Job ID = 6453604 SRX = SRX1299930 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:32:11 prefetch.2.10.7: 1) Downloading 'SRR2546849'... 2020-06-21T08:32:11 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:32:47 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:32:48 prefetch.2.10.7: 'SRR2546849' is valid 2020-06-21T08:32:48 prefetch.2.10.7: 1) 'SRR2546849' was downloaded successfully 2020-06-21T08:32:48 prefetch.2.10.7: 'SRR2546849' has 0 unresolved dependencies Read 1585104 spots for SRR2546849/SRR2546849.sra Written 1585104 spots for SRR2546849/SRR2546849.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: 00:00:25 1585104 reads; of these: 1585104 (100.00%) were unpaired; of these: 436873 (27.56%) aligned 0 times 653216 (41.21%) aligned exactly 1 time 495015 (31.23%) aligned >1 times 72.44% overall alignment rate Time searching: 00:00:25 Overall time: 00:00:25 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_rmdupse_core] 353598 / 1148231 = 0.3080 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 17:34:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1299930/SRX1299930.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1299930/SRX1299930.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1299930/SRX1299930.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1299930/SRX1299930.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 17:34:07: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:34:07: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:34:11: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 17:34:11: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 17:34:11: #1 total tags in treatment: 794633 INFO @ Sun, 21 Jun 2020 17:34:11: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:34:11: #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 17:34:12: #1 tags after filtering in treatment: 794244 INFO @ Sun, 21 Jun 2020 17:34:12: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:34:12: #1 finished! INFO @ Sun, 21 Jun 2020 17:34:12: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:34:12: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:34:12: #2 number of paired peaks: 1379 INFO @ Sun, 21 Jun 2020 17:34:12: start model_add_line... INFO @ Sun, 21 Jun 2020 17:34:12: start X-correlation... INFO @ Sun, 21 Jun 2020 17:34:12: end of X-cor INFO @ Sun, 21 Jun 2020 17:34:12: #2 finished! INFO @ Sun, 21 Jun 2020 17:34:12: #2 predicted fragment length is 112 bps INFO @ Sun, 21 Jun 2020 17:34:12: #2 alternative fragment length(s) may be 68,112,128,168 bps INFO @ Sun, 21 Jun 2020 17:34:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1299930/SRX1299930.05_model.r INFO @ Sun, 21 Jun 2020 17:34:12: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:34:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:34:14: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:34:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1299930/SRX1299930.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:34:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1299930/SRX1299930.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:34:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1299930/SRX1299930.05_summits.bed INFO @ Sun, 21 Jun 2020 17:34:15: Done! pass1 - making usageList (409 chroms): 1 millis pass2 - checking and writing primary data (764 records, 4 fields): 12 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 17:34:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1299930/SRX1299930.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1299930/SRX1299930.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1299930/SRX1299930.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1299930/SRX1299930.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 17:34:37: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:34:37: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:34:41: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 17:34:41: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 17:34:41: #1 total tags in treatment: 794633 INFO @ Sun, 21 Jun 2020 17:34:41: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:34:41: #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 17:34:41: #1 tags after filtering in treatment: 794244 INFO @ Sun, 21 Jun 2020 17:34:41: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:34:41: #1 finished! INFO @ Sun, 21 Jun 2020 17:34:41: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:34:41: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:34:42: #2 number of paired peaks: 1379 INFO @ Sun, 21 Jun 2020 17:34:42: start model_add_line... INFO @ Sun, 21 Jun 2020 17:34:42: start X-correlation... INFO @ Sun, 21 Jun 2020 17:34:42: end of X-cor INFO @ Sun, 21 Jun 2020 17:34:42: #2 finished! INFO @ Sun, 21 Jun 2020 17:34:42: #2 predicted fragment length is 112 bps INFO @ Sun, 21 Jun 2020 17:34:42: #2 alternative fragment length(s) may be 68,112,128,168 bps INFO @ Sun, 21 Jun 2020 17:34:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1299930/SRX1299930.10_model.r INFO @ Sun, 21 Jun 2020 17:34:42: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:34:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:34:44: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:34:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1299930/SRX1299930.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:34:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1299930/SRX1299930.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:34:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1299930/SRX1299930.10_summits.bed INFO @ Sun, 21 Jun 2020 17:34:45: Done! pass1 - making usageList (178 chroms): 0 millis pass2 - checking and writing primary data (256 records, 4 fields): 7 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 17:35:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1299930/SRX1299930.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1299930/SRX1299930.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1299930/SRX1299930.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1299930/SRX1299930.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 17:35:07: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:35:07: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:35:11: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 17:35:11: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 17:35:11: #1 total tags in treatment: 794633 INFO @ Sun, 21 Jun 2020 17:35:11: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:35:11: #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 17:35:11: #1 tags after filtering in treatment: 794244 INFO @ Sun, 21 Jun 2020 17:35:11: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:35:11: #1 finished! INFO @ Sun, 21 Jun 2020 17:35:11: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:35:11: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:35:12: #2 number of paired peaks: 1379 INFO @ Sun, 21 Jun 2020 17:35:12: start model_add_line... INFO @ Sun, 21 Jun 2020 17:35:12: start X-correlation... INFO @ Sun, 21 Jun 2020 17:35:12: end of X-cor INFO @ Sun, 21 Jun 2020 17:35:12: #2 finished! INFO @ Sun, 21 Jun 2020 17:35:12: #2 predicted fragment length is 112 bps INFO @ Sun, 21 Jun 2020 17:35:12: #2 alternative fragment length(s) may be 68,112,128,168 bps INFO @ Sun, 21 Jun 2020 17:35:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1299930/SRX1299930.20_model.r INFO @ Sun, 21 Jun 2020 17:35:12: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:35:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:35:14: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:35:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1299930/SRX1299930.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:35:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1299930/SRX1299930.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:35:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1299930/SRX1299930.20_summits.bed INFO @ Sun, 21 Jun 2020 17:35:15: Done! pass1 - making usageList (60 chroms): 1 millis pass2 - checking and writing primary data (89 records, 4 fields): 4 millis CompletedMACS2peakCalling