Job ID = 5721142 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 2,647,291 reads read : 5,294,582 reads written : 5,294,582 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: 00:04:02 2647291 reads; of these: 2647291 (100.00%) were paired; of these: 465608 (17.59%) aligned concordantly 0 times 1883651 (71.15%) aligned concordantly exactly 1 time 298032 (11.26%) aligned concordantly >1 times ---- 465608 pairs aligned concordantly 0 times; of these: 205434 (44.12%) aligned discordantly 1 time ---- 260174 pairs aligned 0 times concordantly or discordantly; of these: 520348 mates make up the pairs; of these: 278101 (53.45%) aligned 0 times 134749 (25.90%) aligned exactly 1 time 107498 (20.66%) aligned >1 times 94.75% overall alignment rate Time searching: 00:04:02 Overall time: 00:04:02 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_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] 92180 / 2380915 = 0.0387 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 05:22:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6708281/SRX6708281.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6708281/SRX6708281.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6708281/SRX6708281.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6708281/SRX6708281.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 05:22:18: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:22:18: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:22:23: 1000000 INFO @ Thu, 16 Apr 2020 05:22:29: 2000000 INFO @ Thu, 16 Apr 2020 05:22:35: 3000000 INFO @ Thu, 16 Apr 2020 05:22:40: 4000000 INFO @ Thu, 16 Apr 2020 05:22:45: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 05:22:45: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 05:22:45: #1 total tags in treatment: 2095054 INFO @ Thu, 16 Apr 2020 05:22:45: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:22:45: #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 05:22:45: #1 tags after filtering in treatment: 2033118 INFO @ Thu, 16 Apr 2020 05:22:45: #1 Redundant rate of treatment: 0.03 INFO @ Thu, 16 Apr 2020 05:22:45: #1 finished! INFO @ Thu, 16 Apr 2020 05:22:45: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:22:45: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:22:45: #2 number of paired peaks: 4322 INFO @ Thu, 16 Apr 2020 05:22:45: start model_add_line... INFO @ Thu, 16 Apr 2020 05:22:46: start X-correlation... INFO @ Thu, 16 Apr 2020 05:22:46: end of X-cor INFO @ Thu, 16 Apr 2020 05:22:46: #2 finished! INFO @ Thu, 16 Apr 2020 05:22:46: #2 predicted fragment length is 209 bps INFO @ Thu, 16 Apr 2020 05:22:46: #2 alternative fragment length(s) may be 209 bps INFO @ Thu, 16 Apr 2020 05:22:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6708281/SRX6708281.05_model.r INFO @ Thu, 16 Apr 2020 05:22:46: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:22:46: #3 Pre-compute pvalue-qvalue table... 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 05:22:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6708281/SRX6708281.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6708281/SRX6708281.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6708281/SRX6708281.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6708281/SRX6708281.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 05:22:48: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:22:48: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:22:50: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:22:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6708281/SRX6708281.05_peaks.xls INFO @ Thu, 16 Apr 2020 05:22:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6708281/SRX6708281.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:22:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6708281/SRX6708281.05_summits.bed INFO @ Thu, 16 Apr 2020 05:22:53: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3531 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 05:22:53: 1000000 INFO @ Thu, 16 Apr 2020 05:22:58: 2000000 INFO @ Thu, 16 Apr 2020 05:23:03: 3000000 INFO @ Thu, 16 Apr 2020 05:23:08: 4000000 INFO @ Thu, 16 Apr 2020 05:23:12: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 05:23:12: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 05:23:12: #1 total tags in treatment: 2095054 INFO @ Thu, 16 Apr 2020 05:23:12: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:23:12: #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 05:23:12: #1 tags after filtering in treatment: 2033118 INFO @ Thu, 16 Apr 2020 05:23:12: #1 Redundant rate of treatment: 0.03 INFO @ Thu, 16 Apr 2020 05:23:12: #1 finished! INFO @ Thu, 16 Apr 2020 05:23:12: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:23:12: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:23:12: #2 number of paired peaks: 4322 INFO @ Thu, 16 Apr 2020 05:23:12: start model_add_line... INFO @ Thu, 16 Apr 2020 05:23:12: start X-correlation... INFO @ Thu, 16 Apr 2020 05:23:12: end of X-cor INFO @ Thu, 16 Apr 2020 05:23:12: #2 finished! INFO @ Thu, 16 Apr 2020 05:23:12: #2 predicted fragment length is 209 bps INFO @ Thu, 16 Apr 2020 05:23:12: #2 alternative fragment length(s) may be 209 bps INFO @ Thu, 16 Apr 2020 05:23:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6708281/SRX6708281.10_model.r INFO @ Thu, 16 Apr 2020 05:23:12: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:23:12: #3 Pre-compute pvalue-qvalue table... 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 05:23:17: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:23:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6708281/SRX6708281.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6708281/SRX6708281.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6708281/SRX6708281.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6708281/SRX6708281.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 05:23:18: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:23:18: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:23:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6708281/SRX6708281.10_peaks.xls INFO @ Thu, 16 Apr 2020 05:23:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6708281/SRX6708281.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:23:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6708281/SRX6708281.10_summits.bed INFO @ Thu, 16 Apr 2020 05:23:19: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1441 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 05:23:23: 1000000 INFO @ Thu, 16 Apr 2020 05:23:30: 2000000 INFO @ Thu, 16 Apr 2020 05:23:36: 3000000 INFO @ Thu, 16 Apr 2020 05:23:42: 4000000 INFO @ Thu, 16 Apr 2020 05:23:47: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 05:23:47: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 05:23:47: #1 total tags in treatment: 2095054 INFO @ Thu, 16 Apr 2020 05:23:47: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:23:47: #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 05:23:47: #1 tags after filtering in treatment: 2033118 INFO @ Thu, 16 Apr 2020 05:23:47: #1 Redundant rate of treatment: 0.03 INFO @ Thu, 16 Apr 2020 05:23:47: #1 finished! INFO @ Thu, 16 Apr 2020 05:23:47: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:23:47: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:23:48: #2 number of paired peaks: 4322 INFO @ Thu, 16 Apr 2020 05:23:48: start model_add_line... INFO @ Thu, 16 Apr 2020 05:23:48: start X-correlation... INFO @ Thu, 16 Apr 2020 05:23:48: end of X-cor INFO @ Thu, 16 Apr 2020 05:23:48: #2 finished! INFO @ Thu, 16 Apr 2020 05:23:48: #2 predicted fragment length is 209 bps INFO @ Thu, 16 Apr 2020 05:23:48: #2 alternative fragment length(s) may be 209 bps INFO @ Thu, 16 Apr 2020 05:23:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6708281/SRX6708281.20_model.r INFO @ Thu, 16 Apr 2020 05:23:48: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:23:48: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:23:52: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:23:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6708281/SRX6708281.20_peaks.xls INFO @ Thu, 16 Apr 2020 05:23:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6708281/SRX6708281.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:23:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6708281/SRX6708281.20_summits.bed INFO @ Thu, 16 Apr 2020 05:23:55: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (407 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。