Job ID = 6453417 SRX = SRX1134699 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:22:02 prefetch.2.10.7: 1) Downloading 'SRR2147080'... 2020-06-21T08:22:02 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:24:06 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:24:06 prefetch.2.10.7: 'SRR2147080' is valid 2020-06-21T08:24:06 prefetch.2.10.7: 1) 'SRR2147080' was downloaded successfully 2020-06-21T08:24:06 prefetch.2.10.7: 'SRR2147080' has 0 unresolved dependencies Read 13441934 spots for SRR2147080/SRR2147080.sra Written 13441934 spots for SRR2147080/SRR2147080.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: 00:02:46 13441934 reads; of these: 13441934 (100.00%) were unpaired; of these: 1035582 (7.70%) aligned 0 times 10600622 (78.86%) aligned exactly 1 time 1805730 (13.43%) aligned >1 times 92.30% overall alignment rate Time searching: 00:02:47 Overall time: 00:02:47 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] 9900640 / 12406352 = 0.7980 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 17:30:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1134699/SRX1134699.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1134699/SRX1134699.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1134699/SRX1134699.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1134699/SRX1134699.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 17:30:04: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:30:04: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:30:09: 1000000 INFO @ Sun, 21 Jun 2020 17:30:15: 2000000 INFO @ Sun, 21 Jun 2020 17:30:17: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 17:30:17: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 17:30:17: #1 total tags in treatment: 2505712 INFO @ Sun, 21 Jun 2020 17:30:17: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:30:17: #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 17:30:18: #1 tags after filtering in treatment: 2505391 INFO @ Sun, 21 Jun 2020 17:30:18: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:30:18: #1 finished! INFO @ Sun, 21 Jun 2020 17:30:18: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:30:18: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:30:18: #2 number of paired peaks: 5961 INFO @ Sun, 21 Jun 2020 17:30:18: start model_add_line... INFO @ Sun, 21 Jun 2020 17:30:18: start X-correlation... INFO @ Sun, 21 Jun 2020 17:30:18: end of X-cor INFO @ Sun, 21 Jun 2020 17:30:18: #2 finished! INFO @ Sun, 21 Jun 2020 17:30:18: #2 predicted fragment length is 189 bps INFO @ Sun, 21 Jun 2020 17:30:18: #2 alternative fragment length(s) may be 189 bps INFO @ Sun, 21 Jun 2020 17:30:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1134699/SRX1134699.05_model.r INFO @ Sun, 21 Jun 2020 17:30:18: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:30:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:30:26: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:30:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1134699/SRX1134699.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:30:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1134699/SRX1134699.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:30:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1134699/SRX1134699.05_summits.bed INFO @ Sun, 21 Jun 2020 17:30:30: Done! pass1 - making usageList (214 chroms): 1 millis pass2 - checking and writing primary data (5153 records, 4 fields): 11 millis CompletedMACS2peakCalling 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 17:30:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1134699/SRX1134699.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1134699/SRX1134699.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1134699/SRX1134699.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1134699/SRX1134699.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 17:30:35: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:30:35: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:30:40: 1000000 INFO @ Sun, 21 Jun 2020 17:30:45: 2000000 INFO @ Sun, 21 Jun 2020 17:30:48: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 17:30:48: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 17:30:48: #1 total tags in treatment: 2505712 INFO @ Sun, 21 Jun 2020 17:30:48: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:30:48: #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 17:30:48: #1 tags after filtering in treatment: 2505391 INFO @ Sun, 21 Jun 2020 17:30:48: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:30:48: #1 finished! INFO @ Sun, 21 Jun 2020 17:30:48: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:30:48: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:30:48: #2 number of paired peaks: 5961 INFO @ Sun, 21 Jun 2020 17:30:48: start model_add_line... INFO @ Sun, 21 Jun 2020 17:30:48: start X-correlation... INFO @ Sun, 21 Jun 2020 17:30:48: end of X-cor INFO @ Sun, 21 Jun 2020 17:30:48: #2 finished! INFO @ Sun, 21 Jun 2020 17:30:48: #2 predicted fragment length is 189 bps INFO @ Sun, 21 Jun 2020 17:30:48: #2 alternative fragment length(s) may be 189 bps INFO @ Sun, 21 Jun 2020 17:30:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1134699/SRX1134699.10_model.r INFO @ Sun, 21 Jun 2020 17:30:48: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:30:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:30:57: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:31:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1134699/SRX1134699.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:31:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1134699/SRX1134699.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:31:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1134699/SRX1134699.10_summits.bed INFO @ Sun, 21 Jun 2020 17:31:00: Done! pass1 - making usageList (166 chroms): 1 millis pass2 - checking and writing primary data (3709 records, 4 fields): 9 millis CompletedMACS2peakCalling 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 17:31:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1134699/SRX1134699.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1134699/SRX1134699.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1134699/SRX1134699.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1134699/SRX1134699.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 17:31:05: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:31:05: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:31:09: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:31:15: 2000000 INFO @ Sun, 21 Jun 2020 17:31:17: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 17:31:17: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 17:31:17: #1 total tags in treatment: 2505712 INFO @ Sun, 21 Jun 2020 17:31:17: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:31:17: #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 17:31:18: #1 tags after filtering in treatment: 2505391 INFO @ Sun, 21 Jun 2020 17:31:18: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:31:18: #1 finished! INFO @ Sun, 21 Jun 2020 17:31:18: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:31:18: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:31:18: #2 number of paired peaks: 5961 INFO @ Sun, 21 Jun 2020 17:31:18: start model_add_line... INFO @ Sun, 21 Jun 2020 17:31:18: start X-correlation... INFO @ Sun, 21 Jun 2020 17:31:18: end of X-cor INFO @ Sun, 21 Jun 2020 17:31:18: #2 finished! INFO @ Sun, 21 Jun 2020 17:31:18: #2 predicted fragment length is 189 bps INFO @ Sun, 21 Jun 2020 17:31:18: #2 alternative fragment length(s) may be 189 bps INFO @ Sun, 21 Jun 2020 17:31:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1134699/SRX1134699.20_model.r INFO @ Sun, 21 Jun 2020 17:31:18: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:31:18: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:31:26: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:31:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1134699/SRX1134699.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:31:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1134699/SRX1134699.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:31:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1134699/SRX1134699.20_summits.bed INFO @ Sun, 21 Jun 2020 17:31:30: Done! pass1 - making usageList (100 chroms): 1 millis pass2 - checking and writing primary data (2405 records, 4 fields): 6 millis CompletedMACS2peakCalling