Job ID = 5721173 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 13,437,077 reads read : 26,874,154 reads written : 26,874,154 spots read : 13,437,368 reads read : 26,874,736 reads written : 26,874,736 spots read : 13,072,170 reads read : 26,144,340 reads written : 26,144,340 spots read : 13,173,282 reads read : 26,346,564 reads written : 26,346,564 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: 00:10:13 53119897 reads; of these: 53119897 (100.00%) were paired; of these: 51192543 (96.37%) aligned concordantly 0 times 1432249 (2.70%) aligned concordantly exactly 1 time 495105 (0.93%) aligned concordantly >1 times ---- 51192543 pairs aligned concordantly 0 times; of these: 14731 (0.03%) aligned discordantly 1 time ---- 51177812 pairs aligned 0 times concordantly or discordantly; of these: 102355624 mates make up the pairs; of these: 101282994 (98.95%) aligned 0 times 189148 (0.18%) aligned exactly 1 time 883482 (0.86%) aligned >1 times 4.67% overall alignment rate Time searching: 00:10:13 Overall time: 00:10:13 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] 81528 / 1940250 = 0.0420 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 06:11:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6762285/SRX6762285.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6762285/SRX6762285.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6762285/SRX6762285.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6762285/SRX6762285.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 06:11:26: #1 read tag files... INFO @ Thu, 16 Apr 2020 06:11:26: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 06:11:32: 1000000 INFO @ Thu, 16 Apr 2020 06:11:38: 2000000 INFO @ Thu, 16 Apr 2020 06:11:45: 3000000 INFO @ Thu, 16 Apr 2020 06:11:50: 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 06:11:55: #1 tag size is determined as 40 bps INFO @ Thu, 16 Apr 2020 06:11:55: #1 tag size = 40 INFO @ Thu, 16 Apr 2020 06:11:55: #1 total tags in treatment: 1845997 INFO @ Thu, 16 Apr 2020 06:11:55: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:11:55: #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 06:11:55: #1 tags after filtering in treatment: 1718903 INFO @ Thu, 16 Apr 2020 06:11:55: #1 Redundant rate of treatment: 0.07 INFO @ Thu, 16 Apr 2020 06:11:55: #1 finished! INFO @ Thu, 16 Apr 2020 06:11:55: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:11:55: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:11:55: #2 number of paired peaks: 5275 INFO @ Thu, 16 Apr 2020 06:11:55: start model_add_line... INFO @ Thu, 16 Apr 2020 06:11:55: start X-correlation... INFO @ Thu, 16 Apr 2020 06:11:55: end of X-cor INFO @ Thu, 16 Apr 2020 06:11:55: #2 finished! INFO @ Thu, 16 Apr 2020 06:11:55: #2 predicted fragment length is 206 bps INFO @ Thu, 16 Apr 2020 06:11:55: #2 alternative fragment length(s) may be 206 bps INFO @ Thu, 16 Apr 2020 06:11:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6762285/SRX6762285.05_model.r INFO @ Thu, 16 Apr 2020 06:11:55: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:11:55: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 06:11:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6762285/SRX6762285.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6762285/SRX6762285.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6762285/SRX6762285.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6762285/SRX6762285.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 06:11:56: #1 read tag files... INFO @ Thu, 16 Apr 2020 06:11:56: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 06:11:59: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:12:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6762285/SRX6762285.05_peaks.xls INFO @ Thu, 16 Apr 2020 06:12:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6762285/SRX6762285.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:12:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6762285/SRX6762285.05_summits.bed INFO @ Thu, 16 Apr 2020 06:12:01: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (2741 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 06:12:02: 1000000 INFO @ Thu, 16 Apr 2020 06:12:07: 2000000 INFO @ Thu, 16 Apr 2020 06:12:13: 3000000 INFO @ Thu, 16 Apr 2020 06:12:18: 4000000 INFO @ Thu, 16 Apr 2020 06:12:22: #1 tag size is determined as 40 bps INFO @ Thu, 16 Apr 2020 06:12:22: #1 tag size = 40 INFO @ Thu, 16 Apr 2020 06:12:22: #1 total tags in treatment: 1845997 INFO @ Thu, 16 Apr 2020 06:12:22: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:12:22: #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 06:12:22: #1 tags after filtering in treatment: 1718903 INFO @ Thu, 16 Apr 2020 06:12:22: #1 Redundant rate of treatment: 0.07 INFO @ Thu, 16 Apr 2020 06:12:22: #1 finished! INFO @ Thu, 16 Apr 2020 06:12:22: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:12:22: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:12:22: #2 number of paired peaks: 5275 INFO @ Thu, 16 Apr 2020 06:12:22: start model_add_line... INFO @ Thu, 16 Apr 2020 06:12:22: start X-correlation... INFO @ Thu, 16 Apr 2020 06:12:22: end of X-cor INFO @ Thu, 16 Apr 2020 06:12:22: #2 finished! INFO @ Thu, 16 Apr 2020 06:12:22: #2 predicted fragment length is 206 bps INFO @ Thu, 16 Apr 2020 06:12:22: #2 alternative fragment length(s) may be 206 bps INFO @ Thu, 16 Apr 2020 06:12:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6762285/SRX6762285.10_model.r INFO @ Thu, 16 Apr 2020 06:12:22: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:12:22: #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 06:12:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6762285/SRX6762285.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6762285/SRX6762285.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6762285/SRX6762285.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6762285/SRX6762285.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 06:12:26: #1 read tag files... INFO @ Thu, 16 Apr 2020 06:12:26: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 06:12:26: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:12:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6762285/SRX6762285.10_peaks.xls INFO @ Thu, 16 Apr 2020 06:12:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6762285/SRX6762285.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:12:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6762285/SRX6762285.10_summits.bed INFO @ Thu, 16 Apr 2020 06:12:29: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1045 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 06:12:32: 1000000 INFO @ Thu, 16 Apr 2020 06:12:38: 2000000 INFO @ Thu, 16 Apr 2020 06:12:43: 3000000 INFO @ Thu, 16 Apr 2020 06:12:48: 4000000 INFO @ Thu, 16 Apr 2020 06:12:52: #1 tag size is determined as 40 bps INFO @ Thu, 16 Apr 2020 06:12:52: #1 tag size = 40 INFO @ Thu, 16 Apr 2020 06:12:52: #1 total tags in treatment: 1845997 INFO @ Thu, 16 Apr 2020 06:12:52: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:12:52: #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 06:12:52: #1 tags after filtering in treatment: 1718903 INFO @ Thu, 16 Apr 2020 06:12:52: #1 Redundant rate of treatment: 0.07 INFO @ Thu, 16 Apr 2020 06:12:52: #1 finished! INFO @ Thu, 16 Apr 2020 06:12:52: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:12:52: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:12:53: #2 number of paired peaks: 5275 INFO @ Thu, 16 Apr 2020 06:12:53: start model_add_line... INFO @ Thu, 16 Apr 2020 06:12:53: start X-correlation... INFO @ Thu, 16 Apr 2020 06:12:53: end of X-cor INFO @ Thu, 16 Apr 2020 06:12:53: #2 finished! INFO @ Thu, 16 Apr 2020 06:12:53: #2 predicted fragment length is 206 bps INFO @ Thu, 16 Apr 2020 06:12:53: #2 alternative fragment length(s) may be 206 bps INFO @ Thu, 16 Apr 2020 06:12:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6762285/SRX6762285.20_model.r INFO @ Thu, 16 Apr 2020 06:12:53: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:12:53: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 06:12:57: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:12:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6762285/SRX6762285.20_peaks.xls INFO @ Thu, 16 Apr 2020 06:12:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6762285/SRX6762285.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:12:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6762285/SRX6762285.20_summits.bed INFO @ Thu, 16 Apr 2020 06:12:59: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (342 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。