Job ID = 6453046 SRX = SRX101813 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:16:48 prefetch.2.10.7: 1) Downloading 'SRR360699'... 2020-06-21T08:16:48 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:21:28 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:21:28 prefetch.2.10.7: 1) 'SRR360699' was downloaded successfully Read 24729310 spots for SRR360699/SRR360699.sra Written 24729310 spots for SRR360699/SRR360699.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: 00:11:22 24729310 reads; of these: 24729310 (100.00%) were unpaired; of these: 3655257 (14.78%) aligned 0 times 9788703 (39.58%) aligned exactly 1 time 11285350 (45.64%) aligned >1 times 85.22% overall alignment rate Time searching: 00:11:22 Overall time: 00:11:22 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_sort_core] merging from 8 files... [bam_rmdupse_core] 17360145 / 21074053 = 0.8238 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 17:37:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX101813/SRX101813.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX101813/SRX101813.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX101813/SRX101813.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX101813/SRX101813.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 17:37:03: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:37:03: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:37:10: 1000000 INFO @ Sun, 21 Jun 2020 17:37:16: 2000000 INFO @ Sun, 21 Jun 2020 17:37:23: 3000000 INFO @ Sun, 21 Jun 2020 17:37:27: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:37:27: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:37:27: #1 total tags in treatment: 3713908 INFO @ Sun, 21 Jun 2020 17:37:27: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:37:27: #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 17:37:27: #1 tags after filtering in treatment: 3713632 INFO @ Sun, 21 Jun 2020 17:37:27: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:37:27: #1 finished! INFO @ Sun, 21 Jun 2020 17:37:27: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:37:27: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:37:28: #2 number of paired peaks: 5005 INFO @ Sun, 21 Jun 2020 17:37:28: start model_add_line... INFO @ Sun, 21 Jun 2020 17:37:28: start X-correlation... INFO @ Sun, 21 Jun 2020 17:37:28: end of X-cor INFO @ Sun, 21 Jun 2020 17:37:28: #2 finished! INFO @ Sun, 21 Jun 2020 17:37:28: #2 predicted fragment length is 215 bps INFO @ Sun, 21 Jun 2020 17:37:28: #2 alternative fragment length(s) may be 215 bps INFO @ Sun, 21 Jun 2020 17:37:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX101813/SRX101813.05_model.r INFO @ Sun, 21 Jun 2020 17:37:28: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:37:28: #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 17:37:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX101813/SRX101813.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX101813/SRX101813.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX101813/SRX101813.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX101813/SRX101813.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 17:37:33: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:37:33: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:37:38: 1000000 INFO @ Sun, 21 Jun 2020 17:37:39: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:37:43: 2000000 INFO @ Sun, 21 Jun 2020 17:37:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX101813/SRX101813.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:37:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX101813/SRX101813.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:37:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX101813/SRX101813.05_summits.bed INFO @ Sun, 21 Jun 2020 17:37:44: Done! pass1 - making usageList (319 chroms): 2 millis pass2 - checking and writing primary data (8948 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:37:49: 3000000 INFO @ Sun, 21 Jun 2020 17:37:53: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:37:53: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:37:53: #1 total tags in treatment: 3713908 INFO @ Sun, 21 Jun 2020 17:37:53: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:37:53: #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 17:37:53: #1 tags after filtering in treatment: 3713632 INFO @ Sun, 21 Jun 2020 17:37:53: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:37:53: #1 finished! INFO @ Sun, 21 Jun 2020 17:37:53: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:37:53: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:37:53: #2 number of paired peaks: 5005 INFO @ Sun, 21 Jun 2020 17:37:53: start model_add_line... INFO @ Sun, 21 Jun 2020 17:37:53: start X-correlation... INFO @ Sun, 21 Jun 2020 17:37:53: end of X-cor INFO @ Sun, 21 Jun 2020 17:37:53: #2 finished! INFO @ Sun, 21 Jun 2020 17:37:53: #2 predicted fragment length is 215 bps INFO @ Sun, 21 Jun 2020 17:37:53: #2 alternative fragment length(s) may be 215 bps INFO @ Sun, 21 Jun 2020 17:37:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX101813/SRX101813.10_model.r INFO @ Sun, 21 Jun 2020 17:37:53: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:37:53: #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 17:38:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX101813/SRX101813.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX101813/SRX101813.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX101813/SRX101813.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX101813/SRX101813.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 17:38:03: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:38:03: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:38:04: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:38:09: 1000000 INFO @ Sun, 21 Jun 2020 17:38:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX101813/SRX101813.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:38:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX101813/SRX101813.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:38:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX101813/SRX101813.10_summits.bed INFO @ Sun, 21 Jun 2020 17:38:09: Done! pass1 - making usageList (274 chroms): 2 millis pass2 - checking and writing primary data (7002 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:38:14: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:38:19: 3000000 INFO @ Sun, 21 Jun 2020 17:38:23: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:38:23: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:38:23: #1 total tags in treatment: 3713908 INFO @ Sun, 21 Jun 2020 17:38:23: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:38:23: #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 17:38:23: #1 tags after filtering in treatment: 3713632 INFO @ Sun, 21 Jun 2020 17:38:23: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:38:23: #1 finished! INFO @ Sun, 21 Jun 2020 17:38:23: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:38:23: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:38:24: #2 number of paired peaks: 5005 INFO @ Sun, 21 Jun 2020 17:38:24: start model_add_line... INFO @ Sun, 21 Jun 2020 17:38:24: start X-correlation... INFO @ Sun, 21 Jun 2020 17:38:24: end of X-cor INFO @ Sun, 21 Jun 2020 17:38:24: #2 finished! INFO @ Sun, 21 Jun 2020 17:38:24: #2 predicted fragment length is 215 bps INFO @ Sun, 21 Jun 2020 17:38:24: #2 alternative fragment length(s) may be 215 bps INFO @ Sun, 21 Jun 2020 17:38:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX101813/SRX101813.20_model.r INFO @ Sun, 21 Jun 2020 17:38:24: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:38:24: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:38:36: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:38:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX101813/SRX101813.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:38:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX101813/SRX101813.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:38:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX101813/SRX101813.20_summits.bed INFO @ Sun, 21 Jun 2020 17:38:41: Done! pass1 - making usageList (226 chroms): 1 millis pass2 - checking and writing primary data (5054 records, 4 fields): 11 millis CompletedMACS2peakCalling