Job ID = 6507905 SRX = SRX495008 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T13:18:03 prefetch.2.10.7: 1) Downloading 'SRR1198540'... 2020-06-26T13:18:03 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T13:20:30 prefetch.2.10.7: HTTPS download succeed 2020-06-26T13:20:30 prefetch.2.10.7: 1) 'SRR1198540' was downloaded successfully Read 16689254 spots for SRR1198540/SRR1198540.sra Written 16689254 spots for SRR1198540/SRR1198540.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: 00:02:53 16689254 reads; of these: 16689254 (100.00%) were unpaired; of these: 3578676 (21.44%) aligned 0 times 10793058 (64.67%) aligned exactly 1 time 2317520 (13.89%) aligned >1 times 78.56% overall alignment rate Time searching: 00:02:53 Overall time: 00:02:53 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] 7743466 / 13110578 = 0.5906 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 @ Fri, 26 Jun 2020 22:27:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495008/SRX495008.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495008/SRX495008.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495008/SRX495008.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495008/SRX495008.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 @ Fri, 26 Jun 2020 22:27:48: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:27:48: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:27:56: 1000000 INFO @ Fri, 26 Jun 2020 22:28:03: 2000000 INFO @ Fri, 26 Jun 2020 22:28:10: 3000000 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 @ Fri, 26 Jun 2020 22:28:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495008/SRX495008.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495008/SRX495008.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495008/SRX495008.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495008/SRX495008.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 @ Fri, 26 Jun 2020 22:28:17: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:28:17: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:28:18: 4000000 INFO @ Fri, 26 Jun 2020 22:28:25: 5000000 INFO @ Fri, 26 Jun 2020 22:28:25: 1000000 INFO @ Fri, 26 Jun 2020 22:28:27: #1 tag size is determined as 42 bps INFO @ Fri, 26 Jun 2020 22:28:27: #1 tag size = 42 INFO @ Fri, 26 Jun 2020 22:28:27: #1 total tags in treatment: 5367112 INFO @ Fri, 26 Jun 2020 22:28:27: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:28:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 22:28:28: #1 tags after filtering in treatment: 5367112 INFO @ Fri, 26 Jun 2020 22:28:28: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:28:28: #1 finished! INFO @ Fri, 26 Jun 2020 22:28:28: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:28:28: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:28:28: #2 number of paired peaks: 2327 INFO @ Fri, 26 Jun 2020 22:28:28: start model_add_line... INFO @ Fri, 26 Jun 2020 22:28:28: start X-correlation... INFO @ Fri, 26 Jun 2020 22:28:28: end of X-cor INFO @ Fri, 26 Jun 2020 22:28:28: #2 finished! INFO @ Fri, 26 Jun 2020 22:28:28: #2 predicted fragment length is 201 bps INFO @ Fri, 26 Jun 2020 22:28:28: #2 alternative fragment length(s) may be 3,201 bps INFO @ Fri, 26 Jun 2020 22:28:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495008/SRX495008.05_model.r INFO @ Fri, 26 Jun 2020 22:28:28: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:28:28: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:28:33: 2000000 INFO @ Fri, 26 Jun 2020 22:28:41: 3000000 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 @ Fri, 26 Jun 2020 22:28:46: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:28:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495008/SRX495008.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495008/SRX495008.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495008/SRX495008.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495008/SRX495008.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 @ Fri, 26 Jun 2020 22:28:47: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:28:47: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:28:49: 4000000 INFO @ Fri, 26 Jun 2020 22:28:53: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495008/SRX495008.05_peaks.xls INFO @ Fri, 26 Jun 2020 22:28:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495008/SRX495008.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:28:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495008/SRX495008.05_summits.bed INFO @ Fri, 26 Jun 2020 22:28:53: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1716 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 22:28:55: 1000000 INFO @ Fri, 26 Jun 2020 22:28:57: 5000000 INFO @ Fri, 26 Jun 2020 22:28:59: #1 tag size is determined as 42 bps INFO @ Fri, 26 Jun 2020 22:28:59: #1 tag size = 42 INFO @ Fri, 26 Jun 2020 22:28:59: #1 total tags in treatment: 5367112 INFO @ Fri, 26 Jun 2020 22:28:59: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:28:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 22:29:00: #1 tags after filtering in treatment: 5367112 INFO @ Fri, 26 Jun 2020 22:29:00: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:29:00: #1 finished! INFO @ Fri, 26 Jun 2020 22:29:00: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:29:00: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:29:00: #2 number of paired peaks: 2327 INFO @ Fri, 26 Jun 2020 22:29:00: start model_add_line... INFO @ Fri, 26 Jun 2020 22:29:00: start X-correlation... INFO @ Fri, 26 Jun 2020 22:29:00: end of X-cor INFO @ Fri, 26 Jun 2020 22:29:00: #2 finished! INFO @ Fri, 26 Jun 2020 22:29:00: #2 predicted fragment length is 201 bps INFO @ Fri, 26 Jun 2020 22:29:00: #2 alternative fragment length(s) may be 3,201 bps INFO @ Fri, 26 Jun 2020 22:29:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495008/SRX495008.10_model.r INFO @ Fri, 26 Jun 2020 22:29:00: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:29:00: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:29:02: 2000000 INFO @ Fri, 26 Jun 2020 22:29:09: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 22:29:17: 4000000 INFO @ Fri, 26 Jun 2020 22:29:18: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:29:24: 5000000 INFO @ Fri, 26 Jun 2020 22:29:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495008/SRX495008.10_peaks.xls INFO @ Fri, 26 Jun 2020 22:29:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495008/SRX495008.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:29:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495008/SRX495008.10_summits.bed INFO @ Fri, 26 Jun 2020 22:29:25: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (734 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 22:29:26: #1 tag size is determined as 42 bps INFO @ Fri, 26 Jun 2020 22:29:26: #1 tag size = 42 INFO @ Fri, 26 Jun 2020 22:29:26: #1 total tags in treatment: 5367112 INFO @ Fri, 26 Jun 2020 22:29:26: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:29:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 22:29:26: #1 tags after filtering in treatment: 5367112 INFO @ Fri, 26 Jun 2020 22:29:26: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:29:26: #1 finished! INFO @ Fri, 26 Jun 2020 22:29:26: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:29:26: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:29:27: #2 number of paired peaks: 2327 INFO @ Fri, 26 Jun 2020 22:29:27: start model_add_line... INFO @ Fri, 26 Jun 2020 22:29:27: start X-correlation... INFO @ Fri, 26 Jun 2020 22:29:27: end of X-cor INFO @ Fri, 26 Jun 2020 22:29:27: #2 finished! INFO @ Fri, 26 Jun 2020 22:29:27: #2 predicted fragment length is 201 bps INFO @ Fri, 26 Jun 2020 22:29:27: #2 alternative fragment length(s) may be 3,201 bps INFO @ Fri, 26 Jun 2020 22:29:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495008/SRX495008.20_model.r INFO @ Fri, 26 Jun 2020 22:29:27: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:29:27: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 22:29:45: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:29:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495008/SRX495008.20_peaks.xls INFO @ Fri, 26 Jun 2020 22:29:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495008/SRX495008.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:29:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495008/SRX495008.20_summits.bed INFO @ Fri, 26 Jun 2020 22:29:52: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (279 records, 4 fields): 4 millis CompletedMACS2peakCalling