Job ID = 6457820 SRX = SRX4798863 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:57:19 prefetch.2.10.7: 1) Downloading 'SRR7965206'... 2020-06-21T11:57:19 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:58:48 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:58:49 prefetch.2.10.7: 'SRR7965206' is valid 2020-06-21T11:58:49 prefetch.2.10.7: 1) 'SRR7965206' was downloaded successfully Read 12799188 spots for SRR7965206/SRR7965206.sra Written 12799188 spots for SRR7965206/SRR7965206.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: 00:01:20 12799188 reads; of these: 12799188 (100.00%) were unpaired; of these: 9923199 (77.53%) aligned 0 times 2658254 (20.77%) aligned exactly 1 time 217735 (1.70%) aligned >1 times 22.47% overall alignment rate Time searching: 00:01:20 Overall time: 00:01:20 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_rmdupse_core] 696499 / 2875989 = 0.2422 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 @ Sun, 21 Jun 2020 21:02:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4798863/SRX4798863.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4798863/SRX4798863.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4798863/SRX4798863.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4798863/SRX4798863.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Sun, 21 Jun 2020 21:02:07: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:02:07: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:02:12: 1000000 INFO @ Sun, 21 Jun 2020 21:02:18: 2000000 INFO @ Sun, 21 Jun 2020 21:02:19: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 21:02:19: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 21:02:19: #1 total tags in treatment: 2179490 INFO @ Sun, 21 Jun 2020 21:02:19: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:02:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 21:02:20: #1 tags after filtering in treatment: 2178996 INFO @ Sun, 21 Jun 2020 21:02:20: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:02:20: #1 finished! INFO @ Sun, 21 Jun 2020 21:02:20: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:02:20: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:02:20: #2 number of paired peaks: 4279 INFO @ Sun, 21 Jun 2020 21:02:20: start model_add_line... INFO @ Sun, 21 Jun 2020 21:02:20: start X-correlation... INFO @ Sun, 21 Jun 2020 21:02:20: end of X-cor INFO @ Sun, 21 Jun 2020 21:02:20: #2 finished! INFO @ Sun, 21 Jun 2020 21:02:20: #2 predicted fragment length is 161 bps INFO @ Sun, 21 Jun 2020 21:02:20: #2 alternative fragment length(s) may be 161 bps INFO @ Sun, 21 Jun 2020 21:02:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4798863/SRX4798863.05_model.r INFO @ Sun, 21 Jun 2020 21:02:20: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:02:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:02:26: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:02:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4798863/SRX4798863.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:02:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4798863/SRX4798863.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:02:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4798863/SRX4798863.05_summits.bed INFO @ Sun, 21 Jun 2020 21:02:29: Done! pass1 - making usageList (69 chroms): 1 millis pass2 - checking and writing primary data (4679 records, 4 fields): 8 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 @ Sun, 21 Jun 2020 21:02:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4798863/SRX4798863.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4798863/SRX4798863.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4798863/SRX4798863.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4798863/SRX4798863.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Sun, 21 Jun 2020 21:02:37: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:02:37: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:02:43: 1000000 INFO @ Sun, 21 Jun 2020 21:02:49: 2000000 INFO @ Sun, 21 Jun 2020 21:02:51: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 21:02:51: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 21:02:51: #1 total tags in treatment: 2179490 INFO @ Sun, 21 Jun 2020 21:02:51: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:02:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 21:02:51: #1 tags after filtering in treatment: 2178996 INFO @ Sun, 21 Jun 2020 21:02:51: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:02:51: #1 finished! INFO @ Sun, 21 Jun 2020 21:02:51: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:02:51: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:02:51: #2 number of paired peaks: 4279 INFO @ Sun, 21 Jun 2020 21:02:51: start model_add_line... INFO @ Sun, 21 Jun 2020 21:02:51: start X-correlation... INFO @ Sun, 21 Jun 2020 21:02:51: end of X-cor INFO @ Sun, 21 Jun 2020 21:02:51: #2 finished! INFO @ Sun, 21 Jun 2020 21:02:51: #2 predicted fragment length is 161 bps INFO @ Sun, 21 Jun 2020 21:02:51: #2 alternative fragment length(s) may be 161 bps INFO @ Sun, 21 Jun 2020 21:02:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4798863/SRX4798863.10_model.r INFO @ Sun, 21 Jun 2020 21:02:51: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:02:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:02:57: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:03:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4798863/SRX4798863.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:03:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4798863/SRX4798863.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:03:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4798863/SRX4798863.10_summits.bed INFO @ Sun, 21 Jun 2020 21:03:00: Done! pass1 - making usageList (54 chroms): 1 millis pass2 - checking and writing primary data (2455 records, 4 fields): 21 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 @ Sun, 21 Jun 2020 21:03:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4798863/SRX4798863.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4798863/SRX4798863.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4798863/SRX4798863.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4798863/SRX4798863.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Sun, 21 Jun 2020 21:03:07: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:03:07: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:03:13: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:03:20: 2000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:03:22: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 21:03:22: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 21:03:22: #1 total tags in treatment: 2179490 INFO @ Sun, 21 Jun 2020 21:03:22: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:03:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 21:03:22: #1 tags after filtering in treatment: 2178996 INFO @ Sun, 21 Jun 2020 21:03:22: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:03:22: #1 finished! INFO @ Sun, 21 Jun 2020 21:03:22: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:03:22: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:03:22: #2 number of paired peaks: 4279 INFO @ Sun, 21 Jun 2020 21:03:22: start model_add_line... INFO @ Sun, 21 Jun 2020 21:03:22: start X-correlation... INFO @ Sun, 21 Jun 2020 21:03:22: end of X-cor INFO @ Sun, 21 Jun 2020 21:03:22: #2 finished! INFO @ Sun, 21 Jun 2020 21:03:22: #2 predicted fragment length is 161 bps INFO @ Sun, 21 Jun 2020 21:03:22: #2 alternative fragment length(s) may be 161 bps INFO @ Sun, 21 Jun 2020 21:03:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4798863/SRX4798863.20_model.r INFO @ Sun, 21 Jun 2020 21:03:22: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:03:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:03:28: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:03:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4798863/SRX4798863.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:03:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4798863/SRX4798863.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:03:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4798863/SRX4798863.20_summits.bed INFO @ Sun, 21 Jun 2020 21:03:31: Done! pass1 - making usageList (45 chroms): 1 millis pass2 - checking and writing primary data (1038 records, 4 fields): 22 millis CompletedMACS2peakCalling