Job ID = 6453725 SRX = SRX1433368 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:39:32 prefetch.2.10.7: 1) Downloading 'SRR2919833'... 2020-06-21T08:39:32 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:43:11 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:43:12 prefetch.2.10.7: 'SRR2919833' is valid 2020-06-21T08:43:12 prefetch.2.10.7: 1) 'SRR2919833' was downloaded successfully Read 23440045 spots for SRR2919833/SRR2919833.sra Written 23440045 spots for SRR2919833/SRR2919833.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: 00:06:19 23440045 reads; of these: 23440045 (100.00%) were unpaired; of these: 1202745 (5.13%) aligned 0 times 17152019 (73.17%) aligned exactly 1 time 5085281 (21.69%) aligned >1 times 94.87% overall alignment rate Time searching: 00:06:19 Overall time: 00:06:19 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] 5261784 / 22237300 = 0.2366 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 17:54:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1433368/SRX1433368.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1433368/SRX1433368.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1433368/SRX1433368.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1433368/SRX1433368.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 17:54:52: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:54:52: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:54:57: 1000000 INFO @ Sun, 21 Jun 2020 17:55:03: 2000000 INFO @ Sun, 21 Jun 2020 17:55:08: 3000000 INFO @ Sun, 21 Jun 2020 17:55:13: 4000000 INFO @ Sun, 21 Jun 2020 17:55:19: 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 17:55:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1433368/SRX1433368.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1433368/SRX1433368.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1433368/SRX1433368.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1433368/SRX1433368.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 17:55:22: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:55:22: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:55:25: 6000000 INFO @ Sun, 21 Jun 2020 17:55:29: 1000000 INFO @ Sun, 21 Jun 2020 17:55:31: 7000000 INFO @ Sun, 21 Jun 2020 17:55:35: 2000000 INFO @ Sun, 21 Jun 2020 17:55:38: 8000000 INFO @ Sun, 21 Jun 2020 17:55:42: 3000000 INFO @ Sun, 21 Jun 2020 17:55:44: 9000000 INFO @ Sun, 21 Jun 2020 17:55:48: 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 17:55:51: 10000000 INFO @ Sun, 21 Jun 2020 17:55:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1433368/SRX1433368.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1433368/SRX1433368.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1433368/SRX1433368.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1433368/SRX1433368.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 17:55:52: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:55:52: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:55:55: 5000000 INFO @ Sun, 21 Jun 2020 17:55:58: 11000000 INFO @ Sun, 21 Jun 2020 17:55:59: 1000000 INFO @ Sun, 21 Jun 2020 17:56:02: 6000000 INFO @ Sun, 21 Jun 2020 17:56:04: 12000000 INFO @ Sun, 21 Jun 2020 17:56:06: 2000000 INFO @ Sun, 21 Jun 2020 17:56:09: 7000000 INFO @ Sun, 21 Jun 2020 17:56:11: 13000000 INFO @ Sun, 21 Jun 2020 17:56:13: 3000000 INFO @ Sun, 21 Jun 2020 17:56:16: 8000000 INFO @ Sun, 21 Jun 2020 17:56:19: 14000000 INFO @ Sun, 21 Jun 2020 17:56:21: 4000000 INFO @ Sun, 21 Jun 2020 17:56:22: 9000000 INFO @ Sun, 21 Jun 2020 17:56:25: 15000000 INFO @ Sun, 21 Jun 2020 17:56:28: 5000000 INFO @ Sun, 21 Jun 2020 17:56:29: 10000000 INFO @ Sun, 21 Jun 2020 17:56:32: 16000000 INFO @ Sun, 21 Jun 2020 17:56:35: 6000000 INFO @ Sun, 21 Jun 2020 17:56:36: 11000000 INFO @ Sun, 21 Jun 2020 17:56:39: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 17:56:39: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 17:56:39: #1 total tags in treatment: 16975516 INFO @ Sun, 21 Jun 2020 17:56:39: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:56:39: #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 17:56:40: #1 tags after filtering in treatment: 16975440 INFO @ Sun, 21 Jun 2020 17:56:40: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:56:40: #1 finished! INFO @ Sun, 21 Jun 2020 17:56:40: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:56:40: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:56:41: #2 number of paired peaks: 364 WARNING @ Sun, 21 Jun 2020 17:56:41: Fewer paired peaks (364) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 364 pairs to build model! INFO @ Sun, 21 Jun 2020 17:56:41: start model_add_line... INFO @ Sun, 21 Jun 2020 17:56:41: start X-correlation... INFO @ Sun, 21 Jun 2020 17:56:41: end of X-cor INFO @ Sun, 21 Jun 2020 17:56:41: #2 finished! INFO @ Sun, 21 Jun 2020 17:56:41: #2 predicted fragment length is 131 bps INFO @ Sun, 21 Jun 2020 17:56:41: #2 alternative fragment length(s) may be 4,120,131 bps INFO @ Sun, 21 Jun 2020 17:56:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1433368/SRX1433368.05_model.r INFO @ Sun, 21 Jun 2020 17:56:41: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:56:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:56:42: 7000000 INFO @ Sun, 21 Jun 2020 17:56:43: 12000000 INFO @ Sun, 21 Jun 2020 17:56:49: 13000000 INFO @ Sun, 21 Jun 2020 17:56:49: 8000000 INFO @ Sun, 21 Jun 2020 17:56:56: 14000000 INFO @ Sun, 21 Jun 2020 17:56:57: 9000000 INFO @ Sun, 21 Jun 2020 17:57:03: 15000000 INFO @ Sun, 21 Jun 2020 17:57:04: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:57:09: 16000000 INFO @ Sun, 21 Jun 2020 17:57:11: 11000000 INFO @ Sun, 21 Jun 2020 17:57:14: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:57:16: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 17:57:16: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 17:57:16: #1 total tags in treatment: 16975516 INFO @ Sun, 21 Jun 2020 17:57:16: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:57:16: #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 17:57:17: #1 tags after filtering in treatment: 16975440 INFO @ Sun, 21 Jun 2020 17:57:17: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:57:17: #1 finished! INFO @ Sun, 21 Jun 2020 17:57:17: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:57:17: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:57:18: #2 number of paired peaks: 364 WARNING @ Sun, 21 Jun 2020 17:57:18: Fewer paired peaks (364) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 364 pairs to build model! INFO @ Sun, 21 Jun 2020 17:57:18: start model_add_line... INFO @ Sun, 21 Jun 2020 17:57:18: start X-correlation... INFO @ Sun, 21 Jun 2020 17:57:18: end of X-cor INFO @ Sun, 21 Jun 2020 17:57:18: #2 finished! INFO @ Sun, 21 Jun 2020 17:57:18: #2 predicted fragment length is 131 bps INFO @ Sun, 21 Jun 2020 17:57:18: #2 alternative fragment length(s) may be 4,120,131 bps INFO @ Sun, 21 Jun 2020 17:57:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1433368/SRX1433368.10_model.r INFO @ Sun, 21 Jun 2020 17:57:18: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:57:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:57:18: 12000000 INFO @ Sun, 21 Jun 2020 17:57:25: 13000000 INFO @ Sun, 21 Jun 2020 17:57:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1433368/SRX1433368.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:57:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1433368/SRX1433368.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:57:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1433368/SRX1433368.05_summits.bed INFO @ Sun, 21 Jun 2020 17:57:30: Done! pass1 - making usageList (528 chroms): 1 millis pass2 - checking and writing primary data (3088 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:57:32: 14000000 INFO @ Sun, 21 Jun 2020 17:57:38: 15000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:57:45: 16000000 INFO @ Sun, 21 Jun 2020 17:57:51: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:57:51: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 17:57:51: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 17:57:51: #1 total tags in treatment: 16975516 INFO @ Sun, 21 Jun 2020 17:57:51: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:57:51: #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 17:57:52: #1 tags after filtering in treatment: 16975440 INFO @ Sun, 21 Jun 2020 17:57:52: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:57:52: #1 finished! INFO @ Sun, 21 Jun 2020 17:57:52: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:57:52: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:57:53: #2 number of paired peaks: 364 WARNING @ Sun, 21 Jun 2020 17:57:53: Fewer paired peaks (364) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 364 pairs to build model! INFO @ Sun, 21 Jun 2020 17:57:53: start model_add_line... INFO @ Sun, 21 Jun 2020 17:57:53: start X-correlation... INFO @ Sun, 21 Jun 2020 17:57:53: end of X-cor INFO @ Sun, 21 Jun 2020 17:57:53: #2 finished! INFO @ Sun, 21 Jun 2020 17:57:53: #2 predicted fragment length is 131 bps INFO @ Sun, 21 Jun 2020 17:57:53: #2 alternative fragment length(s) may be 4,120,131 bps INFO @ Sun, 21 Jun 2020 17:57:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1433368/SRX1433368.20_model.r INFO @ Sun, 21 Jun 2020 17:57:53: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:57:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:58:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1433368/SRX1433368.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:58:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1433368/SRX1433368.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:58:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1433368/SRX1433368.10_summits.bed INFO @ Sun, 21 Jun 2020 17:58:07: Done! pass1 - making usageList (423 chroms): 2 millis pass2 - checking and writing primary data (1845 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:58:27: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:58:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1433368/SRX1433368.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:58:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1433368/SRX1433368.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:58:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1433368/SRX1433368.20_summits.bed INFO @ Sun, 21 Jun 2020 17:58:44: Done! pass1 - making usageList (228 chroms): 1 millis pass2 - checking and writing primary data (826 records, 4 fields): 7 millis CompletedMACS2peakCalling