Job ID = 6455744 SRX = SRX288038 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:28:21 prefetch.2.10.7: 1) Downloading 'SRR870227'... 2020-06-21T10:28:21 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:32:42 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:32:42 prefetch.2.10.7: 1) 'SRR870227' was downloaded successfully Read 24663092 spots for SRR870227/SRR870227.sra Written 24663092 spots for SRR870227/SRR870227.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:06:23 24663092 reads; of these: 24663092 (100.00%) were unpaired; of these: 1965751 (7.97%) aligned 0 times 16218854 (65.76%) aligned exactly 1 time 6478487 (26.27%) aligned >1 times 92.03% overall alignment rate Time searching: 00:06:24 Overall time: 00:06:24 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_sort_core] merging from 12 files... [bam_rmdupse_core] 4149895 / 22697341 = 0.1828 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 19:47:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX288038/SRX288038.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX288038/SRX288038.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX288038/SRX288038.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX288038/SRX288038.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 19:47:44: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:47:44: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:47:49: 1000000 INFO @ Sun, 21 Jun 2020 19:47:54: 2000000 INFO @ Sun, 21 Jun 2020 19:47:59: 3000000 INFO @ Sun, 21 Jun 2020 19:48:04: 4000000 INFO @ Sun, 21 Jun 2020 19:48:09: 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 19:48:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX288038/SRX288038.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX288038/SRX288038.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX288038/SRX288038.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX288038/SRX288038.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 19:48:14: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:48:14: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:48:14: 6000000 INFO @ Sun, 21 Jun 2020 19:48:20: 7000000 INFO @ Sun, 21 Jun 2020 19:48:20: 1000000 INFO @ Sun, 21 Jun 2020 19:48:25: 8000000 INFO @ Sun, 21 Jun 2020 19:48:25: 2000000 INFO @ Sun, 21 Jun 2020 19:48:30: 9000000 INFO @ Sun, 21 Jun 2020 19:48:31: 3000000 INFO @ Sun, 21 Jun 2020 19:48:36: 10000000 INFO @ Sun, 21 Jun 2020 19:48:36: 4000000 INFO @ Sun, 21 Jun 2020 19:48:41: 11000000 INFO @ Sun, 21 Jun 2020 19:48:42: 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 19:48:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX288038/SRX288038.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX288038/SRX288038.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX288038/SRX288038.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX288038/SRX288038.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 19:48:44: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:48:44: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:48:47: 12000000 INFO @ Sun, 21 Jun 2020 19:48:47: 6000000 INFO @ Sun, 21 Jun 2020 19:48:50: 1000000 INFO @ Sun, 21 Jun 2020 19:48:53: 13000000 INFO @ Sun, 21 Jun 2020 19:48:53: 7000000 INFO @ Sun, 21 Jun 2020 19:48:56: 2000000 INFO @ Sun, 21 Jun 2020 19:48:59: 14000000 INFO @ Sun, 21 Jun 2020 19:48:59: 8000000 INFO @ Sun, 21 Jun 2020 19:49:02: 3000000 INFO @ Sun, 21 Jun 2020 19:49:05: 9000000 INFO @ Sun, 21 Jun 2020 19:49:05: 15000000 INFO @ Sun, 21 Jun 2020 19:49:08: 4000000 INFO @ Sun, 21 Jun 2020 19:49:10: 10000000 INFO @ Sun, 21 Jun 2020 19:49:11: 16000000 INFO @ Sun, 21 Jun 2020 19:49:14: 5000000 INFO @ Sun, 21 Jun 2020 19:49:16: 11000000 INFO @ Sun, 21 Jun 2020 19:49:17: 17000000 INFO @ Sun, 21 Jun 2020 19:49:19: 6000000 INFO @ Sun, 21 Jun 2020 19:49:22: 12000000 INFO @ Sun, 21 Jun 2020 19:49:24: 18000000 INFO @ Sun, 21 Jun 2020 19:49:25: 7000000 INFO @ Sun, 21 Jun 2020 19:49:27: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:49:27: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:49:27: #1 total tags in treatment: 18547446 INFO @ Sun, 21 Jun 2020 19:49:27: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:49:27: #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 19:49:28: 13000000 INFO @ Sun, 21 Jun 2020 19:49:28: #1 tags after filtering in treatment: 18547446 INFO @ Sun, 21 Jun 2020 19:49:28: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:49:28: #1 finished! INFO @ Sun, 21 Jun 2020 19:49:28: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:49:28: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:49:29: #2 number of paired peaks: 598 WARNING @ Sun, 21 Jun 2020 19:49:29: Fewer paired peaks (598) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 598 pairs to build model! INFO @ Sun, 21 Jun 2020 19:49:29: start model_add_line... INFO @ Sun, 21 Jun 2020 19:49:30: start X-correlation... INFO @ Sun, 21 Jun 2020 19:49:30: end of X-cor INFO @ Sun, 21 Jun 2020 19:49:30: #2 finished! INFO @ Sun, 21 Jun 2020 19:49:30: #2 predicted fragment length is 188 bps INFO @ Sun, 21 Jun 2020 19:49:30: #2 alternative fragment length(s) may be 188 bps INFO @ Sun, 21 Jun 2020 19:49:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX288038/SRX288038.05_model.r INFO @ Sun, 21 Jun 2020 19:49:30: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:49:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:49:31: 8000000 INFO @ Sun, 21 Jun 2020 19:49:33: 14000000 INFO @ Sun, 21 Jun 2020 19:49:36: 9000000 INFO @ Sun, 21 Jun 2020 19:49:38: 15000000 INFO @ Sun, 21 Jun 2020 19:49:41: 10000000 INFO @ Sun, 21 Jun 2020 19:49:44: 16000000 INFO @ Sun, 21 Jun 2020 19:49:46: 11000000 INFO @ Sun, 21 Jun 2020 19:49:50: 17000000 INFO @ Sun, 21 Jun 2020 19:49:52: 12000000 INFO @ Sun, 21 Jun 2020 19:49:55: 18000000 INFO @ Sun, 21 Jun 2020 19:49:57: 13000000 INFO @ Sun, 21 Jun 2020 19:49:58: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:49:58: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:49:58: #1 total tags in treatment: 18547446 INFO @ Sun, 21 Jun 2020 19:49:58: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:49:58: #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 19:49:59: #1 tags after filtering in treatment: 18547446 INFO @ Sun, 21 Jun 2020 19:49:59: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:49:59: #1 finished! INFO @ Sun, 21 Jun 2020 19:49:59: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:49:59: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:50:01: #2 number of paired peaks: 598 WARNING @ Sun, 21 Jun 2020 19:50:01: Fewer paired peaks (598) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 598 pairs to build model! INFO @ Sun, 21 Jun 2020 19:50:01: start model_add_line... INFO @ Sun, 21 Jun 2020 19:50:01: start X-correlation... INFO @ Sun, 21 Jun 2020 19:50:01: end of X-cor INFO @ Sun, 21 Jun 2020 19:50:01: #2 finished! INFO @ Sun, 21 Jun 2020 19:50:01: #2 predicted fragment length is 188 bps INFO @ Sun, 21 Jun 2020 19:50:01: #2 alternative fragment length(s) may be 188 bps INFO @ Sun, 21 Jun 2020 19:50:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX288038/SRX288038.10_model.r INFO @ Sun, 21 Jun 2020 19:50:01: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:50:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:50:02: 14000000 INFO @ Sun, 21 Jun 2020 19:50:07: 15000000 INFO @ Sun, 21 Jun 2020 19:50:10: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:50:12: 16000000 INFO @ Sun, 21 Jun 2020 19:50:17: 17000000 INFO @ Sun, 21 Jun 2020 19:50:22: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:50:25: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:50:25: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:50:25: #1 total tags in treatment: 18547446 INFO @ Sun, 21 Jun 2020 19:50:25: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:50:25: #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 19:50:26: #1 tags after filtering in treatment: 18547446 INFO @ Sun, 21 Jun 2020 19:50:26: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:50:26: #1 finished! INFO @ Sun, 21 Jun 2020 19:50:26: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:50:26: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:50:27: #2 number of paired peaks: 598 WARNING @ Sun, 21 Jun 2020 19:50:27: Fewer paired peaks (598) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 598 pairs to build model! INFO @ Sun, 21 Jun 2020 19:50:27: start model_add_line... INFO @ Sun, 21 Jun 2020 19:50:28: start X-correlation... INFO @ Sun, 21 Jun 2020 19:50:28: end of X-cor INFO @ Sun, 21 Jun 2020 19:50:28: #2 finished! INFO @ Sun, 21 Jun 2020 19:50:28: #2 predicted fragment length is 188 bps INFO @ Sun, 21 Jun 2020 19:50:28: #2 alternative fragment length(s) may be 188 bps INFO @ Sun, 21 Jun 2020 19:50:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX288038/SRX288038.20_model.r INFO @ Sun, 21 Jun 2020 19:50:28: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:50:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:50:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX288038/SRX288038.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:50:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX288038/SRX288038.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:50:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX288038/SRX288038.05_summits.bed INFO @ Sun, 21 Jun 2020 19:50:28: Done! pass1 - making usageList (771 chroms): 2 millis pass2 - checking and writing primary data (6452 records, 4 fields): 49 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:50:41: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:50:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX288038/SRX288038.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:50:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX288038/SRX288038.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:50:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX288038/SRX288038.10_summits.bed INFO @ Sun, 21 Jun 2020 19:50:59: Done! pass1 - making usageList (654 chroms): 2 millis pass2 - checking and writing primary data (3896 records, 4 fields): 38 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:51:08: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:51:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX288038/SRX288038.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:51:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX288038/SRX288038.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:51:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX288038/SRX288038.20_summits.bed INFO @ Sun, 21 Jun 2020 19:51:26: Done! pass1 - making usageList (493 chroms): 1 millis pass2 - checking and writing primary data (2170 records, 4 fields): 29 millis CompletedMACS2peakCalling