Job ID = 6369001 SRX = SRX982067 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:37:46 prefetch.2.10.7: 1) Downloading 'SRR1956543'... 2020-06-16T00:37:46 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:39:03 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:39:04 prefetch.2.10.7: 'SRR1956543' is valid 2020-06-16T00:39:04 prefetch.2.10.7: 1) 'SRR1956543' was downloaded successfully Read 7224626 spots for SRR1956543/SRR1956543.sra Written 7224626 spots for SRR1956543/SRR1956543.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: 00:01:21 7224626 reads; of these: 7224626 (100.00%) were unpaired; of these: 1276281 (17.67%) aligned 0 times 5060027 (70.04%) aligned exactly 1 time 888318 (12.30%) aligned >1 times 82.33% overall alignment rate Time searching: 00:01:21 Overall time: 00:01:21 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] 795078 / 5948345 = 0.1337 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 09:42:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX982067/SRX982067.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX982067/SRX982067.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX982067/SRX982067.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX982067/SRX982067.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 09:42:44: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:42:44: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:42:50: 1000000 INFO @ Tue, 16 Jun 2020 09:42:56: 2000000 INFO @ Tue, 16 Jun 2020 09:43:03: 3000000 INFO @ Tue, 16 Jun 2020 09:43:08: 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 @ Tue, 16 Jun 2020 09:43:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX982067/SRX982067.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX982067/SRX982067.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX982067/SRX982067.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX982067/SRX982067.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 09:43:14: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:43:14: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:43:14: 5000000 INFO @ Tue, 16 Jun 2020 09:43:15: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:43:15: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:43:15: #1 total tags in treatment: 5153267 INFO @ Tue, 16 Jun 2020 09:43:15: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:43:15: #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 09:43:15: #1 tags after filtering in treatment: 5153267 INFO @ Tue, 16 Jun 2020 09:43:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:43:15: #1 finished! INFO @ Tue, 16 Jun 2020 09:43:15: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:43:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:43:16: #2 number of paired peaks: 1643 INFO @ Tue, 16 Jun 2020 09:43:16: start model_add_line... INFO @ Tue, 16 Jun 2020 09:43:16: start X-correlation... INFO @ Tue, 16 Jun 2020 09:43:16: end of X-cor INFO @ Tue, 16 Jun 2020 09:43:16: #2 finished! INFO @ Tue, 16 Jun 2020 09:43:16: #2 predicted fragment length is 170 bps INFO @ Tue, 16 Jun 2020 09:43:16: #2 alternative fragment length(s) may be 170 bps INFO @ Tue, 16 Jun 2020 09:43:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX982067/SRX982067.05_model.r INFO @ Tue, 16 Jun 2020 09:43:16: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:43:16: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:43:20: 1000000 INFO @ Tue, 16 Jun 2020 09:43:27: 2000000 INFO @ Tue, 16 Jun 2020 09:43:27: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:43:33: 3000000 INFO @ Tue, 16 Jun 2020 09:43:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX982067/SRX982067.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:43:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX982067/SRX982067.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:43:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX982067/SRX982067.05_summits.bed INFO @ Tue, 16 Jun 2020 09:43:33: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1733 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:43:39: 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 @ Tue, 16 Jun 2020 09:43:44: 5000000 INFO @ Tue, 16 Jun 2020 09:43:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX982067/SRX982067.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX982067/SRX982067.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX982067/SRX982067.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX982067/SRX982067.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 09:43:45: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:43:45: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:43:45: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:43:45: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:43:45: #1 total tags in treatment: 5153267 INFO @ Tue, 16 Jun 2020 09:43:45: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:43:45: #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 09:43:45: #1 tags after filtering in treatment: 5153267 INFO @ Tue, 16 Jun 2020 09:43:45: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:43:45: #1 finished! INFO @ Tue, 16 Jun 2020 09:43:45: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:43:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:43:46: #2 number of paired peaks: 1643 INFO @ Tue, 16 Jun 2020 09:43:46: start model_add_line... INFO @ Tue, 16 Jun 2020 09:43:46: start X-correlation... INFO @ Tue, 16 Jun 2020 09:43:46: end of X-cor INFO @ Tue, 16 Jun 2020 09:43:46: #2 finished! INFO @ Tue, 16 Jun 2020 09:43:46: #2 predicted fragment length is 170 bps INFO @ Tue, 16 Jun 2020 09:43:46: #2 alternative fragment length(s) may be 170 bps INFO @ Tue, 16 Jun 2020 09:43:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX982067/SRX982067.10_model.r INFO @ Tue, 16 Jun 2020 09:43:46: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:43:46: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:43:51: 1000000 INFO @ Tue, 16 Jun 2020 09:43:57: 2000000 INFO @ Tue, 16 Jun 2020 09:43:58: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:44:04: 3000000 INFO @ Tue, 16 Jun 2020 09:44:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX982067/SRX982067.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:44:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX982067/SRX982067.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:44:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX982067/SRX982067.10_summits.bed INFO @ Tue, 16 Jun 2020 09:44:04: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1110 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:44:10: 4000000 INFO @ Tue, 16 Jun 2020 09:44:16: 5000000 INFO @ Tue, 16 Jun 2020 09:44:17: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:44:17: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:44:17: #1 total tags in treatment: 5153267 INFO @ Tue, 16 Jun 2020 09:44:17: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:44:17: #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 09:44:17: #1 tags after filtering in treatment: 5153267 INFO @ Tue, 16 Jun 2020 09:44:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:44:17: #1 finished! INFO @ Tue, 16 Jun 2020 09:44:17: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:44:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:44:17: #2 number of paired peaks: 1643 INFO @ Tue, 16 Jun 2020 09:44:17: start model_add_line... INFO @ Tue, 16 Jun 2020 09:44:18: start X-correlation... INFO @ Tue, 16 Jun 2020 09:44:18: end of X-cor INFO @ Tue, 16 Jun 2020 09:44:18: #2 finished! INFO @ Tue, 16 Jun 2020 09:44:18: #2 predicted fragment length is 170 bps INFO @ Tue, 16 Jun 2020 09:44:18: #2 alternative fragment length(s) may be 170 bps INFO @ Tue, 16 Jun 2020 09:44:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX982067/SRX982067.20_model.r INFO @ Tue, 16 Jun 2020 09:44:18: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:44:18: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:44:30: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:44:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX982067/SRX982067.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:44:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX982067/SRX982067.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:44:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX982067/SRX982067.20_summits.bed INFO @ Tue, 16 Jun 2020 09:44:36: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (501 records, 4 fields): 1 millis CompletedMACS2peakCalling