Job ID = 6454792 SRX = SRX2592395 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:24:00 prefetch.2.10.7: 1) Downloading 'SRR5289672'... 2020-06-21T09:24:00 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:25:33 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:25:33 prefetch.2.10.7: 'SRR5289672' is valid 2020-06-21T09:25:33 prefetch.2.10.7: 1) 'SRR5289672' was downloaded successfully Read 5444932 spots for SRR5289672/SRR5289672.sra Written 5444932 spots for SRR5289672/SRR5289672.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: 00:01:08 5444932 reads; of these: 5444932 (100.00%) were unpaired; of these: 2157472 (39.62%) aligned 0 times 2477565 (45.50%) aligned exactly 1 time 809895 (14.87%) aligned >1 times 60.38% overall alignment rate Time searching: 00:01:08 Overall time: 00:01:08 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] 813149 / 3287460 = 0.2473 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 18:28:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592395/SRX2592395.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592395/SRX2592395.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592395/SRX2592395.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592395/SRX2592395.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 18:28:18: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:28:18: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:28:25: 1000000 INFO @ Sun, 21 Jun 2020 18:28:33: 2000000 INFO @ Sun, 21 Jun 2020 18:28:37: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:28:37: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:28:37: #1 total tags in treatment: 2474311 INFO @ Sun, 21 Jun 2020 18:28:37: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:28:37: #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 18:28:37: #1 tags after filtering in treatment: 2474002 INFO @ Sun, 21 Jun 2020 18:28:37: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:28:37: #1 finished! INFO @ Sun, 21 Jun 2020 18:28:37: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:28:37: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:28:38: #2 number of paired peaks: 577 WARNING @ Sun, 21 Jun 2020 18:28:38: Fewer paired peaks (577) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 577 pairs to build model! INFO @ Sun, 21 Jun 2020 18:28:38: start model_add_line... INFO @ Sun, 21 Jun 2020 18:28:38: start X-correlation... INFO @ Sun, 21 Jun 2020 18:28:38: end of X-cor INFO @ Sun, 21 Jun 2020 18:28:38: #2 finished! INFO @ Sun, 21 Jun 2020 18:28:38: #2 predicted fragment length is 107 bps INFO @ Sun, 21 Jun 2020 18:28:38: #2 alternative fragment length(s) may be 107 bps INFO @ Sun, 21 Jun 2020 18:28:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592395/SRX2592395.05_model.r INFO @ Sun, 21 Jun 2020 18:28:38: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:28:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:28:44: #3 Call peaks for each chromosome... 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 18:28:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592395/SRX2592395.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:28:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592395/SRX2592395.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:28:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592395/SRX2592395.05_summits.bed INFO @ Sun, 21 Jun 2020 18:28:47: Done! pass1 - making usageList (195 chroms): 1 millis pass2 - checking and writing primary data (573 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:28:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592395/SRX2592395.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592395/SRX2592395.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592395/SRX2592395.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592395/SRX2592395.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 18:28:48: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:28:48: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:28:54: 1000000 INFO @ Sun, 21 Jun 2020 18:29:00: 2000000 INFO @ Sun, 21 Jun 2020 18:29:02: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:29:02: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:29:02: #1 total tags in treatment: 2474311 INFO @ Sun, 21 Jun 2020 18:29:02: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:29:02: #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 18:29:03: #1 tags after filtering in treatment: 2474002 INFO @ Sun, 21 Jun 2020 18:29:03: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:29:03: #1 finished! INFO @ Sun, 21 Jun 2020 18:29:03: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:29:03: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:29:03: #2 number of paired peaks: 577 WARNING @ Sun, 21 Jun 2020 18:29:03: Fewer paired peaks (577) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 577 pairs to build model! INFO @ Sun, 21 Jun 2020 18:29:03: start model_add_line... INFO @ Sun, 21 Jun 2020 18:29:03: start X-correlation... INFO @ Sun, 21 Jun 2020 18:29:03: end of X-cor INFO @ Sun, 21 Jun 2020 18:29:03: #2 finished! INFO @ Sun, 21 Jun 2020 18:29:03: #2 predicted fragment length is 107 bps INFO @ Sun, 21 Jun 2020 18:29:03: #2 alternative fragment length(s) may be 107 bps INFO @ Sun, 21 Jun 2020 18:29:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592395/SRX2592395.10_model.r INFO @ Sun, 21 Jun 2020 18:29:03: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:29:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:29:09: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:29:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592395/SRX2592395.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:29:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592395/SRX2592395.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:29:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592395/SRX2592395.10_summits.bed INFO @ Sun, 21 Jun 2020 18:29:12: Done! pass1 - making usageList (86 chroms): 1 millis pass2 - checking and writing primary data (168 records, 4 fields): 4 millis CompletedMACS2peakCalling 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 18:29:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592395/SRX2592395.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592395/SRX2592395.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592395/SRX2592395.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592395/SRX2592395.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 18:29:19: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:29:19: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:29:26: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:29:33: 2000000 INFO @ Sun, 21 Jun 2020 18:29:36: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:29:36: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:29:36: #1 total tags in treatment: 2474311 INFO @ Sun, 21 Jun 2020 18:29:36: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:29:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:29:37: #1 tags after filtering in treatment: 2474002 INFO @ Sun, 21 Jun 2020 18:29:37: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:29:37: #1 finished! INFO @ Sun, 21 Jun 2020 18:29:37: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:29:37: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:29:37: #2 number of paired peaks: 577 WARNING @ Sun, 21 Jun 2020 18:29:37: Fewer paired peaks (577) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 577 pairs to build model! INFO @ Sun, 21 Jun 2020 18:29:37: start model_add_line... INFO @ Sun, 21 Jun 2020 18:29:37: start X-correlation... INFO @ Sun, 21 Jun 2020 18:29:37: end of X-cor INFO @ Sun, 21 Jun 2020 18:29:37: #2 finished! INFO @ Sun, 21 Jun 2020 18:29:37: #2 predicted fragment length is 107 bps INFO @ Sun, 21 Jun 2020 18:29:37: #2 alternative fragment length(s) may be 107 bps INFO @ Sun, 21 Jun 2020 18:29:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592395/SRX2592395.20_model.r INFO @ Sun, 21 Jun 2020 18:29:37: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:29:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:29:43: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:29:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592395/SRX2592395.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:29:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592395/SRX2592395.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:29:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592395/SRX2592395.20_summits.bed INFO @ Sun, 21 Jun 2020 18:29:46: Done! pass1 - making usageList (40 chroms): 1 millis pass2 - checking and writing primary data (71 records, 4 fields): 2 millis CompletedMACS2peakCalling