Job ID = 5790820 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 1,860,017 reads read : 1,860,017 reads written : 1,860,017 spots read : 1,768,138 reads read : 1,768,138 reads written : 1,768,138 spots read : 1,757,820 reads read : 1,757,820 reads written : 1,757,820 spots read : 1,687,919 reads read : 1,687,919 reads written : 1,687,919 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: 00:01:04 7073894 reads; of these: 7073894 (100.00%) were unpaired; of these: 153461 (2.17%) aligned 0 times 5882608 (83.16%) aligned exactly 1 time 1037825 (14.67%) aligned >1 times 97.83% overall alignment rate Time searching: 00:01:04 Overall time: 00:01:04 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 17 sequences. [bam_rmdupse_core] 6723342 / 6920433 = 0.9715 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 @ Wed, 22 Apr 2020 07:46:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2858298/ERX2858298.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2858298/ERX2858298.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2858298/ERX2858298.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2858298/ERX2858298.bam'] # control file = None # effective genome size = 1.21e+07 # 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 @ Wed, 22 Apr 2020 07:46:41: #1 read tag files... INFO @ Wed, 22 Apr 2020 07:46:41: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 07:46:42: #1 tag size is determined as 75 bps INFO @ Wed, 22 Apr 2020 07:46:42: #1 tag size = 75 INFO @ Wed, 22 Apr 2020 07:46:42: #1 total tags in treatment: 197091 INFO @ Wed, 22 Apr 2020 07:46:42: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 07:46:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 07:46:42: #1 tags after filtering in treatment: 197091 INFO @ Wed, 22 Apr 2020 07:46:42: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 07:46:42: #1 finished! INFO @ Wed, 22 Apr 2020 07:46:42: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 07:46:42: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 07:46:43: #2 number of paired peaks: 392 WARNING @ Wed, 22 Apr 2020 07:46:43: Fewer paired peaks (392) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 392 pairs to build model! INFO @ Wed, 22 Apr 2020 07:46:43: start model_add_line... INFO @ Wed, 22 Apr 2020 07:46:43: start X-correlation... INFO @ Wed, 22 Apr 2020 07:46:43: end of X-cor INFO @ Wed, 22 Apr 2020 07:46:43: #2 finished! INFO @ Wed, 22 Apr 2020 07:46:43: #2 predicted fragment length is 188 bps INFO @ Wed, 22 Apr 2020 07:46:43: #2 alternative fragment length(s) may be 3,80,112,188,236,292,403,417,493,507,548,566 bps INFO @ Wed, 22 Apr 2020 07:46:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2858298/ERX2858298.05_model.r INFO @ Wed, 22 Apr 2020 07:46:43: #3 Call peaks... INFO @ Wed, 22 Apr 2020 07:46:43: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 07:46:43: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 07:46:43: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2858298/ERX2858298.05_peaks.xls INFO @ Wed, 22 Apr 2020 07:46:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2858298/ERX2858298.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 07:46:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2858298/ERX2858298.05_summits.bed INFO @ Wed, 22 Apr 2020 07:46:43: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (95 records, 4 fields): 1 millis CompletedMACS2peakCalling 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 @ Wed, 22 Apr 2020 07:47:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2858298/ERX2858298.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2858298/ERX2858298.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2858298/ERX2858298.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2858298/ERX2858298.bam'] # control file = None # effective genome size = 1.21e+07 # 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 @ Wed, 22 Apr 2020 07:47:11: #1 read tag files... INFO @ Wed, 22 Apr 2020 07:47:11: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 07:47:13: #1 tag size is determined as 75 bps INFO @ Wed, 22 Apr 2020 07:47:13: #1 tag size = 75 INFO @ Wed, 22 Apr 2020 07:47:13: #1 total tags in treatment: 197091 INFO @ Wed, 22 Apr 2020 07:47:13: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 07:47:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 07:47:13: #1 tags after filtering in treatment: 197091 INFO @ Wed, 22 Apr 2020 07:47:13: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 07:47:13: #1 finished! INFO @ Wed, 22 Apr 2020 07:47:13: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 07:47:13: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 07:47:13: #2 number of paired peaks: 392 WARNING @ Wed, 22 Apr 2020 07:47:13: Fewer paired peaks (392) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 392 pairs to build model! INFO @ Wed, 22 Apr 2020 07:47:13: start model_add_line... INFO @ Wed, 22 Apr 2020 07:47:13: start X-correlation... INFO @ Wed, 22 Apr 2020 07:47:13: end of X-cor INFO @ Wed, 22 Apr 2020 07:47:13: #2 finished! INFO @ Wed, 22 Apr 2020 07:47:13: #2 predicted fragment length is 188 bps INFO @ Wed, 22 Apr 2020 07:47:13: #2 alternative fragment length(s) may be 3,80,112,188,236,292,403,417,493,507,548,566 bps INFO @ Wed, 22 Apr 2020 07:47:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2858298/ERX2858298.10_model.r INFO @ Wed, 22 Apr 2020 07:47:13: #3 Call peaks... INFO @ Wed, 22 Apr 2020 07:47:13: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 07:47:13: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 07:47:13: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2858298/ERX2858298.10_peaks.xls INFO @ Wed, 22 Apr 2020 07:47:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2858298/ERX2858298.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 07:47:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2858298/ERX2858298.10_summits.bed INFO @ Wed, 22 Apr 2020 07:47:13: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (29 records, 4 fields): 1 millis CompletedMACS2peakCalling 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 @ Wed, 22 Apr 2020 07:47:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2858298/ERX2858298.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2858298/ERX2858298.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2858298/ERX2858298.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2858298/ERX2858298.bam'] # control file = None # effective genome size = 1.21e+07 # 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 @ Wed, 22 Apr 2020 07:47:41: #1 read tag files... INFO @ Wed, 22 Apr 2020 07:47:41: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Wed, 22 Apr 2020 07:47:43: #1 tag size is determined as 75 bps INFO @ Wed, 22 Apr 2020 07:47:43: #1 tag size = 75 INFO @ Wed, 22 Apr 2020 07:47:43: #1 total tags in treatment: 197091 INFO @ Wed, 22 Apr 2020 07:47:43: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 07:47:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 07:47:43: #1 tags after filtering in treatment: 197091 INFO @ Wed, 22 Apr 2020 07:47:43: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 07:47:43: #1 finished! INFO @ Wed, 22 Apr 2020 07:47:43: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 07:47:43: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 07:47:43: #2 number of paired peaks: 392 WARNING @ Wed, 22 Apr 2020 07:47:43: Fewer paired peaks (392) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 392 pairs to build model! INFO @ Wed, 22 Apr 2020 07:47:43: start model_add_line... INFO @ Wed, 22 Apr 2020 07:47:43: start X-correlation... INFO @ Wed, 22 Apr 2020 07:47:43: end of X-cor INFO @ Wed, 22 Apr 2020 07:47:43: #2 finished! INFO @ Wed, 22 Apr 2020 07:47:43: #2 predicted fragment length is 188 bps INFO @ Wed, 22 Apr 2020 07:47:43: #2 alternative fragment length(s) may be 3,80,112,188,236,292,403,417,493,507,548,566 bps INFO @ Wed, 22 Apr 2020 07:47:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2858298/ERX2858298.20_model.r INFO @ Wed, 22 Apr 2020 07:47:43: #3 Call peaks... INFO @ Wed, 22 Apr 2020 07:47:43: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 07:47:43: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 07:47:43: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2858298/ERX2858298.20_peaks.xls INFO @ Wed, 22 Apr 2020 07:47:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2858298/ERX2858298.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 07:47:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2858298/ERX2858298.20_summits.bed INFO @ Wed, 22 Apr 2020 07:47:43: Done! pass1 - making usageList (2 chroms): 0 millis pass2 - checking and writing primary data (2 records, 4 fields): 1 millis CompletedMACS2peakCalling