Job ID = 5720571 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 9,589,506 reads read : 9,589,506 reads written : 9,589,506 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR5289708.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:03:29 9589506 reads; of these: 9589506 (100.00%) were unpaired; of these: 867892 (9.05%) aligned 0 times 6014523 (62.72%) aligned exactly 1 time 2707091 (28.23%) aligned >1 times 90.95% overall alignment rate Time searching: 00:03:30 Overall time: 00:03:30 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] 3339267 / 8721614 = 0.3829 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 00:38:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592431/SRX2592431.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592431/SRX2592431.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592431/SRX2592431.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592431/SRX2592431.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 00:38:23: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:38:23: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:38:28: 1000000 INFO @ Thu, 16 Apr 2020 00:38:34: 2000000 INFO @ Thu, 16 Apr 2020 00:38:39: 3000000 INFO @ Thu, 16 Apr 2020 00:38:45: 4000000 INFO @ Thu, 16 Apr 2020 00:38:50: 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 00:38:52: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 00:38:52: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 00:38:52: #1 total tags in treatment: 5382347 INFO @ Thu, 16 Apr 2020 00:38:52: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:38:52: #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 00:38:52: #1 tags after filtering in treatment: 5382347 INFO @ Thu, 16 Apr 2020 00:38:52: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:38:52: #1 finished! INFO @ Thu, 16 Apr 2020 00:38:52: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:38:52: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:38:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592431/SRX2592431.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592431/SRX2592431.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592431/SRX2592431.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592431/SRX2592431.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 00:38:53: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:38:53: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:38:53: #2 number of paired peaks: 301 WARNING @ Thu, 16 Apr 2020 00:38:53: Fewer paired peaks (301) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 301 pairs to build model! INFO @ Thu, 16 Apr 2020 00:38:53: start model_add_line... INFO @ Thu, 16 Apr 2020 00:38:53: start X-correlation... INFO @ Thu, 16 Apr 2020 00:38:53: end of X-cor INFO @ Thu, 16 Apr 2020 00:38:53: #2 finished! INFO @ Thu, 16 Apr 2020 00:38:53: #2 predicted fragment length is 151 bps INFO @ Thu, 16 Apr 2020 00:38:53: #2 alternative fragment length(s) may be 151 bps INFO @ Thu, 16 Apr 2020 00:38:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592431/SRX2592431.05_model.r INFO @ Thu, 16 Apr 2020 00:38:53: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:38:53: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:38:58: 1000000 INFO @ Thu, 16 Apr 2020 00:39:04: 2000000 INFO @ Thu, 16 Apr 2020 00:39:05: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:39:09: 3000000 INFO @ Thu, 16 Apr 2020 00:39:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592431/SRX2592431.05_peaks.xls INFO @ Thu, 16 Apr 2020 00:39:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592431/SRX2592431.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:39:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592431/SRX2592431.05_summits.bed INFO @ Thu, 16 Apr 2020 00:39:11: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (17541 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 00:39:15: 4000000 INFO @ Thu, 16 Apr 2020 00:39:21: 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 @ Thu, 16 Apr 2020 00:39:23: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 00:39:23: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 00:39:23: #1 total tags in treatment: 5382347 INFO @ Thu, 16 Apr 2020 00:39:23: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:39:23: #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 00:39:23: #1 tags after filtering in treatment: 5382347 INFO @ Thu, 16 Apr 2020 00:39:23: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:39:23: #1 finished! INFO @ Thu, 16 Apr 2020 00:39:23: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:39:23: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:39:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592431/SRX2592431.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592431/SRX2592431.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592431/SRX2592431.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592431/SRX2592431.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 00:39:23: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:39:23: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:39:23: #2 number of paired peaks: 301 WARNING @ Thu, 16 Apr 2020 00:39:23: Fewer paired peaks (301) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 301 pairs to build model! INFO @ Thu, 16 Apr 2020 00:39:23: start model_add_line... INFO @ Thu, 16 Apr 2020 00:39:24: start X-correlation... INFO @ Thu, 16 Apr 2020 00:39:24: end of X-cor INFO @ Thu, 16 Apr 2020 00:39:24: #2 finished! INFO @ Thu, 16 Apr 2020 00:39:24: #2 predicted fragment length is 151 bps INFO @ Thu, 16 Apr 2020 00:39:24: #2 alternative fragment length(s) may be 151 bps INFO @ Thu, 16 Apr 2020 00:39:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592431/SRX2592431.10_model.r INFO @ Thu, 16 Apr 2020 00:39:24: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:39:24: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:39:28: 1000000 INFO @ Thu, 16 Apr 2020 00:39:34: 2000000 INFO @ Thu, 16 Apr 2020 00:39:36: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:39:40: 3000000 INFO @ Thu, 16 Apr 2020 00:39:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592431/SRX2592431.10_peaks.xls INFO @ Thu, 16 Apr 2020 00:39:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592431/SRX2592431.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:39:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592431/SRX2592431.10_summits.bed INFO @ Thu, 16 Apr 2020 00:39:43: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (14446 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 00:39:45: 4000000 INFO @ Thu, 16 Apr 2020 00:39:51: 5000000 INFO @ Thu, 16 Apr 2020 00:39:53: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 00:39:53: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 00:39:53: #1 total tags in treatment: 5382347 INFO @ Thu, 16 Apr 2020 00:39:53: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:39:53: #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 00:39:53: #1 tags after filtering in treatment: 5382347 INFO @ Thu, 16 Apr 2020 00:39:53: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:39:53: #1 finished! INFO @ Thu, 16 Apr 2020 00:39:53: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:39:53: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:39:54: #2 number of paired peaks: 301 WARNING @ Thu, 16 Apr 2020 00:39:54: Fewer paired peaks (301) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 301 pairs to build model! INFO @ Thu, 16 Apr 2020 00:39:54: start model_add_line... INFO @ Thu, 16 Apr 2020 00:39:54: start X-correlation... INFO @ Thu, 16 Apr 2020 00:39:54: end of X-cor INFO @ Thu, 16 Apr 2020 00:39:54: #2 finished! INFO @ Thu, 16 Apr 2020 00:39:54: #2 predicted fragment length is 151 bps INFO @ Thu, 16 Apr 2020 00:39:54: #2 alternative fragment length(s) may be 151 bps INFO @ Thu, 16 Apr 2020 00:39:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592431/SRX2592431.20_model.r INFO @ Thu, 16 Apr 2020 00:39:54: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:39:54: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:40:05: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:40:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592431/SRX2592431.20_peaks.xls INFO @ Thu, 16 Apr 2020 00:40:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592431/SRX2592431.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:40:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592431/SRX2592431.20_summits.bed INFO @ Thu, 16 Apr 2020 00:40:11: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (10375 records, 4 fields): 10 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。