Job ID = 6454195 SRX = SRX187080 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:09:24 prefetch.2.10.7: 1) Downloading 'SRR569908'... 2020-06-21T09:09:24 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:10:41 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:10:41 prefetch.2.10.7: 'SRR569908' is valid 2020-06-21T09:10:41 prefetch.2.10.7: 1) 'SRR569908' was downloaded successfully Read 9135726 spots for SRR569908/SRR569908.sra Written 9135726 spots for SRR569908/SRR569908.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: 00:01:58 9135726 reads; of these: 9135726 (100.00%) were unpaired; of these: 348690 (3.82%) aligned 0 times 6090304 (66.66%) aligned exactly 1 time 2696732 (29.52%) aligned >1 times 96.18% overall alignment rate Time searching: 00:01:58 Overall time: 00:01:58 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] 3159671 / 8787036 = 0.3596 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 18:15:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX187080/SRX187080.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX187080/SRX187080.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX187080/SRX187080.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX187080/SRX187080.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 18:15:04: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:15:04: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:15:08: 1000000 INFO @ Sun, 21 Jun 2020 18:15:13: 2000000 INFO @ Sun, 21 Jun 2020 18:15:18: 3000000 INFO @ Sun, 21 Jun 2020 18:15:22: 4000000 INFO @ Sun, 21 Jun 2020 18:15:27: 5000000 INFO @ Sun, 21 Jun 2020 18:15:30: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 18:15:30: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 18:15:30: #1 total tags in treatment: 5627365 INFO @ Sun, 21 Jun 2020 18:15:30: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:15:30: #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 18:15:30: #1 tags after filtering in treatment: 5627245 INFO @ Sun, 21 Jun 2020 18:15:30: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:15:30: #1 finished! INFO @ Sun, 21 Jun 2020 18:15:30: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:15:30: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:15:31: #2 number of paired peaks: 2768 INFO @ Sun, 21 Jun 2020 18:15:31: start model_add_line... INFO @ Sun, 21 Jun 2020 18:15:31: start X-correlation... INFO @ Sun, 21 Jun 2020 18:15:31: end of X-cor INFO @ Sun, 21 Jun 2020 18:15:31: #2 finished! INFO @ Sun, 21 Jun 2020 18:15:31: #2 predicted fragment length is 98 bps INFO @ Sun, 21 Jun 2020 18:15:31: #2 alternative fragment length(s) may be 98 bps INFO @ Sun, 21 Jun 2020 18:15:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX187080/SRX187080.05_model.r INFO @ Sun, 21 Jun 2020 18:15:31: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:15:31: #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 18:15:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX187080/SRX187080.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX187080/SRX187080.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX187080/SRX187080.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX187080/SRX187080.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 18:15:34: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:15:34: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:15:38: 1000000 INFO @ Sun, 21 Jun 2020 18:15:43: 2000000 INFO @ Sun, 21 Jun 2020 18:15:43: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:15:48: 3000000 INFO @ Sun, 21 Jun 2020 18:15:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX187080/SRX187080.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:15:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX187080/SRX187080.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:15:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX187080/SRX187080.05_summits.bed INFO @ Sun, 21 Jun 2020 18:15:50: Done! pass1 - making usageList (581 chroms): 2 millis pass2 - checking and writing primary data (7323 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:15:52: 4000000 INFO @ Sun, 21 Jun 2020 18:15:57: 5000000 INFO @ Sun, 21 Jun 2020 18:16:00: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 18:16:00: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 18:16:00: #1 total tags in treatment: 5627365 INFO @ Sun, 21 Jun 2020 18:16:00: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:16:00: #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 18:16:00: #1 tags after filtering in treatment: 5627245 INFO @ Sun, 21 Jun 2020 18:16:00: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:16:00: #1 finished! INFO @ Sun, 21 Jun 2020 18:16:00: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:16:00: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:16:01: #2 number of paired peaks: 2768 INFO @ Sun, 21 Jun 2020 18:16:01: start model_add_line... INFO @ Sun, 21 Jun 2020 18:16:01: start X-correlation... INFO @ Sun, 21 Jun 2020 18:16:01: end of X-cor INFO @ Sun, 21 Jun 2020 18:16:01: #2 finished! INFO @ Sun, 21 Jun 2020 18:16:01: #2 predicted fragment length is 98 bps INFO @ Sun, 21 Jun 2020 18:16:01: #2 alternative fragment length(s) may be 98 bps INFO @ Sun, 21 Jun 2020 18:16:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX187080/SRX187080.10_model.r INFO @ Sun, 21 Jun 2020 18:16:01: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:16:01: #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 18:16:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX187080/SRX187080.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX187080/SRX187080.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX187080/SRX187080.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX187080/SRX187080.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 18:16:04: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:16:04: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:16:08: 1000000 INFO @ Sun, 21 Jun 2020 18:16:13: 2000000 INFO @ Sun, 21 Jun 2020 18:16:14: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:16:18: 3000000 INFO @ Sun, 21 Jun 2020 18:16:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX187080/SRX187080.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:16:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX187080/SRX187080.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:16:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX187080/SRX187080.10_summits.bed INFO @ Sun, 21 Jun 2020 18:16:21: Done! pass1 - making usageList (319 chroms): 1 millis pass2 - checking and writing primary data (3409 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:16:22: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:16:27: 5000000 INFO @ Sun, 21 Jun 2020 18:16:30: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 18:16:30: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 18:16:30: #1 total tags in treatment: 5627365 INFO @ Sun, 21 Jun 2020 18:16:30: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:16:30: #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 18:16:30: #1 tags after filtering in treatment: 5627245 INFO @ Sun, 21 Jun 2020 18:16:30: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:16:30: #1 finished! INFO @ Sun, 21 Jun 2020 18:16:30: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:16:30: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:16:31: #2 number of paired peaks: 2768 INFO @ Sun, 21 Jun 2020 18:16:31: start model_add_line... INFO @ Sun, 21 Jun 2020 18:16:31: start X-correlation... INFO @ Sun, 21 Jun 2020 18:16:31: end of X-cor INFO @ Sun, 21 Jun 2020 18:16:31: #2 finished! INFO @ Sun, 21 Jun 2020 18:16:31: #2 predicted fragment length is 98 bps INFO @ Sun, 21 Jun 2020 18:16:31: #2 alternative fragment length(s) may be 98 bps INFO @ Sun, 21 Jun 2020 18:16:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX187080/SRX187080.20_model.r INFO @ Sun, 21 Jun 2020 18:16:31: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:16:31: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:16:44: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:16:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX187080/SRX187080.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:16:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX187080/SRX187080.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:16:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX187080/SRX187080.20_summits.bed INFO @ Sun, 21 Jun 2020 18:16:50: Done! pass1 - making usageList (177 chroms): 1 millis pass2 - checking and writing primary data (1285 records, 4 fields): 7 millis CompletedMACS2peakCalling