Job ID = 6457863 SRX = SRX481129 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:59:48 prefetch.2.10.7: 1) Downloading 'SRR1182752'... 2020-06-21T11:59:48 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:04:32 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:04:33 prefetch.2.10.7: 'SRR1182752' is valid 2020-06-21T12:04:33 prefetch.2.10.7: 1) 'SRR1182752' was downloaded successfully Read 16333147 spots for SRR1182752/SRR1182752.sra Written 16333147 spots for SRR1182752/SRR1182752.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: 00:03:50 16333147 reads; of these: 16333147 (100.00%) were unpaired; of these: 703824 (4.31%) aligned 0 times 13834531 (84.70%) aligned exactly 1 time 1794792 (10.99%) aligned >1 times 95.69% overall alignment rate Time searching: 00:03:50 Overall time: 00:03:50 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] 1671146 / 15629323 = 0.1069 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 21:13:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX481129/SRX481129.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX481129/SRX481129.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX481129/SRX481129.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX481129/SRX481129.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 21:13:47: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:13:47: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:13:53: 1000000 INFO @ Sun, 21 Jun 2020 21:14:00: 2000000 INFO @ Sun, 21 Jun 2020 21:14:06: 3000000 INFO @ Sun, 21 Jun 2020 21:14:13: 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 21:14:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX481129/SRX481129.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX481129/SRX481129.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX481129/SRX481129.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX481129/SRX481129.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 21:14:17: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:14:17: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:14:19: 5000000 INFO @ Sun, 21 Jun 2020 21:14:25: 1000000 INFO @ Sun, 21 Jun 2020 21:14:26: 6000000 INFO @ Sun, 21 Jun 2020 21:14:33: 2000000 INFO @ Sun, 21 Jun 2020 21:14:34: 7000000 INFO @ Sun, 21 Jun 2020 21:14:41: 8000000 INFO @ Sun, 21 Jun 2020 21:14:41: 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 21:14:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX481129/SRX481129.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX481129/SRX481129.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX481129/SRX481129.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX481129/SRX481129.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 21:14:47: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:14:47: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:14:48: 9000000 INFO @ Sun, 21 Jun 2020 21:14:49: 4000000 INFO @ Sun, 21 Jun 2020 21:14:55: 1000000 INFO @ Sun, 21 Jun 2020 21:14:56: 10000000 INFO @ Sun, 21 Jun 2020 21:14:57: 5000000 INFO @ Sun, 21 Jun 2020 21:15:03: 11000000 INFO @ Sun, 21 Jun 2020 21:15:04: 2000000 INFO @ Sun, 21 Jun 2020 21:15:05: 6000000 INFO @ Sun, 21 Jun 2020 21:15:11: 12000000 INFO @ Sun, 21 Jun 2020 21:15:12: 3000000 INFO @ Sun, 21 Jun 2020 21:15:13: 7000000 INFO @ Sun, 21 Jun 2020 21:15:18: 13000000 INFO @ Sun, 21 Jun 2020 21:15:20: 4000000 INFO @ Sun, 21 Jun 2020 21:15:22: 8000000 INFO @ Sun, 21 Jun 2020 21:15:26: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:15:26: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:15:26: #1 total tags in treatment: 13958177 INFO @ Sun, 21 Jun 2020 21:15:26: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:15:26: #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 21:15:26: #1 tags after filtering in treatment: 13958144 INFO @ Sun, 21 Jun 2020 21:15:26: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:15:26: #1 finished! INFO @ Sun, 21 Jun 2020 21:15:26: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:15:26: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:15:27: #2 number of paired peaks: 697 WARNING @ Sun, 21 Jun 2020 21:15:27: Fewer paired peaks (697) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 697 pairs to build model! INFO @ Sun, 21 Jun 2020 21:15:27: start model_add_line... INFO @ Sun, 21 Jun 2020 21:15:27: start X-correlation... INFO @ Sun, 21 Jun 2020 21:15:27: end of X-cor INFO @ Sun, 21 Jun 2020 21:15:27: #2 finished! INFO @ Sun, 21 Jun 2020 21:15:27: #2 predicted fragment length is 202 bps INFO @ Sun, 21 Jun 2020 21:15:27: #2 alternative fragment length(s) may be 202 bps INFO @ Sun, 21 Jun 2020 21:15:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX481129/SRX481129.05_model.r INFO @ Sun, 21 Jun 2020 21:15:27: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:15:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:15:28: 5000000 INFO @ Sun, 21 Jun 2020 21:15:29: 9000000 INFO @ Sun, 21 Jun 2020 21:15:35: 6000000 INFO @ Sun, 21 Jun 2020 21:15:37: 10000000 INFO @ Sun, 21 Jun 2020 21:15:43: 7000000 INFO @ Sun, 21 Jun 2020 21:15:45: 11000000 INFO @ Sun, 21 Jun 2020 21:15:51: 8000000 INFO @ Sun, 21 Jun 2020 21:15:53: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:15:59: 9000000 INFO @ Sun, 21 Jun 2020 21:15:59: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:16:01: 13000000 INFO @ Sun, 21 Jun 2020 21:16:06: 10000000 INFO @ Sun, 21 Jun 2020 21:16:08: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:16:08: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:16:08: #1 total tags in treatment: 13958177 INFO @ Sun, 21 Jun 2020 21:16:08: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:16:08: #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 21:16:09: #1 tags after filtering in treatment: 13958144 INFO @ Sun, 21 Jun 2020 21:16:09: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:16:09: #1 finished! INFO @ Sun, 21 Jun 2020 21:16:09: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:16:09: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:16:10: #2 number of paired peaks: 697 WARNING @ Sun, 21 Jun 2020 21:16:10: Fewer paired peaks (697) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 697 pairs to build model! INFO @ Sun, 21 Jun 2020 21:16:10: start model_add_line... INFO @ Sun, 21 Jun 2020 21:16:10: start X-correlation... INFO @ Sun, 21 Jun 2020 21:16:10: end of X-cor INFO @ Sun, 21 Jun 2020 21:16:10: #2 finished! INFO @ Sun, 21 Jun 2020 21:16:10: #2 predicted fragment length is 202 bps INFO @ Sun, 21 Jun 2020 21:16:10: #2 alternative fragment length(s) may be 202 bps INFO @ Sun, 21 Jun 2020 21:16:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX481129/SRX481129.10_model.r INFO @ Sun, 21 Jun 2020 21:16:10: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:16:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:16:14: 11000000 INFO @ Sun, 21 Jun 2020 21:16:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX481129/SRX481129.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:16:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX481129/SRX481129.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:16:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX481129/SRX481129.05_summits.bed INFO @ Sun, 21 Jun 2020 21:16:16: Done! pass1 - making usageList (128 chroms): 1 millis pass2 - checking and writing primary data (6312 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:16:21: 12000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:16:28: 13000000 INFO @ Sun, 21 Jun 2020 21:16:35: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:16:35: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:16:35: #1 total tags in treatment: 13958177 INFO @ Sun, 21 Jun 2020 21:16:35: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:16:35: #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 21:16:35: #1 tags after filtering in treatment: 13958144 INFO @ Sun, 21 Jun 2020 21:16:35: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:16:35: #1 finished! INFO @ Sun, 21 Jun 2020 21:16:35: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:16:35: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:16:36: #2 number of paired peaks: 697 WARNING @ Sun, 21 Jun 2020 21:16:36: Fewer paired peaks (697) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 697 pairs to build model! INFO @ Sun, 21 Jun 2020 21:16:36: start model_add_line... INFO @ Sun, 21 Jun 2020 21:16:36: start X-correlation... INFO @ Sun, 21 Jun 2020 21:16:37: end of X-cor INFO @ Sun, 21 Jun 2020 21:16:37: #2 finished! INFO @ Sun, 21 Jun 2020 21:16:37: #2 predicted fragment length is 202 bps INFO @ Sun, 21 Jun 2020 21:16:37: #2 alternative fragment length(s) may be 202 bps INFO @ Sun, 21 Jun 2020 21:16:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX481129/SRX481129.20_model.r INFO @ Sun, 21 Jun 2020 21:16:37: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:16:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:16:43: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:17:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX481129/SRX481129.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:17:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX481129/SRX481129.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:17:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX481129/SRX481129.10_summits.bed INFO @ Sun, 21 Jun 2020 21:17:00: Done! pass1 - making usageList (110 chroms): 1 millis pass2 - checking and writing primary data (4534 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:17:11: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:17:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX481129/SRX481129.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:17:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX481129/SRX481129.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:17:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX481129/SRX481129.20_summits.bed INFO @ Sun, 21 Jun 2020 21:17:28: Done! pass1 - making usageList (84 chroms): 1 millis pass2 - checking and writing primary data (2779 records, 4 fields): 7 millis CompletedMACS2peakCalling