Job ID = 6367963 SRX = SRX4456922 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:44:18 prefetch.2.10.7: 1) Downloading 'SRR7591863'... 2020-06-15T23:44:18 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:45:10 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:45:10 prefetch.2.10.7: 'SRR7591863' is valid 2020-06-15T23:45:10 prefetch.2.10.7: 1) 'SRR7591863' was downloaded successfully Read 4120114 spots for SRR7591863/SRR7591863.sra Written 4120114 spots for SRR7591863/SRR7591863.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: 00:00:50 4120114 reads; of these: 4120114 (100.00%) were unpaired; of these: 295746 (7.18%) aligned 0 times 3335723 (80.96%) aligned exactly 1 time 488645 (11.86%) aligned >1 times 92.82% overall alignment rate Time searching: 00:00:50 Overall time: 00:00:50 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] 384009 / 3824368 = 0.1004 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 08:47:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4456922/SRX4456922.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4456922/SRX4456922.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4456922/SRX4456922.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4456922/SRX4456922.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 08:47:26: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:47:26: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:47:31: 1000000 INFO @ Tue, 16 Jun 2020 08:47:37: 2000000 INFO @ Tue, 16 Jun 2020 08:47:42: 3000000 INFO @ Tue, 16 Jun 2020 08:47:45: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:47:45: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:47:45: #1 total tags in treatment: 3440359 INFO @ Tue, 16 Jun 2020 08:47:45: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:47:45: #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 08:47:45: #1 tags after filtering in treatment: 3440359 INFO @ Tue, 16 Jun 2020 08:47:45: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:47:45: #1 finished! INFO @ Tue, 16 Jun 2020 08:47:45: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:47:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:47:45: #2 number of paired peaks: 2611 INFO @ Tue, 16 Jun 2020 08:47:45: start model_add_line... INFO @ Tue, 16 Jun 2020 08:47:45: start X-correlation... INFO @ Tue, 16 Jun 2020 08:47:45: end of X-cor INFO @ Tue, 16 Jun 2020 08:47:45: #2 finished! INFO @ Tue, 16 Jun 2020 08:47:45: #2 predicted fragment length is 163 bps INFO @ Tue, 16 Jun 2020 08:47:45: #2 alternative fragment length(s) may be 163 bps INFO @ Tue, 16 Jun 2020 08:47:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4456922/SRX4456922.05_model.r INFO @ Tue, 16 Jun 2020 08:47:45: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:47:45: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:47:53: #3 Call peaks for each chromosome... 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 08:47:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4456922/SRX4456922.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4456922/SRX4456922.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4456922/SRX4456922.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4456922/SRX4456922.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 08:47:56: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:47:56: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:47:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4456922/SRX4456922.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:47:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4456922/SRX4456922.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:47:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4456922/SRX4456922.05_summits.bed INFO @ Tue, 16 Jun 2020 08:47:57: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (2511 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:48:01: 1000000 INFO @ Tue, 16 Jun 2020 08:48:06: 2000000 INFO @ Tue, 16 Jun 2020 08:48:12: 3000000 INFO @ Tue, 16 Jun 2020 08:48:14: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:48:14: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:48:14: #1 total tags in treatment: 3440359 INFO @ Tue, 16 Jun 2020 08:48:14: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:48:14: #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 08:48:14: #1 tags after filtering in treatment: 3440359 INFO @ Tue, 16 Jun 2020 08:48:14: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:48:14: #1 finished! INFO @ Tue, 16 Jun 2020 08:48:14: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:48:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:48:14: #2 number of paired peaks: 2611 INFO @ Tue, 16 Jun 2020 08:48:14: start model_add_line... INFO @ Tue, 16 Jun 2020 08:48:14: start X-correlation... INFO @ Tue, 16 Jun 2020 08:48:14: end of X-cor INFO @ Tue, 16 Jun 2020 08:48:14: #2 finished! INFO @ Tue, 16 Jun 2020 08:48:14: #2 predicted fragment length is 163 bps INFO @ Tue, 16 Jun 2020 08:48:14: #2 alternative fragment length(s) may be 163 bps INFO @ Tue, 16 Jun 2020 08:48:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4456922/SRX4456922.10_model.r INFO @ Tue, 16 Jun 2020 08:48:14: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:48:14: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:48:22: #3 Call peaks for each chromosome... 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 08:48:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4456922/SRX4456922.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4456922/SRX4456922.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4456922/SRX4456922.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4456922/SRX4456922.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 08:48:26: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:48:26: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:48:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4456922/SRX4456922.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:48:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4456922/SRX4456922.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:48:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4456922/SRX4456922.10_summits.bed INFO @ Tue, 16 Jun 2020 08:48:26: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (1125 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:48:31: 1000000 INFO @ Tue, 16 Jun 2020 08:48:37: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:48:42: 3000000 INFO @ Tue, 16 Jun 2020 08:48:44: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:48:44: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:48:44: #1 total tags in treatment: 3440359 INFO @ Tue, 16 Jun 2020 08:48:44: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:48:44: #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 08:48:44: #1 tags after filtering in treatment: 3440359 INFO @ Tue, 16 Jun 2020 08:48:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:48:44: #1 finished! INFO @ Tue, 16 Jun 2020 08:48:44: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:48:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:48:45: #2 number of paired peaks: 2611 INFO @ Tue, 16 Jun 2020 08:48:45: start model_add_line... INFO @ Tue, 16 Jun 2020 08:48:45: start X-correlation... INFO @ Tue, 16 Jun 2020 08:48:45: end of X-cor INFO @ Tue, 16 Jun 2020 08:48:45: #2 finished! INFO @ Tue, 16 Jun 2020 08:48:45: #2 predicted fragment length is 163 bps INFO @ Tue, 16 Jun 2020 08:48:45: #2 alternative fragment length(s) may be 163 bps INFO @ Tue, 16 Jun 2020 08:48:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4456922/SRX4456922.20_model.r INFO @ Tue, 16 Jun 2020 08:48:45: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:48:45: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:48:53: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:48:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4456922/SRX4456922.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:48:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4456922/SRX4456922.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:48:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4456922/SRX4456922.20_summits.bed INFO @ Tue, 16 Jun 2020 08:48:57: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (362 records, 4 fields): 2 millis CompletedMACS2peakCalling