Job ID = 6454539 SRX = SRX220308 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:10:39 prefetch.2.10.7: 1) Downloading 'SRR653353'... 2020-06-21T09:10:39 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:13:39 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:13:40 prefetch.2.10.7: 'SRR653353' is valid 2020-06-21T09:13:40 prefetch.2.10.7: 1) 'SRR653353' was downloaded successfully Read 8084398 spots for SRR653353/SRR653353.sra Written 8084398 spots for SRR653353/SRR653353.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: 00:01:13 8084398 reads; of these: 8084398 (100.00%) were unpaired; of these: 1449543 (17.93%) aligned 0 times 5649843 (69.89%) aligned exactly 1 time 985012 (12.18%) aligned >1 times 82.07% overall alignment rate Time searching: 00:01:13 Overall time: 00:01:13 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] 3993338 / 6634855 = 0.6019 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 18:16:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX220308/SRX220308.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX220308/SRX220308.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX220308/SRX220308.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX220308/SRX220308.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 18:16:47: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:16:47: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:16:52: 1000000 INFO @ Sun, 21 Jun 2020 18:16:57: 2000000 INFO @ Sun, 21 Jun 2020 18:17:00: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 18:17:00: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 18:17:00: #1 total tags in treatment: 2641517 INFO @ Sun, 21 Jun 2020 18:17:00: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:17:00: #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 18:17:00: #1 tags after filtering in treatment: 2641201 INFO @ Sun, 21 Jun 2020 18:17:00: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:17:00: #1 finished! INFO @ Sun, 21 Jun 2020 18:17:00: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:17:00: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:17:01: #2 number of paired peaks: 3513 INFO @ Sun, 21 Jun 2020 18:17:01: start model_add_line... INFO @ Sun, 21 Jun 2020 18:17:01: start X-correlation... INFO @ Sun, 21 Jun 2020 18:17:01: end of X-cor INFO @ Sun, 21 Jun 2020 18:17:01: #2 finished! INFO @ Sun, 21 Jun 2020 18:17:01: #2 predicted fragment length is 140 bps INFO @ Sun, 21 Jun 2020 18:17:01: #2 alternative fragment length(s) may be 140 bps INFO @ Sun, 21 Jun 2020 18:17:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX220308/SRX220308.05_model.r INFO @ Sun, 21 Jun 2020 18:17:01: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:17:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:17:08: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:17:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX220308/SRX220308.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:17:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX220308/SRX220308.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:17:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX220308/SRX220308.05_summits.bed INFO @ Sun, 21 Jun 2020 18:17:12: Done! pass1 - making usageList (97 chroms): 1 millis pass2 - checking and writing primary data (3267 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 18:17:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX220308/SRX220308.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX220308/SRX220308.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX220308/SRX220308.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX220308/SRX220308.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 18:17:17: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:17:17: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:17:21: 1000000 INFO @ Sun, 21 Jun 2020 18:17:26: 2000000 INFO @ Sun, 21 Jun 2020 18:17:30: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 18:17:30: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 18:17:30: #1 total tags in treatment: 2641517 INFO @ Sun, 21 Jun 2020 18:17:30: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:17:30: #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 18:17:30: #1 tags after filtering in treatment: 2641201 INFO @ Sun, 21 Jun 2020 18:17:30: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:17:30: #1 finished! INFO @ Sun, 21 Jun 2020 18:17:30: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:17:30: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:17:30: #2 number of paired peaks: 3513 INFO @ Sun, 21 Jun 2020 18:17:30: start model_add_line... INFO @ Sun, 21 Jun 2020 18:17:30: start X-correlation... INFO @ Sun, 21 Jun 2020 18:17:30: end of X-cor INFO @ Sun, 21 Jun 2020 18:17:30: #2 finished! INFO @ Sun, 21 Jun 2020 18:17:30: #2 predicted fragment length is 140 bps INFO @ Sun, 21 Jun 2020 18:17:30: #2 alternative fragment length(s) may be 140 bps INFO @ Sun, 21 Jun 2020 18:17:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX220308/SRX220308.10_model.r INFO @ Sun, 21 Jun 2020 18:17:30: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:17:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:17:38: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:17:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX220308/SRX220308.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:17:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX220308/SRX220308.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:17:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX220308/SRX220308.10_summits.bed INFO @ Sun, 21 Jun 2020 18:17:41: Done! pass1 - making usageList (73 chroms): 1 millis pass2 - checking and writing primary data (2418 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 18:17:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX220308/SRX220308.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX220308/SRX220308.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX220308/SRX220308.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX220308/SRX220308.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 18:17:47: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:17:47: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:17:51: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:17:56: 2000000 INFO @ Sun, 21 Jun 2020 18:17:59: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 18:17:59: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 18:17:59: #1 total tags in treatment: 2641517 INFO @ Sun, 21 Jun 2020 18:17:59: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:17:59: #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 18:18:00: #1 tags after filtering in treatment: 2641201 INFO @ Sun, 21 Jun 2020 18:18:00: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:18:00: #1 finished! INFO @ Sun, 21 Jun 2020 18:18:00: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:18:00: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:18:00: #2 number of paired peaks: 3513 INFO @ Sun, 21 Jun 2020 18:18:00: start model_add_line... INFO @ Sun, 21 Jun 2020 18:18:00: start X-correlation... INFO @ Sun, 21 Jun 2020 18:18:00: end of X-cor INFO @ Sun, 21 Jun 2020 18:18:00: #2 finished! INFO @ Sun, 21 Jun 2020 18:18:00: #2 predicted fragment length is 140 bps INFO @ Sun, 21 Jun 2020 18:18:00: #2 alternative fragment length(s) may be 140 bps INFO @ Sun, 21 Jun 2020 18:18:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX220308/SRX220308.20_model.r INFO @ Sun, 21 Jun 2020 18:18:00: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:18:00: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:18:08: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:18:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX220308/SRX220308.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:18:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX220308/SRX220308.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:18:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX220308/SRX220308.20_summits.bed INFO @ Sun, 21 Jun 2020 18:18:11: Done! pass1 - making usageList (46 chroms): 1 millis pass2 - checking and writing primary data (1698 records, 4 fields): 5 millis CompletedMACS2peakCalling