Job ID = 6366385 SRX = SRX1388759 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:38:36 prefetch.2.10.7: 1) Downloading 'SRR2832475'... 2020-06-15T22:38:36 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:39:09 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:39:09 prefetch.2.10.7: 'SRR2832475' is valid 2020-06-15T22:39:09 prefetch.2.10.7: 1) 'SRR2832475' was downloaded successfully Read 4178244 spots for SRR2832475/SRR2832475.sra Written 4178244 spots for SRR2832475/SRR2832475.sra 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: 00:00:58 4178244 reads; of these: 4178244 (100.00%) were unpaired; of these: 253608 (6.07%) aligned 0 times 3446106 (82.48%) aligned exactly 1 time 478530 (11.45%) aligned >1 times 93.93% overall alignment rate Time searching: 00:00:58 Overall time: 00:00:58 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_rmdupse_core] 345658 / 3924636 = 0.0881 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 @ Tue, 16 Jun 2020 07:41:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1388759/SRX1388759.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1388759/SRX1388759.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1388759/SRX1388759.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1388759/SRX1388759.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Tue, 16 Jun 2020 07:41:38: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:41:38: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:41:42: 1000000 INFO @ Tue, 16 Jun 2020 07:41:47: 2000000 INFO @ Tue, 16 Jun 2020 07:41:52: 3000000 INFO @ Tue, 16 Jun 2020 07:41:55: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 07:41:55: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 07:41:55: #1 total tags in treatment: 3578978 INFO @ Tue, 16 Jun 2020 07:41:55: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:41:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 07:41:55: #1 tags after filtering in treatment: 3578978 INFO @ Tue, 16 Jun 2020 07:41:55: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:41:55: #1 finished! INFO @ Tue, 16 Jun 2020 07:41:55: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:41:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:41:55: #2 number of paired peaks: 2679 INFO @ Tue, 16 Jun 2020 07:41:55: start model_add_line... INFO @ Tue, 16 Jun 2020 07:41:55: start X-correlation... INFO @ Tue, 16 Jun 2020 07:41:55: end of X-cor INFO @ Tue, 16 Jun 2020 07:41:55: #2 finished! INFO @ Tue, 16 Jun 2020 07:41:55: #2 predicted fragment length is 167 bps INFO @ Tue, 16 Jun 2020 07:41:55: #2 alternative fragment length(s) may be 167 bps INFO @ Tue, 16 Jun 2020 07:41:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1388759/SRX1388759.05_model.r INFO @ Tue, 16 Jun 2020 07:41:55: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:41:55: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:42:04: #3 Call peaks for each chromosome... 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 @ Tue, 16 Jun 2020 07:42:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1388759/SRX1388759.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1388759/SRX1388759.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1388759/SRX1388759.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1388759/SRX1388759.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Tue, 16 Jun 2020 07:42:08: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:42:08: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:42:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1388759/SRX1388759.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:42:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1388759/SRX1388759.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:42:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1388759/SRX1388759.05_summits.bed INFO @ Tue, 16 Jun 2020 07:42:08: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3453 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:42:12: 1000000 INFO @ Tue, 16 Jun 2020 07:42:17: 2000000 INFO @ Tue, 16 Jun 2020 07:42:22: 3000000 INFO @ Tue, 16 Jun 2020 07:42:25: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 07:42:25: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 07:42:25: #1 total tags in treatment: 3578978 INFO @ Tue, 16 Jun 2020 07:42:25: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:42:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 07:42:25: #1 tags after filtering in treatment: 3578978 INFO @ Tue, 16 Jun 2020 07:42:25: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:42:25: #1 finished! INFO @ Tue, 16 Jun 2020 07:42:25: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:42:25: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:42:25: #2 number of paired peaks: 2679 INFO @ Tue, 16 Jun 2020 07:42:25: start model_add_line... INFO @ Tue, 16 Jun 2020 07:42:25: start X-correlation... INFO @ Tue, 16 Jun 2020 07:42:25: end of X-cor INFO @ Tue, 16 Jun 2020 07:42:25: #2 finished! INFO @ Tue, 16 Jun 2020 07:42:25: #2 predicted fragment length is 167 bps INFO @ Tue, 16 Jun 2020 07:42:25: #2 alternative fragment length(s) may be 167 bps INFO @ Tue, 16 Jun 2020 07:42:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1388759/SRX1388759.10_model.r INFO @ Tue, 16 Jun 2020 07:42:25: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:42:25: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:42:33: #3 Call peaks for each chromosome... 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 @ Tue, 16 Jun 2020 07:42:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1388759/SRX1388759.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:42:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1388759/SRX1388759.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:42:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1388759/SRX1388759.10_summits.bed INFO @ Tue, 16 Jun 2020 07:42:38: Done! INFO @ Tue, 16 Jun 2020 07:42:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1388759/SRX1388759.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1388759/SRX1388759.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1388759/SRX1388759.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1388759/SRX1388759.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Tue, 16 Jun 2020 07:42:38: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:42:38: #1 read treatment tags... pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1626 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:42:43: 1000000 INFO @ Tue, 16 Jun 2020 07:42:48: 2000000 INFO @ Tue, 16 Jun 2020 07:42:52: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:42:55: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 07:42:55: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 07:42:55: #1 total tags in treatment: 3578978 INFO @ Tue, 16 Jun 2020 07:42:55: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:42:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 07:42:55: #1 tags after filtering in treatment: 3578978 INFO @ Tue, 16 Jun 2020 07:42:55: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:42:55: #1 finished! INFO @ Tue, 16 Jun 2020 07:42:55: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:42:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:42:56: #2 number of paired peaks: 2679 INFO @ Tue, 16 Jun 2020 07:42:56: start model_add_line... INFO @ Tue, 16 Jun 2020 07:42:56: start X-correlation... INFO @ Tue, 16 Jun 2020 07:42:56: end of X-cor INFO @ Tue, 16 Jun 2020 07:42:56: #2 finished! INFO @ Tue, 16 Jun 2020 07:42:56: #2 predicted fragment length is 167 bps INFO @ Tue, 16 Jun 2020 07:42:56: #2 alternative fragment length(s) may be 167 bps INFO @ Tue, 16 Jun 2020 07:42:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1388759/SRX1388759.20_model.r INFO @ Tue, 16 Jun 2020 07:42:56: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:42:56: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:43:04: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:43:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1388759/SRX1388759.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:43:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1388759/SRX1388759.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:43:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1388759/SRX1388759.20_summits.bed INFO @ Tue, 16 Jun 2020 07:43:09: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (499 records, 4 fields): 2 millis CompletedMACS2peakCalling