Job ID = 6457104 SRX = SRX4375863 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:29:25 prefetch.2.10.7: 1) Downloading 'SRR7506517'... 2020-06-21T11:29:25 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:30:52 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:30:52 prefetch.2.10.7: 'SRR7506517' is valid 2020-06-21T11:30:52 prefetch.2.10.7: 1) 'SRR7506517' was downloaded successfully Read 5831465 spots for SRR7506517/SRR7506517.sra Written 5831465 spots for SRR7506517/SRR7506517.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: 00:01:37 5831465 reads; of these: 5831465 (100.00%) were unpaired; of these: 1233847 (21.16%) aligned 0 times 3332770 (57.15%) aligned exactly 1 time 1264848 (21.69%) aligned >1 times 78.84% overall alignment rate Time searching: 00:01:37 Overall time: 00:01:37 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] 1817382 / 4597618 = 0.3953 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 20:34:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4375863/SRX4375863.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4375863/SRX4375863.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4375863/SRX4375863.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4375863/SRX4375863.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 20:34:20: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:34:20: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:34:26: 1000000 INFO @ Sun, 21 Jun 2020 20:34:31: 2000000 INFO @ Sun, 21 Jun 2020 20:34:35: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:34:35: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:34:35: #1 total tags in treatment: 2780236 INFO @ Sun, 21 Jun 2020 20:34:35: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:34:35: #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 20:34:35: #1 tags after filtering in treatment: 2780013 INFO @ Sun, 21 Jun 2020 20:34:35: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:34:35: #1 finished! INFO @ Sun, 21 Jun 2020 20:34:35: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:34:35: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:34:36: #2 number of paired peaks: 1390 INFO @ Sun, 21 Jun 2020 20:34:36: start model_add_line... INFO @ Sun, 21 Jun 2020 20:34:36: start X-correlation... INFO @ Sun, 21 Jun 2020 20:34:36: end of X-cor INFO @ Sun, 21 Jun 2020 20:34:36: #2 finished! INFO @ Sun, 21 Jun 2020 20:34:36: #2 predicted fragment length is 104 bps INFO @ Sun, 21 Jun 2020 20:34:36: #2 alternative fragment length(s) may be 104,477 bps INFO @ Sun, 21 Jun 2020 20:34:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4375863/SRX4375863.05_model.r INFO @ Sun, 21 Jun 2020 20:34:36: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:34:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:34:42: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:34:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4375863/SRX4375863.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:34:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4375863/SRX4375863.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:34:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4375863/SRX4375863.05_summits.bed INFO @ Sun, 21 Jun 2020 20:34:45: Done! pass1 - making usageList (506 chroms): 1 millis pass2 - checking and writing primary data (1705 records, 4 fields): 34 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 20:34:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4375863/SRX4375863.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4375863/SRX4375863.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4375863/SRX4375863.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4375863/SRX4375863.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 20:34:50: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:34:50: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:34:57: 1000000 INFO @ Sun, 21 Jun 2020 20:35:03: 2000000 INFO @ Sun, 21 Jun 2020 20:35:08: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:35:08: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:35:08: #1 total tags in treatment: 2780236 INFO @ Sun, 21 Jun 2020 20:35:08: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:35:08: #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 20:35:08: #1 tags after filtering in treatment: 2780013 INFO @ Sun, 21 Jun 2020 20:35:08: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:35:08: #1 finished! INFO @ Sun, 21 Jun 2020 20:35:08: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:35:08: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:35:08: #2 number of paired peaks: 1390 INFO @ Sun, 21 Jun 2020 20:35:08: start model_add_line... INFO @ Sun, 21 Jun 2020 20:35:08: start X-correlation... INFO @ Sun, 21 Jun 2020 20:35:08: end of X-cor INFO @ Sun, 21 Jun 2020 20:35:08: #2 finished! INFO @ Sun, 21 Jun 2020 20:35:08: #2 predicted fragment length is 104 bps INFO @ Sun, 21 Jun 2020 20:35:08: #2 alternative fragment length(s) may be 104,477 bps INFO @ Sun, 21 Jun 2020 20:35:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4375863/SRX4375863.10_model.r INFO @ Sun, 21 Jun 2020 20:35:08: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:35:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:35:15: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:35:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4375863/SRX4375863.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:35:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4375863/SRX4375863.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:35:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4375863/SRX4375863.10_summits.bed INFO @ Sun, 21 Jun 2020 20:35:18: Done! pass1 - making usageList (397 chroms): 1 millis pass2 - checking and writing primary data (912 records, 4 fields): 12 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 20:35:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4375863/SRX4375863.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4375863/SRX4375863.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4375863/SRX4375863.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4375863/SRX4375863.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 20:35:20: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:35:20: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:35:26: 1000000 INFO @ Sun, 21 Jun 2020 20:35:32: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:35:38: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:35:38: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:35:38: #1 total tags in treatment: 2780236 INFO @ Sun, 21 Jun 2020 20:35:38: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:35:38: #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 20:35:38: #1 tags after filtering in treatment: 2780013 INFO @ Sun, 21 Jun 2020 20:35:38: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:35:38: #1 finished! INFO @ Sun, 21 Jun 2020 20:35:38: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:35:38: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:35:38: #2 number of paired peaks: 1390 INFO @ Sun, 21 Jun 2020 20:35:38: start model_add_line... INFO @ Sun, 21 Jun 2020 20:35:38: start X-correlation... INFO @ Sun, 21 Jun 2020 20:35:38: end of X-cor INFO @ Sun, 21 Jun 2020 20:35:38: #2 finished! INFO @ Sun, 21 Jun 2020 20:35:38: #2 predicted fragment length is 104 bps INFO @ Sun, 21 Jun 2020 20:35:38: #2 alternative fragment length(s) may be 104,477 bps INFO @ Sun, 21 Jun 2020 20:35:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4375863/SRX4375863.20_model.r INFO @ Sun, 21 Jun 2020 20:35:38: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:35:38: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:35:45: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:35:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4375863/SRX4375863.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:35:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4375863/SRX4375863.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:35:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4375863/SRX4375863.20_summits.bed INFO @ Sun, 21 Jun 2020 20:35:48: Done! pass1 - making usageList (152 chroms): 1 millis pass2 - checking and writing primary data (238 records, 4 fields): 6 millis CompletedMACS2peakCalling