Job ID = 5721137 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 3,064,436 reads read : 6,128,872 reads written : 6,128,872 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: 00:04:21 3064436 reads; of these: 3064436 (100.00%) were paired; of these: 473775 (15.46%) aligned concordantly 0 times 2229577 (72.76%) aligned concordantly exactly 1 time 361084 (11.78%) aligned concordantly >1 times ---- 473775 pairs aligned concordantly 0 times; of these: 216980 (45.80%) aligned discordantly 1 time ---- 256795 pairs aligned 0 times concordantly or discordantly; of these: 513590 mates make up the pairs; of these: 276293 (53.80%) aligned 0 times 131671 (25.64%) aligned exactly 1 time 105626 (20.57%) aligned >1 times 95.49% overall alignment rate Time searching: 00:04:21 Overall time: 00:04:21 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] 90940 / 2800615 = 0.0325 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 05:20:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6708277/SRX6708277.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6708277/SRX6708277.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6708277/SRX6708277.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6708277/SRX6708277.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 05:20:54: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:20:54: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:21:00: 1000000 INFO @ Thu, 16 Apr 2020 05:21:07: 2000000 INFO @ Thu, 16 Apr 2020 05:21:13: 3000000 INFO @ Thu, 16 Apr 2020 05:21:20: 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 05:21:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6708277/SRX6708277.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6708277/SRX6708277.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6708277/SRX6708277.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6708277/SRX6708277.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 05:21:23: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:21:23: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:21:27: 5000000 INFO @ Thu, 16 Apr 2020 05:21:30: 1000000 INFO @ Thu, 16 Apr 2020 05:21:31: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 05:21:31: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 05:21:31: #1 total tags in treatment: 2505285 INFO @ Thu, 16 Apr 2020 05:21:31: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:21:31: #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 05:21:31: #1 tags after filtering in treatment: 2444480 INFO @ Thu, 16 Apr 2020 05:21:31: #1 Redundant rate of treatment: 0.02 INFO @ Thu, 16 Apr 2020 05:21:31: #1 finished! INFO @ Thu, 16 Apr 2020 05:21:31: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:21:31: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:21:32: #2 number of paired peaks: 2981 INFO @ Thu, 16 Apr 2020 05:21:32: start model_add_line... INFO @ Thu, 16 Apr 2020 05:21:32: start X-correlation... INFO @ Thu, 16 Apr 2020 05:21:32: end of X-cor INFO @ Thu, 16 Apr 2020 05:21:32: #2 finished! INFO @ Thu, 16 Apr 2020 05:21:32: #2 predicted fragment length is 200 bps INFO @ Thu, 16 Apr 2020 05:21:32: #2 alternative fragment length(s) may be 200 bps INFO @ Thu, 16 Apr 2020 05:21:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6708277/SRX6708277.05_model.r INFO @ Thu, 16 Apr 2020 05:21:32: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:21:32: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:21:37: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:21:37: 2000000 INFO @ Thu, 16 Apr 2020 05:21:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6708277/SRX6708277.05_peaks.xls INFO @ Thu, 16 Apr 2020 05:21:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6708277/SRX6708277.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:21:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6708277/SRX6708277.05_summits.bed INFO @ Thu, 16 Apr 2020 05:21:40: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (1510 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 05:21:44: 3000000 INFO @ Thu, 16 Apr 2020 05:21:50: 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 05:21:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6708277/SRX6708277.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6708277/SRX6708277.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6708277/SRX6708277.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6708277/SRX6708277.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 05:21:53: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:21:53: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:21:57: 5000000 INFO @ Thu, 16 Apr 2020 05:22:00: 1000000 INFO @ Thu, 16 Apr 2020 05:22:02: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 05:22:02: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 05:22:02: #1 total tags in treatment: 2505285 INFO @ Thu, 16 Apr 2020 05:22:02: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:22:02: #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 05:22:02: #1 tags after filtering in treatment: 2444480 INFO @ Thu, 16 Apr 2020 05:22:02: #1 Redundant rate of treatment: 0.02 INFO @ Thu, 16 Apr 2020 05:22:02: #1 finished! INFO @ Thu, 16 Apr 2020 05:22:02: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:22:02: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:22:02: #2 number of paired peaks: 2981 INFO @ Thu, 16 Apr 2020 05:22:02: start model_add_line... INFO @ Thu, 16 Apr 2020 05:22:02: start X-correlation... INFO @ Thu, 16 Apr 2020 05:22:02: end of X-cor INFO @ Thu, 16 Apr 2020 05:22:02: #2 finished! INFO @ Thu, 16 Apr 2020 05:22:02: #2 predicted fragment length is 200 bps INFO @ Thu, 16 Apr 2020 05:22:02: #2 alternative fragment length(s) may be 200 bps INFO @ Thu, 16 Apr 2020 05:22:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6708277/SRX6708277.10_model.r INFO @ Thu, 16 Apr 2020 05:22:02: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:22:02: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:22:07: 2000000 INFO @ Thu, 16 Apr 2020 05:22:08: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:22:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6708277/SRX6708277.10_peaks.xls INFO @ Thu, 16 Apr 2020 05:22:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6708277/SRX6708277.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:22:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6708277/SRX6708277.10_summits.bed INFO @ Thu, 16 Apr 2020 05:22:11: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (440 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 05:22:14: 3000000 INFO @ Thu, 16 Apr 2020 05:22:20: 4000000 INFO @ Thu, 16 Apr 2020 05:22:27: 5000000 INFO @ Thu, 16 Apr 2020 05:22:31: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 05:22:31: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 05:22:31: #1 total tags in treatment: 2505285 INFO @ Thu, 16 Apr 2020 05:22:31: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:22:31: #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 05:22:31: #1 tags after filtering in treatment: 2444480 INFO @ Thu, 16 Apr 2020 05:22:31: #1 Redundant rate of treatment: 0.02 INFO @ Thu, 16 Apr 2020 05:22:31: #1 finished! INFO @ Thu, 16 Apr 2020 05:22:31: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:22:31: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:22:32: #2 number of paired peaks: 2981 INFO @ Thu, 16 Apr 2020 05:22:32: start model_add_line... INFO @ Thu, 16 Apr 2020 05:22:32: start X-correlation... INFO @ Thu, 16 Apr 2020 05:22:32: end of X-cor INFO @ Thu, 16 Apr 2020 05:22:32: #2 finished! INFO @ Thu, 16 Apr 2020 05:22:32: #2 predicted fragment length is 200 bps INFO @ Thu, 16 Apr 2020 05:22:32: #2 alternative fragment length(s) may be 200 bps INFO @ Thu, 16 Apr 2020 05:22:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6708277/SRX6708277.20_model.r INFO @ Thu, 16 Apr 2020 05:22:32: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:22:32: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:22:37: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:22:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6708277/SRX6708277.20_peaks.xls INFO @ Thu, 16 Apr 2020 05:22:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6708277/SRX6708277.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:22:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6708277/SRX6708277.20_summits.bed INFO @ Thu, 16 Apr 2020 05:22:40: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (194 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。