Job ID = 6456951 SRX = SRX4158178 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:16:57 prefetch.2.10.7: 1) Downloading 'SRR7253458'... 2020-06-21T11:16:57 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:19:52 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:19:52 prefetch.2.10.7: 'SRR7253458' is valid 2020-06-21T11:19:52 prefetch.2.10.7: 1) 'SRR7253458' was downloaded successfully Read 8469311 spots for SRR7253458/SRR7253458.sra Written 8469311 spots for SRR7253458/SRR7253458.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: 00:01:51 8469311 reads; of these: 8469311 (100.00%) were unpaired; of these: 313889 (3.71%) aligned 0 times 7431667 (87.75%) aligned exactly 1 time 723755 (8.55%) aligned >1 times 96.29% overall alignment rate Time searching: 00:01:51 Overall time: 00:01:51 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] 1583760 / 8155422 = 0.1942 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 20:24:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4158178/SRX4158178.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4158178/SRX4158178.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4158178/SRX4158178.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4158178/SRX4158178.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 20:24:38: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:24:38: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:24:43: 1000000 INFO @ Sun, 21 Jun 2020 20:24:49: 2000000 INFO @ Sun, 21 Jun 2020 20:24:54: 3000000 INFO @ Sun, 21 Jun 2020 20:24:59: 4000000 INFO @ Sun, 21 Jun 2020 20:25:04: 5000000 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 20:25:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4158178/SRX4158178.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4158178/SRX4158178.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4158178/SRX4158178.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4158178/SRX4158178.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 20:25:09: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:25:09: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:25:10: 6000000 INFO @ Sun, 21 Jun 2020 20:25:13: #1 tag size is determined as 49 bps INFO @ Sun, 21 Jun 2020 20:25:13: #1 tag size = 49 INFO @ Sun, 21 Jun 2020 20:25:13: #1 total tags in treatment: 6571662 INFO @ Sun, 21 Jun 2020 20:25:13: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:25:13: #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 20:25:13: #1 tags after filtering in treatment: 6571416 INFO @ Sun, 21 Jun 2020 20:25:13: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:25:13: #1 finished! INFO @ Sun, 21 Jun 2020 20:25:13: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:25:13: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:25:14: 1000000 INFO @ Sun, 21 Jun 2020 20:25:14: #2 number of paired peaks: 8309 INFO @ Sun, 21 Jun 2020 20:25:14: start model_add_line... INFO @ Sun, 21 Jun 2020 20:25:15: start X-correlation... INFO @ Sun, 21 Jun 2020 20:25:15: end of X-cor INFO @ Sun, 21 Jun 2020 20:25:15: #2 finished! INFO @ Sun, 21 Jun 2020 20:25:15: #2 predicted fragment length is 159 bps INFO @ Sun, 21 Jun 2020 20:25:15: #2 alternative fragment length(s) may be 159 bps INFO @ Sun, 21 Jun 2020 20:25:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4158178/SRX4158178.05_model.r INFO @ Sun, 21 Jun 2020 20:25:15: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:25:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:25:19: 2000000 INFO @ Sun, 21 Jun 2020 20:25:25: 3000000 INFO @ Sun, 21 Jun 2020 20:25:30: 4000000 INFO @ Sun, 21 Jun 2020 20:25:34: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:25:35: 5000000 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 20:25:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4158178/SRX4158178.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4158178/SRX4158178.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4158178/SRX4158178.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4158178/SRX4158178.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 20:25:38: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:25:38: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:25:41: 6000000 INFO @ Sun, 21 Jun 2020 20:25:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4158178/SRX4158178.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:25:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4158178/SRX4158178.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:25:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4158178/SRX4158178.05_summits.bed INFO @ Sun, 21 Jun 2020 20:25:44: Done! INFO @ Sun, 21 Jun 2020 20:25:44: #1 tag size is determined as 49 bps INFO @ Sun, 21 Jun 2020 20:25:44: #1 tag size = 49 INFO @ Sun, 21 Jun 2020 20:25:44: #1 total tags in treatment: 6571662 INFO @ Sun, 21 Jun 2020 20:25:44: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:25:44: #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 20:25:44: 1000000 pass1 - making usageList (120 chroms): 1 millis pass2 - checking and writing primary data (6825 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:25:45: #1 tags after filtering in treatment: 6571416 INFO @ Sun, 21 Jun 2020 20:25:45: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:25:45: #1 finished! INFO @ Sun, 21 Jun 2020 20:25:45: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:25:45: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:25:46: #2 number of paired peaks: 8309 INFO @ Sun, 21 Jun 2020 20:25:46: start model_add_line... INFO @ Sun, 21 Jun 2020 20:25:46: start X-correlation... INFO @ Sun, 21 Jun 2020 20:25:46: end of X-cor INFO @ Sun, 21 Jun 2020 20:25:46: #2 finished! INFO @ Sun, 21 Jun 2020 20:25:46: #2 predicted fragment length is 159 bps INFO @ Sun, 21 Jun 2020 20:25:46: #2 alternative fragment length(s) may be 159 bps INFO @ Sun, 21 Jun 2020 20:25:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4158178/SRX4158178.10_model.r INFO @ Sun, 21 Jun 2020 20:25:46: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:25:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:25:50: 2000000 INFO @ Sun, 21 Jun 2020 20:25:56: 3000000 INFO @ Sun, 21 Jun 2020 20:26:02: 4000000 INFO @ Sun, 21 Jun 2020 20:26:06: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:26:08: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:26:14: 6000000 INFO @ Sun, 21 Jun 2020 20:26:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4158178/SRX4158178.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:26:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4158178/SRX4158178.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:26:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4158178/SRX4158178.10_summits.bed INFO @ Sun, 21 Jun 2020 20:26:16: Done! pass1 - making usageList (103 chroms): 2 millis pass2 - checking and writing primary data (6273 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:26:18: #1 tag size is determined as 49 bps INFO @ Sun, 21 Jun 2020 20:26:18: #1 tag size = 49 INFO @ Sun, 21 Jun 2020 20:26:18: #1 total tags in treatment: 6571662 INFO @ Sun, 21 Jun 2020 20:26:18: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:26:18: #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 20:26:18: #1 tags after filtering in treatment: 6571416 INFO @ Sun, 21 Jun 2020 20:26:18: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:26:18: #1 finished! INFO @ Sun, 21 Jun 2020 20:26:18: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:26:18: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:26:19: #2 number of paired peaks: 8309 INFO @ Sun, 21 Jun 2020 20:26:19: start model_add_line... INFO @ Sun, 21 Jun 2020 20:26:19: start X-correlation... INFO @ Sun, 21 Jun 2020 20:26:19: end of X-cor INFO @ Sun, 21 Jun 2020 20:26:19: #2 finished! INFO @ Sun, 21 Jun 2020 20:26:19: #2 predicted fragment length is 159 bps INFO @ Sun, 21 Jun 2020 20:26:19: #2 alternative fragment length(s) may be 159 bps INFO @ Sun, 21 Jun 2020 20:26:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4158178/SRX4158178.20_model.r INFO @ Sun, 21 Jun 2020 20:26:19: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:26:19: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:26:38: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:26:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4158178/SRX4158178.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:26:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4158178/SRX4158178.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:26:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4158178/SRX4158178.20_summits.bed INFO @ Sun, 21 Jun 2020 20:26:48: Done! pass1 - making usageList (77 chroms): 2 millis pass2 - checking and writing primary data (5424 records, 4 fields): 9 millis CompletedMACS2peakCalling