Job ID = 6366529 SRX = SRX1769984 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:48:22 prefetch.2.10.7: 1) Downloading 'SRR3535761'... 2020-06-15T22:48:22 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:49:51 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:49:52 prefetch.2.10.7: 'SRR3535761' is valid 2020-06-15T22:49:52 prefetch.2.10.7: 1) 'SRR3535761' was downloaded successfully Read 11140655 spots for SRR3535761/SRR3535761.sra Written 11140655 spots for SRR3535761/SRR3535761.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: 00:02:08 11140655 reads; of these: 11140655 (100.00%) were unpaired; of these: 3423078 (30.73%) aligned 0 times 5182760 (46.52%) aligned exactly 1 time 2534817 (22.75%) aligned >1 times 69.27% overall alignment rate Time searching: 00:02:08 Overall time: 00:02:08 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] 4249354 / 7717577 = 0.5506 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 07:54:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1769984/SRX1769984.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1769984/SRX1769984.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1769984/SRX1769984.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1769984/SRX1769984.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 07:54:39: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:54:39: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:54:45: 1000000 INFO @ Tue, 16 Jun 2020 07:54:51: 2000000 INFO @ Tue, 16 Jun 2020 07:54:57: 3000000 INFO @ Tue, 16 Jun 2020 07:55:00: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 07:55:00: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 07:55:00: #1 total tags in treatment: 3468223 INFO @ Tue, 16 Jun 2020 07:55:00: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:55:00: #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 07:55:00: #1 tags after filtering in treatment: 3468223 INFO @ Tue, 16 Jun 2020 07:55:00: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:55:00: #1 finished! INFO @ Tue, 16 Jun 2020 07:55:00: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:55:00: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:55:00: #2 number of paired peaks: 1355 INFO @ Tue, 16 Jun 2020 07:55:00: start model_add_line... INFO @ Tue, 16 Jun 2020 07:55:00: start X-correlation... INFO @ Tue, 16 Jun 2020 07:55:00: end of X-cor INFO @ Tue, 16 Jun 2020 07:55:00: #2 finished! INFO @ Tue, 16 Jun 2020 07:55:00: #2 predicted fragment length is 207 bps INFO @ Tue, 16 Jun 2020 07:55:00: #2 alternative fragment length(s) may be 207 bps INFO @ Tue, 16 Jun 2020 07:55:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1769984/SRX1769984.05_model.r INFO @ Tue, 16 Jun 2020 07:55:00: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:55:00: #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 @ Tue, 16 Jun 2020 07:55:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1769984/SRX1769984.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1769984/SRX1769984.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1769984/SRX1769984.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1769984/SRX1769984.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 07:55:09: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:55:09: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:55:10: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:55:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1769984/SRX1769984.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:55:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1769984/SRX1769984.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:55:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1769984/SRX1769984.05_summits.bed INFO @ Tue, 16 Jun 2020 07:55:14: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1595 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:55:15: 1000000 INFO @ Tue, 16 Jun 2020 07:55:21: 2000000 INFO @ Tue, 16 Jun 2020 07:55:27: 3000000 INFO @ Tue, 16 Jun 2020 07:55:29: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 07:55:29: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 07:55:29: #1 total tags in treatment: 3468223 INFO @ Tue, 16 Jun 2020 07:55:29: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:55:29: #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 07:55:29: #1 tags after filtering in treatment: 3468223 INFO @ Tue, 16 Jun 2020 07:55:29: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:55:29: #1 finished! INFO @ Tue, 16 Jun 2020 07:55:29: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:55:29: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:55:30: #2 number of paired peaks: 1355 INFO @ Tue, 16 Jun 2020 07:55:30: start model_add_line... INFO @ Tue, 16 Jun 2020 07:55:30: start X-correlation... INFO @ Tue, 16 Jun 2020 07:55:30: end of X-cor INFO @ Tue, 16 Jun 2020 07:55:30: #2 finished! INFO @ Tue, 16 Jun 2020 07:55:30: #2 predicted fragment length is 207 bps INFO @ Tue, 16 Jun 2020 07:55:30: #2 alternative fragment length(s) may be 207 bps INFO @ Tue, 16 Jun 2020 07:55:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1769984/SRX1769984.10_model.r INFO @ Tue, 16 Jun 2020 07:55:30: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:55:30: #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 @ Tue, 16 Jun 2020 07:55:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1769984/SRX1769984.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1769984/SRX1769984.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1769984/SRX1769984.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1769984/SRX1769984.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 07:55:39: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:55:39: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:55:40: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:55:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1769984/SRX1769984.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:55:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1769984/SRX1769984.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:55:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1769984/SRX1769984.10_summits.bed INFO @ Tue, 16 Jun 2020 07:55:44: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1078 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:55:45: 1000000 INFO @ Tue, 16 Jun 2020 07:55:51: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:55:58: 3000000 INFO @ Tue, 16 Jun 2020 07:56:01: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 07:56:01: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 07:56:01: #1 total tags in treatment: 3468223 INFO @ Tue, 16 Jun 2020 07:56:01: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:56:01: #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 07:56:01: #1 tags after filtering in treatment: 3468223 INFO @ Tue, 16 Jun 2020 07:56:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:56:01: #1 finished! INFO @ Tue, 16 Jun 2020 07:56:01: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:56:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:56:01: #2 number of paired peaks: 1355 INFO @ Tue, 16 Jun 2020 07:56:01: start model_add_line... INFO @ Tue, 16 Jun 2020 07:56:01: start X-correlation... INFO @ Tue, 16 Jun 2020 07:56:01: end of X-cor INFO @ Tue, 16 Jun 2020 07:56:01: #2 finished! INFO @ Tue, 16 Jun 2020 07:56:01: #2 predicted fragment length is 207 bps INFO @ Tue, 16 Jun 2020 07:56:01: #2 alternative fragment length(s) may be 207 bps INFO @ Tue, 16 Jun 2020 07:56:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1769984/SRX1769984.20_model.r INFO @ Tue, 16 Jun 2020 07:56:01: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:56:01: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:56:11: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:56:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1769984/SRX1769984.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:56:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1769984/SRX1769984.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:56:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1769984/SRX1769984.20_summits.bed INFO @ Tue, 16 Jun 2020 07:56:15: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (711 records, 4 fields): 2 millis CompletedMACS2peakCalling