Job ID = 6457047 SRX = SRX4375815 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:38:25 prefetch.2.10.7: 1) Downloading 'SRR7506469'... 2020-06-21T11:38:25 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:39:56 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:39:57 prefetch.2.10.7: 'SRR7506469' is valid 2020-06-21T11:39:57 prefetch.2.10.7: 1) 'SRR7506469' was downloaded successfully Read 8933314 spots for SRR7506469/SRR7506469.sra Written 8933314 spots for SRR7506469/SRR7506469.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: 00:00:54 8933314 reads; of these: 8933314 (100.00%) were unpaired; of these: 7029705 (78.69%) aligned 0 times 1447425 (16.20%) aligned exactly 1 time 456184 (5.11%) aligned >1 times 21.31% overall alignment rate Time searching: 00:00:54 Overall time: 00:00:54 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] 647335 / 1903609 = 0.3401 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 20:42:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4375815/SRX4375815.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4375815/SRX4375815.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4375815/SRX4375815.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4375815/SRX4375815.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 20:42:17: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:42:17: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:42:23: 1000000 INFO @ Sun, 21 Jun 2020 20:42:25: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:42:25: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:42:25: #1 total tags in treatment: 1256274 INFO @ Sun, 21 Jun 2020 20:42:25: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:42:25: #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 20:42:25: #1 tags after filtering in treatment: 1255853 INFO @ Sun, 21 Jun 2020 20:42:25: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:42:25: #1 finished! INFO @ Sun, 21 Jun 2020 20:42:25: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:42:25: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:42:25: #2 number of paired peaks: 3158 INFO @ Sun, 21 Jun 2020 20:42:25: start model_add_line... INFO @ Sun, 21 Jun 2020 20:42:25: start X-correlation... INFO @ Sun, 21 Jun 2020 20:42:25: end of X-cor INFO @ Sun, 21 Jun 2020 20:42:25: #2 finished! INFO @ Sun, 21 Jun 2020 20:42:25: #2 predicted fragment length is 271 bps INFO @ Sun, 21 Jun 2020 20:42:25: #2 alternative fragment length(s) may be 271 bps INFO @ Sun, 21 Jun 2020 20:42:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4375815/SRX4375815.05_model.r INFO @ Sun, 21 Jun 2020 20:42:25: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:42:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:42:29: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:42:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4375815/SRX4375815.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:42:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4375815/SRX4375815.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:42:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4375815/SRX4375815.05_summits.bed INFO @ Sun, 21 Jun 2020 20:42:30: Done! pass1 - making usageList (202 chroms): 1 millis pass2 - checking and writing primary data (1973 records, 4 fields): 8 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 20:42:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4375815/SRX4375815.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4375815/SRX4375815.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4375815/SRX4375815.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4375815/SRX4375815.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 20:42:47: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:42:47: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:42:54: 1000000 INFO @ Sun, 21 Jun 2020 20:42:56: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:42:56: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:42:56: #1 total tags in treatment: 1256274 INFO @ Sun, 21 Jun 2020 20:42:56: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:42:56: #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 20:42:57: #1 tags after filtering in treatment: 1255853 INFO @ Sun, 21 Jun 2020 20:42:57: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:42:57: #1 finished! INFO @ Sun, 21 Jun 2020 20:42:57: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:42:57: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:42:57: #2 number of paired peaks: 3158 INFO @ Sun, 21 Jun 2020 20:42:57: start model_add_line... INFO @ Sun, 21 Jun 2020 20:42:57: start X-correlation... INFO @ Sun, 21 Jun 2020 20:42:57: end of X-cor INFO @ Sun, 21 Jun 2020 20:42:57: #2 finished! INFO @ Sun, 21 Jun 2020 20:42:57: #2 predicted fragment length is 271 bps INFO @ Sun, 21 Jun 2020 20:42:57: #2 alternative fragment length(s) may be 271 bps INFO @ Sun, 21 Jun 2020 20:42:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4375815/SRX4375815.10_model.r INFO @ Sun, 21 Jun 2020 20:42:57: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:42:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:43:00: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:43:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4375815/SRX4375815.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:43:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4375815/SRX4375815.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:43:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4375815/SRX4375815.10_summits.bed INFO @ Sun, 21 Jun 2020 20:43:02: Done! pass1 - making usageList (77 chroms): 1 millis pass2 - checking and writing primary data (881 records, 4 fields): 5 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 20:43:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4375815/SRX4375815.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4375815/SRX4375815.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4375815/SRX4375815.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4375815/SRX4375815.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 20:43:17: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:43:17: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:43:24: 1000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:43:25: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:43:25: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:43:25: #1 total tags in treatment: 1256274 INFO @ Sun, 21 Jun 2020 20:43:25: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:43:25: #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 20:43:26: #1 tags after filtering in treatment: 1255853 INFO @ Sun, 21 Jun 2020 20:43:26: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:43:26: #1 finished! INFO @ Sun, 21 Jun 2020 20:43:26: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:43:26: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:43:26: #2 number of paired peaks: 3158 INFO @ Sun, 21 Jun 2020 20:43:26: start model_add_line... INFO @ Sun, 21 Jun 2020 20:43:26: start X-correlation... INFO @ Sun, 21 Jun 2020 20:43:26: end of X-cor INFO @ Sun, 21 Jun 2020 20:43:26: #2 finished! INFO @ Sun, 21 Jun 2020 20:43:26: #2 predicted fragment length is 271 bps INFO @ Sun, 21 Jun 2020 20:43:26: #2 alternative fragment length(s) may be 271 bps INFO @ Sun, 21 Jun 2020 20:43:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4375815/SRX4375815.20_model.r INFO @ Sun, 21 Jun 2020 20:43:26: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:43:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:43:29: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:43:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4375815/SRX4375815.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:43:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4375815/SRX4375815.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:43:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4375815/SRX4375815.20_summits.bed INFO @ Sun, 21 Jun 2020 20:43:31: Done! pass1 - making usageList (37 chroms): 1 millis pass2 - checking and writing primary data (346 records, 4 fields): 3 millis CompletedMACS2peakCalling