Job ID = 6367214 SRX = SRX3043400 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:26:06 prefetch.2.10.7: 1) Downloading 'SRR5875884'... 2020-06-15T23:26:06 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:27:19 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:27:19 prefetch.2.10.7: 'SRR5875884' is valid 2020-06-15T23:27:19 prefetch.2.10.7: 1) 'SRR5875884' was downloaded successfully Read 8650033 spots for SRR5875884/SRR5875884.sra Written 8650033 spots for SRR5875884/SRR5875884.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: 00:02:17 8650033 reads; of these: 8650033 (100.00%) were unpaired; of these: 106941 (1.24%) aligned 0 times 7665011 (88.61%) aligned exactly 1 time 878081 (10.15%) aligned >1 times 98.76% overall alignment rate Time searching: 00:02:17 Overall time: 00:02:17 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] 1324360 / 8543092 = 0.1550 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 08:32:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3043400/SRX3043400.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3043400/SRX3043400.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3043400/SRX3043400.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3043400/SRX3043400.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 08:32:35: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:32:35: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:32:41: 1000000 INFO @ Tue, 16 Jun 2020 08:32:46: 2000000 INFO @ Tue, 16 Jun 2020 08:32:52: 3000000 INFO @ Tue, 16 Jun 2020 08:32:57: 4000000 INFO @ Tue, 16 Jun 2020 08:33:03: 5000000 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 08:33:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3043400/SRX3043400.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3043400/SRX3043400.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3043400/SRX3043400.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3043400/SRX3043400.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 08:33:05: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:33:05: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:33:08: 6000000 INFO @ Tue, 16 Jun 2020 08:33:11: 1000000 INFO @ Tue, 16 Jun 2020 08:33:14: 7000000 INFO @ Tue, 16 Jun 2020 08:33:15: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:33:15: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:33:15: #1 total tags in treatment: 7218732 INFO @ Tue, 16 Jun 2020 08:33:15: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:33:15: #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 08:33:15: #1 tags after filtering in treatment: 7218732 INFO @ Tue, 16 Jun 2020 08:33:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:33:15: #1 finished! INFO @ Tue, 16 Jun 2020 08:33:15: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:33:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:33:16: #2 number of paired peaks: 2491 INFO @ Tue, 16 Jun 2020 08:33:16: start model_add_line... INFO @ Tue, 16 Jun 2020 08:33:16: start X-correlation... INFO @ Tue, 16 Jun 2020 08:33:16: end of X-cor INFO @ Tue, 16 Jun 2020 08:33:16: #2 finished! INFO @ Tue, 16 Jun 2020 08:33:16: #2 predicted fragment length is 170 bps INFO @ Tue, 16 Jun 2020 08:33:16: #2 alternative fragment length(s) may be 170 bps INFO @ Tue, 16 Jun 2020 08:33:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3043400/SRX3043400.05_model.r INFO @ Tue, 16 Jun 2020 08:33:16: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:33:16: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:33:16: 2000000 INFO @ Tue, 16 Jun 2020 08:33:22: 3000000 INFO @ Tue, 16 Jun 2020 08:33:27: 4000000 INFO @ Tue, 16 Jun 2020 08:33:32: 5000000 INFO @ Tue, 16 Jun 2020 08:33:33: #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 08:33:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3043400/SRX3043400.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3043400/SRX3043400.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3043400/SRX3043400.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3043400/SRX3043400.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 08:33:35: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:33:35: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:33:38: 6000000 INFO @ Tue, 16 Jun 2020 08:33:41: 1000000 INFO @ Tue, 16 Jun 2020 08:33:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3043400/SRX3043400.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:33:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3043400/SRX3043400.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:33:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3043400/SRX3043400.05_summits.bed INFO @ Tue, 16 Jun 2020 08:33:42: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (5857 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:33:44: 7000000 INFO @ Tue, 16 Jun 2020 08:33:45: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:33:45: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:33:45: #1 total tags in treatment: 7218732 INFO @ Tue, 16 Jun 2020 08:33:45: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:33:45: #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 08:33:45: #1 tags after filtering in treatment: 7218732 INFO @ Tue, 16 Jun 2020 08:33:45: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:33:45: #1 finished! INFO @ Tue, 16 Jun 2020 08:33:45: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:33:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:33:46: #2 number of paired peaks: 2491 INFO @ Tue, 16 Jun 2020 08:33:46: start model_add_line... INFO @ Tue, 16 Jun 2020 08:33:46: start X-correlation... INFO @ Tue, 16 Jun 2020 08:33:46: end of X-cor INFO @ Tue, 16 Jun 2020 08:33:46: #2 finished! INFO @ Tue, 16 Jun 2020 08:33:46: #2 predicted fragment length is 170 bps INFO @ Tue, 16 Jun 2020 08:33:46: #2 alternative fragment length(s) may be 170 bps INFO @ Tue, 16 Jun 2020 08:33:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3043400/SRX3043400.10_model.r INFO @ Tue, 16 Jun 2020 08:33:46: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:33:46: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:33:47: 2000000 INFO @ Tue, 16 Jun 2020 08:33:52: 3000000 INFO @ Tue, 16 Jun 2020 08:33:58: 4000000 INFO @ Tue, 16 Jun 2020 08:34:03: 5000000 INFO @ Tue, 16 Jun 2020 08:34:04: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:34:09: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:34:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3043400/SRX3043400.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:34:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3043400/SRX3043400.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:34:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3043400/SRX3043400.10_summits.bed INFO @ Tue, 16 Jun 2020 08:34:13: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (4166 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:34:14: 7000000 INFO @ Tue, 16 Jun 2020 08:34:16: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:34:16: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:34:16: #1 total tags in treatment: 7218732 INFO @ Tue, 16 Jun 2020 08:34:16: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:34:16: #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 08:34:16: #1 tags after filtering in treatment: 7218732 INFO @ Tue, 16 Jun 2020 08:34:16: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:34:16: #1 finished! INFO @ Tue, 16 Jun 2020 08:34:16: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:34:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:34:16: #2 number of paired peaks: 2491 INFO @ Tue, 16 Jun 2020 08:34:16: start model_add_line... INFO @ Tue, 16 Jun 2020 08:34:17: start X-correlation... INFO @ Tue, 16 Jun 2020 08:34:17: end of X-cor INFO @ Tue, 16 Jun 2020 08:34:17: #2 finished! INFO @ Tue, 16 Jun 2020 08:34:17: #2 predicted fragment length is 170 bps INFO @ Tue, 16 Jun 2020 08:34:17: #2 alternative fragment length(s) may be 170 bps INFO @ Tue, 16 Jun 2020 08:34:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3043400/SRX3043400.20_model.r INFO @ Tue, 16 Jun 2020 08:34:17: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:34:17: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:34:34: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:34:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3043400/SRX3043400.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:34:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3043400/SRX3043400.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:34:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3043400/SRX3043400.20_summits.bed INFO @ Tue, 16 Jun 2020 08:34:43: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2646 records, 4 fields): 3 millis CompletedMACS2peakCalling