Job ID = 5720672 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 8,504,566 reads read : 8,504,566 reads written : 8,504,566 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR5289766.sra.cache’: 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: 00:01:52 8504566 reads; of these: 8504566 (100.00%) were unpaired; of these: 2815593 (33.11%) aligned 0 times 4615048 (54.27%) aligned exactly 1 time 1073925 (12.63%) aligned >1 times 66.89% overall alignment rate Time searching: 00:01:52 Overall time: 00:01:52 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] 1337978 / 5688973 = 0.2352 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 00:53:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592489/SRX2592489.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592489/SRX2592489.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592489/SRX2592489.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592489/SRX2592489.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 00:53:36: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:53:36: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:53:42: 1000000 INFO @ Thu, 16 Apr 2020 00:53:48: 2000000 INFO @ Thu, 16 Apr 2020 00:53:54: 3000000 INFO @ Thu, 16 Apr 2020 00:54:00: 4000000 INFO @ Thu, 16 Apr 2020 00:54:02: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 00:54:02: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 00:54:02: #1 total tags in treatment: 4350995 INFO @ Thu, 16 Apr 2020 00:54:02: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:54:02: #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 00:54:02: #1 tags after filtering in treatment: 4350995 INFO @ Thu, 16 Apr 2020 00:54:02: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:54:02: #1 finished! INFO @ Thu, 16 Apr 2020 00:54:02: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:54:02: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:54:03: #2 number of paired peaks: 3230 INFO @ Thu, 16 Apr 2020 00:54:03: start model_add_line... INFO @ Thu, 16 Apr 2020 00:54:03: start X-correlation... INFO @ Thu, 16 Apr 2020 00:54:03: end of X-cor INFO @ Thu, 16 Apr 2020 00:54:03: #2 finished! INFO @ Thu, 16 Apr 2020 00:54:03: #2 predicted fragment length is 137 bps INFO @ Thu, 16 Apr 2020 00:54:03: #2 alternative fragment length(s) may be 137 bps INFO @ Thu, 16 Apr 2020 00:54:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592489/SRX2592489.05_model.r INFO @ Thu, 16 Apr 2020 00:54:03: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:54:03: #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 00:54:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592489/SRX2592489.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592489/SRX2592489.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592489/SRX2592489.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592489/SRX2592489.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 00:54:06: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:54:06: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:54:13: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:54:14: 1000000 INFO @ Thu, 16 Apr 2020 00:54:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592489/SRX2592489.05_peaks.xls INFO @ Thu, 16 Apr 2020 00:54:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592489/SRX2592489.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:54:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592489/SRX2592489.05_summits.bed INFO @ Thu, 16 Apr 2020 00:54:19: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (6870 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 00:54:22: 2000000 INFO @ Thu, 16 Apr 2020 00:54:28: 3000000 BedGraph に変換中... INFO @ Thu, 16 Apr 2020 00:54:34: 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 00:54:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592489/SRX2592489.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592489/SRX2592489.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592489/SRX2592489.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592489/SRX2592489.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 00:54:36: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:54:36: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:54:36: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 00:54:36: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 00:54:36: #1 total tags in treatment: 4350995 INFO @ Thu, 16 Apr 2020 00:54:36: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:54:36: #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 00:54:36: #1 tags after filtering in treatment: 4350995 INFO @ Thu, 16 Apr 2020 00:54:36: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:54:36: #1 finished! INFO @ Thu, 16 Apr 2020 00:54:36: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:54:36: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:54:37: #2 number of paired peaks: 3230 INFO @ Thu, 16 Apr 2020 00:54:37: start model_add_line... INFO @ Thu, 16 Apr 2020 00:54:37: start X-correlation... INFO @ Thu, 16 Apr 2020 00:54:37: end of X-cor INFO @ Thu, 16 Apr 2020 00:54:37: #2 finished! INFO @ Thu, 16 Apr 2020 00:54:37: #2 predicted fragment length is 137 bps INFO @ Thu, 16 Apr 2020 00:54:37: #2 alternative fragment length(s) may be 137 bps INFO @ Thu, 16 Apr 2020 00:54:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592489/SRX2592489.10_model.r INFO @ Thu, 16 Apr 2020 00:54:37: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:54:37: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:54:42: 1000000 INFO @ Thu, 16 Apr 2020 00:54:47: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:54:48: 2000000 INFO @ Thu, 16 Apr 2020 00:54:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592489/SRX2592489.10_peaks.xls INFO @ Thu, 16 Apr 2020 00:54:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592489/SRX2592489.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:54:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592489/SRX2592489.10_summits.bed INFO @ Thu, 16 Apr 2020 00:54:52: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3861 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 00:54:54: 3000000 INFO @ Thu, 16 Apr 2020 00:55:00: 4000000 INFO @ Thu, 16 Apr 2020 00:55:02: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 00:55:02: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 00:55:02: #1 total tags in treatment: 4350995 INFO @ Thu, 16 Apr 2020 00:55:02: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:55:02: #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 00:55:02: #1 tags after filtering in treatment: 4350995 INFO @ Thu, 16 Apr 2020 00:55:02: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:55:02: #1 finished! INFO @ Thu, 16 Apr 2020 00:55:02: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:55:02: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:55:03: #2 number of paired peaks: 3230 INFO @ Thu, 16 Apr 2020 00:55:03: start model_add_line... INFO @ Thu, 16 Apr 2020 00:55:03: start X-correlation... INFO @ Thu, 16 Apr 2020 00:55:03: end of X-cor INFO @ Thu, 16 Apr 2020 00:55:03: #2 finished! INFO @ Thu, 16 Apr 2020 00:55:03: #2 predicted fragment length is 137 bps INFO @ Thu, 16 Apr 2020 00:55:03: #2 alternative fragment length(s) may be 137 bps INFO @ Thu, 16 Apr 2020 00:55:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592489/SRX2592489.20_model.r INFO @ Thu, 16 Apr 2020 00:55:03: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:55:03: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:55:14: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:55:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592489/SRX2592489.20_peaks.xls INFO @ Thu, 16 Apr 2020 00:55:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592489/SRX2592489.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:55:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592489/SRX2592489.20_summits.bed INFO @ Thu, 16 Apr 2020 00:55:19: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1791 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。