Job ID = 5720722 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 7,935,332 reads read : 7,935,332 reads written : 7,935,332 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: 00:02:43 7935332 reads; of these: 7935332 (100.00%) were unpaired; of these: 546858 (6.89%) aligned 0 times 4329225 (54.56%) aligned exactly 1 time 3059249 (38.55%) aligned >1 times 93.11% overall alignment rate Time searching: 00:02:43 Overall time: 00:02:43 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] 1139751 / 7388474 = 0.1543 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 01:10:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4158194/SRX4158194.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4158194/SRX4158194.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4158194/SRX4158194.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4158194/SRX4158194.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 01:10:12: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:10:12: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:10:18: 1000000 INFO @ Thu, 16 Apr 2020 01:10:24: 2000000 INFO @ Thu, 16 Apr 2020 01:10:30: 3000000 INFO @ Thu, 16 Apr 2020 01:10:35: 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 01:10:41: 5000000 INFO @ Thu, 16 Apr 2020 01:10:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4158194/SRX4158194.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4158194/SRX4158194.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4158194/SRX4158194.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4158194/SRX4158194.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 01:10:42: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:10:42: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:10:47: 6000000 INFO @ Thu, 16 Apr 2020 01:10:49: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 01:10:49: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 01:10:49: #1 total tags in treatment: 6248723 INFO @ Thu, 16 Apr 2020 01:10:49: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:10:49: #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 01:10:49: #1 tags after filtering in treatment: 6248723 INFO @ Thu, 16 Apr 2020 01:10:49: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:10:49: #1 finished! INFO @ Thu, 16 Apr 2020 01:10:49: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:10:49: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:10:49: #2 number of paired peaks: 1546 INFO @ Thu, 16 Apr 2020 01:10:49: start model_add_line... INFO @ Thu, 16 Apr 2020 01:10:49: 1000000 INFO @ Thu, 16 Apr 2020 01:10:49: start X-correlation... INFO @ Thu, 16 Apr 2020 01:10:49: end of X-cor INFO @ Thu, 16 Apr 2020 01:10:49: #2 finished! INFO @ Thu, 16 Apr 2020 01:10:49: #2 predicted fragment length is 217 bps INFO @ Thu, 16 Apr 2020 01:10:49: #2 alternative fragment length(s) may be 217 bps INFO @ Thu, 16 Apr 2020 01:10:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4158194/SRX4158194.05_model.r INFO @ Thu, 16 Apr 2020 01:10:49: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:10:49: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:10:56: 2000000 INFO @ Thu, 16 Apr 2020 01:11:03: 3000000 INFO @ Thu, 16 Apr 2020 01:11:03: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:11:09: 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 01:11:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4158194/SRX4158194.05_peaks.xls INFO @ Thu, 16 Apr 2020 01:11:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4158194/SRX4158194.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:11:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4158194/SRX4158194.05_summits.bed INFO @ Thu, 16 Apr 2020 01:11:11: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3408 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 01:11:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4158194/SRX4158194.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4158194/SRX4158194.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4158194/SRX4158194.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4158194/SRX4158194.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 01:11:12: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:11:12: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:11:16: 5000000 INFO @ Thu, 16 Apr 2020 01:11:19: 1000000 INFO @ Thu, 16 Apr 2020 01:11:23: 6000000 INFO @ Thu, 16 Apr 2020 01:11:25: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 01:11:25: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 01:11:25: #1 total tags in treatment: 6248723 INFO @ Thu, 16 Apr 2020 01:11:25: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:11:25: #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 01:11:25: #1 tags after filtering in treatment: 6248723 INFO @ Thu, 16 Apr 2020 01:11:25: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:11:25: #1 finished! INFO @ Thu, 16 Apr 2020 01:11:25: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:11:25: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:11:25: 2000000 INFO @ Thu, 16 Apr 2020 01:11:25: #2 number of paired peaks: 1546 INFO @ Thu, 16 Apr 2020 01:11:25: start model_add_line... INFO @ Thu, 16 Apr 2020 01:11:25: start X-correlation... INFO @ Thu, 16 Apr 2020 01:11:25: end of X-cor INFO @ Thu, 16 Apr 2020 01:11:25: #2 finished! INFO @ Thu, 16 Apr 2020 01:11:25: #2 predicted fragment length is 217 bps INFO @ Thu, 16 Apr 2020 01:11:25: #2 alternative fragment length(s) may be 217 bps INFO @ Thu, 16 Apr 2020 01:11:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4158194/SRX4158194.10_model.r INFO @ Thu, 16 Apr 2020 01:11:25: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:11:25: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:11:31: 3000000 INFO @ Thu, 16 Apr 2020 01:11:36: 4000000 INFO @ Thu, 16 Apr 2020 01:11:40: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:11:42: 5000000 INFO @ Thu, 16 Apr 2020 01:11:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4158194/SRX4158194.10_peaks.xls INFO @ Thu, 16 Apr 2020 01:11:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4158194/SRX4158194.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:11:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4158194/SRX4158194.10_summits.bed INFO @ Thu, 16 Apr 2020 01:11:46: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1581 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 01:11:48: 6000000 INFO @ Thu, 16 Apr 2020 01:11:49: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 01:11:49: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 01:11:49: #1 total tags in treatment: 6248723 INFO @ Thu, 16 Apr 2020 01:11:49: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:11:49: #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 01:11:49: #1 tags after filtering in treatment: 6248723 INFO @ Thu, 16 Apr 2020 01:11:49: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:11:49: #1 finished! INFO @ Thu, 16 Apr 2020 01:11:49: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:11:49: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:11:50: #2 number of paired peaks: 1546 INFO @ Thu, 16 Apr 2020 01:11:50: start model_add_line... INFO @ Thu, 16 Apr 2020 01:11:50: start X-correlation... INFO @ Thu, 16 Apr 2020 01:11:50: end of X-cor INFO @ Thu, 16 Apr 2020 01:11:50: #2 finished! INFO @ Thu, 16 Apr 2020 01:11:50: #2 predicted fragment length is 217 bps INFO @ Thu, 16 Apr 2020 01:11:50: #2 alternative fragment length(s) may be 217 bps INFO @ Thu, 16 Apr 2020 01:11:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4158194/SRX4158194.20_model.r INFO @ Thu, 16 Apr 2020 01:11:50: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:11:50: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:12:04: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:12:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4158194/SRX4158194.20_peaks.xls INFO @ Thu, 16 Apr 2020 01:12:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4158194/SRX4158194.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:12:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4158194/SRX4158194.20_summits.bed INFO @ Thu, 16 Apr 2020 01:12:11: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (693 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。