Job ID = 6455941 SRX = SRX3068977 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:32:35 prefetch.2.10.7: 1) Downloading 'SRR5907453'... 2020-06-21T10:32:35 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:33:59 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:33:59 prefetch.2.10.7: 'SRR5907453' is valid 2020-06-21T10:33:59 prefetch.2.10.7: 1) 'SRR5907453' was downloaded successfully Read 8079238 spots for SRR5907453/SRR5907453.sra Written 8079238 spots for SRR5907453/SRR5907453.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: 00:01:32 8079238 reads; of these: 8079238 (100.00%) were unpaired; of these: 2485586 (30.77%) aligned 0 times 4919568 (60.89%) aligned exactly 1 time 674084 (8.34%) aligned >1 times 69.23% overall alignment rate Time searching: 00:01:32 Overall time: 00:01:32 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] 1729691 / 5593652 = 0.3092 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 19:37:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3068977/SRX3068977.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3068977/SRX3068977.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3068977/SRX3068977.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3068977/SRX3068977.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 19:37:41: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:37:41: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:37:46: 1000000 INFO @ Sun, 21 Jun 2020 19:37:52: 2000000 INFO @ Sun, 21 Jun 2020 19:37:57: 3000000 INFO @ Sun, 21 Jun 2020 19:38:02: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:38:02: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:38:02: #1 total tags in treatment: 3863961 INFO @ Sun, 21 Jun 2020 19:38:02: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:38:02: #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 19:38:02: #1 tags after filtering in treatment: 3863814 INFO @ Sun, 21 Jun 2020 19:38:02: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:38:02: #1 finished! INFO @ Sun, 21 Jun 2020 19:38:02: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:38:02: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:38:03: #2 number of paired peaks: 3560 INFO @ Sun, 21 Jun 2020 19:38:03: start model_add_line... INFO @ Sun, 21 Jun 2020 19:38:03: start X-correlation... INFO @ Sun, 21 Jun 2020 19:38:03: end of X-cor INFO @ Sun, 21 Jun 2020 19:38:03: #2 finished! INFO @ Sun, 21 Jun 2020 19:38:03: #2 predicted fragment length is 171 bps INFO @ Sun, 21 Jun 2020 19:38:03: #2 alternative fragment length(s) may be 171 bps INFO @ Sun, 21 Jun 2020 19:38:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3068977/SRX3068977.05_model.r INFO @ Sun, 21 Jun 2020 19:38:03: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:38:03: #3 Pre-compute pvalue-qvalue table... 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 19:38:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3068977/SRX3068977.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3068977/SRX3068977.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3068977/SRX3068977.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3068977/SRX3068977.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 19:38:11: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:38:11: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:38:12: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:38:16: 1000000 INFO @ Sun, 21 Jun 2020 19:38:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3068977/SRX3068977.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:38:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3068977/SRX3068977.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:38:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3068977/SRX3068977.05_summits.bed INFO @ Sun, 21 Jun 2020 19:38:17: Done! pass1 - making usageList (322 chroms): 1 millis pass2 - checking and writing primary data (5661 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:38:22: 2000000 INFO @ Sun, 21 Jun 2020 19:38:28: 3000000 INFO @ Sun, 21 Jun 2020 19:38:33: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:38:33: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:38:33: #1 total tags in treatment: 3863961 INFO @ Sun, 21 Jun 2020 19:38:33: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:38:33: #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 19:38:33: #1 tags after filtering in treatment: 3863814 INFO @ Sun, 21 Jun 2020 19:38:33: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:38:33: #1 finished! INFO @ Sun, 21 Jun 2020 19:38:33: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:38:33: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:38:33: #2 number of paired peaks: 3560 INFO @ Sun, 21 Jun 2020 19:38:33: start model_add_line... INFO @ Sun, 21 Jun 2020 19:38:34: start X-correlation... INFO @ Sun, 21 Jun 2020 19:38:34: end of X-cor INFO @ Sun, 21 Jun 2020 19:38:34: #2 finished! INFO @ Sun, 21 Jun 2020 19:38:34: #2 predicted fragment length is 171 bps INFO @ Sun, 21 Jun 2020 19:38:34: #2 alternative fragment length(s) may be 171 bps INFO @ Sun, 21 Jun 2020 19:38:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3068977/SRX3068977.10_model.r INFO @ Sun, 21 Jun 2020 19:38:34: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:38:34: #3 Pre-compute pvalue-qvalue table... 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 19:38:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3068977/SRX3068977.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3068977/SRX3068977.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3068977/SRX3068977.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3068977/SRX3068977.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 19:38:41: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:38:41: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:38:44: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:38:46: 1000000 INFO @ Sun, 21 Jun 2020 19:38:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3068977/SRX3068977.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:38:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3068977/SRX3068977.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:38:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3068977/SRX3068977.10_summits.bed INFO @ Sun, 21 Jun 2020 19:38:48: Done! pass1 - making usageList (131 chroms): 1 millis pass2 - checking and writing primary data (3353 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:38:52: 2000000 INFO @ Sun, 21 Jun 2020 19:38:57: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:39:02: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:39:02: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:39:02: #1 total tags in treatment: 3863961 INFO @ Sun, 21 Jun 2020 19:39:02: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:39:02: #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 19:39:02: #1 tags after filtering in treatment: 3863814 INFO @ Sun, 21 Jun 2020 19:39:02: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:39:02: #1 finished! INFO @ Sun, 21 Jun 2020 19:39:02: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:39:02: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:39:03: #2 number of paired peaks: 3560 INFO @ Sun, 21 Jun 2020 19:39:03: start model_add_line... INFO @ Sun, 21 Jun 2020 19:39:03: start X-correlation... INFO @ Sun, 21 Jun 2020 19:39:03: end of X-cor INFO @ Sun, 21 Jun 2020 19:39:03: #2 finished! INFO @ Sun, 21 Jun 2020 19:39:03: #2 predicted fragment length is 171 bps INFO @ Sun, 21 Jun 2020 19:39:03: #2 alternative fragment length(s) may be 171 bps INFO @ Sun, 21 Jun 2020 19:39:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3068977/SRX3068977.20_model.r INFO @ Sun, 21 Jun 2020 19:39:03: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:39:03: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:39:13: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:39:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3068977/SRX3068977.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:39:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3068977/SRX3068977.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:39:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3068977/SRX3068977.20_summits.bed INFO @ Sun, 21 Jun 2020 19:39:18: Done! pass1 - making usageList (62 chroms): 1 millis pass2 - checking and writing primary data (1845 records, 4 fields): 5 millis CompletedMACS2peakCalling