Job ID = 6366710 SRX = SRX2228865 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:02:13 prefetch.2.10.7: 1) Downloading 'SRR4380321'... 2020-06-15T23:02:13 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:03:36 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:03:36 prefetch.2.10.7: 1) 'SRR4380321' was downloaded successfully Read 18668481 spots for SRR4380321/SRR4380321.sra Written 18668481 spots for SRR4380321/SRR4380321.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: 00:04:36 18668481 reads; of these: 18668481 (100.00%) were unpaired; of these: 696521 (3.73%) aligned 0 times 14978352 (80.23%) aligned exactly 1 time 2993608 (16.04%) aligned >1 times 96.27% overall alignment rate Time searching: 00:04:36 Overall time: 00:04:36 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_sort_core] merging from 8 files... [bam_rmdupse_core] 12306852 / 17971960 = 0.6848 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 08:13:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2228865/SRX2228865.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2228865/SRX2228865.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2228865/SRX2228865.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2228865/SRX2228865.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 08:13:19: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:13:19: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:13:25: 1000000 INFO @ Tue, 16 Jun 2020 08:13:31: 2000000 INFO @ Tue, 16 Jun 2020 08:13:37: 3000000 INFO @ Tue, 16 Jun 2020 08:13:43: 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 08:13:48: 5000000 INFO @ Tue, 16 Jun 2020 08:13:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2228865/SRX2228865.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2228865/SRX2228865.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2228865/SRX2228865.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2228865/SRX2228865.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 08:13:49: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:13:49: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:13:53: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:13:53: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:13:53: #1 total tags in treatment: 5665108 INFO @ Tue, 16 Jun 2020 08:13:53: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:13:53: #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 08:13:53: #1 tags after filtering in treatment: 5665108 INFO @ Tue, 16 Jun 2020 08:13:53: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:13:53: #1 finished! INFO @ Tue, 16 Jun 2020 08:13:53: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:13:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:13:53: #2 number of paired peaks: 1036 INFO @ Tue, 16 Jun 2020 08:13:53: start model_add_line... INFO @ Tue, 16 Jun 2020 08:13:53: start X-correlation... INFO @ Tue, 16 Jun 2020 08:13:53: end of X-cor INFO @ Tue, 16 Jun 2020 08:13:53: #2 finished! INFO @ Tue, 16 Jun 2020 08:13:53: #2 predicted fragment length is 134 bps INFO @ Tue, 16 Jun 2020 08:13:53: #2 alternative fragment length(s) may be 134 bps INFO @ Tue, 16 Jun 2020 08:13:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2228865/SRX2228865.05_model.r INFO @ Tue, 16 Jun 2020 08:13:53: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:13:53: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:13:56: 1000000 INFO @ Tue, 16 Jun 2020 08:14:02: 2000000 INFO @ Tue, 16 Jun 2020 08:14:08: 3000000 INFO @ Tue, 16 Jun 2020 08:14:09: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:14:14: 4000000 INFO @ Tue, 16 Jun 2020 08:14:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2228865/SRX2228865.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:14:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2228865/SRX2228865.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:14:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2228865/SRX2228865.05_summits.bed INFO @ Tue, 16 Jun 2020 08:14:16: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1613 records, 4 fields): 3 millis CompletedMACS2peakCalling 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 08:14:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2228865/SRX2228865.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2228865/SRX2228865.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2228865/SRX2228865.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2228865/SRX2228865.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 08:14:19: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:14:19: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:14:20: 5000000 INFO @ Tue, 16 Jun 2020 08:14:24: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:14:24: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:14:24: #1 total tags in treatment: 5665108 INFO @ Tue, 16 Jun 2020 08:14:24: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:14:24: #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 08:14:24: #1 tags after filtering in treatment: 5665108 INFO @ Tue, 16 Jun 2020 08:14:24: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:14:24: #1 finished! INFO @ Tue, 16 Jun 2020 08:14:24: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:14:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:14:25: #2 number of paired peaks: 1036 INFO @ Tue, 16 Jun 2020 08:14:25: start model_add_line... INFO @ Tue, 16 Jun 2020 08:14:25: start X-correlation... INFO @ Tue, 16 Jun 2020 08:14:25: end of X-cor INFO @ Tue, 16 Jun 2020 08:14:25: #2 finished! INFO @ Tue, 16 Jun 2020 08:14:25: #2 predicted fragment length is 134 bps INFO @ Tue, 16 Jun 2020 08:14:25: #2 alternative fragment length(s) may be 134 bps INFO @ Tue, 16 Jun 2020 08:14:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2228865/SRX2228865.10_model.r INFO @ Tue, 16 Jun 2020 08:14:25: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:14:25: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:14:26: 1000000 INFO @ Tue, 16 Jun 2020 08:14:32: 2000000 INFO @ Tue, 16 Jun 2020 08:14:38: 3000000 INFO @ Tue, 16 Jun 2020 08:14:40: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:14:44: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:14:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2228865/SRX2228865.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:14:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2228865/SRX2228865.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:14:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2228865/SRX2228865.10_summits.bed INFO @ Tue, 16 Jun 2020 08:14:48: Done! INFO @ Tue, 16 Jun 2020 08:14:50: 5000000 pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1057 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:14:55: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:14:55: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:14:55: #1 total tags in treatment: 5665108 INFO @ Tue, 16 Jun 2020 08:14:55: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:14:55: #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 08:14:55: #1 tags after filtering in treatment: 5665108 INFO @ Tue, 16 Jun 2020 08:14:55: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:14:55: #1 finished! INFO @ Tue, 16 Jun 2020 08:14:55: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:14:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:14:55: #2 number of paired peaks: 1036 INFO @ Tue, 16 Jun 2020 08:14:55: start model_add_line... INFO @ Tue, 16 Jun 2020 08:14:55: start X-correlation... INFO @ Tue, 16 Jun 2020 08:14:55: end of X-cor INFO @ Tue, 16 Jun 2020 08:14:55: #2 finished! INFO @ Tue, 16 Jun 2020 08:14:55: #2 predicted fragment length is 134 bps INFO @ Tue, 16 Jun 2020 08:14:55: #2 alternative fragment length(s) may be 134 bps INFO @ Tue, 16 Jun 2020 08:14:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2228865/SRX2228865.20_model.r INFO @ Tue, 16 Jun 2020 08:14:55: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:14:55: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:15:11: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:15:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2228865/SRX2228865.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:15:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2228865/SRX2228865.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:15:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2228865/SRX2228865.20_summits.bed INFO @ Tue, 16 Jun 2020 08:15:19: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (644 records, 4 fields): 1 millis CompletedMACS2peakCalling