Apr 2020 05:56:22: end of X-cor INFO @ Thu, 16 Apr 2020 05:56:22: #2 finished! INFO @ Thu, 16 Apr 2020 05:56:22: #2 predicted fragment length is 183 bps INFO @ Thu, 16 Apr 2020 05:56:22: #2 alternative fragment length(s) may be 183 bps INFO @ Thu, 16 Apr 2020 05:56:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6708290/SRX6708290.10_model.r INFO @ Thu, 16 Apr 2020 05:56:22: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:56:22: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:56:23: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:56:29: 14000000 INFO @ Thu, 16 Apr 2020 05:56:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6708290/SRX6708290.05_peaks.xls INFO @ Thu, 16 Apr 2020 05:56:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6708290/SRX6708290.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:56:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6708290/SRX6708290.05_summits.bed INFO @ Thu, 16 Apr 2020 05:56:32: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (8370 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 05:56:37: 15000000 INFO @ Thu, 16 Apr 2020 05:56:41: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:56:45: 16000000 INFO @ Thu, 16 Apr 2020 05:56:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6708290/SRX6708290.10_peaks.xls INFO @ Thu, 16 Apr 2020 05:56:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6708290/SRX6708290.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:56:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6708290/SRX6708290.10_summits.bed INFO @ Thu, 16 Apr 2020 05:56:51: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (6775 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 05:56:53: 17000000 INFO @ Thu, 16 Apr 2020 05:57:00: 18000000 INFO @ Thu, 16 Apr 2020 05:57:07: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 05:57:07: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 05:57:07: #1 total tags in treatment: 9015172 INFO @ Thu, 16 Apr 2020 05:57:07: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:57:07: #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 05:57:07: #1 tags after filtering in treatment: 7678194 INFO @ Thu, 16 Apr 2020 05:57:07: #1 Redundant rate of treatment: 0.15 INFO @ Thu, 16 Apr 2020 05:57:07: #1 finished! INFO @ Thu, 16 Apr 2020 05:57:07: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:57:07: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:57:08: #2 number of paired peaks: 5193 INFO @ Thu, 16 Apr 2020 05:57:08: start model_add_line... INFO @ Thu, 16 Apr 2020 05:57:08: start X-correlation... INFO @ Thu, 16 Apr 2020 05:57:08: end of X-cor INFO @ Thu, 16 Apr 2020 05:57:08: #2 finished! INFO @ Thu, 16 Apr 2020 05:57:08: #2 predicted fragment length is 183 bps INFO @ Thu, 16 Apr 2020 05:57:08: #2 alternative fragment length(s) may be 183 bps INFO @ Thu, 16 Apr 2020 05:57:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6708290/SRX6708290.20_model.r INFO @ Thu, 16 Apr 2020 05:57:08: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:57:08: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 16 Apr 2020 05:57:28: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:57:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6708290/SRX6708290.20_peaks.xls INFO @ Thu, 16 Apr 2020 05:57:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6708290/SRX6708290.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:57:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6708290/SRX6708290.20_summits.bed INFO @ Thu, 16 Apr 2020 05:57:38: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (5173 records, 4 fields): 7 millis CompletedMACS2peakCalling BigWig に変換しました。