Job ID = 6455692 SRX = SRX287993 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:12:36 prefetch.2.10.7: 1) Downloading 'SRR870182'... 2020-06-21T10:12:36 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:16:28 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:16:28 prefetch.2.10.7: 1) 'SRR870182' was downloaded successfully Read 18761386 spots for SRR870182/SRR870182.sra Written 18761386 spots for SRR870182/SRR870182.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: 00:05:03 18761386 reads; of these: 18761386 (100.00%) were unpaired; of these: 1295338 (6.90%) aligned 0 times 12904508 (68.78%) aligned exactly 1 time 4561540 (24.31%) aligned >1 times 93.10% overall alignment rate Time searching: 00:05:03 Overall time: 00:05:03 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 8 files... [bam_rmdupse_core] 2615666 / 17466048 = 0.1498 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 19:27:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287993/SRX287993.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287993/SRX287993.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287993/SRX287993.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287993/SRX287993.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 19:27:01: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:27:01: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:27:08: 1000000 INFO @ Sun, 21 Jun 2020 19:27:14: 2000000 INFO @ Sun, 21 Jun 2020 19:27:21: 3000000 INFO @ Sun, 21 Jun 2020 19:27:27: 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 19:27:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287993/SRX287993.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287993/SRX287993.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287993/SRX287993.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287993/SRX287993.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 19:27:31: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:27:31: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:27:34: 5000000 INFO @ Sun, 21 Jun 2020 19:27:38: 1000000 INFO @ Sun, 21 Jun 2020 19:27:40: 6000000 INFO @ Sun, 21 Jun 2020 19:27:45: 2000000 INFO @ Sun, 21 Jun 2020 19:27:47: 7000000 INFO @ Sun, 21 Jun 2020 19:27:51: 3000000 INFO @ Sun, 21 Jun 2020 19:27:54: 8000000 INFO @ Sun, 21 Jun 2020 19:27:58: 4000000 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 19:28:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287993/SRX287993.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287993/SRX287993.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287993/SRX287993.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287993/SRX287993.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 19:28:01: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:28:01: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:28:02: 9000000 INFO @ Sun, 21 Jun 2020 19:28:05: 5000000 INFO @ Sun, 21 Jun 2020 19:28:08: 1000000 INFO @ Sun, 21 Jun 2020 19:28:09: 10000000 INFO @ Sun, 21 Jun 2020 19:28:11: 6000000 INFO @ Sun, 21 Jun 2020 19:28:14: 2000000 INFO @ Sun, 21 Jun 2020 19:28:16: 11000000 INFO @ Sun, 21 Jun 2020 19:28:18: 7000000 INFO @ Sun, 21 Jun 2020 19:28:20: 3000000 INFO @ Sun, 21 Jun 2020 19:28:23: 12000000 INFO @ Sun, 21 Jun 2020 19:28:25: 8000000 INFO @ Sun, 21 Jun 2020 19:28:26: 4000000 INFO @ Sun, 21 Jun 2020 19:28:30: 13000000 INFO @ Sun, 21 Jun 2020 19:28:32: 9000000 INFO @ Sun, 21 Jun 2020 19:28:33: 5000000 INFO @ Sun, 21 Jun 2020 19:28:38: 14000000 INFO @ Sun, 21 Jun 2020 19:28:38: 10000000 INFO @ Sun, 21 Jun 2020 19:28:39: 6000000 INFO @ Sun, 21 Jun 2020 19:28:44: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:28:44: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:28:44: #1 total tags in treatment: 14850382 INFO @ Sun, 21 Jun 2020 19:28:44: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:28:44: #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 19:28:44: #1 tags after filtering in treatment: 14850381 INFO @ Sun, 21 Jun 2020 19:28:44: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:28:44: #1 finished! INFO @ Sun, 21 Jun 2020 19:28:44: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:28:44: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:28:45: 7000000 INFO @ Sun, 21 Jun 2020 19:28:45: 11000000 INFO @ Sun, 21 Jun 2020 19:28:45: #2 number of paired peaks: 457 WARNING @ Sun, 21 Jun 2020 19:28:45: Fewer paired peaks (457) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 457 pairs to build model! INFO @ Sun, 21 Jun 2020 19:28:45: start model_add_line... INFO @ Sun, 21 Jun 2020 19:28:45: start X-correlation... INFO @ Sun, 21 Jun 2020 19:28:45: end of X-cor INFO @ Sun, 21 Jun 2020 19:28:45: #2 finished! INFO @ Sun, 21 Jun 2020 19:28:45: #2 predicted fragment length is 181 bps INFO @ Sun, 21 Jun 2020 19:28:45: #2 alternative fragment length(s) may be 181 bps INFO @ Sun, 21 Jun 2020 19:28:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287993/SRX287993.05_model.r INFO @ Sun, 21 Jun 2020 19:28:45: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:28:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:28:51: 8000000 INFO @ Sun, 21 Jun 2020 19:28:52: 12000000 INFO @ Sun, 21 Jun 2020 19:28:57: 9000000 INFO @ Sun, 21 Jun 2020 19:28:59: 13000000 INFO @ Sun, 21 Jun 2020 19:29:03: 10000000 INFO @ Sun, 21 Jun 2020 19:29:05: 14000000 INFO @ Sun, 21 Jun 2020 19:29:09: 11000000 INFO @ Sun, 21 Jun 2020 19:29:11: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:29:11: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:29:11: #1 total tags in treatment: 14850382 INFO @ Sun, 21 Jun 2020 19:29:11: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:29:11: #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 19:29:12: #1 tags after filtering in treatment: 14850381 INFO @ Sun, 21 Jun 2020 19:29:12: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:29:12: #1 finished! INFO @ Sun, 21 Jun 2020 19:29:12: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:29:12: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:29:13: #2 number of paired peaks: 457 WARNING @ Sun, 21 Jun 2020 19:29:13: Fewer paired peaks (457) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 457 pairs to build model! INFO @ Sun, 21 Jun 2020 19:29:13: start model_add_line... INFO @ Sun, 21 Jun 2020 19:29:13: start X-correlation... INFO @ Sun, 21 Jun 2020 19:29:13: end of X-cor INFO @ Sun, 21 Jun 2020 19:29:13: #2 finished! INFO @ Sun, 21 Jun 2020 19:29:13: #2 predicted fragment length is 181 bps INFO @ Sun, 21 Jun 2020 19:29:13: #2 alternative fragment length(s) may be 181 bps INFO @ Sun, 21 Jun 2020 19:29:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287993/SRX287993.10_model.r INFO @ Sun, 21 Jun 2020 19:29:13: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:29:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:29:15: 12000000 INFO @ Sun, 21 Jun 2020 19:29:16: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:29:21: 13000000 INFO @ Sun, 21 Jun 2020 19:29:26: 14000000 INFO @ Sun, 21 Jun 2020 19:29:31: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:29:31: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:29:31: #1 total tags in treatment: 14850382 INFO @ Sun, 21 Jun 2020 19:29:31: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:29:31: #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 19:29:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287993/SRX287993.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:29:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287993/SRX287993.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:29:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287993/SRX287993.05_summits.bed INFO @ Sun, 21 Jun 2020 19:29:31: Done! INFO @ Sun, 21 Jun 2020 19:29:32: #1 tags after filtering in treatment: 14850381 INFO @ Sun, 21 Jun 2020 19:29:32: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:29:32: #1 finished! INFO @ Sun, 21 Jun 2020 19:29:32: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:29:32: #2 looking for paired plus/minus strand peaks... pass1 - making usageList (658 chroms): 2 millis pass2 - checking and writing primary data (4424 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:29:33: #2 number of paired peaks: 457 WARNING @ Sun, 21 Jun 2020 19:29:33: Fewer paired peaks (457) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 457 pairs to build model! INFO @ Sun, 21 Jun 2020 19:29:33: start model_add_line... INFO @ Sun, 21 Jun 2020 19:29:33: start X-correlation... INFO @ Sun, 21 Jun 2020 19:29:33: end of X-cor INFO @ Sun, 21 Jun 2020 19:29:33: #2 finished! INFO @ Sun, 21 Jun 2020 19:29:33: #2 predicted fragment length is 181 bps INFO @ Sun, 21 Jun 2020 19:29:33: #2 alternative fragment length(s) may be 181 bps INFO @ Sun, 21 Jun 2020 19:29:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287993/SRX287993.20_model.r INFO @ Sun, 21 Jun 2020 19:29:33: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:29:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:29:44: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:29:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287993/SRX287993.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:29:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287993/SRX287993.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:29:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287993/SRX287993.10_summits.bed INFO @ Sun, 21 Jun 2020 19:29:59: Done! pass1 - making usageList (553 chroms): 1 millis pass2 - checking and writing primary data (3060 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:30:03: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:30:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287993/SRX287993.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:30:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287993/SRX287993.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:30:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287993/SRX287993.20_summits.bed INFO @ Sun, 21 Jun 2020 19:30:18: Done! pass1 - making usageList (429 chroms): 1 millis pass2 - checking and writing primary data (2021 records, 4 fields): 14 millis CompletedMACS2peakCalling