Job ID = 6459885 SRX = SRX969917 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T13:46:34 prefetch.2.10.7: 1) Downloading 'SRR1931633'... 2020-06-21T13:46:34 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:48:17 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:48:18 prefetch.2.10.7: 'SRR1931633' is valid 2020-06-21T13:48:18 prefetch.2.10.7: 1) 'SRR1931633' was downloaded successfully Read 16439552 spots for SRR1931633/SRR1931633.sra Written 16439552 spots for SRR1931633/SRR1931633.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: 00:04:32 16439552 reads; of these: 16439552 (100.00%) were unpaired; of these: 699812 (4.26%) aligned 0 times 12451515 (75.74%) aligned exactly 1 time 3288225 (20.00%) aligned >1 times 95.74% overall alignment rate Time searching: 00:04:32 Overall time: 00:04:32 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] 2118206 / 15739740 = 0.1346 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 22:57:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX969917/SRX969917.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX969917/SRX969917.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX969917/SRX969917.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX969917/SRX969917.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 22:57:49: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:57:49: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:57:54: 1000000 INFO @ Sun, 21 Jun 2020 22:57:59: 2000000 INFO @ Sun, 21 Jun 2020 22:58:05: 3000000 INFO @ Sun, 21 Jun 2020 22:58:10: 4000000 INFO @ Sun, 21 Jun 2020 22:58:15: 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 22:58:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX969917/SRX969917.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX969917/SRX969917.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX969917/SRX969917.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX969917/SRX969917.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 22:58:19: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:58:19: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:58:20: 6000000 INFO @ Sun, 21 Jun 2020 22:58:25: 1000000 INFO @ Sun, 21 Jun 2020 22:58:26: 7000000 INFO @ Sun, 21 Jun 2020 22:58:30: 2000000 INFO @ Sun, 21 Jun 2020 22:58:31: 8000000 INFO @ Sun, 21 Jun 2020 22:58:36: 3000000 INFO @ Sun, 21 Jun 2020 22:58:37: 9000000 INFO @ Sun, 21 Jun 2020 22:58:42: 4000000 INFO @ Sun, 21 Jun 2020 22:58:42: 10000000 INFO @ Sun, 21 Jun 2020 22:58:47: 5000000 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 22:58:47: 11000000 INFO @ Sun, 21 Jun 2020 22:58:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX969917/SRX969917.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX969917/SRX969917.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX969917/SRX969917.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX969917/SRX969917.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 22:58:49: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:58:49: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:58:53: 6000000 INFO @ Sun, 21 Jun 2020 22:58:53: 12000000 INFO @ Sun, 21 Jun 2020 22:58:55: 1000000 INFO @ Sun, 21 Jun 2020 22:58:58: 7000000 INFO @ Sun, 21 Jun 2020 22:58:59: 13000000 INFO @ Sun, 21 Jun 2020 22:59:00: 2000000 INFO @ Sun, 21 Jun 2020 22:59:03: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:59:03: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:59:03: #1 total tags in treatment: 13621534 INFO @ Sun, 21 Jun 2020 22:59:03: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:59:03: #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 22:59:03: #1 tags after filtering in treatment: 13621478 INFO @ Sun, 21 Jun 2020 22:59:03: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:59:03: #1 finished! INFO @ Sun, 21 Jun 2020 22:59:03: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:59:03: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:59:04: 8000000 INFO @ Sun, 21 Jun 2020 22:59:04: #2 number of paired peaks: 372 WARNING @ Sun, 21 Jun 2020 22:59:04: Fewer paired peaks (372) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 372 pairs to build model! INFO @ Sun, 21 Jun 2020 22:59:04: start model_add_line... INFO @ Sun, 21 Jun 2020 22:59:04: start X-correlation... INFO @ Sun, 21 Jun 2020 22:59:04: end of X-cor INFO @ Sun, 21 Jun 2020 22:59:04: #2 finished! INFO @ Sun, 21 Jun 2020 22:59:04: #2 predicted fragment length is 174 bps INFO @ Sun, 21 Jun 2020 22:59:04: #2 alternative fragment length(s) may be 174 bps INFO @ Sun, 21 Jun 2020 22:59:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX969917/SRX969917.05_model.r INFO @ Sun, 21 Jun 2020 22:59:04: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:59:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:59:06: 3000000 INFO @ Sun, 21 Jun 2020 22:59:09: 9000000 INFO @ Sun, 21 Jun 2020 22:59:11: 4000000 INFO @ Sun, 21 Jun 2020 22:59:15: 10000000 INFO @ Sun, 21 Jun 2020 22:59:17: 5000000 INFO @ Sun, 21 Jun 2020 22:59:21: 11000000 INFO @ Sun, 21 Jun 2020 22:59:23: 6000000 INFO @ Sun, 21 Jun 2020 22:59:26: 12000000 INFO @ Sun, 21 Jun 2020 22:59:28: 7000000 INFO @ Sun, 21 Jun 2020 22:59:32: 13000000 INFO @ Sun, 21 Jun 2020 22:59:32: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:59:34: 8000000 INFO @ Sun, 21 Jun 2020 22:59:36: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:59:36: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:59:36: #1 total tags in treatment: 13621534 INFO @ Sun, 21 Jun 2020 22:59:36: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:59:36: #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 22:59:36: #1 tags after filtering in treatment: 13621478 INFO @ Sun, 21 Jun 2020 22:59:36: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:59:36: #1 finished! INFO @ Sun, 21 Jun 2020 22:59:36: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:59:36: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:59:37: #2 number of paired peaks: 372 WARNING @ Sun, 21 Jun 2020 22:59:37: Fewer paired peaks (372) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 372 pairs to build model! INFO @ Sun, 21 Jun 2020 22:59:37: start model_add_line... INFO @ Sun, 21 Jun 2020 22:59:37: start X-correlation... INFO @ Sun, 21 Jun 2020 22:59:37: end of X-cor INFO @ Sun, 21 Jun 2020 22:59:37: #2 finished! INFO @ Sun, 21 Jun 2020 22:59:37: #2 predicted fragment length is 174 bps INFO @ Sun, 21 Jun 2020 22:59:37: #2 alternative fragment length(s) may be 174 bps INFO @ Sun, 21 Jun 2020 22:59:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX969917/SRX969917.10_model.r INFO @ Sun, 21 Jun 2020 22:59:37: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:59:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:59:39: 9000000 INFO @ Sun, 21 Jun 2020 22:59:44: 10000000 INFO @ Sun, 21 Jun 2020 22:59:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX969917/SRX969917.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:59:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX969917/SRX969917.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:59:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX969917/SRX969917.05_summits.bed INFO @ Sun, 21 Jun 2020 22:59:46: Done! pass1 - making usageList (400 chroms): 1 millis pass2 - checking and writing primary data (4393 records, 4 fields): 14 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:59:49: 11000000 INFO @ Sun, 21 Jun 2020 22:59:55: 12000000 INFO @ Sun, 21 Jun 2020 23:00:00: 13000000 INFO @ Sun, 21 Jun 2020 23:00:03: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 23:00:03: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 23:00:03: #1 total tags in treatment: 13621534 INFO @ Sun, 21 Jun 2020 23:00:03: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 23:00:03: #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 23:00:04: #1 tags after filtering in treatment: 13621478 INFO @ Sun, 21 Jun 2020 23:00:04: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 23:00:04: #1 finished! INFO @ Sun, 21 Jun 2020 23:00:04: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 23:00:04: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 23:00:05: #2 number of paired peaks: 372 WARNING @ Sun, 21 Jun 2020 23:00:05: Fewer paired peaks (372) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 372 pairs to build model! INFO @ Sun, 21 Jun 2020 23:00:05: start model_add_line... INFO @ Sun, 21 Jun 2020 23:00:05: start X-correlation... INFO @ Sun, 21 Jun 2020 23:00:05: end of X-cor INFO @ Sun, 21 Jun 2020 23:00:05: #2 finished! INFO @ Sun, 21 Jun 2020 23:00:05: #2 predicted fragment length is 174 bps INFO @ Sun, 21 Jun 2020 23:00:05: #2 alternative fragment length(s) may be 174 bps INFO @ Sun, 21 Jun 2020 23:00:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX969917/SRX969917.20_model.r INFO @ Sun, 21 Jun 2020 23:00:05: #3 Call peaks... INFO @ Sun, 21 Jun 2020 23:00:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 23:00:07: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 23:00:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX969917/SRX969917.10_peaks.xls INFO @ Sun, 21 Jun 2020 23:00:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX969917/SRX969917.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 23:00:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX969917/SRX969917.10_summits.bed INFO @ Sun, 21 Jun 2020 23:00:23: Done! pass1 - making usageList (297 chroms): 1 millis pass2 - checking and writing primary data (2646 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 23:00:33: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 23:00:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX969917/SRX969917.20_peaks.xls INFO @ Sun, 21 Jun 2020 23:00:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX969917/SRX969917.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 23:00:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX969917/SRX969917.20_summits.bed INFO @ Sun, 21 Jun 2020 23:00:46: Done! pass1 - making usageList (198 chroms): 1 millis pass2 - checking and writing primary data (1274 records, 4 fields): 7 millis CompletedMACS2peakCalling