Job ID = 6367753 SRX = SRX4082367 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:33:50 prefetch.2.10.7: 1) Downloading 'SRR7164185'... 2020-06-15T23:33:50 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:35:12 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:35:12 prefetch.2.10.7: 'SRR7164185' is valid 2020-06-15T23:35:12 prefetch.2.10.7: 1) 'SRR7164185' was downloaded successfully 2020-06-15T23:35:12 prefetch.2.10.7: 'SRR7164185' has 0 unresolved dependencies Read 8069989 spots for SRR7164185/SRR7164185.sra Written 8069989 spots for SRR7164185/SRR7164185.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: 00:01:39 8069989 reads; of these: 8069989 (100.00%) were unpaired; of these: 1423718 (17.64%) aligned 0 times 6083432 (75.38%) aligned exactly 1 time 562839 (6.97%) aligned >1 times 82.36% overall alignment rate Time searching: 00:01:39 Overall time: 00:01:39 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] 4222909 / 6646271 = 0.6354 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 08:38:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4082367/SRX4082367.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4082367/SRX4082367.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4082367/SRX4082367.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4082367/SRX4082367.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 08:38:51: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:38:51: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:38:57: 1000000 INFO @ Tue, 16 Jun 2020 08:39:03: 2000000 INFO @ Tue, 16 Jun 2020 08:39:05: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:39:05: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:39:05: #1 total tags in treatment: 2423362 INFO @ Tue, 16 Jun 2020 08:39:05: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:39:05: #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 08:39:05: #1 tags after filtering in treatment: 2423362 INFO @ Tue, 16 Jun 2020 08:39:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:39:05: #1 finished! INFO @ Tue, 16 Jun 2020 08:39:05: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:39:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:39:05: #2 number of paired peaks: 6025 INFO @ Tue, 16 Jun 2020 08:39:05: start model_add_line... INFO @ Tue, 16 Jun 2020 08:39:06: start X-correlation... INFO @ Tue, 16 Jun 2020 08:39:06: end of X-cor INFO @ Tue, 16 Jun 2020 08:39:06: #2 finished! INFO @ Tue, 16 Jun 2020 08:39:06: #2 predicted fragment length is 197 bps INFO @ Tue, 16 Jun 2020 08:39:06: #2 alternative fragment length(s) may be 4,197 bps INFO @ Tue, 16 Jun 2020 08:39:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4082367/SRX4082367.05_model.r INFO @ Tue, 16 Jun 2020 08:39:06: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:39:06: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:39:11: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:39:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4082367/SRX4082367.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:39:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4082367/SRX4082367.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:39:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4082367/SRX4082367.05_summits.bed INFO @ Tue, 16 Jun 2020 08:39:14: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (2899 records, 4 fields): 4 millis CompletedMACS2peakCalling 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 08:39:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4082367/SRX4082367.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4082367/SRX4082367.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4082367/SRX4082367.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4082367/SRX4082367.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 08:39:21: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:39:21: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:39:27: 1000000 INFO @ Tue, 16 Jun 2020 08:39:33: 2000000 INFO @ Tue, 16 Jun 2020 08:39:35: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:39:35: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:39:35: #1 total tags in treatment: 2423362 INFO @ Tue, 16 Jun 2020 08:39:35: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:39:35: #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 08:39:35: #1 tags after filtering in treatment: 2423362 INFO @ Tue, 16 Jun 2020 08:39:35: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:39:35: #1 finished! INFO @ Tue, 16 Jun 2020 08:39:35: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:39:35: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:39:36: #2 number of paired peaks: 6025 INFO @ Tue, 16 Jun 2020 08:39:36: start model_add_line... INFO @ Tue, 16 Jun 2020 08:39:36: start X-correlation... INFO @ Tue, 16 Jun 2020 08:39:36: end of X-cor INFO @ Tue, 16 Jun 2020 08:39:36: #2 finished! INFO @ Tue, 16 Jun 2020 08:39:36: #2 predicted fragment length is 197 bps INFO @ Tue, 16 Jun 2020 08:39:36: #2 alternative fragment length(s) may be 4,197 bps INFO @ Tue, 16 Jun 2020 08:39:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4082367/SRX4082367.10_model.r INFO @ Tue, 16 Jun 2020 08:39:36: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:39:36: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:39:41: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:39:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4082367/SRX4082367.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:39:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4082367/SRX4082367.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:39:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4082367/SRX4082367.10_summits.bed INFO @ Tue, 16 Jun 2020 08:39:44: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (514 records, 4 fields): 1 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 08:39:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4082367/SRX4082367.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4082367/SRX4082367.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4082367/SRX4082367.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4082367/SRX4082367.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 08:39:51: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:39:51: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:39:57: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:40:02: 2000000 INFO @ Tue, 16 Jun 2020 08:40:05: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:40:05: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:40:05: #1 total tags in treatment: 2423362 INFO @ Tue, 16 Jun 2020 08:40:05: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:40:05: #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 08:40:05: #1 tags after filtering in treatment: 2423362 INFO @ Tue, 16 Jun 2020 08:40:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:40:05: #1 finished! INFO @ Tue, 16 Jun 2020 08:40:05: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:40:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:40:05: #2 number of paired peaks: 6025 INFO @ Tue, 16 Jun 2020 08:40:05: start model_add_line... INFO @ Tue, 16 Jun 2020 08:40:05: start X-correlation... INFO @ Tue, 16 Jun 2020 08:40:05: end of X-cor INFO @ Tue, 16 Jun 2020 08:40:05: #2 finished! INFO @ Tue, 16 Jun 2020 08:40:05: #2 predicted fragment length is 197 bps INFO @ Tue, 16 Jun 2020 08:40:05: #2 alternative fragment length(s) may be 4,197 bps INFO @ Tue, 16 Jun 2020 08:40:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4082367/SRX4082367.20_model.r INFO @ Tue, 16 Jun 2020 08:40:05: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:40:05: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:40:11: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:40:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4082367/SRX4082367.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:40:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4082367/SRX4082367.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:40:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4082367/SRX4082367.20_summits.bed INFO @ Tue, 16 Jun 2020 08:40:13: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (30 records, 4 fields): 1 millis CompletedMACS2peakCalling