Job ID = 6452440 SRX = SRX013060 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T07:34:57 prefetch.2.10.7: 1) Downloading 'SRR030326'... 2020-06-21T07:34:57 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:35:33 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:35:33 prefetch.2.10.7: 'SRR030326' is valid 2020-06-21T07:35:33 prefetch.2.10.7: 1) 'SRR030326' was downloaded successfully Read 2503024 spots for SRR030326/SRR030326.sra Written 2503024 spots for SRR030326/SRR030326.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: 00:00:01 Multiseed full-index search: 00:00:25 2503024 reads; of these: 2503024 (100.00%) were unpaired; of these: 495192 (19.78%) aligned 0 times 1691429 (67.58%) aligned exactly 1 time 316403 (12.64%) aligned >1 times 80.22% overall alignment rate Time searching: 00:00:26 Overall time: 00:00:26 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] 90770 / 2007832 = 0.0452 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 16:37:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX013060/SRX013060.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX013060/SRX013060.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX013060/SRX013060.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX013060/SRX013060.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 16:37:07: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:37:07: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:37:12: 1000000 INFO @ Sun, 21 Jun 2020 16:37:17: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:37:17: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:37:17: #1 total tags in treatment: 1917062 INFO @ Sun, 21 Jun 2020 16:37:17: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:37:17: #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 16:37:17: #1 tags after filtering in treatment: 1916664 INFO @ Sun, 21 Jun 2020 16:37:17: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:37:17: #1 finished! INFO @ Sun, 21 Jun 2020 16:37:17: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:37:17: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:37:18: #2 number of paired peaks: 210 WARNING @ Sun, 21 Jun 2020 16:37:18: Fewer paired peaks (210) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 210 pairs to build model! INFO @ Sun, 21 Jun 2020 16:37:18: start model_add_line... INFO @ Sun, 21 Jun 2020 16:37:18: start X-correlation... INFO @ Sun, 21 Jun 2020 16:37:18: end of X-cor INFO @ Sun, 21 Jun 2020 16:37:18: #2 finished! INFO @ Sun, 21 Jun 2020 16:37:18: #2 predicted fragment length is 91 bps INFO @ Sun, 21 Jun 2020 16:37:18: #2 alternative fragment length(s) may be 47,91,576,583 bps INFO @ Sun, 21 Jun 2020 16:37:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX013060/SRX013060.05_model.r INFO @ Sun, 21 Jun 2020 16:37:18: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:37:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:37:22: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:37:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX013060/SRX013060.05_peaks.xls INFO @ Sun, 21 Jun 2020 16:37:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX013060/SRX013060.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:37:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX013060/SRX013060.05_summits.bed INFO @ Sun, 21 Jun 2020 16:37:25: Done! pass1 - making usageList (67 chroms): 1 millis pass2 - checking and writing primary data (163 records, 4 fields): 4 millis CompletedMACS2peakCalling 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 16:37:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX013060/SRX013060.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX013060/SRX013060.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX013060/SRX013060.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX013060/SRX013060.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 16:37:37: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:37:37: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:37:42: 1000000 INFO @ Sun, 21 Jun 2020 16:37:47: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:37:47: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:37:47: #1 total tags in treatment: 1917062 INFO @ Sun, 21 Jun 2020 16:37:47: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:37:47: #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 16:37:47: #1 tags after filtering in treatment: 1916664 INFO @ Sun, 21 Jun 2020 16:37:47: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:37:47: #1 finished! INFO @ Sun, 21 Jun 2020 16:37:47: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:37:47: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:37:48: #2 number of paired peaks: 210 WARNING @ Sun, 21 Jun 2020 16:37:48: Fewer paired peaks (210) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 210 pairs to build model! INFO @ Sun, 21 Jun 2020 16:37:48: start model_add_line... INFO @ Sun, 21 Jun 2020 16:37:48: start X-correlation... INFO @ Sun, 21 Jun 2020 16:37:48: end of X-cor INFO @ Sun, 21 Jun 2020 16:37:48: #2 finished! INFO @ Sun, 21 Jun 2020 16:37:48: #2 predicted fragment length is 91 bps INFO @ Sun, 21 Jun 2020 16:37:48: #2 alternative fragment length(s) may be 47,91,576,583 bps INFO @ Sun, 21 Jun 2020 16:37:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX013060/SRX013060.10_model.r INFO @ Sun, 21 Jun 2020 16:37:48: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:37:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:37:53: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:37:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX013060/SRX013060.10_peaks.xls INFO @ Sun, 21 Jun 2020 16:37:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX013060/SRX013060.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:37:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX013060/SRX013060.10_summits.bed INFO @ Sun, 21 Jun 2020 16:37:55: Done! pass1 - making usageList (48 chroms): 1 millis pass2 - checking and writing primary data (89 records, 4 fields): 2 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 16:38:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX013060/SRX013060.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX013060/SRX013060.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX013060/SRX013060.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX013060/SRX013060.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 16:38:07: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:38:07: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:38:13: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 16:38:18: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:38:18: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:38:18: #1 total tags in treatment: 1917062 INFO @ Sun, 21 Jun 2020 16:38:18: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:38:18: #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 16:38:18: #1 tags after filtering in treatment: 1916664 INFO @ Sun, 21 Jun 2020 16:38:18: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:38:18: #1 finished! INFO @ Sun, 21 Jun 2020 16:38:18: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:38:18: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:38:18: #2 number of paired peaks: 210 WARNING @ Sun, 21 Jun 2020 16:38:18: Fewer paired peaks (210) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 210 pairs to build model! INFO @ Sun, 21 Jun 2020 16:38:18: start model_add_line... INFO @ Sun, 21 Jun 2020 16:38:18: start X-correlation... INFO @ Sun, 21 Jun 2020 16:38:19: end of X-cor INFO @ Sun, 21 Jun 2020 16:38:19: #2 finished! INFO @ Sun, 21 Jun 2020 16:38:19: #2 predicted fragment length is 91 bps INFO @ Sun, 21 Jun 2020 16:38:19: #2 alternative fragment length(s) may be 47,91,576,583 bps INFO @ Sun, 21 Jun 2020 16:38:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX013060/SRX013060.20_model.r INFO @ Sun, 21 Jun 2020 16:38:19: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:38:19: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 16:38:24: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:38:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX013060/SRX013060.20_peaks.xls INFO @ Sun, 21 Jun 2020 16:38:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX013060/SRX013060.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:38:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX013060/SRX013060.20_summits.bed INFO @ Sun, 21 Jun 2020 16:38:26: Done! pass1 - making usageList (31 chroms): 1 millis pass2 - checking and writing primary data (46 records, 4 fields): 2 millis CompletedMACS2peakCalling