Job ID = 5721139 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 2,562,464 reads read : 5,124,928 reads written : 5,124,928 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: 00:04:14 2562464 reads; of these: 2562464 (100.00%) were paired; of these: 363657 (14.19%) aligned concordantly 0 times 1845093 (72.00%) aligned concordantly exactly 1 time 353714 (13.80%) aligned concordantly >1 times ---- 363657 pairs aligned concordantly 0 times; of these: 147686 (40.61%) aligned discordantly 1 time ---- 215971 pairs aligned 0 times concordantly or discordantly; of these: 431942 mates make up the pairs; of these: 261769 (60.60%) aligned 0 times 94087 (21.78%) aligned exactly 1 time 76086 (17.61%) aligned >1 times 94.89% overall alignment rate Time searching: 00:04:14 Overall time: 00:04:14 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] 88323 / 2340933 = 0.0377 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 05:20:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6708278/SRX6708278.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6708278/SRX6708278.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6708278/SRX6708278.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6708278/SRX6708278.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 05:20:48: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:20:48: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:20:54: 1000000 INFO @ Thu, 16 Apr 2020 05:20:59: 2000000 INFO @ Thu, 16 Apr 2020 05:21:04: 3000000 INFO @ Thu, 16 Apr 2020 05:21:09: 4000000 INFO @ Thu, 16 Apr 2020 05:21:12: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 05:21:12: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 05:21:12: #1 total tags in treatment: 2114457 INFO @ Thu, 16 Apr 2020 05:21:12: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:21:12: #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 05:21:12: #1 tags after filtering in treatment: 2055331 INFO @ Thu, 16 Apr 2020 05:21:12: #1 Redundant rate of treatment: 0.03 INFO @ Thu, 16 Apr 2020 05:21:12: #1 finished! INFO @ Thu, 16 Apr 2020 05:21:12: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:21:12: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:21:12: #2 number of paired peaks: 3129 INFO @ Thu, 16 Apr 2020 05:21:12: start model_add_line... INFO @ Thu, 16 Apr 2020 05:21:12: start X-correlation... INFO @ Thu, 16 Apr 2020 05:21:12: end of X-cor INFO @ Thu, 16 Apr 2020 05:21:12: #2 finished! INFO @ Thu, 16 Apr 2020 05:21:12: #2 predicted fragment length is 176 bps INFO @ Thu, 16 Apr 2020 05:21:12: #2 alternative fragment length(s) may be 176 bps INFO @ Thu, 16 Apr 2020 05:21:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6708278/SRX6708278.05_model.r INFO @ Thu, 16 Apr 2020 05:21:12: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:21:12: #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 05:21:17: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:21:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6708278/SRX6708278.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6708278/SRX6708278.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6708278/SRX6708278.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6708278/SRX6708278.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 05:21:18: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:21:18: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:21:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6708278/SRX6708278.05_peaks.xls INFO @ Thu, 16 Apr 2020 05:21:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6708278/SRX6708278.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:21:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6708278/SRX6708278.05_summits.bed INFO @ Thu, 16 Apr 2020 05:21:20: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (2915 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 05:21:24: 1000000 INFO @ Thu, 16 Apr 2020 05:21:29: 2000000 INFO @ Thu, 16 Apr 2020 05:21:34: 3000000 INFO @ Thu, 16 Apr 2020 05:21:39: 4000000 INFO @ Thu, 16 Apr 2020 05:21:42: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 05:21:42: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 05:21:42: #1 total tags in treatment: 2114457 INFO @ Thu, 16 Apr 2020 05:21:42: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:21:42: #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 05:21:42: #1 tags after filtering in treatment: 2055331 INFO @ Thu, 16 Apr 2020 05:21:42: #1 Redundant rate of treatment: 0.03 INFO @ Thu, 16 Apr 2020 05:21:42: #1 finished! INFO @ Thu, 16 Apr 2020 05:21:42: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:21:42: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:21:42: #2 number of paired peaks: 3129 INFO @ Thu, 16 Apr 2020 05:21:42: start model_add_line... INFO @ Thu, 16 Apr 2020 05:21:42: start X-correlation... INFO @ Thu, 16 Apr 2020 05:21:42: end of X-cor INFO @ Thu, 16 Apr 2020 05:21:42: #2 finished! INFO @ Thu, 16 Apr 2020 05:21:42: #2 predicted fragment length is 176 bps INFO @ Thu, 16 Apr 2020 05:21:42: #2 alternative fragment length(s) may be 176 bps INFO @ Thu, 16 Apr 2020 05:21:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6708278/SRX6708278.10_model.r INFO @ Thu, 16 Apr 2020 05:21:42: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:21:42: #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 05:21:47: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:21:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6708278/SRX6708278.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6708278/SRX6708278.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6708278/SRX6708278.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6708278/SRX6708278.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 05:21:48: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:21:48: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:21:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6708278/SRX6708278.10_peaks.xls INFO @ Thu, 16 Apr 2020 05:21:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6708278/SRX6708278.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:21:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6708278/SRX6708278.10_summits.bed INFO @ Thu, 16 Apr 2020 05:21:50: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (1061 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 05:21:54: 1000000 INFO @ Thu, 16 Apr 2020 05:21:59: 2000000 INFO @ Thu, 16 Apr 2020 05:22:03: 3000000 INFO @ Thu, 16 Apr 2020 05:22:08: 4000000 INFO @ Thu, 16 Apr 2020 05:22:12: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 05:22:12: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 05:22:12: #1 total tags in treatment: 2114457 INFO @ Thu, 16 Apr 2020 05:22:12: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:22:12: #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 05:22:12: #1 tags after filtering in treatment: 2055331 INFO @ Thu, 16 Apr 2020 05:22:12: #1 Redundant rate of treatment: 0.03 INFO @ Thu, 16 Apr 2020 05:22:12: #1 finished! INFO @ Thu, 16 Apr 2020 05:22:12: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:22:12: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:22:12: #2 number of paired peaks: 3129 INFO @ Thu, 16 Apr 2020 05:22:12: start model_add_line... INFO @ Thu, 16 Apr 2020 05:22:12: start X-correlation... INFO @ Thu, 16 Apr 2020 05:22:12: end of X-cor INFO @ Thu, 16 Apr 2020 05:22:12: #2 finished! INFO @ Thu, 16 Apr 2020 05:22:12: #2 predicted fragment length is 176 bps INFO @ Thu, 16 Apr 2020 05:22:12: #2 alternative fragment length(s) may be 176 bps INFO @ Thu, 16 Apr 2020 05:22:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6708278/SRX6708278.20_model.r INFO @ Thu, 16 Apr 2020 05:22:12: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:22:12: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:22:17: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:22:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6708278/SRX6708278.20_peaks.xls INFO @ Thu, 16 Apr 2020 05:22:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6708278/SRX6708278.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:22:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6708278/SRX6708278.20_summits.bed INFO @ Thu, 16 Apr 2020 05:22:20: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (313 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。