Job ID = 6457794 SRX = SRX4798830 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:10:49 prefetch.2.10.7: 1) Downloading 'SRR7965239'... 2020-06-21T12:10:49 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:12:47 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:12:48 prefetch.2.10.7: 'SRR7965239' is valid 2020-06-21T12:12:48 prefetch.2.10.7: 1) 'SRR7965239' was downloaded successfully Read 12377165 spots for SRR7965239/SRR7965239.sra Written 12377165 spots for SRR7965239/SRR7965239.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: 00:02:02 12377165 reads; of these: 12377165 (100.00%) were unpaired; of these: 5238847 (42.33%) aligned 0 times 6385166 (51.59%) aligned exactly 1 time 753152 (6.09%) aligned >1 times 57.67% overall alignment rate Time searching: 00:02:02 Overall time: 00:02:02 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] 2110475 / 7138318 = 0.2957 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 21:17:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4798830/SRX4798830.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4798830/SRX4798830.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4798830/SRX4798830.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4798830/SRX4798830.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 21:17:52: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:17:52: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:17:58: 1000000 INFO @ Sun, 21 Jun 2020 21:18:03: 2000000 INFO @ Sun, 21 Jun 2020 21:18:08: 3000000 INFO @ Sun, 21 Jun 2020 21:18:14: 4000000 INFO @ Sun, 21 Jun 2020 21:18:19: 5000000 INFO @ Sun, 21 Jun 2020 21:18:19: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 21:18:19: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 21:18:19: #1 total tags in treatment: 5027843 INFO @ Sun, 21 Jun 2020 21:18:19: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:18:19: #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 21:18:20: #1 tags after filtering in treatment: 5027588 INFO @ Sun, 21 Jun 2020 21:18:20: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:18:20: #1 finished! INFO @ Sun, 21 Jun 2020 21:18:20: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:18:20: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:18:20: #2 number of paired peaks: 582 WARNING @ Sun, 21 Jun 2020 21:18:20: Fewer paired peaks (582) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 582 pairs to build model! INFO @ Sun, 21 Jun 2020 21:18:20: start model_add_line... INFO @ Sun, 21 Jun 2020 21:18:20: start X-correlation... INFO @ Sun, 21 Jun 2020 21:18:20: end of X-cor INFO @ Sun, 21 Jun 2020 21:18:20: #2 finished! INFO @ Sun, 21 Jun 2020 21:18:20: #2 predicted fragment length is 160 bps INFO @ Sun, 21 Jun 2020 21:18:20: #2 alternative fragment length(s) may be 160 bps INFO @ Sun, 21 Jun 2020 21:18:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4798830/SRX4798830.05_model.r INFO @ Sun, 21 Jun 2020 21:18:20: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:18:20: #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 21:18:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4798830/SRX4798830.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4798830/SRX4798830.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4798830/SRX4798830.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4798830/SRX4798830.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 21:18:22: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:18:22: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:18:28: 1000000 INFO @ Sun, 21 Jun 2020 21:18:32: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:18:33: 2000000 INFO @ Sun, 21 Jun 2020 21:18:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4798830/SRX4798830.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:18:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4798830/SRX4798830.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:18:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4798830/SRX4798830.05_summits.bed INFO @ Sun, 21 Jun 2020 21:18:38: Done! pass1 - making usageList (177 chroms): 2 millis pass2 - checking and writing primary data (3123 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:18:38: 3000000 INFO @ Sun, 21 Jun 2020 21:18:44: 4000000 INFO @ Sun, 21 Jun 2020 21:18:50: 5000000 INFO @ Sun, 21 Jun 2020 21:18:50: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 21:18:50: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 21:18:50: #1 total tags in treatment: 5027843 INFO @ Sun, 21 Jun 2020 21:18:50: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:18:50: #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 21:18:50: #1 tags after filtering in treatment: 5027588 INFO @ Sun, 21 Jun 2020 21:18:50: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:18:50: #1 finished! INFO @ Sun, 21 Jun 2020 21:18:50: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:18:50: #2 looking for paired plus/minus strand peaks... 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 21:18:51: #2 number of paired peaks: 582 WARNING @ Sun, 21 Jun 2020 21:18:51: Fewer paired peaks (582) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 582 pairs to build model! INFO @ Sun, 21 Jun 2020 21:18:51: start model_add_line... INFO @ Sun, 21 Jun 2020 21:18:51: start X-correlation... INFO @ Sun, 21 Jun 2020 21:18:51: end of X-cor INFO @ Sun, 21 Jun 2020 21:18:51: #2 finished! INFO @ Sun, 21 Jun 2020 21:18:51: #2 predicted fragment length is 160 bps INFO @ Sun, 21 Jun 2020 21:18:51: #2 alternative fragment length(s) may be 160 bps INFO @ Sun, 21 Jun 2020 21:18:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4798830/SRX4798830.10_model.r INFO @ Sun, 21 Jun 2020 21:18:51: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:18:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:18:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4798830/SRX4798830.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4798830/SRX4798830.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4798830/SRX4798830.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4798830/SRX4798830.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 21:18:52: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:18:52: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:18:58: 1000000 INFO @ Sun, 21 Jun 2020 21:19:03: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:19:03: 2000000 INFO @ Sun, 21 Jun 2020 21:19:09: 3000000 INFO @ Sun, 21 Jun 2020 21:19:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4798830/SRX4798830.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:19:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4798830/SRX4798830.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:19:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4798830/SRX4798830.10_summits.bed INFO @ Sun, 21 Jun 2020 21:19:09: Done! pass1 - making usageList (66 chroms): 0 millis pass2 - checking and writing primary data (835 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:19:15: 4000000 INFO @ Sun, 21 Jun 2020 21:19:20: 5000000 INFO @ Sun, 21 Jun 2020 21:19:21: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 21:19:21: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 21:19:21: #1 total tags in treatment: 5027843 INFO @ Sun, 21 Jun 2020 21:19:21: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:19:21: #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 21:19:21: #1 tags after filtering in treatment: 5027588 INFO @ Sun, 21 Jun 2020 21:19:21: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:19:21: #1 finished! INFO @ Sun, 21 Jun 2020 21:19:21: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:19:21: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:19:21: #2 number of paired peaks: 582 WARNING @ Sun, 21 Jun 2020 21:19:21: Fewer paired peaks (582) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 582 pairs to build model! INFO @ Sun, 21 Jun 2020 21:19:21: start model_add_line... INFO @ Sun, 21 Jun 2020 21:19:21: start X-correlation... INFO @ Sun, 21 Jun 2020 21:19:21: end of X-cor INFO @ Sun, 21 Jun 2020 21:19:21: #2 finished! INFO @ Sun, 21 Jun 2020 21:19:21: #2 predicted fragment length is 160 bps INFO @ Sun, 21 Jun 2020 21:19:21: #2 alternative fragment length(s) may be 160 bps INFO @ Sun, 21 Jun 2020 21:19:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4798830/SRX4798830.20_model.r INFO @ Sun, 21 Jun 2020 21:19:21: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:19:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:19:34: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:19:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4798830/SRX4798830.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:19:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4798830/SRX4798830.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:19:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4798830/SRX4798830.20_summits.bed INFO @ Sun, 21 Jun 2020 21:19:40: Done! pass1 - making usageList (41 chroms): 1 millis pass2 - checking and writing primary data (132 records, 4 fields): 4 millis CompletedMACS2peakCalling