Job ID = 6452755 SRX = SRX030959 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:02:53 prefetch.2.10.7: 1) Downloading 'SRR072386'... 2020-06-21T08:02:53 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:06:05 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:06:06 prefetch.2.10.7: 'SRR072386' is valid 2020-06-21T08:06:06 prefetch.2.10.7: 1) 'SRR072386' was downloaded successfully Read 23012193 spots for SRR072386/SRR072386.sra Written 23012193 spots for SRR072386/SRR072386.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: 00:04:58 23012193 reads; of these: 23012193 (100.00%) were unpaired; of these: 1112758 (4.84%) aligned 0 times 17000775 (73.88%) aligned exactly 1 time 4898660 (21.29%) aligned >1 times 95.16% overall alignment rate Time searching: 00:04:58 Overall time: 00:04:58 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] 4032421 / 21899435 = 0.1841 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 17:16:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX030959/SRX030959.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX030959/SRX030959.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX030959/SRX030959.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX030959/SRX030959.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 17:16:51: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:16:51: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:16:57: 1000000 INFO @ Sun, 21 Jun 2020 17:17:03: 2000000 INFO @ Sun, 21 Jun 2020 17:17:09: 3000000 INFO @ Sun, 21 Jun 2020 17:17:15: 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 17:17:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX030959/SRX030959.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX030959/SRX030959.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX030959/SRX030959.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX030959/SRX030959.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 17:17:21: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:17:21: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:17:21: 5000000 INFO @ Sun, 21 Jun 2020 17:17:28: 6000000 INFO @ Sun, 21 Jun 2020 17:17:28: 1000000 INFO @ Sun, 21 Jun 2020 17:17:35: 7000000 INFO @ Sun, 21 Jun 2020 17:17:35: 2000000 INFO @ Sun, 21 Jun 2020 17:17:42: 8000000 INFO @ Sun, 21 Jun 2020 17:17:42: 3000000 INFO @ Sun, 21 Jun 2020 17:17:48: 9000000 INFO @ Sun, 21 Jun 2020 17:17:49: 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 17:17:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX030959/SRX030959.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX030959/SRX030959.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX030959/SRX030959.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX030959/SRX030959.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 17:17:51: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:17:51: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:17:55: 10000000 INFO @ Sun, 21 Jun 2020 17:17:56: 5000000 INFO @ Sun, 21 Jun 2020 17:17:58: 1000000 INFO @ Sun, 21 Jun 2020 17:18:02: 11000000 INFO @ Sun, 21 Jun 2020 17:18:03: 6000000 INFO @ Sun, 21 Jun 2020 17:18:05: 2000000 INFO @ Sun, 21 Jun 2020 17:18:09: 12000000 INFO @ Sun, 21 Jun 2020 17:18:10: 7000000 INFO @ Sun, 21 Jun 2020 17:18:12: 3000000 INFO @ Sun, 21 Jun 2020 17:18:16: 13000000 INFO @ Sun, 21 Jun 2020 17:18:16: 8000000 INFO @ Sun, 21 Jun 2020 17:18:19: 4000000 INFO @ Sun, 21 Jun 2020 17:18:23: 14000000 INFO @ Sun, 21 Jun 2020 17:18:23: 9000000 INFO @ Sun, 21 Jun 2020 17:18:25: 5000000 INFO @ Sun, 21 Jun 2020 17:18:30: 15000000 INFO @ Sun, 21 Jun 2020 17:18:30: 10000000 INFO @ Sun, 21 Jun 2020 17:18:32: 6000000 INFO @ Sun, 21 Jun 2020 17:18:37: 16000000 INFO @ Sun, 21 Jun 2020 17:18:37: 11000000 INFO @ Sun, 21 Jun 2020 17:18:39: 7000000 INFO @ Sun, 21 Jun 2020 17:18:44: 17000000 INFO @ Sun, 21 Jun 2020 17:18:44: 12000000 INFO @ Sun, 21 Jun 2020 17:18:46: 8000000 INFO @ Sun, 21 Jun 2020 17:18:50: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:18:50: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:18:50: #1 total tags in treatment: 17867014 INFO @ Sun, 21 Jun 2020 17:18:50: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:18:50: #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 17:18:50: #1 tags after filtering in treatment: 17867004 INFO @ Sun, 21 Jun 2020 17:18:50: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:18:50: #1 finished! INFO @ Sun, 21 Jun 2020 17:18:50: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:18:50: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:18:51: 13000000 INFO @ Sun, 21 Jun 2020 17:18:52: #2 number of paired peaks: 242 WARNING @ Sun, 21 Jun 2020 17:18:52: Fewer paired peaks (242) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 242 pairs to build model! INFO @ Sun, 21 Jun 2020 17:18:52: start model_add_line... INFO @ Sun, 21 Jun 2020 17:18:52: start X-correlation... INFO @ Sun, 21 Jun 2020 17:18:52: end of X-cor INFO @ Sun, 21 Jun 2020 17:18:52: #2 finished! INFO @ Sun, 21 Jun 2020 17:18:52: #2 predicted fragment length is 147 bps INFO @ Sun, 21 Jun 2020 17:18:52: #2 alternative fragment length(s) may be 147 bps INFO @ Sun, 21 Jun 2020 17:18:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX030959/SRX030959.05_model.r INFO @ Sun, 21 Jun 2020 17:18:52: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:18:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:18:53: 9000000 INFO @ Sun, 21 Jun 2020 17:18:58: 14000000 INFO @ Sun, 21 Jun 2020 17:18:59: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:19:06: 15000000 INFO @ Sun, 21 Jun 2020 17:19:06: 11000000 INFO @ Sun, 21 Jun 2020 17:19:12: 12000000 INFO @ Sun, 21 Jun 2020 17:19:12: 16000000 INFO @ Sun, 21 Jun 2020 17:19:19: 13000000 INFO @ Sun, 21 Jun 2020 17:19:19: 17000000 INFO @ Sun, 21 Jun 2020 17:19:26: 14000000 INFO @ Sun, 21 Jun 2020 17:19:26: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:19:26: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:19:26: #1 total tags in treatment: 17867014 INFO @ Sun, 21 Jun 2020 17:19:26: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:19:26: #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 17:19:26: #1 tags after filtering in treatment: 17867004 INFO @ Sun, 21 Jun 2020 17:19:26: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:19:26: #1 finished! INFO @ Sun, 21 Jun 2020 17:19:26: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:19:26: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:19:27: #2 number of paired peaks: 242 WARNING @ Sun, 21 Jun 2020 17:19:27: Fewer paired peaks (242) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 242 pairs to build model! INFO @ Sun, 21 Jun 2020 17:19:27: start model_add_line... INFO @ Sun, 21 Jun 2020 17:19:28: start X-correlation... INFO @ Sun, 21 Jun 2020 17:19:28: end of X-cor INFO @ Sun, 21 Jun 2020 17:19:28: #2 finished! INFO @ Sun, 21 Jun 2020 17:19:28: #2 predicted fragment length is 147 bps INFO @ Sun, 21 Jun 2020 17:19:28: #2 alternative fragment length(s) may be 147 bps INFO @ Sun, 21 Jun 2020 17:19:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX030959/SRX030959.10_model.r INFO @ Sun, 21 Jun 2020 17:19:28: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:19:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:19:28: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:19:32: 15000000 INFO @ Sun, 21 Jun 2020 17:19:39: 16000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:19:45: 17000000 INFO @ Sun, 21 Jun 2020 17:19:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX030959/SRX030959.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:19:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX030959/SRX030959.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:19:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX030959/SRX030959.05_summits.bed INFO @ Sun, 21 Jun 2020 17:19:46: Done! pass1 - making usageList (639 chroms): 2 millis pass2 - checking and writing primary data (8897 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:19:51: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:19:51: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:19:51: #1 total tags in treatment: 17867014 INFO @ Sun, 21 Jun 2020 17:19:51: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:19:51: #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 17:19:51: #1 tags after filtering in treatment: 17867004 INFO @ Sun, 21 Jun 2020 17:19:51: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:19:51: #1 finished! INFO @ Sun, 21 Jun 2020 17:19:51: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:19:51: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:19:52: #2 number of paired peaks: 242 WARNING @ Sun, 21 Jun 2020 17:19:52: Fewer paired peaks (242) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 242 pairs to build model! INFO @ Sun, 21 Jun 2020 17:19:52: start model_add_line... INFO @ Sun, 21 Jun 2020 17:19:52: start X-correlation... INFO @ Sun, 21 Jun 2020 17:19:52: end of X-cor INFO @ Sun, 21 Jun 2020 17:19:52: #2 finished! INFO @ Sun, 21 Jun 2020 17:19:52: #2 predicted fragment length is 147 bps INFO @ Sun, 21 Jun 2020 17:19:52: #2 alternative fragment length(s) may be 147 bps INFO @ Sun, 21 Jun 2020 17:19:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX030959/SRX030959.20_model.r INFO @ Sun, 21 Jun 2020 17:19:52: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:19:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:20:07: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:20:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX030959/SRX030959.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:20:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX030959/SRX030959.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:20:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX030959/SRX030959.10_summits.bed INFO @ Sun, 21 Jun 2020 17:20:28: Done! pass1 - making usageList (463 chroms): 2 millis pass2 - checking and writing primary data (2589 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:20:31: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:20:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX030959/SRX030959.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:20:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX030959/SRX030959.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:20:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX030959/SRX030959.20_summits.bed INFO @ Sun, 21 Jun 2020 17:20:50: Done! pass1 - making usageList (215 chroms): 1 millis pass2 - checking and writing primary data (566 records, 4 fields): 7 millis CompletedMACS2peakCalling