Job ID = 6367272 SRX = SRX330984 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:33:35 prefetch.2.10.7: 1) Downloading 'SRR947189'... 2020-06-15T23:33:35 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:35:21 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:35:21 prefetch.2.10.7: 'SRR947189' is valid 2020-06-15T23:35:21 prefetch.2.10.7: 1) 'SRR947189' was downloaded successfully Read 7074941 spots for SRR947189/SRR947189.sra Written 7074941 spots for SRR947189/SRR947189.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: 00:01:48 7074941 reads; of these: 7074941 (100.00%) were unpaired; of these: 494861 (6.99%) aligned 0 times 5018468 (70.93%) aligned exactly 1 time 1561612 (22.07%) aligned >1 times 93.01% 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: 7 sequences. [bam_rmdupse_core] 1822131 / 6580080 = 0.2769 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 08:39:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX330984/SRX330984.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX330984/SRX330984.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX330984/SRX330984.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX330984/SRX330984.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 08:39:33: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:39:33: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:39:39: 1000000 INFO @ Tue, 16 Jun 2020 08:39:44: 2000000 INFO @ Tue, 16 Jun 2020 08:39:49: 3000000 INFO @ Tue, 16 Jun 2020 08:39:54: 4000000 INFO @ Tue, 16 Jun 2020 08:39:58: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:39:58: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:39:58: #1 total tags in treatment: 4757949 INFO @ Tue, 16 Jun 2020 08:39:58: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:39:58: #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 08:39:58: #1 tags after filtering in treatment: 4757949 INFO @ Tue, 16 Jun 2020 08:39:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:39:58: #1 finished! INFO @ Tue, 16 Jun 2020 08:39:58: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:39:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:39:58: #2 number of paired peaks: 1262 INFO @ Tue, 16 Jun 2020 08:39:58: start model_add_line... INFO @ Tue, 16 Jun 2020 08:39:59: start X-correlation... INFO @ Tue, 16 Jun 2020 08:39:59: end of X-cor INFO @ Tue, 16 Jun 2020 08:39:59: #2 finished! INFO @ Tue, 16 Jun 2020 08:39:59: #2 predicted fragment length is 174 bps INFO @ Tue, 16 Jun 2020 08:39:59: #2 alternative fragment length(s) may be 174 bps INFO @ Tue, 16 Jun 2020 08:39:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX330984/SRX330984.05_model.r INFO @ Tue, 16 Jun 2020 08:39:59: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:39:59: #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 08:40:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX330984/SRX330984.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX330984/SRX330984.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX330984/SRX330984.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX330984/SRX330984.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 08:40:03: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:40:03: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:40:08: 1000000 INFO @ Tue, 16 Jun 2020 08:40:10: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:40:14: 2000000 INFO @ Tue, 16 Jun 2020 08:40:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX330984/SRX330984.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:40:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX330984/SRX330984.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:40:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX330984/SRX330984.05_summits.bed INFO @ Tue, 16 Jun 2020 08:40:15: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2608 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:40:19: 3000000 INFO @ Tue, 16 Jun 2020 08:40:24: 4000000 INFO @ Tue, 16 Jun 2020 08:40:28: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:40:28: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:40:28: #1 total tags in treatment: 4757949 INFO @ Tue, 16 Jun 2020 08:40:28: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:40:28: #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 08:40:28: #1 tags after filtering in treatment: 4757949 INFO @ Tue, 16 Jun 2020 08:40:28: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:40:28: #1 finished! INFO @ Tue, 16 Jun 2020 08:40:28: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:40:28: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:40:28: #2 number of paired peaks: 1262 INFO @ Tue, 16 Jun 2020 08:40:28: start model_add_line... INFO @ Tue, 16 Jun 2020 08:40:28: start X-correlation... INFO @ Tue, 16 Jun 2020 08:40:28: end of X-cor INFO @ Tue, 16 Jun 2020 08:40:28: #2 finished! INFO @ Tue, 16 Jun 2020 08:40:28: #2 predicted fragment length is 174 bps INFO @ Tue, 16 Jun 2020 08:40:28: #2 alternative fragment length(s) may be 174 bps INFO @ Tue, 16 Jun 2020 08:40:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX330984/SRX330984.10_model.r INFO @ Tue, 16 Jun 2020 08:40:28: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:40:28: #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 08:40:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX330984/SRX330984.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX330984/SRX330984.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX330984/SRX330984.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX330984/SRX330984.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 08:40:33: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:40:33: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:40:39: 1000000 INFO @ Tue, 16 Jun 2020 08:40:39: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:40:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX330984/SRX330984.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:40:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX330984/SRX330984.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:40:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX330984/SRX330984.10_summits.bed INFO @ Tue, 16 Jun 2020 08:40:45: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1697 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:40:45: 2000000 INFO @ Tue, 16 Jun 2020 08:40:51: 3000000 INFO @ Tue, 16 Jun 2020 08:40:57: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:41:02: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:41:02: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:41:02: #1 total tags in treatment: 4757949 INFO @ Tue, 16 Jun 2020 08:41:02: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:41:02: #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 08:41:02: #1 tags after filtering in treatment: 4757949 INFO @ Tue, 16 Jun 2020 08:41:02: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:41:02: #1 finished! INFO @ Tue, 16 Jun 2020 08:41:02: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:41:02: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:41:02: #2 number of paired peaks: 1262 INFO @ Tue, 16 Jun 2020 08:41:02: start model_add_line... INFO @ Tue, 16 Jun 2020 08:41:02: start X-correlation... INFO @ Tue, 16 Jun 2020 08:41:02: end of X-cor INFO @ Tue, 16 Jun 2020 08:41:02: #2 finished! INFO @ Tue, 16 Jun 2020 08:41:02: #2 predicted fragment length is 174 bps INFO @ Tue, 16 Jun 2020 08:41:02: #2 alternative fragment length(s) may be 174 bps INFO @ Tue, 16 Jun 2020 08:41:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX330984/SRX330984.20_model.r INFO @ Tue, 16 Jun 2020 08:41:02: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:41:02: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:41:13: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:41:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX330984/SRX330984.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:41:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX330984/SRX330984.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:41:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX330984/SRX330984.20_summits.bed INFO @ Tue, 16 Jun 2020 08:41:18: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (908 records, 4 fields): 3 millis CompletedMACS2peakCalling