Job ID = 5720937 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 13,107,189 reads read : 13,107,189 reads written : 13,107,189 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR9624468.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: 00:02:54 13107189 reads; of these: 13107189 (100.00%) were unpaired; of these: 5712326 (43.58%) aligned 0 times 5444266 (41.54%) aligned exactly 1 time 1950597 (14.88%) aligned >1 times 56.42% overall alignment rate Time searching: 00:02:54 Overall time: 00:02:54 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_rmdupse_core] 2226393 / 7394863 = 0.3011 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 03:24:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6386736/SRX6386736.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6386736/SRX6386736.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6386736/SRX6386736.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6386736/SRX6386736.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 03:24:37: #1 read tag files... INFO @ Thu, 16 Apr 2020 03:24:37: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 03:24:43: 1000000 INFO @ Thu, 16 Apr 2020 03:24:48: 2000000 INFO @ Thu, 16 Apr 2020 03:24:54: 3000000 INFO @ Thu, 16 Apr 2020 03:24:59: 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 @ Thu, 16 Apr 2020 03:25:05: 5000000 INFO @ Thu, 16 Apr 2020 03:25:05: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 03:25:05: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 03:25:05: #1 total tags in treatment: 5168470 INFO @ Thu, 16 Apr 2020 03:25:05: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 03:25:05: #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 03:25:06: #1 tags after filtering in treatment: 5168470 INFO @ Thu, 16 Apr 2020 03:25:06: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 03:25:06: #1 finished! INFO @ Thu, 16 Apr 2020 03:25:06: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 03:25:06: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 03:25:06: #2 number of paired peaks: 338 WARNING @ Thu, 16 Apr 2020 03:25:06: Fewer paired peaks (338) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 338 pairs to build model! INFO @ Thu, 16 Apr 2020 03:25:06: start model_add_line... INFO @ Thu, 16 Apr 2020 03:25:06: start X-correlation... INFO @ Thu, 16 Apr 2020 03:25:06: end of X-cor INFO @ Thu, 16 Apr 2020 03:25:06: #2 finished! INFO @ Thu, 16 Apr 2020 03:25:06: #2 predicted fragment length is 146 bps INFO @ Thu, 16 Apr 2020 03:25:06: #2 alternative fragment length(s) may be 146 bps INFO @ Thu, 16 Apr 2020 03:25:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6386736/SRX6386736.05_model.r INFO @ Thu, 16 Apr 2020 03:25:06: #3 Call peaks... INFO @ Thu, 16 Apr 2020 03:25:06: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 03:25:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6386736/SRX6386736.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6386736/SRX6386736.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6386736/SRX6386736.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6386736/SRX6386736.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 03:25:06: #1 read tag files... INFO @ Thu, 16 Apr 2020 03:25:06: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 03:25:12: 1000000 INFO @ Thu, 16 Apr 2020 03:25:17: 2000000 INFO @ Thu, 16 Apr 2020 03:25:17: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 03:25:22: 3000000 INFO @ Thu, 16 Apr 2020 03:25:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6386736/SRX6386736.05_peaks.xls INFO @ Thu, 16 Apr 2020 03:25:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6386736/SRX6386736.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 03:25:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6386736/SRX6386736.05_summits.bed INFO @ Thu, 16 Apr 2020 03:25:23: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (1852 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 03:25:27: 4000000 INFO @ Thu, 16 Apr 2020 03:25:33: 5000000 INFO @ Thu, 16 Apr 2020 03:25:34: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 03:25:34: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 03:25:34: #1 total tags in treatment: 5168470 INFO @ Thu, 16 Apr 2020 03:25:34: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 03:25:34: #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 03:25:34: #1 tags after filtering in treatment: 5168470 INFO @ Thu, 16 Apr 2020 03:25:34: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 03:25:34: #1 finished! INFO @ Thu, 16 Apr 2020 03:25:34: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 03:25:34: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 03:25:34: #2 number of paired peaks: 338 WARNING @ Thu, 16 Apr 2020 03:25:34: Fewer paired peaks (338) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 338 pairs to build model! INFO @ Thu, 16 Apr 2020 03:25:34: start model_add_line... INFO @ Thu, 16 Apr 2020 03:25:34: start X-correlation... INFO @ Thu, 16 Apr 2020 03:25:34: end of X-cor INFO @ Thu, 16 Apr 2020 03:25:34: #2 finished! INFO @ Thu, 16 Apr 2020 03:25:34: #2 predicted fragment length is 146 bps INFO @ Thu, 16 Apr 2020 03:25:34: #2 alternative fragment length(s) may be 146 bps INFO @ Thu, 16 Apr 2020 03:25:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6386736/SRX6386736.10_model.r INFO @ Thu, 16 Apr 2020 03:25:34: #3 Call peaks... INFO @ Thu, 16 Apr 2020 03:25:34: #3 Pre-compute pvalue-qvalue table... 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 03:25:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6386736/SRX6386736.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6386736/SRX6386736.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6386736/SRX6386736.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6386736/SRX6386736.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 03:25:36: #1 read tag files... INFO @ Thu, 16 Apr 2020 03:25:36: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 03:25:42: 1000000 INFO @ Thu, 16 Apr 2020 03:25:45: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 03:25:47: 2000000 INFO @ Thu, 16 Apr 2020 03:25:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6386736/SRX6386736.10_peaks.xls INFO @ Thu, 16 Apr 2020 03:25:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6386736/SRX6386736.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 03:25:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6386736/SRX6386736.10_summits.bed INFO @ Thu, 16 Apr 2020 03:25:51: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (994 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 03:25:52: 3000000 INFO @ Thu, 16 Apr 2020 03:25:58: 4000000 INFO @ Thu, 16 Apr 2020 03:26:03: 5000000 INFO @ Thu, 16 Apr 2020 03:26:04: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 03:26:04: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 03:26:04: #1 total tags in treatment: 5168470 INFO @ Thu, 16 Apr 2020 03:26:04: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 03:26:04: #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 03:26:04: #1 tags after filtering in treatment: 5168470 INFO @ Thu, 16 Apr 2020 03:26:04: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 03:26:04: #1 finished! INFO @ Thu, 16 Apr 2020 03:26:04: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 03:26:04: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 03:26:04: #2 number of paired peaks: 338 WARNING @ Thu, 16 Apr 2020 03:26:04: Fewer paired peaks (338) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 338 pairs to build model! INFO @ Thu, 16 Apr 2020 03:26:04: start model_add_line... INFO @ Thu, 16 Apr 2020 03:26:04: start X-correlation... INFO @ Thu, 16 Apr 2020 03:26:04: end of X-cor INFO @ Thu, 16 Apr 2020 03:26:04: #2 finished! INFO @ Thu, 16 Apr 2020 03:26:04: #2 predicted fragment length is 146 bps INFO @ Thu, 16 Apr 2020 03:26:04: #2 alternative fragment length(s) may be 146 bps INFO @ Thu, 16 Apr 2020 03:26:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6386736/SRX6386736.20_model.r INFO @ Thu, 16 Apr 2020 03:26:04: #3 Call peaks... INFO @ Thu, 16 Apr 2020 03:26:04: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 03:26:16: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 03:26:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6386736/SRX6386736.20_peaks.xls INFO @ Thu, 16 Apr 2020 03:26:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6386736/SRX6386736.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 03:26:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6386736/SRX6386736.20_summits.bed INFO @ Thu, 16 Apr 2020 03:26:21: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (426 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。