Job ID = 6455180 SRX = SRX2829097 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:54:10 prefetch.2.10.7: 1) Downloading 'SRR5569907'... 2020-06-21T09:54:10 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:57:20 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:57:20 prefetch.2.10.7: 1) 'SRR5569907' was downloaded successfully Read 20266485 spots for SRR5569907/SRR5569907.sra Written 20266485 spots for SRR5569907/SRR5569907.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: 00:03:58 20266485 reads; of these: 20266485 (100.00%) were unpaired; of these: 3553831 (17.54%) aligned 0 times 14384507 (70.98%) aligned exactly 1 time 2328147 (11.49%) aligned >1 times 82.46% overall alignment rate Time searching: 00:03:58 Overall time: 00:03:58 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] 7608791 / 16712654 = 0.4553 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 19:06:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2829097/SRX2829097.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2829097/SRX2829097.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2829097/SRX2829097.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2829097/SRX2829097.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 19:06:09: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:06:09: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:06:14: 1000000 INFO @ Sun, 21 Jun 2020 19:06:20: 2000000 INFO @ Sun, 21 Jun 2020 19:06:26: 3000000 INFO @ Sun, 21 Jun 2020 19:06:32: 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 19:06:37: 5000000 INFO @ Sun, 21 Jun 2020 19:06:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2829097/SRX2829097.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2829097/SRX2829097.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2829097/SRX2829097.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2829097/SRX2829097.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 19:06:39: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:06:39: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:06:44: 6000000 INFO @ Sun, 21 Jun 2020 19:06:46: 1000000 INFO @ Sun, 21 Jun 2020 19:06:51: 7000000 INFO @ Sun, 21 Jun 2020 19:06:54: 2000000 INFO @ Sun, 21 Jun 2020 19:06:59: 8000000 INFO @ Sun, 21 Jun 2020 19:07:01: 3000000 INFO @ Sun, 21 Jun 2020 19:07:06: 9000000 INFO @ Sun, 21 Jun 2020 19:07:07: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:07:07: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:07:07: #1 total tags in treatment: 9103863 INFO @ Sun, 21 Jun 2020 19:07:07: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:07:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) 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 19:07:07: #1 tags after filtering in treatment: 9103847 INFO @ Sun, 21 Jun 2020 19:07:07: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:07:07: #1 finished! INFO @ Sun, 21 Jun 2020 19:07:07: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:07:07: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:07:08: #2 number of paired peaks: 7334 INFO @ Sun, 21 Jun 2020 19:07:08: start model_add_line... INFO @ Sun, 21 Jun 2020 19:07:08: start X-correlation... INFO @ Sun, 21 Jun 2020 19:07:08: end of X-cor INFO @ Sun, 21 Jun 2020 19:07:08: #2 finished! INFO @ Sun, 21 Jun 2020 19:07:08: #2 predicted fragment length is 183 bps INFO @ Sun, 21 Jun 2020 19:07:08: #2 alternative fragment length(s) may be 4,183 bps INFO @ Sun, 21 Jun 2020 19:07:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2829097/SRX2829097.05_model.r INFO @ Sun, 21 Jun 2020 19:07:08: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:07:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:07:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2829097/SRX2829097.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2829097/SRX2829097.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2829097/SRX2829097.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2829097/SRX2829097.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 19:07:09: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:07:09: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:07:09: 4000000 INFO @ Sun, 21 Jun 2020 19:07:16: 1000000 INFO @ Sun, 21 Jun 2020 19:07:17: 5000000 INFO @ Sun, 21 Jun 2020 19:07:23: 2000000 INFO @ Sun, 21 Jun 2020 19:07:24: 6000000 INFO @ Sun, 21 Jun 2020 19:07:30: 3000000 INFO @ Sun, 21 Jun 2020 19:07:32: 7000000 INFO @ Sun, 21 Jun 2020 19:07:32: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:07:38: 4000000 INFO @ Sun, 21 Jun 2020 19:07:40: 8000000 INFO @ Sun, 21 Jun 2020 19:07:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2829097/SRX2829097.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:07:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2829097/SRX2829097.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:07:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2829097/SRX2829097.05_summits.bed INFO @ Sun, 21 Jun 2020 19:07:43: Done! pass1 - making usageList (303 chroms): 2 millis pass2 - checking and writing primary data (8030 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:07:45: 5000000 INFO @ Sun, 21 Jun 2020 19:07:48: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:07:49: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:07:49: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:07:49: #1 total tags in treatment: 9103863 INFO @ Sun, 21 Jun 2020 19:07:49: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:07:49: #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 19:07:49: #1 tags after filtering in treatment: 9103847 INFO @ Sun, 21 Jun 2020 19:07:49: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:07:49: #1 finished! INFO @ Sun, 21 Jun 2020 19:07:49: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:07:49: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:07:50: #2 number of paired peaks: 7334 INFO @ Sun, 21 Jun 2020 19:07:50: start model_add_line... INFO @ Sun, 21 Jun 2020 19:07:50: start X-correlation... INFO @ Sun, 21 Jun 2020 19:07:51: end of X-cor INFO @ Sun, 21 Jun 2020 19:07:51: #2 finished! INFO @ Sun, 21 Jun 2020 19:07:51: #2 predicted fragment length is 183 bps INFO @ Sun, 21 Jun 2020 19:07:51: #2 alternative fragment length(s) may be 4,183 bps INFO @ Sun, 21 Jun 2020 19:07:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2829097/SRX2829097.10_model.r INFO @ Sun, 21 Jun 2020 19:07:51: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:07:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:07:51: 6000000 INFO @ Sun, 21 Jun 2020 19:07:58: 7000000 INFO @ Sun, 21 Jun 2020 19:08:04: 8000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:08:10: 9000000 INFO @ Sun, 21 Jun 2020 19:08:11: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:08:11: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:08:11: #1 total tags in treatment: 9103863 INFO @ Sun, 21 Jun 2020 19:08:11: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:08:11: #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 19:08:11: #1 tags after filtering in treatment: 9103847 INFO @ Sun, 21 Jun 2020 19:08:11: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:08:11: #1 finished! INFO @ Sun, 21 Jun 2020 19:08:11: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:08:11: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:08:12: #2 number of paired peaks: 7334 INFO @ Sun, 21 Jun 2020 19:08:12: start model_add_line... INFO @ Sun, 21 Jun 2020 19:08:12: start X-correlation... INFO @ Sun, 21 Jun 2020 19:08:12: end of X-cor INFO @ Sun, 21 Jun 2020 19:08:12: #2 finished! INFO @ Sun, 21 Jun 2020 19:08:12: #2 predicted fragment length is 183 bps INFO @ Sun, 21 Jun 2020 19:08:12: #2 alternative fragment length(s) may be 4,183 bps INFO @ Sun, 21 Jun 2020 19:08:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2829097/SRX2829097.20_model.r INFO @ Sun, 21 Jun 2020 19:08:12: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:08:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:08:15: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:08:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2829097/SRX2829097.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:08:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2829097/SRX2829097.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:08:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2829097/SRX2829097.10_summits.bed INFO @ Sun, 21 Jun 2020 19:08:27: Done! pass1 - making usageList (244 chroms): 1 millis pass2 - checking and writing primary data (5349 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:08:37: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:08:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2829097/SRX2829097.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:08:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2829097/SRX2829097.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:08:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2829097/SRX2829097.20_summits.bed INFO @ Sun, 21 Jun 2020 19:08:50: Done! pass1 - making usageList (166 chroms): 1 millis pass2 - checking and writing primary data (2182 records, 4 fields): 9 millis CompletedMACS2peakCalling