Job ID = 6459880 SRX = SRX969913 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T13:46:04 prefetch.2.10.7: 1) Downloading 'SRR1931629'... 2020-06-21T13:46:04 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:48:26 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:48:27 prefetch.2.10.7: 'SRR1931629' is valid 2020-06-21T13:48:27 prefetch.2.10.7: 1) 'SRR1931629' was downloaded successfully Read 23032705 spots for SRR1931629/SRR1931629.sra Written 23032705 spots for SRR1931629/SRR1931629.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: 00:06:49 23032705 reads; of these: 23032705 (100.00%) were unpaired; of these: 1587419 (6.89%) aligned 0 times 16828899 (73.07%) aligned exactly 1 time 4616387 (20.04%) aligned >1 times 93.11% overall alignment rate Time searching: 00:06:49 Overall time: 00:06:49 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 12 files... [bam_rmdupse_core] 5394797 / 21445286 = 0.2516 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 23:00:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX969913/SRX969913.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX969913/SRX969913.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX969913/SRX969913.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX969913/SRX969913.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 23:00:43: #1 read tag files... INFO @ Sun, 21 Jun 2020 23:00:43: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 23:00:48: 1000000 INFO @ Sun, 21 Jun 2020 23:00:53: 2000000 INFO @ Sun, 21 Jun 2020 23:00:59: 3000000 INFO @ Sun, 21 Jun 2020 23:01:04: 4000000 INFO @ Sun, 21 Jun 2020 23:01:09: 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 23:01:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX969913/SRX969913.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX969913/SRX969913.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX969913/SRX969913.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX969913/SRX969913.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 23:01:13: #1 read tag files... INFO @ Sun, 21 Jun 2020 23:01:13: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 23:01:15: 6000000 INFO @ Sun, 21 Jun 2020 23:01:19: 1000000 INFO @ Sun, 21 Jun 2020 23:01:20: 7000000 INFO @ Sun, 21 Jun 2020 23:01:24: 2000000 INFO @ Sun, 21 Jun 2020 23:01:26: 8000000 INFO @ Sun, 21 Jun 2020 23:01:30: 3000000 INFO @ Sun, 21 Jun 2020 23:01:31: 9000000 INFO @ Sun, 21 Jun 2020 23:01:36: 4000000 INFO @ Sun, 21 Jun 2020 23:01:37: 10000000 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 23:01:41: 5000000 INFO @ Sun, 21 Jun 2020 23:01:42: 11000000 INFO @ Sun, 21 Jun 2020 23:01:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX969913/SRX969913.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX969913/SRX969913.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX969913/SRX969913.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX969913/SRX969913.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 23:01:43: #1 read tag files... INFO @ Sun, 21 Jun 2020 23:01:43: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 23:01:47: 6000000 INFO @ Sun, 21 Jun 2020 23:01:48: 12000000 INFO @ Sun, 21 Jun 2020 23:01:49: 1000000 INFO @ Sun, 21 Jun 2020 23:01:53: 7000000 INFO @ Sun, 21 Jun 2020 23:01:54: 13000000 INFO @ Sun, 21 Jun 2020 23:01:54: 2000000 INFO @ Sun, 21 Jun 2020 23:01:58: 8000000 INFO @ Sun, 21 Jun 2020 23:02:00: 14000000 INFO @ Sun, 21 Jun 2020 23:02:00: 3000000 INFO @ Sun, 21 Jun 2020 23:02:04: 9000000 INFO @ Sun, 21 Jun 2020 23:02:06: 15000000 INFO @ Sun, 21 Jun 2020 23:02:06: 4000000 INFO @ Sun, 21 Jun 2020 23:02:10: 10000000 INFO @ Sun, 21 Jun 2020 23:02:11: 5000000 INFO @ Sun, 21 Jun 2020 23:02:11: 16000000 INFO @ Sun, 21 Jun 2020 23:02:12: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 23:02:12: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 23:02:12: #1 total tags in treatment: 16050489 INFO @ Sun, 21 Jun 2020 23:02:12: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 23:02:12: #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 23:02:12: #1 tags after filtering in treatment: 16050488 INFO @ Sun, 21 Jun 2020 23:02:12: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 23:02:12: #1 finished! INFO @ Sun, 21 Jun 2020 23:02:12: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 23:02:12: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 23:02:14: #2 number of paired peaks: 1071 INFO @ Sun, 21 Jun 2020 23:02:14: start model_add_line... INFO @ Sun, 21 Jun 2020 23:02:14: start X-correlation... INFO @ Sun, 21 Jun 2020 23:02:14: end of X-cor INFO @ Sun, 21 Jun 2020 23:02:14: #2 finished! INFO @ Sun, 21 Jun 2020 23:02:14: #2 predicted fragment length is 194 bps INFO @ Sun, 21 Jun 2020 23:02:14: #2 alternative fragment length(s) may be 194 bps INFO @ Sun, 21 Jun 2020 23:02:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX969913/SRX969913.05_model.r INFO @ Sun, 21 Jun 2020 23:02:14: #3 Call peaks... INFO @ Sun, 21 Jun 2020 23:02:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 23:02:15: 11000000 INFO @ Sun, 21 Jun 2020 23:02:17: 6000000 INFO @ Sun, 21 Jun 2020 23:02:21: 12000000 INFO @ Sun, 21 Jun 2020 23:02:23: 7000000 INFO @ Sun, 21 Jun 2020 23:02:27: 13000000 INFO @ Sun, 21 Jun 2020 23:02:28: 8000000 INFO @ Sun, 21 Jun 2020 23:02:32: 14000000 INFO @ Sun, 21 Jun 2020 23:02:34: 9000000 INFO @ Sun, 21 Jun 2020 23:02:38: 15000000 INFO @ Sun, 21 Jun 2020 23:02:39: 10000000 INFO @ Sun, 21 Jun 2020 23:02:44: 16000000 INFO @ Sun, 21 Jun 2020 23:02:44: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 23:02:44: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 23:02:44: #1 total tags in treatment: 16050489 INFO @ Sun, 21 Jun 2020 23:02:44: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 23:02:44: #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 23:02:45: #1 tags after filtering in treatment: 16050488 INFO @ Sun, 21 Jun 2020 23:02:45: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 23:02:45: #1 finished! INFO @ Sun, 21 Jun 2020 23:02:45: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 23:02:45: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 23:02:45: 11000000 INFO @ Sun, 21 Jun 2020 23:02:46: #2 number of paired peaks: 1071 INFO @ Sun, 21 Jun 2020 23:02:46: start model_add_line... INFO @ Sun, 21 Jun 2020 23:02:46: start X-correlation... INFO @ Sun, 21 Jun 2020 23:02:46: end of X-cor INFO @ Sun, 21 Jun 2020 23:02:46: #2 finished! INFO @ Sun, 21 Jun 2020 23:02:46: #2 predicted fragment length is 194 bps INFO @ Sun, 21 Jun 2020 23:02:46: #2 alternative fragment length(s) may be 194 bps INFO @ Sun, 21 Jun 2020 23:02:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX969913/SRX969913.10_model.r INFO @ Sun, 21 Jun 2020 23:02:46: #3 Call peaks... INFO @ Sun, 21 Jun 2020 23:02:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 23:02:47: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 23:02:50: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 23:02:56: 13000000 INFO @ Sun, 21 Jun 2020 23:03:01: 14000000 INFO @ Sun, 21 Jun 2020 23:03:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX969913/SRX969913.05_peaks.xls INFO @ Sun, 21 Jun 2020 23:03:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX969913/SRX969913.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 23:03:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX969913/SRX969913.05_summits.bed INFO @ Sun, 21 Jun 2020 23:03:04: Done! pass1 - making usageList (602 chroms): 2 millis pass2 - checking and writing primary data (7530 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 23:03:06: 15000000 INFO @ Sun, 21 Jun 2020 23:03:12: 16000000 INFO @ Sun, 21 Jun 2020 23:03:12: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 23:03:12: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 23:03:12: #1 total tags in treatment: 16050489 INFO @ Sun, 21 Jun 2020 23:03:12: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 23:03:12: #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 23:03:13: #1 tags after filtering in treatment: 16050488 INFO @ Sun, 21 Jun 2020 23:03:13: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 23:03:13: #1 finished! INFO @ Sun, 21 Jun 2020 23:03:13: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 23:03:13: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 23:03:14: #2 number of paired peaks: 1071 INFO @ Sun, 21 Jun 2020 23:03:14: start model_add_line... INFO @ Sun, 21 Jun 2020 23:03:14: start X-correlation... INFO @ Sun, 21 Jun 2020 23:03:14: end of X-cor INFO @ Sun, 21 Jun 2020 23:03:14: #2 finished! INFO @ Sun, 21 Jun 2020 23:03:14: #2 predicted fragment length is 194 bps INFO @ Sun, 21 Jun 2020 23:03:14: #2 alternative fragment length(s) may be 194 bps INFO @ Sun, 21 Jun 2020 23:03:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX969913/SRX969913.20_model.r INFO @ Sun, 21 Jun 2020 23:03:14: #3 Call peaks... INFO @ Sun, 21 Jun 2020 23:03:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 23:03:21: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 23:03:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX969913/SRX969913.10_peaks.xls INFO @ Sun, 21 Jun 2020 23:03:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX969913/SRX969913.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 23:03:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX969913/SRX969913.10_summits.bed INFO @ Sun, 21 Jun 2020 23:03:38: Done! pass1 - making usageList (494 chroms): 1 millis pass2 - checking and writing primary data (5741 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 23:03:48: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 23:04:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX969913/SRX969913.20_peaks.xls INFO @ Sun, 21 Jun 2020 23:04:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX969913/SRX969913.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 23:04:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX969913/SRX969913.20_summits.bed INFO @ Sun, 21 Jun 2020 23:04:04: Done! pass1 - making usageList (366 chroms): 1 millis pass2 - checking and writing primary data (3975 records, 4 fields): 14 millis CompletedMACS2peakCalling