Job ID = 6455016 SRX = SRX2638363 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:53:40 prefetch.2.10.7: 1) Downloading 'SRR5341689'... 2020-06-21T09:53:40 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:57:47 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:57:47 prefetch.2.10.7: 1) 'SRR5341689' was downloaded successfully Read 23386320 spots for SRR5341689/SRR5341689.sra Written 23386320 spots for SRR5341689/SRR5341689.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:06:30 23386320 reads; of these: 23386320 (100.00%) were unpaired; of these: 14333214 (61.29%) aligned 0 times 3560488 (15.22%) aligned exactly 1 time 5492618 (23.49%) aligned >1 times 38.71% overall alignment rate Time searching: 00:06:31 Overall time: 00:06:31 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] 7568472 / 9053106 = 0.8360 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 19:08:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2638363/SRX2638363.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2638363/SRX2638363.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2638363/SRX2638363.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2638363/SRX2638363.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 19:08:08: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:08:08: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:08:15: 1000000 INFO @ Sun, 21 Jun 2020 19:08:19: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:08:19: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:08:19: #1 total tags in treatment: 1484634 INFO @ Sun, 21 Jun 2020 19:08:19: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:08:19: #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 19:08:19: #1 tags after filtering in treatment: 1484352 INFO @ Sun, 21 Jun 2020 19:08:19: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:08:19: #1 finished! INFO @ Sun, 21 Jun 2020 19:08:19: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:08:19: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:08:20: #2 number of paired peaks: 3242 INFO @ Sun, 21 Jun 2020 19:08:20: start model_add_line... INFO @ Sun, 21 Jun 2020 19:08:20: start X-correlation... INFO @ Sun, 21 Jun 2020 19:08:20: end of X-cor INFO @ Sun, 21 Jun 2020 19:08:20: #2 finished! INFO @ Sun, 21 Jun 2020 19:08:20: #2 predicted fragment length is 149 bps INFO @ Sun, 21 Jun 2020 19:08:20: #2 alternative fragment length(s) may be 149 bps INFO @ Sun, 21 Jun 2020 19:08:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2638363/SRX2638363.05_model.r INFO @ Sun, 21 Jun 2020 19:08:20: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:08:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:08:24: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:08:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2638363/SRX2638363.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:08:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2638363/SRX2638363.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:08:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2638363/SRX2638363.05_summits.bed INFO @ Sun, 21 Jun 2020 19:08:26: Done! pass1 - making usageList (587 chroms): 1 millis pass2 - checking and writing primary data (3525 records, 4 fields): 37 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 19:08:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2638363/SRX2638363.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2638363/SRX2638363.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2638363/SRX2638363.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2638363/SRX2638363.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 19:08:38: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:08:38: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:08:45: 1000000 INFO @ Sun, 21 Jun 2020 19:08:50: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:08:50: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:08:50: #1 total tags in treatment: 1484634 INFO @ Sun, 21 Jun 2020 19:08:50: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:08:50: #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 19:08:50: #1 tags after filtering in treatment: 1484352 INFO @ Sun, 21 Jun 2020 19:08:50: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:08:50: #1 finished! INFO @ Sun, 21 Jun 2020 19:08:50: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:08:50: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:08:50: #2 number of paired peaks: 3242 INFO @ Sun, 21 Jun 2020 19:08:50: start model_add_line... INFO @ Sun, 21 Jun 2020 19:08:50: start X-correlation... INFO @ Sun, 21 Jun 2020 19:08:50: end of X-cor INFO @ Sun, 21 Jun 2020 19:08:50: #2 finished! INFO @ Sun, 21 Jun 2020 19:08:50: #2 predicted fragment length is 149 bps INFO @ Sun, 21 Jun 2020 19:08:50: #2 alternative fragment length(s) may be 149 bps INFO @ Sun, 21 Jun 2020 19:08:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2638363/SRX2638363.10_model.r INFO @ Sun, 21 Jun 2020 19:08:50: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:08:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:08:55: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:08:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2638363/SRX2638363.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:08:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2638363/SRX2638363.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:08:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2638363/SRX2638363.10_summits.bed INFO @ Sun, 21 Jun 2020 19:08:57: Done! pass1 - making usageList (380 chroms): 1 millis pass2 - checking and writing primary data (1606 records, 4 fields): 23 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 19:09:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2638363/SRX2638363.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2638363/SRX2638363.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2638363/SRX2638363.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2638363/SRX2638363.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 19:09:08: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:09:08: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:09:14: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:09:18: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:09:18: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:09:18: #1 total tags in treatment: 1484634 INFO @ Sun, 21 Jun 2020 19:09:18: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:09:18: #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 19:09:19: #1 tags after filtering in treatment: 1484352 INFO @ Sun, 21 Jun 2020 19:09:19: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:09:19: #1 finished! INFO @ Sun, 21 Jun 2020 19:09:19: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:09:19: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:09:19: #2 number of paired peaks: 3242 INFO @ Sun, 21 Jun 2020 19:09:19: start model_add_line... INFO @ Sun, 21 Jun 2020 19:09:19: start X-correlation... INFO @ Sun, 21 Jun 2020 19:09:19: end of X-cor INFO @ Sun, 21 Jun 2020 19:09:19: #2 finished! INFO @ Sun, 21 Jun 2020 19:09:19: #2 predicted fragment length is 149 bps INFO @ Sun, 21 Jun 2020 19:09:19: #2 alternative fragment length(s) may be 149 bps INFO @ Sun, 21 Jun 2020 19:09:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2638363/SRX2638363.20_model.r INFO @ Sun, 21 Jun 2020 19:09:19: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:09:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:09:23: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:09:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2638363/SRX2638363.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:09:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2638363/SRX2638363.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:09:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2638363/SRX2638363.20_summits.bed INFO @ Sun, 21 Jun 2020 19:09:25: Done! pass1 - making usageList (143 chroms): 1 millis pass2 - checking and writing primary data (628 records, 4 fields): 10 millis CompletedMACS2peakCalling