Job ID = 5720702 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 4,162,103 reads read : 4,162,103 reads written : 4,162,103 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: 00:00:57 4162103 reads; of these: 4162103 (100.00%) were unpaired; of these: 167362 (4.02%) aligned 0 times 3627121 (87.15%) aligned exactly 1 time 367620 (8.83%) aligned >1 times 95.98% overall alignment rate Time searching: 00:00:57 Overall time: 00:00:57 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] 402054 / 3994741 = 0.1006 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 01:01:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4158166/SRX4158166.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4158166/SRX4158166.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4158166/SRX4158166.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4158166/SRX4158166.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 01:01:16: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:01:16: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:01:22: 1000000 INFO @ Thu, 16 Apr 2020 01:01:27: 2000000 INFO @ Thu, 16 Apr 2020 01:01:32: 3000000 INFO @ Thu, 16 Apr 2020 01:01:35: #1 tag size is determined as 49 bps INFO @ Thu, 16 Apr 2020 01:01:35: #1 tag size = 49 INFO @ Thu, 16 Apr 2020 01:01:35: #1 total tags in treatment: 3592687 INFO @ Thu, 16 Apr 2020 01:01:35: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:01:35: #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 01:01:35: #1 tags after filtering in treatment: 3592687 INFO @ Thu, 16 Apr 2020 01:01:35: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:01:35: #1 finished! INFO @ Thu, 16 Apr 2020 01:01:35: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:01:35: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:01:36: #2 number of paired peaks: 6993 INFO @ Thu, 16 Apr 2020 01:01:36: start model_add_line... INFO @ Thu, 16 Apr 2020 01:01:36: start X-correlation... INFO @ Thu, 16 Apr 2020 01:01:36: end of X-cor INFO @ Thu, 16 Apr 2020 01:01:36: #2 finished! INFO @ Thu, 16 Apr 2020 01:01:36: #2 predicted fragment length is 167 bps INFO @ Thu, 16 Apr 2020 01:01:36: #2 alternative fragment length(s) may be 167 bps INFO @ Thu, 16 Apr 2020 01:01:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4158166/SRX4158166.05_model.r INFO @ Thu, 16 Apr 2020 01:01:36: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:01:36: #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 01:01:46: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:01:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4158166/SRX4158166.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4158166/SRX4158166.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4158166/SRX4158166.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4158166/SRX4158166.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 01:01:46: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:01:46: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:01:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4158166/SRX4158166.05_peaks.xls INFO @ Thu, 16 Apr 2020 01:01:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4158166/SRX4158166.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:01:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4158166/SRX4158166.05_summits.bed INFO @ Thu, 16 Apr 2020 01:01:51: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (6091 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 01:01:51: 1000000 INFO @ Thu, 16 Apr 2020 01:01:57: 2000000 INFO @ Thu, 16 Apr 2020 01:02:02: 3000000 INFO @ Thu, 16 Apr 2020 01:02:05: #1 tag size is determined as 49 bps INFO @ Thu, 16 Apr 2020 01:02:05: #1 tag size = 49 INFO @ Thu, 16 Apr 2020 01:02:05: #1 total tags in treatment: 3592687 INFO @ Thu, 16 Apr 2020 01:02:05: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:02:05: #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 01:02:05: #1 tags after filtering in treatment: 3592687 INFO @ Thu, 16 Apr 2020 01:02:05: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:02:05: #1 finished! INFO @ Thu, 16 Apr 2020 01:02:05: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:02:05: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:02:06: #2 number of paired peaks: 6993 INFO @ Thu, 16 Apr 2020 01:02:06: start model_add_line... INFO @ Thu, 16 Apr 2020 01:02:06: start X-correlation... INFO @ Thu, 16 Apr 2020 01:02:06: end of X-cor INFO @ Thu, 16 Apr 2020 01:02:06: #2 finished! INFO @ Thu, 16 Apr 2020 01:02:06: #2 predicted fragment length is 167 bps INFO @ Thu, 16 Apr 2020 01:02:06: #2 alternative fragment length(s) may be 167 bps INFO @ Thu, 16 Apr 2020 01:02:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4158166/SRX4158166.10_model.r INFO @ Thu, 16 Apr 2020 01:02:06: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:02:06: #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 01:02:16: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:02:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4158166/SRX4158166.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4158166/SRX4158166.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4158166/SRX4158166.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4158166/SRX4158166.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 01:02:16: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:02:16: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:02:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4158166/SRX4158166.10_peaks.xls INFO @ Thu, 16 Apr 2020 01:02:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4158166/SRX4158166.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:02:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4158166/SRX4158166.10_summits.bed INFO @ Thu, 16 Apr 2020 01:02:21: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (5154 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 01:02:22: 1000000 INFO @ Thu, 16 Apr 2020 01:02:27: 2000000 INFO @ Thu, 16 Apr 2020 01:02:32: 3000000 INFO @ Thu, 16 Apr 2020 01:02:35: #1 tag size is determined as 49 bps INFO @ Thu, 16 Apr 2020 01:02:35: #1 tag size = 49 INFO @ Thu, 16 Apr 2020 01:02:35: #1 total tags in treatment: 3592687 INFO @ Thu, 16 Apr 2020 01:02:35: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:02:35: #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 01:02:35: #1 tags after filtering in treatment: 3592687 INFO @ Thu, 16 Apr 2020 01:02:35: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:02:35: #1 finished! INFO @ Thu, 16 Apr 2020 01:02:35: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:02:35: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:02:36: #2 number of paired peaks: 6993 INFO @ Thu, 16 Apr 2020 01:02:36: start model_add_line... INFO @ Thu, 16 Apr 2020 01:02:36: start X-correlation... INFO @ Thu, 16 Apr 2020 01:02:36: end of X-cor INFO @ Thu, 16 Apr 2020 01:02:36: #2 finished! INFO @ Thu, 16 Apr 2020 01:02:36: #2 predicted fragment length is 167 bps INFO @ Thu, 16 Apr 2020 01:02:36: #2 alternative fragment length(s) may be 167 bps INFO @ Thu, 16 Apr 2020 01:02:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4158166/SRX4158166.20_model.r INFO @ Thu, 16 Apr 2020 01:02:36: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:02:36: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:02:47: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:02:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4158166/SRX4158166.20_peaks.xls INFO @ Thu, 16 Apr 2020 01:02:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4158166/SRX4158166.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:02:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4158166/SRX4158166.20_summits.bed INFO @ Thu, 16 Apr 2020 01:02:52: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (3764 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。