Job ID = 6459465 SRX = SRX681824 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T13:17:17 prefetch.2.10.7: 1) Downloading 'SRR1552293'... 2020-06-21T13:17:17 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:25:32 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:25:32 prefetch.2.10.7: 1) 'SRR1552293' was downloaded successfully Read 40635891 spots for SRR1552293/SRR1552293.sra Written 40635891 spots for SRR1552293/SRR1552293.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: 00:08:45 40635891 reads; of these: 40635891 (100.00%) were unpaired; of these: 8160628 (20.08%) aligned 0 times 28770404 (70.80%) aligned exactly 1 time 3704859 (9.12%) aligned >1 times 79.92% overall alignment rate Time searching: 00:08:45 Overall time: 00:08:45 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 16 files... [bam_rmdupse_core] 12788632 / 32475263 = 0.3938 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 22:43:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX681824/SRX681824.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX681824/SRX681824.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX681824/SRX681824.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX681824/SRX681824.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 22:43:38: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:43:38: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:43:44: 1000000 INFO @ Sun, 21 Jun 2020 22:43:50: 2000000 INFO @ Sun, 21 Jun 2020 22:43:56: 3000000 INFO @ Sun, 21 Jun 2020 22:44:02: 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 22:44:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX681824/SRX681824.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX681824/SRX681824.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX681824/SRX681824.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX681824/SRX681824.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 22:44:08: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:44:08: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:44:08: 5000000 INFO @ Sun, 21 Jun 2020 22:44:15: 6000000 INFO @ Sun, 21 Jun 2020 22:44:16: 1000000 INFO @ Sun, 21 Jun 2020 22:44:23: 7000000 INFO @ Sun, 21 Jun 2020 22:44:23: 2000000 INFO @ Sun, 21 Jun 2020 22:44:30: 8000000 INFO @ Sun, 21 Jun 2020 22:44:31: 3000000 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 22:44:37: 9000000 INFO @ Sun, 21 Jun 2020 22:44:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX681824/SRX681824.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX681824/SRX681824.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX681824/SRX681824.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX681824/SRX681824.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 22:44:38: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:44:38: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:44:38: 4000000 INFO @ Sun, 21 Jun 2020 22:44:45: 10000000 INFO @ Sun, 21 Jun 2020 22:44:45: 1000000 INFO @ Sun, 21 Jun 2020 22:44:46: 5000000 INFO @ Sun, 21 Jun 2020 22:44:52: 11000000 INFO @ Sun, 21 Jun 2020 22:44:53: 2000000 INFO @ Sun, 21 Jun 2020 22:44:53: 6000000 INFO @ Sun, 21 Jun 2020 22:44:59: 12000000 INFO @ Sun, 21 Jun 2020 22:45:00: 3000000 INFO @ Sun, 21 Jun 2020 22:45:01: 7000000 INFO @ Sun, 21 Jun 2020 22:45:07: 13000000 INFO @ Sun, 21 Jun 2020 22:45:07: 4000000 INFO @ Sun, 21 Jun 2020 22:45:08: 8000000 INFO @ Sun, 21 Jun 2020 22:45:14: 14000000 INFO @ Sun, 21 Jun 2020 22:45:15: 5000000 INFO @ Sun, 21 Jun 2020 22:45:16: 9000000 INFO @ Sun, 21 Jun 2020 22:45:21: 15000000 INFO @ Sun, 21 Jun 2020 22:45:22: 6000000 INFO @ Sun, 21 Jun 2020 22:45:23: 10000000 INFO @ Sun, 21 Jun 2020 22:45:29: 16000000 INFO @ Sun, 21 Jun 2020 22:45:29: 7000000 INFO @ Sun, 21 Jun 2020 22:45:31: 11000000 INFO @ Sun, 21 Jun 2020 22:45:37: 8000000 INFO @ Sun, 21 Jun 2020 22:45:37: 17000000 INFO @ Sun, 21 Jun 2020 22:45:38: 12000000 INFO @ Sun, 21 Jun 2020 22:45:44: 9000000 INFO @ Sun, 21 Jun 2020 22:45:44: 18000000 INFO @ Sun, 21 Jun 2020 22:45:45: 13000000 INFO @ Sun, 21 Jun 2020 22:45:51: 10000000 INFO @ Sun, 21 Jun 2020 22:45:52: 19000000 INFO @ Sun, 21 Jun 2020 22:45:53: 14000000 INFO @ Sun, 21 Jun 2020 22:45:57: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:45:57: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:45:57: #1 total tags in treatment: 19686631 INFO @ Sun, 21 Jun 2020 22:45:57: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:45:57: #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 22:45:58: #1 tags after filtering in treatment: 19686624 INFO @ Sun, 21 Jun 2020 22:45:58: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:45:58: #1 finished! INFO @ Sun, 21 Jun 2020 22:45:58: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:45:58: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:45:58: 11000000 INFO @ Sun, 21 Jun 2020 22:45:59: #2 number of paired peaks: 345 WARNING @ Sun, 21 Jun 2020 22:45:59: Fewer paired peaks (345) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 345 pairs to build model! INFO @ Sun, 21 Jun 2020 22:45:59: start model_add_line... INFO @ Sun, 21 Jun 2020 22:45:59: start X-correlation... INFO @ Sun, 21 Jun 2020 22:45:59: end of X-cor INFO @ Sun, 21 Jun 2020 22:45:59: #2 finished! INFO @ Sun, 21 Jun 2020 22:45:59: #2 predicted fragment length is 155 bps INFO @ Sun, 21 Jun 2020 22:45:59: #2 alternative fragment length(s) may be 155 bps INFO @ Sun, 21 Jun 2020 22:45:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX681824/SRX681824.05_model.r INFO @ Sun, 21 Jun 2020 22:45:59: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:45:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:46:00: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:46:06: 12000000 INFO @ Sun, 21 Jun 2020 22:46:08: 16000000 INFO @ Sun, 21 Jun 2020 22:46:13: 13000000 INFO @ Sun, 21 Jun 2020 22:46:15: 17000000 INFO @ Sun, 21 Jun 2020 22:46:20: 14000000 INFO @ Sun, 21 Jun 2020 22:46:22: 18000000 INFO @ Sun, 21 Jun 2020 22:46:27: 15000000 INFO @ Sun, 21 Jun 2020 22:46:30: 19000000 INFO @ Sun, 21 Jun 2020 22:46:34: 16000000 INFO @ Sun, 21 Jun 2020 22:46:35: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:46:35: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:46:35: #1 total tags in treatment: 19686631 INFO @ Sun, 21 Jun 2020 22:46:35: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:46:35: #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 22:46:36: #1 tags after filtering in treatment: 19686624 INFO @ Sun, 21 Jun 2020 22:46:36: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:46:36: #1 finished! INFO @ Sun, 21 Jun 2020 22:46:36: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:46:36: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:46:37: #2 number of paired peaks: 345 WARNING @ Sun, 21 Jun 2020 22:46:37: Fewer paired peaks (345) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 345 pairs to build model! INFO @ Sun, 21 Jun 2020 22:46:37: start model_add_line... INFO @ Sun, 21 Jun 2020 22:46:37: start X-correlation... INFO @ Sun, 21 Jun 2020 22:46:37: end of X-cor INFO @ Sun, 21 Jun 2020 22:46:37: #2 finished! INFO @ Sun, 21 Jun 2020 22:46:37: #2 predicted fragment length is 155 bps INFO @ Sun, 21 Jun 2020 22:46:37: #2 alternative fragment length(s) may be 155 bps INFO @ Sun, 21 Jun 2020 22:46:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX681824/SRX681824.10_model.r INFO @ Sun, 21 Jun 2020 22:46:37: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:46:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:46:41: 17000000 INFO @ Sun, 21 Jun 2020 22:46:43: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:46:47: 18000000 INFO @ Sun, 21 Jun 2020 22:46:54: 19000000 INFO @ Sun, 21 Jun 2020 22:46:58: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:46:58: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:46:58: #1 total tags in treatment: 19686631 INFO @ Sun, 21 Jun 2020 22:46:58: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:46:58: #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 22:46:59: #1 tags after filtering in treatment: 19686624 INFO @ Sun, 21 Jun 2020 22:46:59: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:46:59: #1 finished! INFO @ Sun, 21 Jun 2020 22:46:59: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:46:59: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:47:00: #2 number of paired peaks: 345 WARNING @ Sun, 21 Jun 2020 22:47:00: Fewer paired peaks (345) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 345 pairs to build model! INFO @ Sun, 21 Jun 2020 22:47:00: start model_add_line... INFO @ Sun, 21 Jun 2020 22:47:01: start X-correlation... INFO @ Sun, 21 Jun 2020 22:47:01: end of X-cor INFO @ Sun, 21 Jun 2020 22:47:01: #2 finished! INFO @ Sun, 21 Jun 2020 22:47:01: #2 predicted fragment length is 155 bps INFO @ Sun, 21 Jun 2020 22:47:01: #2 alternative fragment length(s) may be 155 bps INFO @ Sun, 21 Jun 2020 22:47:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX681824/SRX681824.20_model.r INFO @ Sun, 21 Jun 2020 22:47:01: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:47:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:47:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX681824/SRX681824.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:47:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX681824/SRX681824.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:47:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX681824/SRX681824.05_summits.bed INFO @ Sun, 21 Jun 2020 22:47:07: Done! pass1 - making usageList (334 chroms): 4 millis pass2 - checking and writing primary data (29012 records, 4 fields): 37 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:47:22: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:47:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX681824/SRX681824.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:47:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX681824/SRX681824.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:47:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX681824/SRX681824.10_summits.bed INFO @ Sun, 21 Jun 2020 22:47:46: Done! pass1 - making usageList (252 chroms): 3 millis pass2 - checking and writing primary data (14712 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:47:47: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:48:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX681824/SRX681824.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:48:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX681824/SRX681824.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:48:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX681824/SRX681824.20_summits.bed INFO @ Sun, 21 Jun 2020 22:48:11: Done! pass1 - making usageList (140 chroms): 1 millis pass2 - checking and writing primary data (4725 records, 4 fields): 11 millis CompletedMACS2peakCalling