Job ID = 6454918 SRX = SRX2592500 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:40:55 prefetch.2.10.7: 1) Downloading 'SRR5289777'... 2020-06-21T09:40:55 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:44:15 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:44:15 prefetch.2.10.7: 1) 'SRR5289777' was downloaded successfully Read 20046457 spots for SRR5289777/SRR5289777.sra Written 20046457 spots for SRR5289777/SRR5289777.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: 00:04:07 20046457 reads; of these: 20046457 (100.00%) were unpaired; of these: 2325233 (11.60%) aligned 0 times 15723259 (78.43%) aligned exactly 1 time 1997965 (9.97%) aligned >1 times 88.40% overall alignment rate Time searching: 00:04:07 Overall time: 00:04:07 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] 5635799 / 17721224 = 0.3180 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 18:53:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592500/SRX2592500.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592500/SRX2592500.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592500/SRX2592500.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592500/SRX2592500.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 18:53:52: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:53:52: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:53:59: 1000000 INFO @ Sun, 21 Jun 2020 18:54:05: 2000000 INFO @ Sun, 21 Jun 2020 18:54:11: 3000000 INFO @ Sun, 21 Jun 2020 18:54:17: 4000000 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 18:54:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592500/SRX2592500.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592500/SRX2592500.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592500/SRX2592500.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592500/SRX2592500.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 18:54:23: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:54:23: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:54:24: 5000000 INFO @ Sun, 21 Jun 2020 18:54:30: 1000000 INFO @ Sun, 21 Jun 2020 18:54:31: 6000000 INFO @ Sun, 21 Jun 2020 18:54:37: 2000000 INFO @ Sun, 21 Jun 2020 18:54:38: 7000000 INFO @ Sun, 21 Jun 2020 18:54:44: 3000000 INFO @ Sun, 21 Jun 2020 18:54:44: 8000000 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 18:54:51: 4000000 INFO @ Sun, 21 Jun 2020 18:54:51: 9000000 INFO @ Sun, 21 Jun 2020 18:54:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592500/SRX2592500.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592500/SRX2592500.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592500/SRX2592500.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592500/SRX2592500.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 18:54:52: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:54:52: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:54:58: 5000000 INFO @ Sun, 21 Jun 2020 18:54:59: 10000000 INFO @ Sun, 21 Jun 2020 18:54:59: 1000000 INFO @ Sun, 21 Jun 2020 18:55:06: 6000000 INFO @ Sun, 21 Jun 2020 18:55:06: 11000000 INFO @ Sun, 21 Jun 2020 18:55:07: 2000000 INFO @ Sun, 21 Jun 2020 18:55:13: 7000000 INFO @ Sun, 21 Jun 2020 18:55:13: 12000000 INFO @ Sun, 21 Jun 2020 18:55:14: 3000000 INFO @ Sun, 21 Jun 2020 18:55:14: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:55:14: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:55:14: #1 total tags in treatment: 12085425 INFO @ Sun, 21 Jun 2020 18:55:14: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:55:14: #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 18:55:14: #1 tags after filtering in treatment: 12085267 INFO @ Sun, 21 Jun 2020 18:55:14: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:55:14: #1 finished! INFO @ Sun, 21 Jun 2020 18:55:14: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:55:14: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:55:16: #2 number of paired peaks: 9196 INFO @ Sun, 21 Jun 2020 18:55:16: start model_add_line... INFO @ Sun, 21 Jun 2020 18:55:16: start X-correlation... INFO @ Sun, 21 Jun 2020 18:55:16: end of X-cor INFO @ Sun, 21 Jun 2020 18:55:16: #2 finished! INFO @ Sun, 21 Jun 2020 18:55:16: #2 predicted fragment length is 211 bps INFO @ Sun, 21 Jun 2020 18:55:16: #2 alternative fragment length(s) may be 211 bps INFO @ Sun, 21 Jun 2020 18:55:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592500/SRX2592500.05_model.r INFO @ Sun, 21 Jun 2020 18:55:16: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:55:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:55:20: 8000000 INFO @ Sun, 21 Jun 2020 18:55:21: 4000000 INFO @ Sun, 21 Jun 2020 18:55:27: 9000000 INFO @ Sun, 21 Jun 2020 18:55:27: 5000000 INFO @ Sun, 21 Jun 2020 18:55:34: 10000000 INFO @ Sun, 21 Jun 2020 18:55:34: 6000000 INFO @ Sun, 21 Jun 2020 18:55:41: 11000000 INFO @ Sun, 21 Jun 2020 18:55:41: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:55:48: 12000000 INFO @ Sun, 21 Jun 2020 18:55:49: 8000000 INFO @ Sun, 21 Jun 2020 18:55:49: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:55:49: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:55:49: #1 total tags in treatment: 12085425 INFO @ Sun, 21 Jun 2020 18:55:49: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:55:49: #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 18:55:49: #1 tags after filtering in treatment: 12085267 INFO @ Sun, 21 Jun 2020 18:55:49: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:55:49: #1 finished! INFO @ Sun, 21 Jun 2020 18:55:49: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:55:49: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:55:51: #2 number of paired peaks: 9196 INFO @ Sun, 21 Jun 2020 18:55:51: start model_add_line... INFO @ Sun, 21 Jun 2020 18:55:51: start X-correlation... INFO @ Sun, 21 Jun 2020 18:55:51: end of X-cor INFO @ Sun, 21 Jun 2020 18:55:51: #2 finished! INFO @ Sun, 21 Jun 2020 18:55:51: #2 predicted fragment length is 211 bps INFO @ Sun, 21 Jun 2020 18:55:51: #2 alternative fragment length(s) may be 211 bps INFO @ Sun, 21 Jun 2020 18:55:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592500/SRX2592500.10_model.r INFO @ Sun, 21 Jun 2020 18:55:51: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:55:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:55:55: 9000000 INFO @ Sun, 21 Jun 2020 18:55:57: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:56:02: 10000000 INFO @ Sun, 21 Jun 2020 18:56:09: 11000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:56:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592500/SRX2592500.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:56:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592500/SRX2592500.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:56:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592500/SRX2592500.05_summits.bed INFO @ Sun, 21 Jun 2020 18:56:15: Done! pass1 - making usageList (108 chroms): 2 millis pass2 - checking and writing primary data (11916 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:56:16: 12000000 INFO @ Sun, 21 Jun 2020 18:56:16: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:56:16: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:56:16: #1 total tags in treatment: 12085425 INFO @ Sun, 21 Jun 2020 18:56:16: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:56:16: #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 18:56:17: #1 tags after filtering in treatment: 12085267 INFO @ Sun, 21 Jun 2020 18:56:17: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:56:17: #1 finished! INFO @ Sun, 21 Jun 2020 18:56:17: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:56:17: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:56:19: #2 number of paired peaks: 9196 INFO @ Sun, 21 Jun 2020 18:56:19: start model_add_line... INFO @ Sun, 21 Jun 2020 18:56:19: start X-correlation... INFO @ Sun, 21 Jun 2020 18:56:19: end of X-cor INFO @ Sun, 21 Jun 2020 18:56:19: #2 finished! INFO @ Sun, 21 Jun 2020 18:56:19: #2 predicted fragment length is 211 bps INFO @ Sun, 21 Jun 2020 18:56:19: #2 alternative fragment length(s) may be 211 bps INFO @ Sun, 21 Jun 2020 18:56:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592500/SRX2592500.20_model.r INFO @ Sun, 21 Jun 2020 18:56:19: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:56:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:56:33: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:56:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592500/SRX2592500.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:56:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592500/SRX2592500.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:56:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592500/SRX2592500.10_summits.bed INFO @ Sun, 21 Jun 2020 18:56:51: Done! pass1 - making usageList (83 chroms): 2 millis pass2 - checking and writing primary data (9670 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:57:00: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:57:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592500/SRX2592500.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:57:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592500/SRX2592500.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:57:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592500/SRX2592500.20_summits.bed INFO @ Sun, 21 Jun 2020 18:57:18: Done! pass1 - making usageList (54 chroms): 2 millis pass2 - checking and writing primary data (7234 records, 4 fields): 11 millis CompletedMACS2peakCalling