Job ID = 6530029 SRX = SRX6468482 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 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: 00:06:33 27439551 reads; of these: 27439551 (100.00%) were unpaired; of these: 1538049 (5.61%) aligned 0 times 19762464 (72.02%) aligned exactly 1 time 6139038 (22.37%) aligned >1 times 94.39% overall alignment rate Time searching: 00:06:34 Overall time: 00:06:34 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] 11874369 / 25901502 = 0.4584 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 @ Tue, 30 Jun 2020 03:19:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6468482/SRX6468482.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6468482/SRX6468482.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6468482/SRX6468482.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6468482/SRX6468482.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 @ Tue, 30 Jun 2020 03:19:31: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:19:31: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:19:37: 1000000 INFO @ Tue, 30 Jun 2020 03:19:43: 2000000 INFO @ Tue, 30 Jun 2020 03:19:50: 3000000 INFO @ Tue, 30 Jun 2020 03:19:56: 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 @ Tue, 30 Jun 2020 03:20:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6468482/SRX6468482.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6468482/SRX6468482.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6468482/SRX6468482.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6468482/SRX6468482.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 @ Tue, 30 Jun 2020 03:20:01: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:20:01: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:20:02: 5000000 INFO @ Tue, 30 Jun 2020 03:20:08: 1000000 INFO @ Tue, 30 Jun 2020 03:20:08: 6000000 INFO @ Tue, 30 Jun 2020 03:20:14: 2000000 INFO @ Tue, 30 Jun 2020 03:20:15: 7000000 INFO @ Tue, 30 Jun 2020 03:20:21: 3000000 INFO @ Tue, 30 Jun 2020 03:20:22: 8000000 INFO @ Tue, 30 Jun 2020 03:20:27: 4000000 INFO @ Tue, 30 Jun 2020 03:20:28: 9000000 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 @ Tue, 30 Jun 2020 03:20:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6468482/SRX6468482.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6468482/SRX6468482.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6468482/SRX6468482.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6468482/SRX6468482.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 @ Tue, 30 Jun 2020 03:20:31: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:20:31: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:20:34: 5000000 INFO @ Tue, 30 Jun 2020 03:20:35: 10000000 INFO @ Tue, 30 Jun 2020 03:20:38: 1000000 INFO @ Tue, 30 Jun 2020 03:20:41: 6000000 INFO @ Tue, 30 Jun 2020 03:20:42: 11000000 INFO @ Tue, 30 Jun 2020 03:20:44: 2000000 INFO @ Tue, 30 Jun 2020 03:20:47: 7000000 INFO @ Tue, 30 Jun 2020 03:20:49: 12000000 INFO @ Tue, 30 Jun 2020 03:20:51: 3000000 INFO @ Tue, 30 Jun 2020 03:20:54: 8000000 INFO @ Tue, 30 Jun 2020 03:20:56: 13000000 INFO @ Tue, 30 Jun 2020 03:20:58: 4000000 INFO @ Tue, 30 Jun 2020 03:21:00: 9000000 INFO @ Tue, 30 Jun 2020 03:21:03: 14000000 INFO @ Tue, 30 Jun 2020 03:21:03: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 03:21:03: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 03:21:03: #1 total tags in treatment: 14027133 INFO @ Tue, 30 Jun 2020 03:21:03: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:21:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 03:21:04: #1 tags after filtering in treatment: 14027133 INFO @ Tue, 30 Jun 2020 03:21:04: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:21:04: #1 finished! INFO @ Tue, 30 Jun 2020 03:21:04: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:21:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:21:04: 5000000 INFO @ Tue, 30 Jun 2020 03:21:05: #2 number of paired peaks: 234 WARNING @ Tue, 30 Jun 2020 03:21:05: Fewer paired peaks (234) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 234 pairs to build model! INFO @ Tue, 30 Jun 2020 03:21:05: start model_add_line... INFO @ Tue, 30 Jun 2020 03:21:05: start X-correlation... INFO @ Tue, 30 Jun 2020 03:21:05: end of X-cor INFO @ Tue, 30 Jun 2020 03:21:05: #2 finished! INFO @ Tue, 30 Jun 2020 03:21:05: #2 predicted fragment length is 203 bps INFO @ Tue, 30 Jun 2020 03:21:05: #2 alternative fragment length(s) may be 3,190,203 bps INFO @ Tue, 30 Jun 2020 03:21:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6468482/SRX6468482.05_model.r INFO @ Tue, 30 Jun 2020 03:21:05: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:21:05: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:21:07: 10000000 INFO @ Tue, 30 Jun 2020 03:21:11: 6000000 INFO @ Tue, 30 Jun 2020 03:21:13: 11000000 INFO @ Tue, 30 Jun 2020 03:21:18: 7000000 INFO @ Tue, 30 Jun 2020 03:21:20: 12000000 INFO @ Tue, 30 Jun 2020 03:21:25: 8000000 INFO @ Tue, 30 Jun 2020 03:21:27: 13000000 INFO @ Tue, 30 Jun 2020 03:21:31: 9000000 INFO @ Tue, 30 Jun 2020 03:21:34: 14000000 INFO @ Tue, 30 Jun 2020 03:21:34: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 03:21:34: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 03:21:34: #1 total tags in treatment: 14027133 INFO @ Tue, 30 Jun 2020 03:21:34: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:21:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 03:21:34: #1 tags after filtering in treatment: 14027133 INFO @ Tue, 30 Jun 2020 03:21:34: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:21:34: #1 finished! INFO @ Tue, 30 Jun 2020 03:21:34: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:21:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:21:35: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:21:35: #2 number of paired peaks: 234 WARNING @ Tue, 30 Jun 2020 03:21:35: Fewer paired peaks (234) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 234 pairs to build model! INFO @ Tue, 30 Jun 2020 03:21:35: start model_add_line... INFO @ Tue, 30 Jun 2020 03:21:35: start X-correlation... INFO @ Tue, 30 Jun 2020 03:21:35: end of X-cor INFO @ Tue, 30 Jun 2020 03:21:35: #2 finished! INFO @ Tue, 30 Jun 2020 03:21:35: #2 predicted fragment length is 203 bps INFO @ Tue, 30 Jun 2020 03:21:35: #2 alternative fragment length(s) may be 3,190,203 bps INFO @ Tue, 30 Jun 2020 03:21:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6468482/SRX6468482.10_model.r INFO @ Tue, 30 Jun 2020 03:21:35: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:21:35: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:21:38: 10000000 INFO @ Tue, 30 Jun 2020 03:21:44: 11000000 INFO @ Tue, 30 Jun 2020 03:21:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6468482/SRX6468482.05_peaks.xls INFO @ Tue, 30 Jun 2020 03:21:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6468482/SRX6468482.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:21:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6468482/SRX6468482.05_summits.bed INFO @ Tue, 30 Jun 2020 03:21:51: Done! INFO @ Tue, 30 Jun 2020 03:21:51: 12000000 pass1 - making usageList (563 chroms): 1 millis pass2 - checking and writing primary data (5773 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:21:57: 13000000 INFO @ Tue, 30 Jun 2020 03:22:03: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:22:04: 14000000 INFO @ Tue, 30 Jun 2020 03:22:04: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 03:22:04: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 03:22:04: #1 total tags in treatment: 14027133 INFO @ Tue, 30 Jun 2020 03:22:04: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:22:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 03:22:05: #1 tags after filtering in treatment: 14027133 INFO @ Tue, 30 Jun 2020 03:22:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:22:05: #1 finished! INFO @ Tue, 30 Jun 2020 03:22:05: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:22:05: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 03:22:06: #2 number of paired peaks: 234 WARNING @ Tue, 30 Jun 2020 03:22:06: Fewer paired peaks (234) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 234 pairs to build model! INFO @ Tue, 30 Jun 2020 03:22:06: start model_add_line... INFO @ Tue, 30 Jun 2020 03:22:06: start X-correlation... INFO @ Tue, 30 Jun 2020 03:22:06: end of X-cor INFO @ Tue, 30 Jun 2020 03:22:06: #2 finished! INFO @ Tue, 30 Jun 2020 03:22:06: #2 predicted fragment length is 203 bps INFO @ Tue, 30 Jun 2020 03:22:06: #2 alternative fragment length(s) may be 3,190,203 bps INFO @ Tue, 30 Jun 2020 03:22:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6468482/SRX6468482.20_model.r INFO @ Tue, 30 Jun 2020 03:22:06: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:22:06: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:22:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6468482/SRX6468482.10_peaks.xls INFO @ Tue, 30 Jun 2020 03:22:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6468482/SRX6468482.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:22:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6468482/SRX6468482.10_summits.bed INFO @ Tue, 30 Jun 2020 03:22:17: Done! pass1 - making usageList (322 chroms): 1 millis pass2 - checking and writing primary data (2390 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:22:33: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:22:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6468482/SRX6468482.20_peaks.xls INFO @ Tue, 30 Jun 2020 03:22:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6468482/SRX6468482.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:22:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6468482/SRX6468482.20_summits.bed INFO @ Tue, 30 Jun 2020 03:22:46: Done! pass1 - making usageList (114 chroms): 1 millis pass2 - checking and writing primary data (386 records, 4 fields): 4 millis CompletedMACS2peakCalling