Job ID = 6456908 SRX = SRX4053335 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:15:24 prefetch.2.10.7: 1) Downloading 'SRR7132378'... 2020-06-21T11:15:24 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:15:47 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:15:47 prefetch.2.10.7: 'SRR7132378' is valid 2020-06-21T11:15:47 prefetch.2.10.7: 1) 'SRR7132378' was downloaded successfully 2020-06-21T11:15:47 prefetch.2.10.7: 'SRR7132378' has 0 unresolved dependencies Read 3596931 spots for SRR7132378/SRR7132378.sra Written 3596931 spots for SRR7132378/SRR7132378.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: 00:00:43 3596931 reads; of these: 3596931 (100.00%) were unpaired; of these: 474180 (13.18%) aligned 0 times 2928446 (81.42%) aligned exactly 1 time 194305 (5.40%) aligned >1 times 86.82% overall alignment rate Time searching: 00:00:43 Overall time: 00:00:43 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] 642969 / 3122751 = 0.2059 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 20:17:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4053335/SRX4053335.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4053335/SRX4053335.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4053335/SRX4053335.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4053335/SRX4053335.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 20:17:46: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:17:46: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:17:51: 1000000 INFO @ Sun, 21 Jun 2020 20:17:57: 2000000 INFO @ Sun, 21 Jun 2020 20:18:00: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:18:00: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:18:00: #1 total tags in treatment: 2479782 INFO @ Sun, 21 Jun 2020 20:18:00: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:18:00: #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 20:18:00: #1 tags after filtering in treatment: 2479222 INFO @ Sun, 21 Jun 2020 20:18:00: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:18:00: #1 finished! INFO @ Sun, 21 Jun 2020 20:18:00: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:18:00: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:18:00: #2 number of paired peaks: 9415 INFO @ Sun, 21 Jun 2020 20:18:00: start model_add_line... INFO @ Sun, 21 Jun 2020 20:18:00: start X-correlation... INFO @ Sun, 21 Jun 2020 20:18:00: end of X-cor INFO @ Sun, 21 Jun 2020 20:18:00: #2 finished! INFO @ Sun, 21 Jun 2020 20:18:00: #2 predicted fragment length is 199 bps INFO @ Sun, 21 Jun 2020 20:18:00: #2 alternative fragment length(s) may be 199 bps INFO @ Sun, 21 Jun 2020 20:18:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4053335/SRX4053335.05_model.r INFO @ Sun, 21 Jun 2020 20:18:00: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:18:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:18:07: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:18:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4053335/SRX4053335.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:18:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4053335/SRX4053335.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:18:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4053335/SRX4053335.05_summits.bed INFO @ Sun, 21 Jun 2020 20:18:11: Done! pass1 - making usageList (56 chroms): 2 millis pass2 - checking and writing primary data (5523 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 20:18:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4053335/SRX4053335.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4053335/SRX4053335.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4053335/SRX4053335.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4053335/SRX4053335.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 20:18:16: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:18:16: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:18:21: 1000000 INFO @ Sun, 21 Jun 2020 20:18:27: 2000000 INFO @ Sun, 21 Jun 2020 20:18:30: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:18:30: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:18:30: #1 total tags in treatment: 2479782 INFO @ Sun, 21 Jun 2020 20:18:30: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:18:30: #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 20:18:30: #1 tags after filtering in treatment: 2479222 INFO @ Sun, 21 Jun 2020 20:18:30: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:18:30: #1 finished! INFO @ Sun, 21 Jun 2020 20:18:30: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:18:30: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:18:30: #2 number of paired peaks: 9415 INFO @ Sun, 21 Jun 2020 20:18:30: start model_add_line... INFO @ Sun, 21 Jun 2020 20:18:30: start X-correlation... INFO @ Sun, 21 Jun 2020 20:18:30: end of X-cor INFO @ Sun, 21 Jun 2020 20:18:30: #2 finished! INFO @ Sun, 21 Jun 2020 20:18:30: #2 predicted fragment length is 199 bps INFO @ Sun, 21 Jun 2020 20:18:30: #2 alternative fragment length(s) may be 199 bps INFO @ Sun, 21 Jun 2020 20:18:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4053335/SRX4053335.10_model.r INFO @ Sun, 21 Jun 2020 20:18:30: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:18:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:18:37: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:18:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4053335/SRX4053335.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:18:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4053335/SRX4053335.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:18:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4053335/SRX4053335.10_summits.bed INFO @ Sun, 21 Jun 2020 20:18:41: Done! pass1 - making usageList (48 chroms): 2 millis pass2 - checking and writing primary data (5197 records, 4 fields): 8 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 20:18:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4053335/SRX4053335.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4053335/SRX4053335.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4053335/SRX4053335.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4053335/SRX4053335.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 20:18:46: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:18:46: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:18:52: 1000000 INFO @ Sun, 21 Jun 2020 20:18:57: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:19:00: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:19:00: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:19:00: #1 total tags in treatment: 2479782 INFO @ Sun, 21 Jun 2020 20:19:00: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:19:00: #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 20:19:00: #1 tags after filtering in treatment: 2479222 INFO @ Sun, 21 Jun 2020 20:19:00: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:19:00: #1 finished! INFO @ Sun, 21 Jun 2020 20:19:00: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:19:00: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:19:00: #2 number of paired peaks: 9415 INFO @ Sun, 21 Jun 2020 20:19:00: start model_add_line... INFO @ Sun, 21 Jun 2020 20:19:01: start X-correlation... INFO @ Sun, 21 Jun 2020 20:19:01: end of X-cor INFO @ Sun, 21 Jun 2020 20:19:01: #2 finished! INFO @ Sun, 21 Jun 2020 20:19:01: #2 predicted fragment length is 199 bps INFO @ Sun, 21 Jun 2020 20:19:01: #2 alternative fragment length(s) may be 199 bps INFO @ Sun, 21 Jun 2020 20:19:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4053335/SRX4053335.20_model.r INFO @ Sun, 21 Jun 2020 20:19:01: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:19:01: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:19:07: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:19:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4053335/SRX4053335.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:19:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4053335/SRX4053335.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:19:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4053335/SRX4053335.20_summits.bed INFO @ Sun, 21 Jun 2020 20:19:11: Done! pass1 - making usageList (36 chroms): 2 millis pass2 - checking and writing primary data (4314 records, 4 fields): 8 millis CompletedMACS2peakCalling