Job ID = 6453413 SRX = SRX1134695 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:21:17 prefetch.2.10.7: 1) Downloading 'SRR2147076'... 2020-06-21T08:21:17 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:25:01 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:25:02 prefetch.2.10.7: 'SRR2147076' is valid 2020-06-21T08:25:02 prefetch.2.10.7: 1) 'SRR2147076' was downloaded successfully 2020-06-21T08:25:02 prefetch.2.10.7: 'SRR2147076' has 0 unresolved dependencies Read 11854057 spots for SRR2147076/SRR2147076.sra Written 11854057 spots for SRR2147076/SRR2147076.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: 00:02:25 11854057 reads; of these: 11854057 (100.00%) were unpaired; of these: 1188997 (10.03%) aligned 0 times 9555206 (80.61%) aligned exactly 1 time 1109854 (9.36%) aligned >1 times 89.97% overall alignment rate Time searching: 00:02:25 Overall time: 00:02:25 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] 7714926 / 10665060 = 0.7234 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 17:30:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1134695/SRX1134695.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1134695/SRX1134695.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1134695/SRX1134695.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1134695/SRX1134695.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 17:30:24: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:30:24: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:30:30: 1000000 INFO @ Sun, 21 Jun 2020 17:30:35: 2000000 INFO @ Sun, 21 Jun 2020 17:30:41: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 17:30:41: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 17:30:41: #1 total tags in treatment: 2950134 INFO @ Sun, 21 Jun 2020 17:30:41: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:30:41: #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 17:30:42: #1 tags after filtering in treatment: 2949817 INFO @ Sun, 21 Jun 2020 17:30:42: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:30:42: #1 finished! INFO @ Sun, 21 Jun 2020 17:30:42: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:30:42: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:30:42: #2 number of paired peaks: 5408 INFO @ Sun, 21 Jun 2020 17:30:42: start model_add_line... INFO @ Sun, 21 Jun 2020 17:30:42: start X-correlation... INFO @ Sun, 21 Jun 2020 17:30:42: end of X-cor INFO @ Sun, 21 Jun 2020 17:30:42: #2 finished! INFO @ Sun, 21 Jun 2020 17:30:42: #2 predicted fragment length is 210 bps INFO @ Sun, 21 Jun 2020 17:30:42: #2 alternative fragment length(s) may be 210 bps INFO @ Sun, 21 Jun 2020 17:30:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1134695/SRX1134695.05_model.r INFO @ Sun, 21 Jun 2020 17:30:42: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:30:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:30:51: #3 Call peaks for each chromosome... 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 17:30:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1134695/SRX1134695.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1134695/SRX1134695.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1134695/SRX1134695.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1134695/SRX1134695.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 17:30:54: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:30:54: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:30:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1134695/SRX1134695.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:30:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1134695/SRX1134695.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:30:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1134695/SRX1134695.05_summits.bed INFO @ Sun, 21 Jun 2020 17:30:56: Done! pass1 - making usageList (105 chroms): 2 millis pass2 - checking and writing primary data (4595 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:31:01: 1000000 INFO @ Sun, 21 Jun 2020 17:31:07: 2000000 INFO @ Sun, 21 Jun 2020 17:31:14: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 17:31:14: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 17:31:14: #1 total tags in treatment: 2950134 INFO @ Sun, 21 Jun 2020 17:31:14: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:31:14: #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 17:31:15: #1 tags after filtering in treatment: 2949817 INFO @ Sun, 21 Jun 2020 17:31:15: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:31:15: #1 finished! INFO @ Sun, 21 Jun 2020 17:31:15: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:31:15: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:31:15: #2 number of paired peaks: 5408 INFO @ Sun, 21 Jun 2020 17:31:15: start model_add_line... INFO @ Sun, 21 Jun 2020 17:31:15: start X-correlation... INFO @ Sun, 21 Jun 2020 17:31:15: end of X-cor INFO @ Sun, 21 Jun 2020 17:31:15: #2 finished! INFO @ Sun, 21 Jun 2020 17:31:15: #2 predicted fragment length is 210 bps INFO @ Sun, 21 Jun 2020 17:31:15: #2 alternative fragment length(s) may be 210 bps INFO @ Sun, 21 Jun 2020 17:31:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1134695/SRX1134695.10_model.r INFO @ Sun, 21 Jun 2020 17:31:15: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:31:15: #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 17:31:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1134695/SRX1134695.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1134695/SRX1134695.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1134695/SRX1134695.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1134695/SRX1134695.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 17:31:24: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:31:24: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:31:25: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:31:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1134695/SRX1134695.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:31:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1134695/SRX1134695.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:31:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1134695/SRX1134695.10_summits.bed INFO @ Sun, 21 Jun 2020 17:31:29: Done! pass1 - making usageList (90 chroms): 1 millis pass2 - checking and writing primary data (3449 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:31:31: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:31:38: 2000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:31:44: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 17:31:44: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 17:31:44: #1 total tags in treatment: 2950134 INFO @ Sun, 21 Jun 2020 17:31:44: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:31:44: #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 17:31:45: #1 tags after filtering in treatment: 2949817 INFO @ Sun, 21 Jun 2020 17:31:45: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:31:45: #1 finished! INFO @ Sun, 21 Jun 2020 17:31:45: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:31:45: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:31:45: #2 number of paired peaks: 5408 INFO @ Sun, 21 Jun 2020 17:31:45: start model_add_line... INFO @ Sun, 21 Jun 2020 17:31:45: start X-correlation... INFO @ Sun, 21 Jun 2020 17:31:45: end of X-cor INFO @ Sun, 21 Jun 2020 17:31:45: #2 finished! INFO @ Sun, 21 Jun 2020 17:31:45: #2 predicted fragment length is 210 bps INFO @ Sun, 21 Jun 2020 17:31:45: #2 alternative fragment length(s) may be 210 bps INFO @ Sun, 21 Jun 2020 17:31:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1134695/SRX1134695.20_model.r INFO @ Sun, 21 Jun 2020 17:31:45: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:31:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:31:55: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:31:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1134695/SRX1134695.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:31:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1134695/SRX1134695.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:31:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1134695/SRX1134695.20_summits.bed INFO @ Sun, 21 Jun 2020 17:31:58: Done! pass1 - making usageList (74 chroms): 1 millis pass2 - checking and writing primary data (2381 records, 4 fields): 7 millis CompletedMACS2peakCalling