Job ID = 5721117 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 11,044,547 reads read : 22,089,094 reads written : 22,089,094 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: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:23:35 11044547 reads; of these: 11044547 (100.00%) were paired; of these: 1288743 (11.67%) aligned concordantly 0 times 6853463 (62.05%) aligned concordantly exactly 1 time 2902341 (26.28%) aligned concordantly >1 times ---- 1288743 pairs aligned concordantly 0 times; of these: 456751 (35.44%) aligned discordantly 1 time ---- 831992 pairs aligned 0 times concordantly or discordantly; of these: 1663984 mates make up the pairs; of these: 912651 (54.85%) aligned 0 times 358851 (21.57%) aligned exactly 1 time 392482 (23.59%) aligned >1 times 95.87% overall alignment rate Time searching: 00:23:36 Overall time: 00:23:36 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] 792482 / 10154945 = 0.0780 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 05:31:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6708260/SRX6708260.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6708260/SRX6708260.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6708260/SRX6708260.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6708260/SRX6708260.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 05:31:12: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:31:12: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:31:19: 1000000 INFO @ Thu, 16 Apr 2020 05:31:25: 2000000 INFO @ Thu, 16 Apr 2020 05:31:31: 3000000 INFO @ Thu, 16 Apr 2020 05:31:36: 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 05:31:42: 5000000 INFO @ Thu, 16 Apr 2020 05:31:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6708260/SRX6708260.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6708260/SRX6708260.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6708260/SRX6708260.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6708260/SRX6708260.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 05:31:43: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:31:43: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:31:49: 6000000 INFO @ Thu, 16 Apr 2020 05:31:49: 1000000 INFO @ Thu, 16 Apr 2020 05:31:55: 7000000 INFO @ Thu, 16 Apr 2020 05:31:55: 2000000 INFO @ Thu, 16 Apr 2020 05:32:01: 8000000 INFO @ Thu, 16 Apr 2020 05:32:02: 3000000 INFO @ Thu, 16 Apr 2020 05:32:08: 9000000 INFO @ Thu, 16 Apr 2020 05:32:08: 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 05:32:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6708260/SRX6708260.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6708260/SRX6708260.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6708260/SRX6708260.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6708260/SRX6708260.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 05:32:13: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:32:13: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:32:14: 10000000 INFO @ Thu, 16 Apr 2020 05:32:14: 5000000 INFO @ Thu, 16 Apr 2020 05:32:19: 1000000 INFO @ Thu, 16 Apr 2020 05:32:21: 11000000 INFO @ Thu, 16 Apr 2020 05:32:21: 6000000 INFO @ Thu, 16 Apr 2020 05:32:25: 2000000 INFO @ Thu, 16 Apr 2020 05:32:27: 12000000 INFO @ Thu, 16 Apr 2020 05:32:27: 7000000 INFO @ Thu, 16 Apr 2020 05:32:32: 3000000 INFO @ Thu, 16 Apr 2020 05:32:33: 13000000 INFO @ Thu, 16 Apr 2020 05:32:33: 8000000 INFO @ Thu, 16 Apr 2020 05:32:38: 4000000 INFO @ Thu, 16 Apr 2020 05:32:39: 14000000 INFO @ Thu, 16 Apr 2020 05:32:40: 9000000 INFO @ Thu, 16 Apr 2020 05:32:44: 5000000 INFO @ Thu, 16 Apr 2020 05:32:46: 15000000 INFO @ Thu, 16 Apr 2020 05:32:46: 10000000 INFO @ Thu, 16 Apr 2020 05:32:51: 6000000 INFO @ Thu, 16 Apr 2020 05:32:52: 16000000 INFO @ Thu, 16 Apr 2020 05:32:52: 11000000 INFO @ Thu, 16 Apr 2020 05:32:57: 7000000 INFO @ Thu, 16 Apr 2020 05:32:58: 17000000 INFO @ Thu, 16 Apr 2020 05:32:59: 12000000 INFO @ Thu, 16 Apr 2020 05:33:03: 8000000 INFO @ Thu, 16 Apr 2020 05:33:05: 18000000 INFO @ Thu, 16 Apr 2020 05:33:05: 13000000 INFO @ Thu, 16 Apr 2020 05:33:10: 9000000 INFO @ Thu, 16 Apr 2020 05:33:11: 19000000 INFO @ Thu, 16 Apr 2020 05:33:11: 14000000 INFO @ Thu, 16 Apr 2020 05:33:15: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 05:33:15: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 05:33:15: #1 total tags in treatment: 8983371 INFO @ Thu, 16 Apr 2020 05:33:15: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:33:15: #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 05:33:15: #1 tags after filtering in treatment: 8365898 INFO @ Thu, 16 Apr 2020 05:33:15: #1 Redundant rate of treatment: 0.07 INFO @ Thu, 16 Apr 2020 05:33:15: #1 finished! INFO @ Thu, 16 Apr 2020 05:33:15: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:33:15: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:33:16: #2 number of paired peaks: 1178 INFO @ Thu, 16 Apr 2020 05:33:16: start model_add_line... INFO @ Thu, 16 Apr 2020 05:33:16: start X-correlation... INFO @ Thu, 16 Apr 2020 05:33:16: end of X-cor INFO @ Thu, 16 Apr 2020 05:33:16: #2 finished! INFO @ Thu, 16 Apr 2020 05:33:16: #2 predicted fragment length is 183 bps INFO @ Thu, 16 Apr 2020 05:33:16: #2 alternative fragment length(s) may be 183 bps INFO @ Thu, 16 Apr 2020 05:33:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6708260/SRX6708260.05_model.r INFO @ Thu, 16 Apr 2020 05:33:16: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:33:16: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:33:16: 10000000 INFO @ Thu, 16 Apr 2020 05:33:18: 15000000 INFO @ Thu, 16 Apr 2020 05:33:22: 11000000 INFO @ Thu, 16 Apr 2020 05:33:24: 16000000 INFO @ Thu, 16 Apr 2020 05:33:29: 12000000 INFO @ Thu, 16 Apr 2020 05:33:30: 17000000 INFO @ Thu, 16 Apr 2020 05:33:35: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:33:35: 13000000 INFO @ Thu, 16 Apr 2020 05:33:37: 18000000 INFO @ Thu, 16 Apr 2020 05:33:41: 14000000 INFO @ Thu, 16 Apr 2020 05:33:43: 19000000 INFO @ Thu, 16 Apr 2020 05:33:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6708260/SRX6708260.05_peaks.xls INFO @ Thu, 16 Apr 2020 05:33:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6708260/SRX6708260.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:33:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6708260/SRX6708260.05_summits.bed INFO @ Thu, 16 Apr 2020 05:33:43: Done! INFO @ Thu, 16 Apr 2020 05:33:46: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 05:33:46: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 05:33:46: #1 total tags in treatment: 8983371 INFO @ Thu, 16 Apr 2020 05:33:46: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:33:46: #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 05:33:47: #1 tags after filtering in treatment: 8365898 INFO @ Thu, 16 Apr 2020 05:33:47: #1 Redundant rate of treatment: 0.07 INFO @ Thu, 16 Apr 2020 05:33:47: #1 finished! INFO @ Thu, 16 Apr 2020 05:33:47: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:33:47: #2 looking for paired plus/minus strand peaks... pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1950 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 05:33:47: 15000000 INFO @ Thu, 16 Apr 2020 05:33:47: #2 number of paired peaks: 1178 INFO @ Thu, 16 Apr 2020 05:33:47: start model_add_line... INFO @ Thu, 16 Apr 2020 05:33:47: start X-correlation... INFO @ Thu, 16 Apr 2020 05:33:47: end of X-cor INFO @ Thu, 16 Apr 2020 05:33:47: #2 finished! INFO @ Thu, 16 Apr 2020 05:33:47: #2 predicted fragment length is 183 bps INFO @ Thu, 16 Apr 2020 05:33:47: #2 alternative fragment length(s) may be 183 bps INFO @ Thu, 16 Apr 2020 05:33:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6708260/SRX6708260.10_model.r INFO @ Thu, 16 Apr 2020 05:33:47: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:33:47: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:33:53: 16000000 INFO @ Thu, 16 Apr 2020 05:33:59: 17000000 INFO @ Thu, 16 Apr 2020 05:34:05: 18000000 INFO @ Thu, 16 Apr 2020 05:34:07: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:34:11: 19000000 INFO @ Thu, 16 Apr 2020 05:34:14: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 05:34:14: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 05:34:14: #1 total tags in treatment: 8983371 INFO @ Thu, 16 Apr 2020 05:34:14: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:34:14: #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 05:34:14: #1 tags after filtering in treatment: 8365898 INFO @ Thu, 16 Apr 2020 05:34:14: #1 Redundant rate of treatment: 0.07 INFO @ Thu, 16 Apr 2020 05:34:14: #1 finished! INFO @ Thu, 16 Apr 2020 05:34:14: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:34:14: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:34:15: #2 number of paired peaks: 1178 INFO @ Thu, 16 Apr 2020 05:34:15: start model_add_line... INFO @ Thu, 16 Apr 2020 05:34:15: start X-correlation... INFO @ Thu, 16 Apr 2020 05:34:15: end of X-cor INFO @ Thu, 16 Apr 2020 05:34:15: #2 finished! INFO @ Thu, 16 Apr 2020 05:34:15: #2 predicted fragment length is 183 bps INFO @ Thu, 16 Apr 2020 05:34:15: #2 alternative fragment length(s) may be 183 bps INFO @ Thu, 16 Apr 2020 05:34:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6708260/SRX6708260.20_model.r INFO @ Thu, 16 Apr 2020 05:34:15: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:34:15: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:34:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6708260/SRX6708260.10_peaks.xls INFO @ Thu, 16 Apr 2020 05:34:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6708260/SRX6708260.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:34:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6708260/SRX6708260.10_summits.bed INFO @ Thu, 16 Apr 2020 05:34:15: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (1169 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 05:34:33: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:34:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6708260/SRX6708260.20_peaks.xls INFO @ Thu, 16 Apr 2020 05:34:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6708260/SRX6708260.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:34:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6708260/SRX6708260.20_summits.bed INFO @ Thu, 16 Apr 2020 05:34:42: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (631 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。