Job ID = 6458367 SRX = SRX507383 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:29:04 prefetch.2.10.7: 1) Downloading 'SRR1213170'... 2020-06-21T12:29:04 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:30:08 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:30:09 prefetch.2.10.7: 'SRR1213170' is valid 2020-06-21T12:30:09 prefetch.2.10.7: 1) 'SRR1213170' was downloaded successfully Read 10390495 spots for SRR1213170/SRR1213170.sra Written 10390495 spots for SRR1213170/SRR1213170.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: 00:02:01 10390495 reads; of these: 10390495 (100.00%) were unpaired; of these: 458694 (4.41%) aligned 0 times 8521810 (82.02%) aligned exactly 1 time 1409991 (13.57%) aligned >1 times 95.59% overall alignment rate Time searching: 00:02:01 Overall time: 00:02:01 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] 2541963 / 9931801 = 0.2559 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 21:36:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX507383/SRX507383.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX507383/SRX507383.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX507383/SRX507383.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX507383/SRX507383.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 21:36:04: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:36:04: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:36:09: 1000000 INFO @ Sun, 21 Jun 2020 21:36:14: 2000000 INFO @ Sun, 21 Jun 2020 21:36:19: 3000000 INFO @ Sun, 21 Jun 2020 21:36:25: 4000000 INFO @ Sun, 21 Jun 2020 21:36:30: 5000000 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 21:36:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX507383/SRX507383.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX507383/SRX507383.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX507383/SRX507383.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX507383/SRX507383.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 21:36:34: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:36:34: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:36:36: 6000000 INFO @ Sun, 21 Jun 2020 21:36:39: 1000000 INFO @ Sun, 21 Jun 2020 21:36:42: 7000000 INFO @ Sun, 21 Jun 2020 21:36:45: 2000000 INFO @ Sun, 21 Jun 2020 21:36:45: #1 tag size is determined as 44 bps INFO @ Sun, 21 Jun 2020 21:36:45: #1 tag size = 44 INFO @ Sun, 21 Jun 2020 21:36:45: #1 total tags in treatment: 7389838 INFO @ Sun, 21 Jun 2020 21:36:45: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:36:45: #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 21:36:46: #1 tags after filtering in treatment: 7389684 INFO @ Sun, 21 Jun 2020 21:36:46: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:36:46: #1 finished! INFO @ Sun, 21 Jun 2020 21:36:46: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:36:46: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:36:46: #2 number of paired peaks: 701 WARNING @ Sun, 21 Jun 2020 21:36:46: Fewer paired peaks (701) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 701 pairs to build model! INFO @ Sun, 21 Jun 2020 21:36:46: start model_add_line... INFO @ Sun, 21 Jun 2020 21:36:46: start X-correlation... INFO @ Sun, 21 Jun 2020 21:36:46: end of X-cor INFO @ Sun, 21 Jun 2020 21:36:46: #2 finished! INFO @ Sun, 21 Jun 2020 21:36:46: #2 predicted fragment length is 124 bps INFO @ Sun, 21 Jun 2020 21:36:46: #2 alternative fragment length(s) may be 4,124 bps INFO @ Sun, 21 Jun 2020 21:36:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX507383/SRX507383.05_model.r INFO @ Sun, 21 Jun 2020 21:36:46: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:36:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:36:50: 3000000 INFO @ Sun, 21 Jun 2020 21:36:56: 4000000 INFO @ Sun, 21 Jun 2020 21:37:01: 5000000 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 21:37:03: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:37:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX507383/SRX507383.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX507383/SRX507383.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX507383/SRX507383.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX507383/SRX507383.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 21:37:04: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:37:04: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:37:08: 6000000 INFO @ Sun, 21 Jun 2020 21:37:10: 1000000 INFO @ Sun, 21 Jun 2020 21:37:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX507383/SRX507383.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:37:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX507383/SRX507383.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:37:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX507383/SRX507383.05_summits.bed INFO @ Sun, 21 Jun 2020 21:37:12: Done! pass1 - making usageList (366 chroms): 2 millis pass2 - checking and writing primary data (5958 records, 4 fields): 27 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:37:15: 7000000 INFO @ Sun, 21 Jun 2020 21:37:15: 2000000 INFO @ Sun, 21 Jun 2020 21:37:18: #1 tag size is determined as 44 bps INFO @ Sun, 21 Jun 2020 21:37:18: #1 tag size = 44 INFO @ Sun, 21 Jun 2020 21:37:18: #1 total tags in treatment: 7389838 INFO @ Sun, 21 Jun 2020 21:37:18: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:37:18: #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 21:37:19: #1 tags after filtering in treatment: 7389684 INFO @ Sun, 21 Jun 2020 21:37:19: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:37:19: #1 finished! INFO @ Sun, 21 Jun 2020 21:37:19: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:37:19: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:37:19: #2 number of paired peaks: 701 WARNING @ Sun, 21 Jun 2020 21:37:19: Fewer paired peaks (701) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 701 pairs to build model! INFO @ Sun, 21 Jun 2020 21:37:19: start model_add_line... INFO @ Sun, 21 Jun 2020 21:37:19: start X-correlation... INFO @ Sun, 21 Jun 2020 21:37:19: end of X-cor INFO @ Sun, 21 Jun 2020 21:37:19: #2 finished! INFO @ Sun, 21 Jun 2020 21:37:19: #2 predicted fragment length is 124 bps INFO @ Sun, 21 Jun 2020 21:37:19: #2 alternative fragment length(s) may be 4,124 bps INFO @ Sun, 21 Jun 2020 21:37:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX507383/SRX507383.10_model.r INFO @ Sun, 21 Jun 2020 21:37:19: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:37:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:37:20: 3000000 INFO @ Sun, 21 Jun 2020 21:37:26: 4000000 INFO @ Sun, 21 Jun 2020 21:37:31: 5000000 INFO @ Sun, 21 Jun 2020 21:37:35: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:37:38: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:37:44: 7000000 INFO @ Sun, 21 Jun 2020 21:37:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX507383/SRX507383.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:37:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX507383/SRX507383.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:37:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX507383/SRX507383.10_summits.bed INFO @ Sun, 21 Jun 2020 21:37:44: Done! pass1 - making usageList (172 chroms): 1 millis pass2 - checking and writing primary data (1382 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:37:47: #1 tag size is determined as 44 bps INFO @ Sun, 21 Jun 2020 21:37:47: #1 tag size = 44 INFO @ Sun, 21 Jun 2020 21:37:47: #1 total tags in treatment: 7389838 INFO @ Sun, 21 Jun 2020 21:37:47: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:37:47: #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 21:37:48: #1 tags after filtering in treatment: 7389684 INFO @ Sun, 21 Jun 2020 21:37:48: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:37:48: #1 finished! INFO @ Sun, 21 Jun 2020 21:37:48: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:37:48: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:37:48: #2 number of paired peaks: 701 WARNING @ Sun, 21 Jun 2020 21:37:48: Fewer paired peaks (701) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 701 pairs to build model! INFO @ Sun, 21 Jun 2020 21:37:48: start model_add_line... INFO @ Sun, 21 Jun 2020 21:37:48: start X-correlation... INFO @ Sun, 21 Jun 2020 21:37:48: end of X-cor INFO @ Sun, 21 Jun 2020 21:37:48: #2 finished! INFO @ Sun, 21 Jun 2020 21:37:48: #2 predicted fragment length is 124 bps INFO @ Sun, 21 Jun 2020 21:37:48: #2 alternative fragment length(s) may be 4,124 bps INFO @ Sun, 21 Jun 2020 21:37:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX507383/SRX507383.20_model.r INFO @ Sun, 21 Jun 2020 21:37:48: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:37:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:38:04: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:38:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX507383/SRX507383.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:38:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX507383/SRX507383.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:38:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX507383/SRX507383.20_summits.bed INFO @ Sun, 21 Jun 2020 21:38:13: Done! pass1 - making usageList (90 chroms): 2 millis pass2 - checking and writing primary data (176 records, 4 fields): 6 millis CompletedMACS2peakCalling