Job ID = 5720673 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 7,758,661 reads read : 7,758,661 reads written : 7,758,661 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR5289767.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: 00:01:48 7758661 reads; of these: 7758661 (100.00%) were unpaired; of these: 3610494 (46.54%) aligned 0 times 3278607 (42.26%) aligned exactly 1 time 869560 (11.21%) aligned >1 times 53.46% overall alignment rate Time searching: 00:01:48 Overall time: 00:01:48 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] 420772 / 4148167 = 0.1014 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 00:54:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592490/SRX2592490.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592490/SRX2592490.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592490/SRX2592490.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592490/SRX2592490.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 00:54:18: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:54:18: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:54:25: 1000000 INFO @ Thu, 16 Apr 2020 00:54:31: 2000000 INFO @ Thu, 16 Apr 2020 00:54:37: 3000000 INFO @ Thu, 16 Apr 2020 00:54:42: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 00:54:42: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 00:54:42: #1 total tags in treatment: 3727395 INFO @ Thu, 16 Apr 2020 00:54:42: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:54:42: #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 00:54:42: #1 tags after filtering in treatment: 3727395 INFO @ Thu, 16 Apr 2020 00:54:42: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:54:42: #1 finished! INFO @ Thu, 16 Apr 2020 00:54:42: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:54:42: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:54:42: #2 number of paired peaks: 2964 INFO @ Thu, 16 Apr 2020 00:54:42: start model_add_line... INFO @ Thu, 16 Apr 2020 00:54:42: start X-correlation... INFO @ Thu, 16 Apr 2020 00:54:43: end of X-cor INFO @ Thu, 16 Apr 2020 00:54:43: #2 finished! INFO @ Thu, 16 Apr 2020 00:54:43: #2 predicted fragment length is 133 bps INFO @ Thu, 16 Apr 2020 00:54:43: #2 alternative fragment length(s) may be 133 bps INFO @ Thu, 16 Apr 2020 00:54:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592490/SRX2592490.05_model.r INFO @ Thu, 16 Apr 2020 00:54:43: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:54:43: #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 00:54:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592490/SRX2592490.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592490/SRX2592490.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592490/SRX2592490.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592490/SRX2592490.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 00:54:47: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:54:47: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:54:51: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:54:54: 1000000 INFO @ Thu, 16 Apr 2020 00:54:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592490/SRX2592490.05_peaks.xls INFO @ Thu, 16 Apr 2020 00:54:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592490/SRX2592490.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:54:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592490/SRX2592490.05_summits.bed INFO @ Thu, 16 Apr 2020 00:54:56: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (5646 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 00:54:59: 2000000 INFO @ Thu, 16 Apr 2020 00:55:05: 3000000 INFO @ Thu, 16 Apr 2020 00:55:09: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 00:55:09: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 00:55:09: #1 total tags in treatment: 3727395 INFO @ Thu, 16 Apr 2020 00:55:09: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:55:09: #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 00:55:09: #1 tags after filtering in treatment: 3727395 INFO @ Thu, 16 Apr 2020 00:55:09: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:55:09: #1 finished! INFO @ Thu, 16 Apr 2020 00:55:09: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:55:09: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:55:09: #2 number of paired peaks: 2964 INFO @ Thu, 16 Apr 2020 00:55:09: start model_add_line... INFO @ Thu, 16 Apr 2020 00:55:09: start X-correlation... INFO @ Thu, 16 Apr 2020 00:55:09: end of X-cor INFO @ Thu, 16 Apr 2020 00:55:09: #2 finished! INFO @ Thu, 16 Apr 2020 00:55:09: #2 predicted fragment length is 133 bps INFO @ Thu, 16 Apr 2020 00:55:09: #2 alternative fragment length(s) may be 133 bps INFO @ Thu, 16 Apr 2020 00:55:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592490/SRX2592490.10_model.r INFO @ Thu, 16 Apr 2020 00:55:09: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:55:09: #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 00:55:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592490/SRX2592490.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592490/SRX2592490.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592490/SRX2592490.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592490/SRX2592490.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 00:55:17: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:55:17: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:55:18: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:55:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592490/SRX2592490.10_peaks.xls INFO @ Thu, 16 Apr 2020 00:55:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592490/SRX2592490.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:55:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592490/SRX2592490.10_summits.bed INFO @ Thu, 16 Apr 2020 00:55:23: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (3037 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 00:55:24: 1000000 INFO @ Thu, 16 Apr 2020 00:55:30: 2000000 INFO @ Thu, 16 Apr 2020 00:55:36: 3000000 INFO @ Thu, 16 Apr 2020 00:55:41: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 00:55:41: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 00:55:41: #1 total tags in treatment: 3727395 INFO @ Thu, 16 Apr 2020 00:55:41: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:55:41: #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 00:55:41: #1 tags after filtering in treatment: 3727395 INFO @ Thu, 16 Apr 2020 00:55:41: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:55:41: #1 finished! INFO @ Thu, 16 Apr 2020 00:55:41: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:55:41: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:55:41: #2 number of paired peaks: 2964 INFO @ Thu, 16 Apr 2020 00:55:41: start model_add_line... INFO @ Thu, 16 Apr 2020 00:55:41: start X-correlation... INFO @ Thu, 16 Apr 2020 00:55:41: end of X-cor INFO @ Thu, 16 Apr 2020 00:55:41: #2 finished! INFO @ Thu, 16 Apr 2020 00:55:41: #2 predicted fragment length is 133 bps INFO @ Thu, 16 Apr 2020 00:55:41: #2 alternative fragment length(s) may be 133 bps INFO @ Thu, 16 Apr 2020 00:55:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592490/SRX2592490.20_model.r INFO @ Thu, 16 Apr 2020 00:55:41: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:55:41: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:55:50: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:55:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592490/SRX2592490.20_peaks.xls INFO @ Thu, 16 Apr 2020 00:55:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592490/SRX2592490.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:55:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592490/SRX2592490.20_summits.bed INFO @ Thu, 16 Apr 2020 00:55:55: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (1353 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。