Job ID = 6456104 SRX = SRX318780 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:30:36 prefetch.2.10.7: 1) Downloading 'SRR927096'... 2020-06-21T10:30:36 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:34:35 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:34:36 prefetch.2.10.7: 'SRR927096' is valid 2020-06-21T10:34:36 prefetch.2.10.7: 1) 'SRR927096' was downloaded successfully Read 14464779 spots for SRR927096/SRR927096.sra Written 14464779 spots for SRR927096/SRR927096.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: 00:03:41 14464779 reads; of these: 14464779 (100.00%) were unpaired; of these: 1143425 (7.90%) aligned 0 times 10663036 (73.72%) aligned exactly 1 time 2658318 (18.38%) aligned >1 times 92.10% overall alignment rate Time searching: 00:03:41 Overall time: 00:03:41 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] 2790278 / 13321354 = 0.2095 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 19:42:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX318780/SRX318780.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX318780/SRX318780.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX318780/SRX318780.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX318780/SRX318780.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 19:42:35: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:42:35: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:42:40: 1000000 INFO @ Sun, 21 Jun 2020 19:42:44: 2000000 INFO @ Sun, 21 Jun 2020 19:42:49: 3000000 INFO @ Sun, 21 Jun 2020 19:42:54: 4000000 INFO @ Sun, 21 Jun 2020 19:42:59: 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 19:43:03: 6000000 INFO @ Sun, 21 Jun 2020 19:43:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX318780/SRX318780.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX318780/SRX318780.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX318780/SRX318780.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX318780/SRX318780.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 19:43:04: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:43:04: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:43:08: 7000000 INFO @ Sun, 21 Jun 2020 19:43:10: 1000000 INFO @ Sun, 21 Jun 2020 19:43:13: 8000000 INFO @ Sun, 21 Jun 2020 19:43:16: 2000000 INFO @ Sun, 21 Jun 2020 19:43:19: 9000000 INFO @ Sun, 21 Jun 2020 19:43:22: 3000000 INFO @ Sun, 21 Jun 2020 19:43:24: 10000000 INFO @ Sun, 21 Jun 2020 19:43:27: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:43:27: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:43:27: #1 total tags in treatment: 10531076 INFO @ Sun, 21 Jun 2020 19:43:27: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:43:27: #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 19:43:27: #1 tags after filtering in treatment: 10531071 INFO @ Sun, 21 Jun 2020 19:43:27: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:43:27: #1 finished! INFO @ Sun, 21 Jun 2020 19:43:27: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:43:27: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:43:28: #2 number of paired peaks: 395 WARNING @ Sun, 21 Jun 2020 19:43:28: Fewer paired peaks (395) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 395 pairs to build model! INFO @ Sun, 21 Jun 2020 19:43:28: start model_add_line... INFO @ Sun, 21 Jun 2020 19:43:28: 4000000 INFO @ Sun, 21 Jun 2020 19:43:28: start X-correlation... INFO @ Sun, 21 Jun 2020 19:43:28: end of X-cor INFO @ Sun, 21 Jun 2020 19:43:28: #2 finished! INFO @ Sun, 21 Jun 2020 19:43:28: #2 predicted fragment length is 129 bps INFO @ Sun, 21 Jun 2020 19:43:28: #2 alternative fragment length(s) may be 129 bps INFO @ Sun, 21 Jun 2020 19:43:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX318780/SRX318780.05_model.r INFO @ Sun, 21 Jun 2020 19:43:28: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:43:28: #3 Pre-compute pvalue-qvalue table... 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 19:43:34: 5000000 INFO @ Sun, 21 Jun 2020 19:43:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX318780/SRX318780.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX318780/SRX318780.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX318780/SRX318780.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX318780/SRX318780.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 19:43:34: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:43:34: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:43:39: 6000000 INFO @ Sun, 21 Jun 2020 19:43:41: 1000000 INFO @ Sun, 21 Jun 2020 19:43:45: 7000000 INFO @ Sun, 21 Jun 2020 19:43:48: 2000000 INFO @ Sun, 21 Jun 2020 19:43:50: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:43:51: 8000000 INFO @ Sun, 21 Jun 2020 19:43:55: 3000000 INFO @ Sun, 21 Jun 2020 19:43:57: 9000000 INFO @ Sun, 21 Jun 2020 19:44:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX318780/SRX318780.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:44:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX318780/SRX318780.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:44:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX318780/SRX318780.05_summits.bed INFO @ Sun, 21 Jun 2020 19:44:01: 4000000 INFO @ Sun, 21 Jun 2020 19:44:01: Done! pass1 - making usageList (478 chroms): 1 millis pass2 - checking and writing primary data (3210 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:44:02: 10000000 INFO @ Sun, 21 Jun 2020 19:44:06: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:44:06: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:44:06: #1 total tags in treatment: 10531076 INFO @ Sun, 21 Jun 2020 19:44:06: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:44:06: #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 19:44:06: #1 tags after filtering in treatment: 10531071 INFO @ Sun, 21 Jun 2020 19:44:06: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:44:06: #1 finished! INFO @ Sun, 21 Jun 2020 19:44:06: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:44:06: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:44:07: #2 number of paired peaks: 395 WARNING @ Sun, 21 Jun 2020 19:44:07: Fewer paired peaks (395) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 395 pairs to build model! INFO @ Sun, 21 Jun 2020 19:44:07: start model_add_line... INFO @ Sun, 21 Jun 2020 19:44:07: start X-correlation... INFO @ Sun, 21 Jun 2020 19:44:07: end of X-cor INFO @ Sun, 21 Jun 2020 19:44:07: #2 finished! INFO @ Sun, 21 Jun 2020 19:44:07: #2 predicted fragment length is 129 bps INFO @ Sun, 21 Jun 2020 19:44:07: #2 alternative fragment length(s) may be 129 bps INFO @ Sun, 21 Jun 2020 19:44:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX318780/SRX318780.10_model.r INFO @ Sun, 21 Jun 2020 19:44:07: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:44:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:44:07: 5000000 INFO @ Sun, 21 Jun 2020 19:44:13: 6000000 INFO @ Sun, 21 Jun 2020 19:44:19: 7000000 INFO @ Sun, 21 Jun 2020 19:44:24: 8000000 INFO @ Sun, 21 Jun 2020 19:44:29: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:44:31: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:44:37: 10000000 INFO @ Sun, 21 Jun 2020 19:44:40: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:44:40: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:44:40: #1 total tags in treatment: 10531076 INFO @ Sun, 21 Jun 2020 19:44:40: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:44:40: #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 19:44:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX318780/SRX318780.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:44:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX318780/SRX318780.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:44:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX318780/SRX318780.10_summits.bed INFO @ Sun, 21 Jun 2020 19:44:40: Done! pass1 - making usageList (351 chroms): 1 millis pass2 - checking and writing primary data (1645 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:44:40: #1 tags after filtering in treatment: 10531071 INFO @ Sun, 21 Jun 2020 19:44:40: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:44:40: #1 finished! INFO @ Sun, 21 Jun 2020 19:44:40: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:44:40: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:44:41: #2 number of paired peaks: 395 WARNING @ Sun, 21 Jun 2020 19:44:41: Fewer paired peaks (395) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 395 pairs to build model! INFO @ Sun, 21 Jun 2020 19:44:41: start model_add_line... INFO @ Sun, 21 Jun 2020 19:44:41: start X-correlation... INFO @ Sun, 21 Jun 2020 19:44:41: end of X-cor INFO @ Sun, 21 Jun 2020 19:44:41: #2 finished! INFO @ Sun, 21 Jun 2020 19:44:41: #2 predicted fragment length is 129 bps INFO @ Sun, 21 Jun 2020 19:44:41: #2 alternative fragment length(s) may be 129 bps INFO @ Sun, 21 Jun 2020 19:44:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX318780/SRX318780.20_model.r INFO @ Sun, 21 Jun 2020 19:44:41: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:44:41: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:45:04: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:45:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX318780/SRX318780.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:45:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX318780/SRX318780.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:45:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX318780/SRX318780.20_summits.bed INFO @ Sun, 21 Jun 2020 19:45:15: Done! pass1 - making usageList (149 chroms): 1 millis pass2 - checking and writing primary data (689 records, 4 fields): 6 millis CompletedMACS2peakCalling