Job ID = 6458306 SRX = SRX5011059 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:18:07 prefetch.2.10.7: 1) Downloading 'SRR8191508'... 2020-06-21T12:18:07 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:22:36 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:22:36 prefetch.2.10.7: 1) 'SRR8191508' was downloaded successfully 2020-06-21T12:22:36 prefetch.2.10.7: 'SRR8191508' has 0 unresolved dependencies Read 43905501 spots for SRR8191508/SRR8191508.sra Written 43905501 spots for SRR8191508/SRR8191508.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: 00:00:01 Multiseed full-index search: 00:10:36 43905501 reads; of these: 43905501 (100.00%) were unpaired; of these: 4176230 (9.51%) aligned 0 times 30635855 (69.78%) aligned exactly 1 time 9093416 (20.71%) aligned >1 times 90.49% overall alignment rate Time searching: 00:10:37 Overall time: 00:10:37 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 20 files... [bam_rmdupse_core] 16003182 / 39729271 = 0.4028 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 21:41:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5011059/SRX5011059.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5011059/SRX5011059.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5011059/SRX5011059.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5011059/SRX5011059.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 21:41:41: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:41:41: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:41:47: 1000000 INFO @ Sun, 21 Jun 2020 21:41:52: 2000000 INFO @ Sun, 21 Jun 2020 21:41:58: 3000000 INFO @ Sun, 21 Jun 2020 21:42:04: 4000000 INFO @ Sun, 21 Jun 2020 21:42:09: 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 21:42:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5011059/SRX5011059.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5011059/SRX5011059.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5011059/SRX5011059.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5011059/SRX5011059.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 21:42:11: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:42:11: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:42:16: 6000000 INFO @ Sun, 21 Jun 2020 21:42:19: 1000000 INFO @ Sun, 21 Jun 2020 21:42:23: 7000000 INFO @ Sun, 21 Jun 2020 21:42:28: 2000000 INFO @ Sun, 21 Jun 2020 21:42:30: 8000000 INFO @ Sun, 21 Jun 2020 21:42:36: 3000000 INFO @ Sun, 21 Jun 2020 21:42:37: 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 @ Sun, 21 Jun 2020 21:42:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5011059/SRX5011059.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5011059/SRX5011059.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5011059/SRX5011059.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5011059/SRX5011059.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 21:42:41: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:42:41: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:42:44: 4000000 INFO @ Sun, 21 Jun 2020 21:42:45: 10000000 INFO @ Sun, 21 Jun 2020 21:42:49: 1000000 INFO @ Sun, 21 Jun 2020 21:42:52: 11000000 INFO @ Sun, 21 Jun 2020 21:42:52: 5000000 INFO @ Sun, 21 Jun 2020 21:42:56: 2000000 INFO @ Sun, 21 Jun 2020 21:42:59: 12000000 INFO @ Sun, 21 Jun 2020 21:43:00: 6000000 INFO @ Sun, 21 Jun 2020 21:43:03: 3000000 INFO @ Sun, 21 Jun 2020 21:43:06: 13000000 INFO @ Sun, 21 Jun 2020 21:43:08: 7000000 INFO @ Sun, 21 Jun 2020 21:43:10: 4000000 INFO @ Sun, 21 Jun 2020 21:43:14: 14000000 INFO @ Sun, 21 Jun 2020 21:43:16: 8000000 INFO @ Sun, 21 Jun 2020 21:43:18: 5000000 INFO @ Sun, 21 Jun 2020 21:43:21: 15000000 INFO @ Sun, 21 Jun 2020 21:43:24: 9000000 INFO @ Sun, 21 Jun 2020 21:43:25: 6000000 INFO @ Sun, 21 Jun 2020 21:43:28: 16000000 INFO @ Sun, 21 Jun 2020 21:43:32: 10000000 INFO @ Sun, 21 Jun 2020 21:43:32: 7000000 INFO @ Sun, 21 Jun 2020 21:43:36: 17000000 INFO @ Sun, 21 Jun 2020 21:43:39: 11000000 INFO @ Sun, 21 Jun 2020 21:43:40: 8000000 INFO @ Sun, 21 Jun 2020 21:43:43: 18000000 INFO @ Sun, 21 Jun 2020 21:43:47: 9000000 INFO @ Sun, 21 Jun 2020 21:43:47: 12000000 INFO @ Sun, 21 Jun 2020 21:43:50: 19000000 INFO @ Sun, 21 Jun 2020 21:43:54: 10000000 INFO @ Sun, 21 Jun 2020 21:43:55: 13000000 INFO @ Sun, 21 Jun 2020 21:43:58: 20000000 INFO @ Sun, 21 Jun 2020 21:44:01: 11000000 INFO @ Sun, 21 Jun 2020 21:44:03: 14000000 INFO @ Sun, 21 Jun 2020 21:44:05: 21000000 INFO @ Sun, 21 Jun 2020 21:44:09: 12000000 INFO @ Sun, 21 Jun 2020 21:44:11: 15000000 INFO @ Sun, 21 Jun 2020 21:44:12: 22000000 INFO @ Sun, 21 Jun 2020 21:44:16: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:44:19: 16000000 INFO @ Sun, 21 Jun 2020 21:44:20: 23000000 INFO @ Sun, 21 Jun 2020 21:44:23: 14000000 INFO @ Sun, 21 Jun 2020 21:44:25: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:44:25: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:44:25: #1 total tags in treatment: 23726089 INFO @ Sun, 21 Jun 2020 21:44:25: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:44:25: #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 21:44:26: #1 tags after filtering in treatment: 23726005 INFO @ Sun, 21 Jun 2020 21:44:26: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:44:26: #1 finished! INFO @ Sun, 21 Jun 2020 21:44:26: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:44:26: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:44:27: #2 number of paired peaks: 699 WARNING @ Sun, 21 Jun 2020 21:44:27: Fewer paired peaks (699) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 699 pairs to build model! INFO @ Sun, 21 Jun 2020 21:44:27: start model_add_line... INFO @ Sun, 21 Jun 2020 21:44:27: start X-correlation... INFO @ Sun, 21 Jun 2020 21:44:27: end of X-cor INFO @ Sun, 21 Jun 2020 21:44:27: #2 finished! INFO @ Sun, 21 Jun 2020 21:44:27: #2 predicted fragment length is 115 bps INFO @ Sun, 21 Jun 2020 21:44:27: #2 alternative fragment length(s) may be 3,115 bps INFO @ Sun, 21 Jun 2020 21:44:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5011059/SRX5011059.05_model.r INFO @ Sun, 21 Jun 2020 21:44:27: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:44:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:44:28: 17000000 INFO @ Sun, 21 Jun 2020 21:44:30: 15000000 INFO @ Sun, 21 Jun 2020 21:44:36: 18000000 INFO @ Sun, 21 Jun 2020 21:44:38: 16000000 INFO @ Sun, 21 Jun 2020 21:44:44: 19000000 INFO @ Sun, 21 Jun 2020 21:44:45: 17000000 INFO @ Sun, 21 Jun 2020 21:44:52: 18000000 INFO @ Sun, 21 Jun 2020 21:44:52: 20000000 INFO @ Sun, 21 Jun 2020 21:45:00: 19000000 INFO @ Sun, 21 Jun 2020 21:45:01: 21000000 INFO @ Sun, 21 Jun 2020 21:45:07: 20000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:45:09: 22000000 INFO @ Sun, 21 Jun 2020 21:45:12: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:45:14: 21000000 INFO @ Sun, 21 Jun 2020 21:45:17: 23000000 INFO @ Sun, 21 Jun 2020 21:45:21: 22000000 INFO @ Sun, 21 Jun 2020 21:45:23: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:45:23: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:45:23: #1 total tags in treatment: 23726089 INFO @ Sun, 21 Jun 2020 21:45:23: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:45:23: #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 21:45:24: #1 tags after filtering in treatment: 23726005 INFO @ Sun, 21 Jun 2020 21:45:24: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:45:24: #1 finished! INFO @ Sun, 21 Jun 2020 21:45:24: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:45:24: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:45:25: #2 number of paired peaks: 699 WARNING @ Sun, 21 Jun 2020 21:45:25: Fewer paired peaks (699) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 699 pairs to build model! INFO @ Sun, 21 Jun 2020 21:45:25: start model_add_line... INFO @ Sun, 21 Jun 2020 21:45:25: start X-correlation... INFO @ Sun, 21 Jun 2020 21:45:25: end of X-cor INFO @ Sun, 21 Jun 2020 21:45:25: #2 finished! INFO @ Sun, 21 Jun 2020 21:45:25: #2 predicted fragment length is 115 bps INFO @ Sun, 21 Jun 2020 21:45:25: #2 alternative fragment length(s) may be 3,115 bps INFO @ Sun, 21 Jun 2020 21:45:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5011059/SRX5011059.10_model.r INFO @ Sun, 21 Jun 2020 21:45:25: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:45:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:45:28: 23000000 INFO @ Sun, 21 Jun 2020 21:45:33: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:45:33: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:45:33: #1 total tags in treatment: 23726089 INFO @ Sun, 21 Jun 2020 21:45:33: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:45:33: #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 21:45:33: #1 tags after filtering in treatment: 23726005 INFO @ Sun, 21 Jun 2020 21:45:33: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:45:33: #1 finished! INFO @ Sun, 21 Jun 2020 21:45:33: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:45:33: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:45:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5011059/SRX5011059.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:45:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5011059/SRX5011059.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:45:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5011059/SRX5011059.05_summits.bed INFO @ Sun, 21 Jun 2020 21:45:34: Done! pass1 - making usageList (643 chroms): 2 millis pass2 - checking and writing primary data (5270 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:45:35: #2 number of paired peaks: 699 WARNING @ Sun, 21 Jun 2020 21:45:35: Fewer paired peaks (699) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 699 pairs to build model! INFO @ Sun, 21 Jun 2020 21:45:35: start model_add_line... INFO @ Sun, 21 Jun 2020 21:45:35: start X-correlation... INFO @ Sun, 21 Jun 2020 21:45:35: end of X-cor INFO @ Sun, 21 Jun 2020 21:45:35: #2 finished! INFO @ Sun, 21 Jun 2020 21:45:35: #2 predicted fragment length is 115 bps INFO @ Sun, 21 Jun 2020 21:45:35: #2 alternative fragment length(s) may be 3,115 bps INFO @ Sun, 21 Jun 2020 21:45:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5011059/SRX5011059.20_model.r INFO @ Sun, 21 Jun 2020 21:45:35: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:45:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:46:11: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:46:20: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:46:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5011059/SRX5011059.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:46:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5011059/SRX5011059.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:46:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5011059/SRX5011059.10_summits.bed INFO @ Sun, 21 Jun 2020 21:46:34: Done! pass1 - making usageList (458 chroms): 2 millis pass2 - checking and writing primary data (2337 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:46:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5011059/SRX5011059.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:46:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5011059/SRX5011059.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:46:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5011059/SRX5011059.20_summits.bed INFO @ Sun, 21 Jun 2020 21:46:41: Done! pass1 - making usageList (345 chroms): 0 millis pass2 - checking and writing primary data (1423 records, 4 fields): 11 millis CompletedMACS2peakCalling