Job ID = 5720612 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 15,062,772 reads read : 15,062,772 reads written : 15,062,772 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR5289730.sra.cache’: No such file or directory 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: 00:06:08 15062772 reads; of these: 15062772 (100.00%) were unpaired; of these: 1798684 (11.94%) aligned 0 times 8588487 (57.02%) aligned exactly 1 time 4675601 (31.04%) aligned >1 times 88.06% overall alignment rate Time searching: 00:06:08 Overall time: 00:06:08 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 3966067 / 13264088 = 0.2990 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 @ Thu, 16 Apr 2020 00:54:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592453/SRX2592453.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592453/SRX2592453.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592453/SRX2592453.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592453/SRX2592453.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 @ Thu, 16 Apr 2020 00:54:47: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:54:47: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:54:52: 1000000 INFO @ Thu, 16 Apr 2020 00:54:57: 2000000 INFO @ Thu, 16 Apr 2020 00:55:03: 3000000 INFO @ Thu, 16 Apr 2020 00:55:08: 4000000 INFO @ Thu, 16 Apr 2020 00:55:13: 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 @ Thu, 16 Apr 2020 00:55:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592453/SRX2592453.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592453/SRX2592453.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592453/SRX2592453.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592453/SRX2592453.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 @ Thu, 16 Apr 2020 00:55:17: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:55:17: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:55:18: 6000000 INFO @ Thu, 16 Apr 2020 00:55:23: 1000000 INFO @ Thu, 16 Apr 2020 00:55:23: 7000000 INFO @ Thu, 16 Apr 2020 00:55:29: 2000000 INFO @ Thu, 16 Apr 2020 00:55:29: 8000000 INFO @ Thu, 16 Apr 2020 00:55:34: 9000000 INFO @ Thu, 16 Apr 2020 00:55:35: 3000000 INFO @ Thu, 16 Apr 2020 00:55:36: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 00:55:36: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 00:55:36: #1 total tags in treatment: 9298021 INFO @ Thu, 16 Apr 2020 00:55:36: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:55:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 00:55:36: #1 tags after filtering in treatment: 9298021 INFO @ Thu, 16 Apr 2020 00:55:36: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:55:36: #1 finished! INFO @ Thu, 16 Apr 2020 00:55:36: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:55:36: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:55:37: #2 number of paired peaks: 296 WARNING @ Thu, 16 Apr 2020 00:55:37: Fewer paired peaks (296) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 296 pairs to build model! INFO @ Thu, 16 Apr 2020 00:55:37: start model_add_line... INFO @ Thu, 16 Apr 2020 00:55:37: start X-correlation... INFO @ Thu, 16 Apr 2020 00:55:37: end of X-cor INFO @ Thu, 16 Apr 2020 00:55:37: #2 finished! INFO @ Thu, 16 Apr 2020 00:55:37: #2 predicted fragment length is 275 bps INFO @ Thu, 16 Apr 2020 00:55:37: #2 alternative fragment length(s) may be 275 bps INFO @ Thu, 16 Apr 2020 00:55:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592453/SRX2592453.05_model.r INFO @ Thu, 16 Apr 2020 00:55:37: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:55:37: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:55:40: 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 @ Thu, 16 Apr 2020 00:55:46: 5000000 INFO @ Thu, 16 Apr 2020 00:55:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592453/SRX2592453.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592453/SRX2592453.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592453/SRX2592453.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592453/SRX2592453.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 @ Thu, 16 Apr 2020 00:55:47: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:55:47: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:55:52: 6000000 INFO @ Thu, 16 Apr 2020 00:55:53: 1000000 INFO @ Thu, 16 Apr 2020 00:55:58: 7000000 INFO @ Thu, 16 Apr 2020 00:55:59: 2000000 INFO @ Thu, 16 Apr 2020 00:56:00: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:56:04: 8000000 INFO @ Thu, 16 Apr 2020 00:56:05: 3000000 INFO @ Thu, 16 Apr 2020 00:56:10: 9000000 INFO @ Thu, 16 Apr 2020 00:56:11: 4000000 INFO @ Thu, 16 Apr 2020 00:56:12: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 00:56:12: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 00:56:12: #1 total tags in treatment: 9298021 INFO @ Thu, 16 Apr 2020 00:56:12: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:56:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 00:56:12: #1 tags after filtering in treatment: 9298021 INFO @ Thu, 16 Apr 2020 00:56:12: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:56:12: #1 finished! INFO @ Thu, 16 Apr 2020 00:56:12: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:56:12: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:56:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592453/SRX2592453.05_peaks.xls INFO @ Thu, 16 Apr 2020 00:56:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592453/SRX2592453.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:56:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592453/SRX2592453.05_summits.bed INFO @ Thu, 16 Apr 2020 00:56:13: Done! INFO @ Thu, 16 Apr 2020 00:56:13: #2 number of paired peaks: 296 WARNING @ Thu, 16 Apr 2020 00:56:13: Fewer paired peaks (296) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 296 pairs to build model! INFO @ Thu, 16 Apr 2020 00:56:13: start model_add_line... INFO @ Thu, 16 Apr 2020 00:56:13: start X-correlation... INFO @ Thu, 16 Apr 2020 00:56:13: end of X-cor INFO @ Thu, 16 Apr 2020 00:56:13: #2 finished! INFO @ Thu, 16 Apr 2020 00:56:13: #2 predicted fragment length is 275 bps INFO @ Thu, 16 Apr 2020 00:56:13: #2 alternative fragment length(s) may be 275 bps INFO @ Thu, 16 Apr 2020 00:56:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592453/SRX2592453.10_model.r INFO @ Thu, 16 Apr 2020 00:56:14: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:56:14: #3 Pre-compute pvalue-qvalue table... pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (14745 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 00:56:17: 5000000 INFO @ Thu, 16 Apr 2020 00:56:23: 6000000 INFO @ Thu, 16 Apr 2020 00:56:29: 7000000 INFO @ Thu, 16 Apr 2020 00:56:35: 8000000 INFO @ Thu, 16 Apr 2020 00:56:36: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:56:41: 9000000 INFO @ Thu, 16 Apr 2020 00:56:43: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 00:56:43: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 00:56:43: #1 total tags in treatment: 9298021 INFO @ Thu, 16 Apr 2020 00:56:43: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:56:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 00:56:43: #1 tags after filtering in treatment: 9298021 INFO @ Thu, 16 Apr 2020 00:56:43: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:56:43: #1 finished! INFO @ Thu, 16 Apr 2020 00:56:43: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:56:43: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:56:44: #2 number of paired peaks: 296 WARNING @ Thu, 16 Apr 2020 00:56:44: Fewer paired peaks (296) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 296 pairs to build model! INFO @ Thu, 16 Apr 2020 00:56:44: start model_add_line... INFO @ Thu, 16 Apr 2020 00:56:44: start X-correlation... INFO @ Thu, 16 Apr 2020 00:56:44: end of X-cor INFO @ Thu, 16 Apr 2020 00:56:44: #2 finished! INFO @ Thu, 16 Apr 2020 00:56:44: #2 predicted fragment length is 275 bps INFO @ Thu, 16 Apr 2020 00:56:44: #2 alternative fragment length(s) may be 275 bps INFO @ Thu, 16 Apr 2020 00:56:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592453/SRX2592453.20_model.r INFO @ Thu, 16 Apr 2020 00:56:44: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:56:44: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:56:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592453/SRX2592453.10_peaks.xls INFO @ Thu, 16 Apr 2020 00:56:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592453/SRX2592453.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:56:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592453/SRX2592453.10_summits.bed INFO @ Thu, 16 Apr 2020 00:56:50: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (10471 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 00:57:08: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:57:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592453/SRX2592453.20_peaks.xls INFO @ Thu, 16 Apr 2020 00:57:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592453/SRX2592453.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:57:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592453/SRX2592453.20_summits.bed INFO @ Thu, 16 Apr 2020 00:57:20: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (6766 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。