Job ID = 6455944 SRX = SRX3068980 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:51:01 prefetch.2.10.7: 1) Downloading 'SRR5907456'... 2020-06-21T10:51:01 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:53:00 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:53:01 prefetch.2.10.7: 'SRR5907456' is valid 2020-06-21T10:53:01 prefetch.2.10.7: 1) 'SRR5907456' was downloaded successfully Read 15073686 spots for SRR5907456/SRR5907456.sra Written 15073686 spots for SRR5907456/SRR5907456.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: 00:03:41 15073686 reads; of these: 15073686 (100.00%) were unpaired; of these: 1139769 (7.56%) aligned 0 times 11873519 (78.77%) aligned exactly 1 time 2060398 (13.67%) aligned >1 times 92.44% overall alignment rate Time searching: 00:03:41 Overall time: 00:03:41 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_sort_core] merging from 8 files... [bam_rmdupse_core] 5096867 / 13933917 = 0.3658 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 20:02:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3068980/SRX3068980.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3068980/SRX3068980.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3068980/SRX3068980.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3068980/SRX3068980.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 20:02:06: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:02:06: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:02:15: 1000000 INFO @ Sun, 21 Jun 2020 20:02:25: 2000000 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 20:02:35: 3000000 INFO @ Sun, 21 Jun 2020 20:02:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3068980/SRX3068980.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3068980/SRX3068980.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3068980/SRX3068980.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3068980/SRX3068980.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 20:02:36: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:02:36: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:02:45: 4000000 INFO @ Sun, 21 Jun 2020 20:02:46: 1000000 INFO @ Sun, 21 Jun 2020 20:02:55: 5000000 INFO @ Sun, 21 Jun 2020 20:02:56: 2000000 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 20:03:05: 6000000 INFO @ Sun, 21 Jun 2020 20:03:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3068980/SRX3068980.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3068980/SRX3068980.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3068980/SRX3068980.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3068980/SRX3068980.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 20:03:06: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:03:06: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:03:07: 3000000 INFO @ Sun, 21 Jun 2020 20:03:14: 1000000 INFO @ Sun, 21 Jun 2020 20:03:16: 7000000 INFO @ Sun, 21 Jun 2020 20:03:17: 4000000 INFO @ Sun, 21 Jun 2020 20:03:23: 2000000 INFO @ Sun, 21 Jun 2020 20:03:27: 8000000 INFO @ Sun, 21 Jun 2020 20:03:27: 5000000 INFO @ Sun, 21 Jun 2020 20:03:31: 3000000 INFO @ Sun, 21 Jun 2020 20:03:35: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:03:35: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:03:35: #1 total tags in treatment: 8837050 INFO @ Sun, 21 Jun 2020 20:03:35: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:03:35: #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 20:03:36: #1 tags after filtering in treatment: 8837042 INFO @ Sun, 21 Jun 2020 20:03:36: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:03:36: #1 finished! INFO @ Sun, 21 Jun 2020 20:03:36: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:03:36: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:03:37: #2 number of paired peaks: 1889 INFO @ Sun, 21 Jun 2020 20:03:37: start model_add_line... INFO @ Sun, 21 Jun 2020 20:03:37: start X-correlation... INFO @ Sun, 21 Jun 2020 20:03:37: 6000000 INFO @ Sun, 21 Jun 2020 20:03:37: end of X-cor INFO @ Sun, 21 Jun 2020 20:03:37: #2 finished! INFO @ Sun, 21 Jun 2020 20:03:37: #2 predicted fragment length is 207 bps INFO @ Sun, 21 Jun 2020 20:03:37: #2 alternative fragment length(s) may be 207 bps INFO @ Sun, 21 Jun 2020 20:03:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3068980/SRX3068980.05_model.r INFO @ Sun, 21 Jun 2020 20:03:37: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:03:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:03:39: 4000000 INFO @ Sun, 21 Jun 2020 20:03:47: 7000000 INFO @ Sun, 21 Jun 2020 20:03:48: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:03:56: 6000000 INFO @ Sun, 21 Jun 2020 20:03:58: 8000000 INFO @ Sun, 21 Jun 2020 20:03:59: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:04:04: 7000000 INFO @ Sun, 21 Jun 2020 20:04:08: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:04:08: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:04:08: #1 total tags in treatment: 8837050 INFO @ Sun, 21 Jun 2020 20:04:08: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:04:08: #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 20:04:08: #1 tags after filtering in treatment: 8837042 INFO @ Sun, 21 Jun 2020 20:04:08: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:04:08: #1 finished! INFO @ Sun, 21 Jun 2020 20:04:08: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:04:08: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:04:09: #2 number of paired peaks: 1889 INFO @ Sun, 21 Jun 2020 20:04:09: start model_add_line... INFO @ Sun, 21 Jun 2020 20:04:09: start X-correlation... INFO @ Sun, 21 Jun 2020 20:04:09: end of X-cor INFO @ Sun, 21 Jun 2020 20:04:09: #2 finished! INFO @ Sun, 21 Jun 2020 20:04:09: #2 predicted fragment length is 207 bps INFO @ Sun, 21 Jun 2020 20:04:09: #2 alternative fragment length(s) may be 207 bps INFO @ Sun, 21 Jun 2020 20:04:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3068980/SRX3068980.10_model.r INFO @ Sun, 21 Jun 2020 20:04:09: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:04:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:04:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3068980/SRX3068980.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:04:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3068980/SRX3068980.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:04:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3068980/SRX3068980.05_summits.bed INFO @ Sun, 21 Jun 2020 20:04:11: Done! pass1 - making usageList (483 chroms): 3 millis pass2 - checking and writing primary data (8604 records, 4 fields): 35 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:04:13: 8000000 INFO @ Sun, 21 Jun 2020 20:04:20: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:04:20: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:04:20: #1 total tags in treatment: 8837050 INFO @ Sun, 21 Jun 2020 20:04:20: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:04:20: #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 20:04:21: #1 tags after filtering in treatment: 8837042 INFO @ Sun, 21 Jun 2020 20:04:21: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:04:21: #1 finished! INFO @ Sun, 21 Jun 2020 20:04:21: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:04:21: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:04:21: #2 number of paired peaks: 1889 INFO @ Sun, 21 Jun 2020 20:04:21: start model_add_line... INFO @ Sun, 21 Jun 2020 20:04:22: start X-correlation... INFO @ Sun, 21 Jun 2020 20:04:22: end of X-cor INFO @ Sun, 21 Jun 2020 20:04:22: #2 finished! INFO @ Sun, 21 Jun 2020 20:04:22: #2 predicted fragment length is 207 bps INFO @ Sun, 21 Jun 2020 20:04:22: #2 alternative fragment length(s) may be 207 bps INFO @ Sun, 21 Jun 2020 20:04:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3068980/SRX3068980.20_model.r INFO @ Sun, 21 Jun 2020 20:04:22: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:04:22: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:04:31: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:04:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3068980/SRX3068980.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:04:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3068980/SRX3068980.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:04:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3068980/SRX3068980.10_summits.bed INFO @ Sun, 21 Jun 2020 20:04:43: Done! INFO @ Sun, 21 Jun 2020 20:04:43: #3 Call peaks for each chromosome... pass1 - making usageList (427 chroms): 2 millis pass2 - checking and writing primary data (5957 records, 4 fields): 30 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:04:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3068980/SRX3068980.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:04:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3068980/SRX3068980.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:04:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3068980/SRX3068980.20_summits.bed INFO @ Sun, 21 Jun 2020 20:04:54: Done! pass1 - making usageList (350 chroms): 2 millis pass2 - checking and writing primary data (2905 records, 4 fields): 23 millis CompletedMACS2peakCalling