Job ID = 6458508 SRX = SRX5247958 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:29:37 prefetch.2.10.7: 1) Downloading 'SRR8440605'... 2020-06-21T12:29:37 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:31:04 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:31:04 prefetch.2.10.7: 'SRR8440605' is valid 2020-06-21T12:31:04 prefetch.2.10.7: 1) 'SRR8440605' was downloaded successfully Read 9024515 spots for SRR8440605/SRR8440605.sra Written 9024515 spots for SRR8440605/SRR8440605.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: 00:02:24 9024515 reads; of these: 9024515 (100.00%) were unpaired; of these: 628762 (6.97%) aligned 0 times 5551884 (61.52%) aligned exactly 1 time 2843869 (31.51%) aligned >1 times 93.03% overall alignment rate Time searching: 00:02:24 Overall time: 00:02:24 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] 497316 / 8395753 = 0.0592 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 21:36:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5247958/SRX5247958.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5247958/SRX5247958.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5247958/SRX5247958.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5247958/SRX5247958.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 21:36:24: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:36:24: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:36:30: 1000000 INFO @ Sun, 21 Jun 2020 21:36:35: 2000000 INFO @ Sun, 21 Jun 2020 21:36:41: 3000000 INFO @ Sun, 21 Jun 2020 21:36:47: 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 21:36:52: 5000000 INFO @ Sun, 21 Jun 2020 21:36:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5247958/SRX5247958.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5247958/SRX5247958.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5247958/SRX5247958.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5247958/SRX5247958.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 21:36:54: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:36:54: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:36:59: 6000000 INFO @ Sun, 21 Jun 2020 21:37:02: 1000000 INFO @ Sun, 21 Jun 2020 21:37:06: 7000000 INFO @ Sun, 21 Jun 2020 21:37:09: 2000000 INFO @ Sun, 21 Jun 2020 21:37:13: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:37:13: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:37:13: #1 total tags in treatment: 7898437 INFO @ Sun, 21 Jun 2020 21:37:13: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:37:13: #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 21:37:13: #1 tags after filtering in treatment: 7898351 INFO @ Sun, 21 Jun 2020 21:37:13: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:37:13: #1 finished! INFO @ Sun, 21 Jun 2020 21:37:13: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:37:13: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:37:14: #2 number of paired peaks: 907 WARNING @ Sun, 21 Jun 2020 21:37:14: Fewer paired peaks (907) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 907 pairs to build model! INFO @ Sun, 21 Jun 2020 21:37:14: start model_add_line... INFO @ Sun, 21 Jun 2020 21:37:14: start X-correlation... INFO @ Sun, 21 Jun 2020 21:37:14: end of X-cor INFO @ Sun, 21 Jun 2020 21:37:14: #2 finished! INFO @ Sun, 21 Jun 2020 21:37:14: #2 predicted fragment length is 136 bps INFO @ Sun, 21 Jun 2020 21:37:14: #2 alternative fragment length(s) may be 4,89,136 bps INFO @ Sun, 21 Jun 2020 21:37:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5247958/SRX5247958.05_model.r INFO @ Sun, 21 Jun 2020 21:37:14: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:37:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:37:16: 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 21:37:23: 4000000 INFO @ Sun, 21 Jun 2020 21:37:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5247958/SRX5247958.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5247958/SRX5247958.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5247958/SRX5247958.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5247958/SRX5247958.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 21:37:26: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:37:26: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:37:30: 5000000 INFO @ Sun, 21 Jun 2020 21:37:33: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:37:33: 1000000 INFO @ Sun, 21 Jun 2020 21:37:38: 6000000 INFO @ Sun, 21 Jun 2020 21:37:40: 2000000 INFO @ Sun, 21 Jun 2020 21:37:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5247958/SRX5247958.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:37:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5247958/SRX5247958.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:37:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5247958/SRX5247958.05_summits.bed INFO @ Sun, 21 Jun 2020 21:37:42: Done! pass1 - making usageList (316 chroms): 1 millis pass2 - checking and writing primary data (1958 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:37:46: 7000000 INFO @ Sun, 21 Jun 2020 21:37:48: 3000000 INFO @ Sun, 21 Jun 2020 21:37:53: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:37:53: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:37:53: #1 total tags in treatment: 7898437 INFO @ Sun, 21 Jun 2020 21:37:53: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:37:53: #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 21:37:53: #1 tags after filtering in treatment: 7898351 INFO @ Sun, 21 Jun 2020 21:37:53: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:37:53: #1 finished! INFO @ Sun, 21 Jun 2020 21:37:53: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:37:53: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:37:54: #2 number of paired peaks: 907 WARNING @ Sun, 21 Jun 2020 21:37:54: Fewer paired peaks (907) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 907 pairs to build model! INFO @ Sun, 21 Jun 2020 21:37:54: start model_add_line... INFO @ Sun, 21 Jun 2020 21:37:54: start X-correlation... INFO @ Sun, 21 Jun 2020 21:37:54: end of X-cor INFO @ Sun, 21 Jun 2020 21:37:54: #2 finished! INFO @ Sun, 21 Jun 2020 21:37:54: #2 predicted fragment length is 136 bps INFO @ Sun, 21 Jun 2020 21:37:54: #2 alternative fragment length(s) may be 4,89,136 bps INFO @ Sun, 21 Jun 2020 21:37:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5247958/SRX5247958.10_model.r INFO @ Sun, 21 Jun 2020 21:37:54: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:37:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:37:55: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:38:02: 5000000 INFO @ Sun, 21 Jun 2020 21:38:09: 6000000 INFO @ Sun, 21 Jun 2020 21:38:12: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:38:17: 7000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:38:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5247958/SRX5247958.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:38:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5247958/SRX5247958.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:38:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5247958/SRX5247958.10_summits.bed INFO @ Sun, 21 Jun 2020 21:38:21: Done! pass1 - making usageList (232 chroms): 1 millis pass2 - checking and writing primary data (762 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:38:23: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:38:23: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:38:23: #1 total tags in treatment: 7898437 INFO @ Sun, 21 Jun 2020 21:38:23: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:38:23: #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 21:38:24: #1 tags after filtering in treatment: 7898351 INFO @ Sun, 21 Jun 2020 21:38:24: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:38:24: #1 finished! INFO @ Sun, 21 Jun 2020 21:38:24: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:38:24: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:38:24: #2 number of paired peaks: 907 WARNING @ Sun, 21 Jun 2020 21:38:24: Fewer paired peaks (907) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 907 pairs to build model! INFO @ Sun, 21 Jun 2020 21:38:24: start model_add_line... INFO @ Sun, 21 Jun 2020 21:38:24: start X-correlation... INFO @ Sun, 21 Jun 2020 21:38:24: end of X-cor INFO @ Sun, 21 Jun 2020 21:38:24: #2 finished! INFO @ Sun, 21 Jun 2020 21:38:24: #2 predicted fragment length is 136 bps INFO @ Sun, 21 Jun 2020 21:38:24: #2 alternative fragment length(s) may be 4,89,136 bps INFO @ Sun, 21 Jun 2020 21:38:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5247958/SRX5247958.20_model.r INFO @ Sun, 21 Jun 2020 21:38:24: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:38:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:38:43: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:38:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5247958/SRX5247958.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:38:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5247958/SRX5247958.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:38:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5247958/SRX5247958.20_summits.bed INFO @ Sun, 21 Jun 2020 21:38:53: Done! pass1 - making usageList (126 chroms): 1 millis pass2 - checking and writing primary data (252 records, 4 fields): 5 millis CompletedMACS2peakCalling