Job ID = 6455940 SRX = SRX3068976 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:27:21 prefetch.2.10.7: 1) Downloading 'SRR5907452'... 2020-06-21T10:27:21 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:29:38 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:29:38 prefetch.2.10.7: 'SRR5907452' is valid 2020-06-21T10:29:38 prefetch.2.10.7: 1) 'SRR5907452' was downloaded successfully Read 9648594 spots for SRR5907452/SRR5907452.sra Written 9648594 spots for SRR5907452/SRR5907452.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: 00:02:13 9648594 reads; of these: 9648594 (100.00%) were unpaired; of these: 1213075 (12.57%) aligned 0 times 7134235 (73.94%) aligned exactly 1 time 1301284 (13.49%) aligned >1 times 87.43% overall alignment rate Time searching: 00:02:13 Overall time: 00:02:13 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] 2793186 / 8435519 = 0.3311 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 19:34:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3068976/SRX3068976.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3068976/SRX3068976.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3068976/SRX3068976.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3068976/SRX3068976.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 19:34:46: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:34:46: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:34:53: 1000000 INFO @ Sun, 21 Jun 2020 19:35:00: 2000000 INFO @ Sun, 21 Jun 2020 19:35:07: 3000000 INFO @ Sun, 21 Jun 2020 19:35:14: 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 @ Sun, 21 Jun 2020 19:35:21: 5000000 INFO @ Sun, 21 Jun 2020 19:35:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3068976/SRX3068976.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3068976/SRX3068976.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3068976/SRX3068976.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3068976/SRX3068976.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 19:35:21: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:35:21: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:35:26: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:35:26: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:35:26: #1 total tags in treatment: 5642333 INFO @ Sun, 21 Jun 2020 19:35:26: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:35:26: #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 19:35:26: #1 tags after filtering in treatment: 5642278 INFO @ Sun, 21 Jun 2020 19:35:26: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:35:26: #1 finished! INFO @ Sun, 21 Jun 2020 19:35:26: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:35:26: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:35:27: #2 number of paired peaks: 2039 INFO @ Sun, 21 Jun 2020 19:35:27: start model_add_line... INFO @ Sun, 21 Jun 2020 19:35:27: start X-correlation... INFO @ Sun, 21 Jun 2020 19:35:27: end of X-cor INFO @ Sun, 21 Jun 2020 19:35:27: #2 finished! INFO @ Sun, 21 Jun 2020 19:35:27: #2 predicted fragment length is 173 bps INFO @ Sun, 21 Jun 2020 19:35:27: #2 alternative fragment length(s) may be 173 bps INFO @ Sun, 21 Jun 2020 19:35:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3068976/SRX3068976.05_model.r INFO @ Sun, 21 Jun 2020 19:35:27: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:35:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:35:29: 1000000 INFO @ Sun, 21 Jun 2020 19:35:36: 2000000 INFO @ Sun, 21 Jun 2020 19:35:40: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:35:43: 3000000 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 19:35:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3068976/SRX3068976.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3068976/SRX3068976.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3068976/SRX3068976.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3068976/SRX3068976.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 19:35:46: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:35:46: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:35:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3068976/SRX3068976.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:35:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3068976/SRX3068976.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:35:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3068976/SRX3068976.05_summits.bed INFO @ Sun, 21 Jun 2020 19:35:47: Done! pass1 - making usageList (460 chroms): 1 millis pass2 - checking and writing primary data (5770 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:35:50: 4000000 INFO @ Sun, 21 Jun 2020 19:35:53: 1000000 INFO @ Sun, 21 Jun 2020 19:35:58: 5000000 INFO @ Sun, 21 Jun 2020 19:36:00: 2000000 INFO @ Sun, 21 Jun 2020 19:36:03: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:36:03: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:36:03: #1 total tags in treatment: 5642333 INFO @ Sun, 21 Jun 2020 19:36:03: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:36:03: #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 19:36:04: #1 tags after filtering in treatment: 5642278 INFO @ Sun, 21 Jun 2020 19:36:04: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:36:04: #1 finished! INFO @ Sun, 21 Jun 2020 19:36:04: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:36:04: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:36:04: #2 number of paired peaks: 2039 INFO @ Sun, 21 Jun 2020 19:36:04: start model_add_line... INFO @ Sun, 21 Jun 2020 19:36:04: start X-correlation... INFO @ Sun, 21 Jun 2020 19:36:04: end of X-cor INFO @ Sun, 21 Jun 2020 19:36:04: #2 finished! INFO @ Sun, 21 Jun 2020 19:36:04: #2 predicted fragment length is 173 bps INFO @ Sun, 21 Jun 2020 19:36:04: #2 alternative fragment length(s) may be 173 bps INFO @ Sun, 21 Jun 2020 19:36:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3068976/SRX3068976.10_model.r INFO @ Sun, 21 Jun 2020 19:36:04: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:36:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:36:07: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:36:13: 4000000 INFO @ Sun, 21 Jun 2020 19:36:18: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:36:19: 5000000 INFO @ Sun, 21 Jun 2020 19:36:23: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:36:23: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:36:23: #1 total tags in treatment: 5642333 INFO @ Sun, 21 Jun 2020 19:36:23: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:36:23: #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 19:36:24: #1 tags after filtering in treatment: 5642278 INFO @ Sun, 21 Jun 2020 19:36:24: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:36:24: #1 finished! INFO @ Sun, 21 Jun 2020 19:36:24: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:36:24: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:36:24: #2 number of paired peaks: 2039 INFO @ Sun, 21 Jun 2020 19:36:24: start model_add_line... INFO @ Sun, 21 Jun 2020 19:36:24: start X-correlation... INFO @ Sun, 21 Jun 2020 19:36:24: end of X-cor INFO @ Sun, 21 Jun 2020 19:36:24: #2 finished! INFO @ Sun, 21 Jun 2020 19:36:24: #2 predicted fragment length is 173 bps INFO @ Sun, 21 Jun 2020 19:36:24: #2 alternative fragment length(s) may be 173 bps INFO @ Sun, 21 Jun 2020 19:36:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3068976/SRX3068976.20_model.r INFO @ Sun, 21 Jun 2020 19:36:24: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:36:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:36:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3068976/SRX3068976.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:36:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3068976/SRX3068976.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:36:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3068976/SRX3068976.10_summits.bed INFO @ Sun, 21 Jun 2020 19:36:24: Done! BigWig に変換しました。 pass1 - making usageList (400 chroms): 1 millis pass2 - checking and writing primary data (3362 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:36:37: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:36:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3068976/SRX3068976.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:36:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3068976/SRX3068976.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:36:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3068976/SRX3068976.20_summits.bed INFO @ Sun, 21 Jun 2020 19:36:44: Done! pass1 - making usageList (247 chroms): 1 millis pass2 - checking and writing primary data (1513 records, 4 fields): 10 millis CompletedMACS2peakCalling