Job ID = 6366538 SRX = SRX1769993 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:48:38 prefetch.2.10.7: 1) Downloading 'SRR3535772'... 2020-06-15T22:48:38 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:50:16 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:50:16 prefetch.2.10.7: 1) 'SRR3535772' was downloaded successfully Read 18925488 spots for SRR3535772/SRR3535772.sra Written 18925488 spots for SRR3535772/SRR3535772.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: 00:00:01 Multiseed full-index search: 00:03:49 18925488 reads; of these: 18925488 (100.00%) were unpaired; of these: 8182143 (43.23%) aligned 0 times 5972322 (31.56%) aligned exactly 1 time 4771023 (25.21%) aligned >1 times 56.77% overall alignment rate Time searching: 00:03:50 Overall time: 00:03:50 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_sort_core] merging from 8 files... [bam_rmdupse_core] 5898266 / 10743345 = 0.5490 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 07:57:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1769993/SRX1769993.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1769993/SRX1769993.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1769993/SRX1769993.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1769993/SRX1769993.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 07:57:50: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:57:50: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:57:56: 1000000 INFO @ Tue, 16 Jun 2020 07:58:02: 2000000 INFO @ Tue, 16 Jun 2020 07:58:08: 3000000 INFO @ Tue, 16 Jun 2020 07:58:14: 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 07:58:20: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 07:58:20: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 07:58:20: #1 total tags in treatment: 4845079 INFO @ Tue, 16 Jun 2020 07:58:20: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:58:20: #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 07:58:20: #1 tags after filtering in treatment: 4845079 INFO @ Tue, 16 Jun 2020 07:58:20: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:58:20: #1 finished! INFO @ Tue, 16 Jun 2020 07:58:20: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:58:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:58:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1769993/SRX1769993.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1769993/SRX1769993.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1769993/SRX1769993.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1769993/SRX1769993.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 07:58:20: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:58:20: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:58:20: #2 number of paired peaks: 1067 INFO @ Tue, 16 Jun 2020 07:58:20: start model_add_line... INFO @ Tue, 16 Jun 2020 07:58:20: start X-correlation... INFO @ Tue, 16 Jun 2020 07:58:20: end of X-cor INFO @ Tue, 16 Jun 2020 07:58:20: #2 finished! INFO @ Tue, 16 Jun 2020 07:58:20: #2 predicted fragment length is 221 bps INFO @ Tue, 16 Jun 2020 07:58:20: #2 alternative fragment length(s) may be 221 bps INFO @ Tue, 16 Jun 2020 07:58:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1769993/SRX1769993.05_model.r INFO @ Tue, 16 Jun 2020 07:58:20: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:58:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:58:26: 1000000 INFO @ Tue, 16 Jun 2020 07:58:33: 2000000 INFO @ Tue, 16 Jun 2020 07:58:34: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:58:39: 3000000 INFO @ Tue, 16 Jun 2020 07:58:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1769993/SRX1769993.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:58:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1769993/SRX1769993.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:58:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1769993/SRX1769993.05_summits.bed INFO @ Tue, 16 Jun 2020 07:58:41: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (842 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:58:45: 4000000 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 07:58:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1769993/SRX1769993.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1769993/SRX1769993.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1769993/SRX1769993.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1769993/SRX1769993.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 07:58:50: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:58:50: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:58:51: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 07:58:51: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 07:58:51: #1 total tags in treatment: 4845079 INFO @ Tue, 16 Jun 2020 07:58:51: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:58:51: #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 07:58:51: #1 tags after filtering in treatment: 4845079 INFO @ Tue, 16 Jun 2020 07:58:51: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:58:51: #1 finished! INFO @ Tue, 16 Jun 2020 07:58:51: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:58:51: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:58:51: #2 number of paired peaks: 1067 INFO @ Tue, 16 Jun 2020 07:58:51: start model_add_line... INFO @ Tue, 16 Jun 2020 07:58:52: start X-correlation... INFO @ Tue, 16 Jun 2020 07:58:52: end of X-cor INFO @ Tue, 16 Jun 2020 07:58:52: #2 finished! INFO @ Tue, 16 Jun 2020 07:58:52: #2 predicted fragment length is 221 bps INFO @ Tue, 16 Jun 2020 07:58:52: #2 alternative fragment length(s) may be 221 bps INFO @ Tue, 16 Jun 2020 07:58:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1769993/SRX1769993.10_model.r INFO @ Tue, 16 Jun 2020 07:58:52: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:58:52: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:58:56: 1000000 INFO @ Tue, 16 Jun 2020 07:59:03: 2000000 INFO @ Tue, 16 Jun 2020 07:59:05: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:59:09: 3000000 INFO @ Tue, 16 Jun 2020 07:59:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1769993/SRX1769993.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:59:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1769993/SRX1769993.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:59:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1769993/SRX1769993.10_summits.bed INFO @ Tue, 16 Jun 2020 07:59:11: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (657 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:59:15: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:59:20: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 07:59:20: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 07:59:20: #1 total tags in treatment: 4845079 INFO @ Tue, 16 Jun 2020 07:59:20: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:59:20: #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 07:59:20: #1 tags after filtering in treatment: 4845079 INFO @ Tue, 16 Jun 2020 07:59:20: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:59:20: #1 finished! INFO @ Tue, 16 Jun 2020 07:59:20: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:59:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:59:21: #2 number of paired peaks: 1067 INFO @ Tue, 16 Jun 2020 07:59:21: start model_add_line... INFO @ Tue, 16 Jun 2020 07:59:21: start X-correlation... INFO @ Tue, 16 Jun 2020 07:59:21: end of X-cor INFO @ Tue, 16 Jun 2020 07:59:21: #2 finished! INFO @ Tue, 16 Jun 2020 07:59:21: #2 predicted fragment length is 221 bps INFO @ Tue, 16 Jun 2020 07:59:21: #2 alternative fragment length(s) may be 221 bps INFO @ Tue, 16 Jun 2020 07:59:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1769993/SRX1769993.20_model.r INFO @ Tue, 16 Jun 2020 07:59:21: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:59:21: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:59:35: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:59:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1769993/SRX1769993.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:59:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1769993/SRX1769993.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:59:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1769993/SRX1769993.20_summits.bed INFO @ Tue, 16 Jun 2020 07:59:41: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (529 records, 4 fields): 1 millis CompletedMACS2peakCalling