Job ID = 6454808 SRX = SRX2592408 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:42:10 prefetch.2.10.7: 1) Downloading 'SRR5289685'... 2020-06-21T09:42:10 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:43:50 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:43:50 prefetch.2.10.7: 'SRR5289685' is valid 2020-06-21T09:43:50 prefetch.2.10.7: 1) 'SRR5289685' was downloaded successfully Read 7821684 spots for SRR5289685/SRR5289685.sra Written 7821684 spots for SRR5289685/SRR5289685.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: 00:01:57 7821684 reads; of these: 7821684 (100.00%) were unpaired; of these: 1604497 (20.51%) aligned 0 times 4742437 (60.63%) aligned exactly 1 time 1474750 (18.85%) aligned >1 times 79.49% overall alignment rate Time searching: 00:01:57 Overall time: 00:01:57 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] 1262976 / 6217187 = 0.2031 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 18:48:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592408/SRX2592408.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592408/SRX2592408.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592408/SRX2592408.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592408/SRX2592408.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 18:48:24: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:48:24: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:48:30: 1000000 INFO @ Sun, 21 Jun 2020 18:48:36: 2000000 INFO @ Sun, 21 Jun 2020 18:48:43: 3000000 INFO @ Sun, 21 Jun 2020 18:48:49: 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 18:48:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592408/SRX2592408.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592408/SRX2592408.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592408/SRX2592408.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592408/SRX2592408.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 18:48:54: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:48:54: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:48:55: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:48:55: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:48:55: #1 total tags in treatment: 4954211 INFO @ Sun, 21 Jun 2020 18:48:55: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:48:55: #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 18:48:55: #1 tags after filtering in treatment: 4953999 INFO @ Sun, 21 Jun 2020 18:48:55: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:48:55: #1 finished! INFO @ Sun, 21 Jun 2020 18:48:55: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:48:55: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:48:56: #2 number of paired peaks: 570 WARNING @ Sun, 21 Jun 2020 18:48:56: Fewer paired peaks (570) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 570 pairs to build model! INFO @ Sun, 21 Jun 2020 18:48:56: start model_add_line... INFO @ Sun, 21 Jun 2020 18:48:56: start X-correlation... INFO @ Sun, 21 Jun 2020 18:48:56: end of X-cor INFO @ Sun, 21 Jun 2020 18:48:56: #2 finished! INFO @ Sun, 21 Jun 2020 18:48:56: #2 predicted fragment length is 108 bps INFO @ Sun, 21 Jun 2020 18:48:56: #2 alternative fragment length(s) may be 108 bps INFO @ Sun, 21 Jun 2020 18:48:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592408/SRX2592408.05_model.r INFO @ Sun, 21 Jun 2020 18:48:56: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:48:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:49:02: 1000000 INFO @ Sun, 21 Jun 2020 18:49:08: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:49:09: 2000000 INFO @ Sun, 21 Jun 2020 18:49:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592408/SRX2592408.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:49:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592408/SRX2592408.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:49:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592408/SRX2592408.05_summits.bed INFO @ Sun, 21 Jun 2020 18:49:14: Done! pass1 - making usageList (443 chroms): 2 millis pass2 - checking and writing primary data (1781 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:49:16: 3000000 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 18:49:23: 4000000 INFO @ Sun, 21 Jun 2020 18:49:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592408/SRX2592408.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592408/SRX2592408.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592408/SRX2592408.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592408/SRX2592408.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 18:49:24: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:49:24: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:49:30: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:49:30: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:49:30: #1 total tags in treatment: 4954211 INFO @ Sun, 21 Jun 2020 18:49:30: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:49:30: #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 18:49:31: #1 tags after filtering in treatment: 4953999 INFO @ Sun, 21 Jun 2020 18:49:31: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:49:31: #1 finished! INFO @ Sun, 21 Jun 2020 18:49:31: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:49:31: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:49:31: #2 number of paired peaks: 570 WARNING @ Sun, 21 Jun 2020 18:49:31: Fewer paired peaks (570) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 570 pairs to build model! INFO @ Sun, 21 Jun 2020 18:49:31: start model_add_line... INFO @ Sun, 21 Jun 2020 18:49:31: start X-correlation... INFO @ Sun, 21 Jun 2020 18:49:31: end of X-cor INFO @ Sun, 21 Jun 2020 18:49:31: #2 finished! INFO @ Sun, 21 Jun 2020 18:49:31: #2 predicted fragment length is 108 bps INFO @ Sun, 21 Jun 2020 18:49:31: #2 alternative fragment length(s) may be 108 bps INFO @ Sun, 21 Jun 2020 18:49:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592408/SRX2592408.10_model.r INFO @ Sun, 21 Jun 2020 18:49:31: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:49:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:49:31: 1000000 INFO @ Sun, 21 Jun 2020 18:49:38: 2000000 INFO @ Sun, 21 Jun 2020 18:49:43: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:49:45: 3000000 INFO @ Sun, 21 Jun 2020 18:49:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592408/SRX2592408.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:49:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592408/SRX2592408.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:49:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592408/SRX2592408.10_summits.bed INFO @ Sun, 21 Jun 2020 18:49:48: Done! pass1 - making usageList (246 chroms): 1 millis pass2 - checking and writing primary data (557 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:49:51: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:49:57: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:49:57: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:49:57: #1 total tags in treatment: 4954211 INFO @ Sun, 21 Jun 2020 18:49:57: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:49:57: #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 18:49:58: #1 tags after filtering in treatment: 4953999 INFO @ Sun, 21 Jun 2020 18:49:58: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:49:58: #1 finished! INFO @ Sun, 21 Jun 2020 18:49:58: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:49:58: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:49:58: #2 number of paired peaks: 570 WARNING @ Sun, 21 Jun 2020 18:49:58: Fewer paired peaks (570) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 570 pairs to build model! INFO @ Sun, 21 Jun 2020 18:49:58: start model_add_line... INFO @ Sun, 21 Jun 2020 18:49:58: start X-correlation... INFO @ Sun, 21 Jun 2020 18:49:58: end of X-cor INFO @ Sun, 21 Jun 2020 18:49:58: #2 finished! INFO @ Sun, 21 Jun 2020 18:49:58: #2 predicted fragment length is 108 bps INFO @ Sun, 21 Jun 2020 18:49:58: #2 alternative fragment length(s) may be 108 bps INFO @ Sun, 21 Jun 2020 18:49:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592408/SRX2592408.20_model.r INFO @ Sun, 21 Jun 2020 18:49:58: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:49:58: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:50:11: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:50:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592408/SRX2592408.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:50:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592408/SRX2592408.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:50:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592408/SRX2592408.20_summits.bed INFO @ Sun, 21 Jun 2020 18:50:17: Done! pass1 - making usageList (92 chroms): 1 millis pass2 - checking and writing primary data (165 records, 4 fields): 4 millis CompletedMACS2peakCalling