Job ID = 6454838 SRX = SRX2592434 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:31:29 prefetch.2.10.7: 1) Downloading 'SRR5289711'... 2020-06-21T09:31:29 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:33:55 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:33:55 prefetch.2.10.7: 'SRR5289711' is valid 2020-06-21T09:33:55 prefetch.2.10.7: 1) 'SRR5289711' was downloaded successfully Read 11212934 spots for SRR5289711/SRR5289711.sra Written 11212934 spots for SRR5289711/SRR5289711.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: 00:02:57 11212934 reads; of these: 11212934 (100.00%) were unpaired; of these: 1090608 (9.73%) aligned 0 times 9124450 (81.37%) aligned exactly 1 time 997876 (8.90%) aligned >1 times 90.27% overall alignment rate Time searching: 00:02:57 Overall time: 00:02:57 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] 5387108 / 10122326 = 0.5322 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 18:40:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592434/SRX2592434.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592434/SRX2592434.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592434/SRX2592434.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592434/SRX2592434.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 18:40:21: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:40:21: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:40:26: 1000000 INFO @ Sun, 21 Jun 2020 18:40:32: 2000000 INFO @ Sun, 21 Jun 2020 18:40:37: 3000000 INFO @ Sun, 21 Jun 2020 18:40:43: 4000000 INFO @ Sun, 21 Jun 2020 18:40:47: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:40:47: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:40:47: #1 total tags in treatment: 4735218 INFO @ Sun, 21 Jun 2020 18:40:47: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:40:47: #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 18:40:47: #1 tags after filtering in treatment: 4734762 INFO @ Sun, 21 Jun 2020 18:40:47: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:40:47: #1 finished! INFO @ Sun, 21 Jun 2020 18:40:47: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:40:47: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:40:48: #2 number of paired peaks: 328 WARNING @ Sun, 21 Jun 2020 18:40:48: Fewer paired peaks (328) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 328 pairs to build model! INFO @ Sun, 21 Jun 2020 18:40:48: start model_add_line... INFO @ Sun, 21 Jun 2020 18:40:48: start X-correlation... INFO @ Sun, 21 Jun 2020 18:40:48: end of X-cor INFO @ Sun, 21 Jun 2020 18:40:48: #2 finished! INFO @ Sun, 21 Jun 2020 18:40:48: #2 predicted fragment length is 186 bps INFO @ Sun, 21 Jun 2020 18:40:48: #2 alternative fragment length(s) may be 186 bps INFO @ Sun, 21 Jun 2020 18:40:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592434/SRX2592434.05_model.r INFO @ Sun, 21 Jun 2020 18:40:48: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:40:48: #3 Pre-compute pvalue-qvalue table... 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 18:40:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592434/SRX2592434.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592434/SRX2592434.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592434/SRX2592434.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592434/SRX2592434.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 18:40:51: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:40:51: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:40:56: 1000000 INFO @ Sun, 21 Jun 2020 18:41:02: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:41:02: 2000000 INFO @ Sun, 21 Jun 2020 18:41:07: 3000000 INFO @ Sun, 21 Jun 2020 18:41:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592434/SRX2592434.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:41:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592434/SRX2592434.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:41:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592434/SRX2592434.05_summits.bed INFO @ Sun, 21 Jun 2020 18:41:09: Done! pass1 - making usageList (194 chroms): 3 millis pass2 - checking and writing primary data (14649 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:41:13: 4000000 INFO @ Sun, 21 Jun 2020 18:41:17: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:41:17: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:41:17: #1 total tags in treatment: 4735218 INFO @ Sun, 21 Jun 2020 18:41:17: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:41:17: #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 18:41:17: #1 tags after filtering in treatment: 4734762 INFO @ Sun, 21 Jun 2020 18:41:17: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:41:17: #1 finished! INFO @ Sun, 21 Jun 2020 18:41:17: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:41:17: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:41:18: #2 number of paired peaks: 328 WARNING @ Sun, 21 Jun 2020 18:41:18: Fewer paired peaks (328) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 328 pairs to build model! INFO @ Sun, 21 Jun 2020 18:41:18: start model_add_line... INFO @ Sun, 21 Jun 2020 18:41:18: start X-correlation... INFO @ Sun, 21 Jun 2020 18:41:18: end of X-cor INFO @ Sun, 21 Jun 2020 18:41:18: #2 finished! INFO @ Sun, 21 Jun 2020 18:41:18: #2 predicted fragment length is 186 bps INFO @ Sun, 21 Jun 2020 18:41:18: #2 alternative fragment length(s) may be 186 bps INFO @ Sun, 21 Jun 2020 18:41:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592434/SRX2592434.10_model.r INFO @ Sun, 21 Jun 2020 18:41:18: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:41:18: #3 Pre-compute pvalue-qvalue table... 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 18:41:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592434/SRX2592434.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592434/SRX2592434.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592434/SRX2592434.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592434/SRX2592434.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 18:41:21: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:41:21: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:41:26: 1000000 INFO @ Sun, 21 Jun 2020 18:41:32: 2000000 INFO @ Sun, 21 Jun 2020 18:41:32: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:41:37: 3000000 INFO @ Sun, 21 Jun 2020 18:41:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592434/SRX2592434.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:41:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592434/SRX2592434.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:41:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592434/SRX2592434.10_summits.bed INFO @ Sun, 21 Jun 2020 18:41:40: Done! pass1 - making usageList (156 chroms): 2 millis pass2 - checking and writing primary data (12506 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:41:43: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:41:47: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:41:47: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:41:47: #1 total tags in treatment: 4735218 INFO @ Sun, 21 Jun 2020 18:41:47: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:41:47: #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 18:41:47: #1 tags after filtering in treatment: 4734762 INFO @ Sun, 21 Jun 2020 18:41:47: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:41:47: #1 finished! INFO @ Sun, 21 Jun 2020 18:41:47: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:41:47: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:41:48: #2 number of paired peaks: 328 WARNING @ Sun, 21 Jun 2020 18:41:48: Fewer paired peaks (328) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 328 pairs to build model! INFO @ Sun, 21 Jun 2020 18:41:48: start model_add_line... INFO @ Sun, 21 Jun 2020 18:41:48: start X-correlation... INFO @ Sun, 21 Jun 2020 18:41:48: end of X-cor INFO @ Sun, 21 Jun 2020 18:41:48: #2 finished! INFO @ Sun, 21 Jun 2020 18:41:48: #2 predicted fragment length is 186 bps INFO @ Sun, 21 Jun 2020 18:41:48: #2 alternative fragment length(s) may be 186 bps INFO @ Sun, 21 Jun 2020 18:41:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592434/SRX2592434.20_model.r INFO @ Sun, 21 Jun 2020 18:41:48: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:41:48: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:42:02: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:42:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592434/SRX2592434.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:42:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592434/SRX2592434.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:42:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592434/SRX2592434.20_summits.bed INFO @ Sun, 21 Jun 2020 18:42:09: Done! pass1 - making usageList (98 chroms): 2 millis pass2 - checking and writing primary data (9660 records, 4 fields): 15 millis CompletedMACS2peakCalling