Job ID = 6454856 SRX = SRX2592448 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:35:10 prefetch.2.10.7: 1) Downloading 'SRR5289725'... 2020-06-21T09:35:10 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:37:57 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:37:58 prefetch.2.10.7: 'SRR5289725' is valid 2020-06-21T09:37:58 prefetch.2.10.7: 1) 'SRR5289725' was downloaded successfully Read 10885172 spots for SRR5289725/SRR5289725.sra Written 10885172 spots for SRR5289725/SRR5289725.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: 00:03:23 10885172 reads; of these: 10885172 (100.00%) were unpaired; of these: 2080543 (19.11%) aligned 0 times 6802736 (62.50%) aligned exactly 1 time 2001893 (18.39%) aligned >1 times 80.89% overall alignment rate Time searching: 00:03:23 Overall time: 00:03:23 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_rmdupse_core] 2666574 / 8804629 = 0.3029 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 18:44:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592448/SRX2592448.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592448/SRX2592448.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592448/SRX2592448.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592448/SRX2592448.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 18:44:45: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:44:45: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:44:51: 1000000 INFO @ Sun, 21 Jun 2020 18:44:56: 2000000 INFO @ Sun, 21 Jun 2020 18:45:02: 3000000 INFO @ Sun, 21 Jun 2020 18:45:08: 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 18:45:14: 5000000 INFO @ Sun, 21 Jun 2020 18:45:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592448/SRX2592448.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592448/SRX2592448.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592448/SRX2592448.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592448/SRX2592448.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 18:45:15: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:45:15: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:45:20: 6000000 INFO @ Sun, 21 Jun 2020 18:45:21: 1000000 INFO @ Sun, 21 Jun 2020 18:45:21: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:45:21: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:45:21: #1 total tags in treatment: 6138055 INFO @ Sun, 21 Jun 2020 18:45:21: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:45:21: #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 18:45:21: #1 tags after filtering in treatment: 6137889 INFO @ Sun, 21 Jun 2020 18:45:21: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:45:21: #1 finished! INFO @ Sun, 21 Jun 2020 18:45:21: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:45:21: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:45:22: #2 number of paired peaks: 556 WARNING @ Sun, 21 Jun 2020 18:45:22: Fewer paired peaks (556) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 556 pairs to build model! INFO @ Sun, 21 Jun 2020 18:45:22: start model_add_line... INFO @ Sun, 21 Jun 2020 18:45:22: start X-correlation... INFO @ Sun, 21 Jun 2020 18:45:22: end of X-cor INFO @ Sun, 21 Jun 2020 18:45:22: #2 finished! INFO @ Sun, 21 Jun 2020 18:45:22: #2 predicted fragment length is 147 bps INFO @ Sun, 21 Jun 2020 18:45:22: #2 alternative fragment length(s) may be 147 bps INFO @ Sun, 21 Jun 2020 18:45:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592448/SRX2592448.05_model.r INFO @ Sun, 21 Jun 2020 18:45:22: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:45:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:45:26: 2000000 INFO @ Sun, 21 Jun 2020 18:45:32: 3000000 INFO @ Sun, 21 Jun 2020 18:45:36: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:45:37: 4000000 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 18:45:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592448/SRX2592448.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:45:43: 5000000 INFO @ Sun, 21 Jun 2020 18:45:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592448/SRX2592448.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:45:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592448/SRX2592448.05_summits.bed INFO @ Sun, 21 Jun 2020 18:45:43: Done! pass1 - making usageList (313 chroms): 2 millis pass2 - checking and writing primary data (4878 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:45:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592448/SRX2592448.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592448/SRX2592448.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592448/SRX2592448.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592448/SRX2592448.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 18:45:45: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:45:45: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:45:49: 6000000 INFO @ Sun, 21 Jun 2020 18:45:50: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:45:50: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:45:50: #1 total tags in treatment: 6138055 INFO @ Sun, 21 Jun 2020 18:45:50: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:45:50: #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 18:45:50: #1 tags after filtering in treatment: 6137889 INFO @ Sun, 21 Jun 2020 18:45:50: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:45:50: #1 finished! INFO @ Sun, 21 Jun 2020 18:45:50: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:45:50: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:45:51: 1000000 INFO @ Sun, 21 Jun 2020 18:45:51: #2 number of paired peaks: 556 WARNING @ Sun, 21 Jun 2020 18:45:51: Fewer paired peaks (556) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 556 pairs to build model! INFO @ Sun, 21 Jun 2020 18:45:51: start model_add_line... INFO @ Sun, 21 Jun 2020 18:45:51: start X-correlation... INFO @ Sun, 21 Jun 2020 18:45:51: end of X-cor INFO @ Sun, 21 Jun 2020 18:45:51: #2 finished! INFO @ Sun, 21 Jun 2020 18:45:51: #2 predicted fragment length is 147 bps INFO @ Sun, 21 Jun 2020 18:45:51: #2 alternative fragment length(s) may be 147 bps INFO @ Sun, 21 Jun 2020 18:45:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592448/SRX2592448.10_model.r INFO @ Sun, 21 Jun 2020 18:45:51: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:45:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:45:56: 2000000 INFO @ Sun, 21 Jun 2020 18:46:01: 3000000 INFO @ Sun, 21 Jun 2020 18:46:05: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:46:07: 4000000 INFO @ Sun, 21 Jun 2020 18:46:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592448/SRX2592448.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:46:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592448/SRX2592448.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:46:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592448/SRX2592448.10_summits.bed INFO @ Sun, 21 Jun 2020 18:46:12: Done! pass1 - making usageList (221 chroms): 1 millis pass2 - checking and writing primary data (2093 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:46:13: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:46:18: 6000000 INFO @ Sun, 21 Jun 2020 18:46:19: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:46:19: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:46:19: #1 total tags in treatment: 6138055 INFO @ Sun, 21 Jun 2020 18:46:19: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:46:19: #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 18:46:19: #1 tags after filtering in treatment: 6137889 INFO @ Sun, 21 Jun 2020 18:46:19: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:46:19: #1 finished! INFO @ Sun, 21 Jun 2020 18:46:19: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:46:19: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:46:20: #2 number of paired peaks: 556 WARNING @ Sun, 21 Jun 2020 18:46:20: Fewer paired peaks (556) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 556 pairs to build model! INFO @ Sun, 21 Jun 2020 18:46:20: start model_add_line... INFO @ Sun, 21 Jun 2020 18:46:20: start X-correlation... INFO @ Sun, 21 Jun 2020 18:46:20: end of X-cor INFO @ Sun, 21 Jun 2020 18:46:20: #2 finished! INFO @ Sun, 21 Jun 2020 18:46:20: #2 predicted fragment length is 147 bps INFO @ Sun, 21 Jun 2020 18:46:20: #2 alternative fragment length(s) may be 147 bps INFO @ Sun, 21 Jun 2020 18:46:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592448/SRX2592448.20_model.r INFO @ Sun, 21 Jun 2020 18:46:20: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:46:20: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:46:34: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:46:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592448/SRX2592448.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:46:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592448/SRX2592448.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:46:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592448/SRX2592448.20_summits.bed INFO @ Sun, 21 Jun 2020 18:46:41: Done! pass1 - making usageList (115 chroms): 0 millis pass2 - checking and writing primary data (447 records, 4 fields): 5 millis CompletedMACS2peakCalling