Job ID = 6453834 SRX = SRX151962 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:47:47 prefetch.2.10.7: 1) Downloading 'SRR504796'... 2020-06-21T08:47:47 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:48:31 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:48:31 prefetch.2.10.7: 'SRR504796' is valid 2020-06-21T08:48:31 prefetch.2.10.7: 1) 'SRR504796' was downloaded successfully Read 6063648 spots for SRR504796/SRR504796.sra Written 6063648 spots for SRR504796/SRR504796.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: 00:01:11 6063648 reads; of these: 6063648 (100.00%) were unpaired; of these: 227436 (3.75%) aligned 0 times 4529626 (74.70%) aligned exactly 1 time 1306586 (21.55%) aligned >1 times 96.25% overall alignment rate Time searching: 00:01:11 Overall time: 00:01:11 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] 935857 / 5836212 = 0.1604 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 17:51:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX151962/SRX151962.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX151962/SRX151962.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX151962/SRX151962.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX151962/SRX151962.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 17:51:35: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:51:35: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:51:40: 1000000 INFO @ Sun, 21 Jun 2020 17:51:44: 2000000 INFO @ Sun, 21 Jun 2020 17:51:49: 3000000 INFO @ Sun, 21 Jun 2020 17:51:53: 4000000 INFO @ Sun, 21 Jun 2020 17:51:58: #1 tag size is determined as 30 bps INFO @ Sun, 21 Jun 2020 17:51:58: #1 tag size = 30 INFO @ Sun, 21 Jun 2020 17:51:58: #1 total tags in treatment: 4900355 INFO @ Sun, 21 Jun 2020 17:51:58: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:51:58: #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 17:51:58: #1 tags after filtering in treatment: 4900301 INFO @ Sun, 21 Jun 2020 17:51:58: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:51:58: #1 finished! INFO @ Sun, 21 Jun 2020 17:51:58: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:51:58: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:51:59: #2 number of paired peaks: 4586 INFO @ Sun, 21 Jun 2020 17:51:59: start model_add_line... INFO @ Sun, 21 Jun 2020 17:51:59: start X-correlation... INFO @ Sun, 21 Jun 2020 17:51:59: end of X-cor INFO @ Sun, 21 Jun 2020 17:51:59: #2 finished! INFO @ Sun, 21 Jun 2020 17:51:59: #2 predicted fragment length is 104 bps INFO @ Sun, 21 Jun 2020 17:51:59: #2 alternative fragment length(s) may be 104 bps INFO @ Sun, 21 Jun 2020 17:51:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX151962/SRX151962.05_model.r INFO @ Sun, 21 Jun 2020 17:51:59: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:51:59: #3 Pre-compute pvalue-qvalue table... 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 17:52:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX151962/SRX151962.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX151962/SRX151962.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX151962/SRX151962.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX151962/SRX151962.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 17:52:05: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:52:05: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:52:10: 1000000 INFO @ Sun, 21 Jun 2020 17:52:11: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:52:15: 2000000 INFO @ Sun, 21 Jun 2020 17:52:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX151962/SRX151962.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:52:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX151962/SRX151962.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:52:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX151962/SRX151962.05_summits.bed INFO @ Sun, 21 Jun 2020 17:52:16: Done! pass1 - making usageList (231 chroms): 2 millis pass2 - checking and writing primary data (6557 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:52:19: 3000000 INFO @ Sun, 21 Jun 2020 17:52:24: 4000000 INFO @ Sun, 21 Jun 2020 17:52:29: #1 tag size is determined as 30 bps INFO @ Sun, 21 Jun 2020 17:52:29: #1 tag size = 30 INFO @ Sun, 21 Jun 2020 17:52:29: #1 total tags in treatment: 4900355 INFO @ Sun, 21 Jun 2020 17:52:29: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:52:29: #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 17:52:29: #1 tags after filtering in treatment: 4900301 INFO @ Sun, 21 Jun 2020 17:52:29: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:52:29: #1 finished! INFO @ Sun, 21 Jun 2020 17:52:29: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:52:29: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:52:29: #2 number of paired peaks: 4586 INFO @ Sun, 21 Jun 2020 17:52:29: start model_add_line... INFO @ Sun, 21 Jun 2020 17:52:30: start X-correlation... INFO @ Sun, 21 Jun 2020 17:52:30: end of X-cor INFO @ Sun, 21 Jun 2020 17:52:30: #2 finished! INFO @ Sun, 21 Jun 2020 17:52:30: #2 predicted fragment length is 104 bps INFO @ Sun, 21 Jun 2020 17:52:30: #2 alternative fragment length(s) may be 104 bps INFO @ Sun, 21 Jun 2020 17:52:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX151962/SRX151962.10_model.r INFO @ Sun, 21 Jun 2020 17:52:30: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:52:30: #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 17:52:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX151962/SRX151962.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX151962/SRX151962.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX151962/SRX151962.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX151962/SRX151962.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 17:52:35: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:52:35: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:52:40: 1000000 INFO @ Sun, 21 Jun 2020 17:52:42: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:52:44: 2000000 INFO @ Sun, 21 Jun 2020 17:52:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX151962/SRX151962.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:52:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX151962/SRX151962.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:52:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX151962/SRX151962.10_summits.bed INFO @ Sun, 21 Jun 2020 17:52:48: Done! pass1 - making usageList (174 chroms): 2 millis pass2 - checking and writing primary data (5027 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:52:49: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:52:53: 4000000 INFO @ Sun, 21 Jun 2020 17:52:58: #1 tag size is determined as 30 bps INFO @ Sun, 21 Jun 2020 17:52:58: #1 tag size = 30 INFO @ Sun, 21 Jun 2020 17:52:58: #1 total tags in treatment: 4900355 INFO @ Sun, 21 Jun 2020 17:52:58: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:52:58: #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 17:52:59: #1 tags after filtering in treatment: 4900301 INFO @ Sun, 21 Jun 2020 17:52:59: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:52:59: #1 finished! INFO @ Sun, 21 Jun 2020 17:52:59: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:52:59: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:52:59: #2 number of paired peaks: 4586 INFO @ Sun, 21 Jun 2020 17:52:59: start model_add_line... INFO @ Sun, 21 Jun 2020 17:52:59: start X-correlation... INFO @ Sun, 21 Jun 2020 17:52:59: end of X-cor INFO @ Sun, 21 Jun 2020 17:52:59: #2 finished! INFO @ Sun, 21 Jun 2020 17:52:59: #2 predicted fragment length is 104 bps INFO @ Sun, 21 Jun 2020 17:52:59: #2 alternative fragment length(s) may be 104 bps INFO @ Sun, 21 Jun 2020 17:52:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX151962/SRX151962.20_model.r INFO @ Sun, 21 Jun 2020 17:52:59: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:52:59: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:53:12: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:53:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX151962/SRX151962.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:53:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX151962/SRX151962.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:53:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX151962/SRX151962.20_summits.bed INFO @ Sun, 21 Jun 2020 17:53:19: Done! pass1 - making usageList (126 chroms): 1 millis pass2 - checking and writing primary data (3398 records, 4 fields): 8 millis CompletedMACS2peakCalling