Job ID = 5721284 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 9,829,976 reads read : 19,659,952 reads written : 9,829,976 reads 0-length : 9,829,976 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: 00:02:23 9829976 reads; of these: 9829976 (100.00%) were unpaired; of these: 272104 (2.77%) aligned 0 times 8154721 (82.96%) aligned exactly 1 time 1403151 (14.27%) aligned >1 times 97.23% overall alignment rate Time searching: 00:02:23 Overall time: 00:02:23 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_rmdupse_core] 1117501 / 9557872 = 0.1169 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 06:19:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7299241/SRX7299241.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7299241/SRX7299241.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7299241/SRX7299241.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7299241/SRX7299241.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 06:19:39: #1 read tag files... INFO @ Thu, 16 Apr 2020 06:19:39: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 06:19:44: 1000000 INFO @ Thu, 16 Apr 2020 06:19:49: 2000000 INFO @ Thu, 16 Apr 2020 06:19:54: 3000000 INFO @ Thu, 16 Apr 2020 06:19:59: 4000000 INFO @ Thu, 16 Apr 2020 06:20:04: 5000000 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 06:20:09: 6000000 INFO @ Thu, 16 Apr 2020 06:20:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7299241/SRX7299241.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7299241/SRX7299241.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7299241/SRX7299241.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7299241/SRX7299241.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 06:20:09: #1 read tag files... INFO @ Thu, 16 Apr 2020 06:20:09: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 06:20:14: 7000000 INFO @ Thu, 16 Apr 2020 06:20:14: 1000000 INFO @ Thu, 16 Apr 2020 06:20:19: 8000000 INFO @ Thu, 16 Apr 2020 06:20:19: 2000000 INFO @ Thu, 16 Apr 2020 06:20:21: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 06:20:21: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 06:20:21: #1 total tags in treatment: 8440371 INFO @ Thu, 16 Apr 2020 06:20:21: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:20:21: #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 06:20:21: #1 tags after filtering in treatment: 8440371 INFO @ Thu, 16 Apr 2020 06:20:21: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 06:20:21: #1 finished! INFO @ Thu, 16 Apr 2020 06:20:21: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:20:21: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:20:22: #2 number of paired peaks: 3859 INFO @ Thu, 16 Apr 2020 06:20:22: start model_add_line... INFO @ Thu, 16 Apr 2020 06:20:22: start X-correlation... INFO @ Thu, 16 Apr 2020 06:20:22: end of X-cor INFO @ Thu, 16 Apr 2020 06:20:22: #2 finished! INFO @ Thu, 16 Apr 2020 06:20:22: #2 predicted fragment length is 162 bps INFO @ Thu, 16 Apr 2020 06:20:22: #2 alternative fragment length(s) may be 162 bps INFO @ Thu, 16 Apr 2020 06:20:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7299241/SRX7299241.05_model.r INFO @ Thu, 16 Apr 2020 06:20:22: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:20:22: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 06:20:24: 3000000 INFO @ Thu, 16 Apr 2020 06:20:29: 4000000 INFO @ Thu, 16 Apr 2020 06:20:34: 5000000 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 06:20:39: 6000000 INFO @ Thu, 16 Apr 2020 06:20:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7299241/SRX7299241.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7299241/SRX7299241.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7299241/SRX7299241.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7299241/SRX7299241.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 06:20:39: #1 read tag files... INFO @ Thu, 16 Apr 2020 06:20:39: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 06:20:43: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:20:44: 7000000 INFO @ Thu, 16 Apr 2020 06:20:45: 1000000 INFO @ Thu, 16 Apr 2020 06:20:49: 8000000 INFO @ Thu, 16 Apr 2020 06:20:50: 2000000 INFO @ Thu, 16 Apr 2020 06:20:51: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 06:20:51: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 06:20:51: #1 total tags in treatment: 8440371 INFO @ Thu, 16 Apr 2020 06:20:51: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:20:51: #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 06:20:51: #1 tags after filtering in treatment: 8440371 INFO @ Thu, 16 Apr 2020 06:20:51: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 06:20:51: #1 finished! INFO @ Thu, 16 Apr 2020 06:20:51: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:20:51: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:20:52: #2 number of paired peaks: 3859 INFO @ Thu, 16 Apr 2020 06:20:52: start model_add_line... INFO @ Thu, 16 Apr 2020 06:20:52: start X-correlation... INFO @ Thu, 16 Apr 2020 06:20:52: end of X-cor INFO @ Thu, 16 Apr 2020 06:20:52: #2 finished! INFO @ Thu, 16 Apr 2020 06:20:52: #2 predicted fragment length is 162 bps INFO @ Thu, 16 Apr 2020 06:20:52: #2 alternative fragment length(s) may be 162 bps INFO @ Thu, 16 Apr 2020 06:20:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7299241/SRX7299241.10_model.r INFO @ Thu, 16 Apr 2020 06:20:52: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:20:52: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 06:20:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7299241/SRX7299241.05_peaks.xls INFO @ Thu, 16 Apr 2020 06:20:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7299241/SRX7299241.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:20:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7299241/SRX7299241.05_summits.bed INFO @ Thu, 16 Apr 2020 06:20:53: Done! pass1 - making usageList (12 chroms): 2 millis pass2 - checking and writing primary data (10064 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 06:20:55: 3000000 INFO @ Thu, 16 Apr 2020 06:21:01: 4000000 INFO @ Thu, 16 Apr 2020 06:21:06: 5000000 INFO @ Thu, 16 Apr 2020 06:21:11: 6000000 INFO @ Thu, 16 Apr 2020 06:21:14: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:21:16: 7000000 INFO @ Thu, 16 Apr 2020 06:21:21: 8000000 INFO @ Thu, 16 Apr 2020 06:21:23: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 06:21:23: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 06:21:23: #1 total tags in treatment: 8440371 INFO @ Thu, 16 Apr 2020 06:21:23: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:21:23: #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 06:21:23: #1 tags after filtering in treatment: 8440371 INFO @ Thu, 16 Apr 2020 06:21:23: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 06:21:23: #1 finished! INFO @ Thu, 16 Apr 2020 06:21:23: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:21:23: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:21:24: #2 number of paired peaks: 3859 INFO @ Thu, 16 Apr 2020 06:21:24: start model_add_line... INFO @ Thu, 16 Apr 2020 06:21:24: start X-correlation... INFO @ Thu, 16 Apr 2020 06:21:24: end of X-cor INFO @ Thu, 16 Apr 2020 06:21:24: #2 finished! INFO @ Thu, 16 Apr 2020 06:21:24: #2 predicted fragment length is 162 bps INFO @ Thu, 16 Apr 2020 06:21:24: #2 alternative fragment length(s) may be 162 bps INFO @ Thu, 16 Apr 2020 06:21:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7299241/SRX7299241.20_model.r INFO @ Thu, 16 Apr 2020 06:21:24: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:21:24: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 06:21:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7299241/SRX7299241.10_peaks.xls INFO @ Thu, 16 Apr 2020 06:21:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7299241/SRX7299241.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:21:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7299241/SRX7299241.10_summits.bed INFO @ Thu, 16 Apr 2020 06:21:25: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (6837 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 06:21:44: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:21:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7299241/SRX7299241.20_peaks.xls INFO @ Thu, 16 Apr 2020 06:21:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7299241/SRX7299241.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:21:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7299241/SRX7299241.20_summits.bed INFO @ Thu, 16 Apr 2020 06:21:54: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (3835 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。