Job ID = 6455922 SRX = SRX3068961 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:25:36 prefetch.2.10.7: 1) Downloading 'SRR5907437'... 2020-06-21T10:25:36 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:27:02 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:27:02 prefetch.2.10.7: 'SRR5907437' is valid 2020-06-21T10:27:02 prefetch.2.10.7: 1) 'SRR5907437' was downloaded successfully Read 6730523 spots for SRR5907437/SRR5907437.sra Written 6730523 spots for SRR5907437/SRR5907437.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: 00:01:02 6730523 reads; of these: 6730523 (100.00%) were unpaired; of these: 2682425 (39.85%) aligned 0 times 3587563 (53.30%) aligned exactly 1 time 460535 (6.84%) aligned >1 times 60.15% overall alignment rate Time searching: 00:01:02 Overall time: 00:01:02 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] 1605634 / 4048098 = 0.3966 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 19:29:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3068961/SRX3068961.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3068961/SRX3068961.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3068961/SRX3068961.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3068961/SRX3068961.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 19:29:46: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:29:46: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:29:51: 1000000 INFO @ Sun, 21 Jun 2020 19:29:57: 2000000 INFO @ Sun, 21 Jun 2020 19:29:59: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:29:59: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:29:59: #1 total tags in treatment: 2442464 INFO @ Sun, 21 Jun 2020 19:29:59: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:29:59: #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 19:30:00: #1 tags after filtering in treatment: 2442193 INFO @ Sun, 21 Jun 2020 19:30:00: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:30:00: #1 finished! INFO @ Sun, 21 Jun 2020 19:30:00: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:30:00: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:30:00: #2 number of paired peaks: 1710 INFO @ Sun, 21 Jun 2020 19:30:00: start model_add_line... INFO @ Sun, 21 Jun 2020 19:30:00: start X-correlation... INFO @ Sun, 21 Jun 2020 19:30:00: end of X-cor INFO @ Sun, 21 Jun 2020 19:30:00: #2 finished! INFO @ Sun, 21 Jun 2020 19:30:00: #2 predicted fragment length is 154 bps INFO @ Sun, 21 Jun 2020 19:30:00: #2 alternative fragment length(s) may be 154 bps INFO @ Sun, 21 Jun 2020 19:30:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3068961/SRX3068961.05_model.r INFO @ Sun, 21 Jun 2020 19:30:00: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:30:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:30:06: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:30:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3068961/SRX3068961.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:30:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3068961/SRX3068961.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:30:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3068961/SRX3068961.05_summits.bed INFO @ Sun, 21 Jun 2020 19:30:09: Done! pass1 - making usageList (220 chroms): 1 millis pass2 - checking and writing primary data (3227 records, 4 fields): 9 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 19:30:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3068961/SRX3068961.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3068961/SRX3068961.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3068961/SRX3068961.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3068961/SRX3068961.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 19:30:16: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:30:16: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:30:21: 1000000 INFO @ Sun, 21 Jun 2020 19:30:27: 2000000 INFO @ Sun, 21 Jun 2020 19:30:29: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:30:29: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:30:29: #1 total tags in treatment: 2442464 INFO @ Sun, 21 Jun 2020 19:30:29: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:30:29: #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 19:30:30: #1 tags after filtering in treatment: 2442193 INFO @ Sun, 21 Jun 2020 19:30:30: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:30:30: #1 finished! INFO @ Sun, 21 Jun 2020 19:30:30: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:30:30: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:30:30: #2 number of paired peaks: 1710 INFO @ Sun, 21 Jun 2020 19:30:30: start model_add_line... INFO @ Sun, 21 Jun 2020 19:30:30: start X-correlation... INFO @ Sun, 21 Jun 2020 19:30:30: end of X-cor INFO @ Sun, 21 Jun 2020 19:30:30: #2 finished! INFO @ Sun, 21 Jun 2020 19:30:30: #2 predicted fragment length is 154 bps INFO @ Sun, 21 Jun 2020 19:30:30: #2 alternative fragment length(s) may be 154 bps INFO @ Sun, 21 Jun 2020 19:30:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3068961/SRX3068961.10_model.r INFO @ Sun, 21 Jun 2020 19:30:30: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:30:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:30:36: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:30:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3068961/SRX3068961.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:30:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3068961/SRX3068961.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:30:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3068961/SRX3068961.10_summits.bed INFO @ Sun, 21 Jun 2020 19:30:39: Done! pass1 - making usageList (64 chroms): 1 millis pass2 - checking and writing primary data (1372 records, 4 fields): 4 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 19:30:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3068961/SRX3068961.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3068961/SRX3068961.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3068961/SRX3068961.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3068961/SRX3068961.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 19:30:46: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:30:46: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:30:51: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:30:57: 2000000 INFO @ Sun, 21 Jun 2020 19:30:59: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:30:59: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:30:59: #1 total tags in treatment: 2442464 INFO @ Sun, 21 Jun 2020 19:30:59: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:30:59: #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 19:31:00: #1 tags after filtering in treatment: 2442193 INFO @ Sun, 21 Jun 2020 19:31:00: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:31:00: #1 finished! INFO @ Sun, 21 Jun 2020 19:31:00: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:31:00: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:31:00: #2 number of paired peaks: 1710 INFO @ Sun, 21 Jun 2020 19:31:00: start model_add_line... INFO @ Sun, 21 Jun 2020 19:31:00: start X-correlation... INFO @ Sun, 21 Jun 2020 19:31:00: end of X-cor INFO @ Sun, 21 Jun 2020 19:31:00: #2 finished! INFO @ Sun, 21 Jun 2020 19:31:00: #2 predicted fragment length is 154 bps INFO @ Sun, 21 Jun 2020 19:31:00: #2 alternative fragment length(s) may be 154 bps INFO @ Sun, 21 Jun 2020 19:31:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3068961/SRX3068961.20_model.r INFO @ Sun, 21 Jun 2020 19:31:00: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:31:00: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:31:06: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:31:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3068961/SRX3068961.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:31:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3068961/SRX3068961.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:31:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3068961/SRX3068961.20_summits.bed INFO @ Sun, 21 Jun 2020 19:31:09: Done! pass1 - making usageList (38 chroms): 1 millis pass2 - checking and writing primary data (635 records, 4 fields): 3 millis CompletedMACS2peakCalling