Job ID = 14521051 SRX = ERX4123672 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 20296595 spots for ERR4157927/ERR4157927.sra Written 20296595 spots for ERR4157927/ERR4157927.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: 00:02:59 20296595 reads; of these: 20296595 (100.00%) were unpaired; of these: 4148301 (20.44%) aligned 0 times 7916112 (39.00%) aligned exactly 1 time 8232182 (40.56%) aligned >1 times 79.56% overall alignment rate Time searching: 00:02:59 Overall time: 00:02:59 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_sort_core] merging from 8 files... [bam_rmdupse_core] 13747933 / 16148294 = 0.8514 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 15 Jan 2022 20:26:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4123672/ERX4123672.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4123672/ERX4123672.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4123672/ERX4123672.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4123672/ERX4123672.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 @ Sat, 15 Jan 2022 20:26:47: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:26:47: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:26:53: 1000000 INFO @ Sat, 15 Jan 2022 20:26:58: 2000000 INFO @ Sat, 15 Jan 2022 20:27:01: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:27:01: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:27:01: #1 total tags in treatment: 2400361 INFO @ Sat, 15 Jan 2022 20:27:01: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:27:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Jan 2022 20:27:01: #1 tags after filtering in treatment: 2400361 INFO @ Sat, 15 Jan 2022 20:27:01: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 20:27:01: #1 finished! INFO @ Sat, 15 Jan 2022 20:27:01: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:27:01: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:27:01: #2 number of paired peaks: 232 WARNING @ Sat, 15 Jan 2022 20:27:01: Fewer paired peaks (232) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 232 pairs to build model! INFO @ Sat, 15 Jan 2022 20:27:01: start model_add_line... INFO @ Sat, 15 Jan 2022 20:27:01: start X-correlation... INFO @ Sat, 15 Jan 2022 20:27:01: end of X-cor INFO @ Sat, 15 Jan 2022 20:27:01: #2 finished! INFO @ Sat, 15 Jan 2022 20:27:01: #2 predicted fragment length is 188 bps INFO @ Sat, 15 Jan 2022 20:27:01: #2 alternative fragment length(s) may be 188 bps INFO @ Sat, 15 Jan 2022 20:27:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX4123672/ERX4123672.05_model.r INFO @ Sat, 15 Jan 2022 20:27:01: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:27:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:27:10: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:27:13: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX4123672/ERX4123672.05_peaks.xls INFO @ Sat, 15 Jan 2022 20:27:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX4123672/ERX4123672.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:27:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX4123672/ERX4123672.05_summits.bed INFO @ Sat, 15 Jan 2022 20:27:13: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (934 records, 4 fields): 4 millis CompletedMACS2peakCalling WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 15 Jan 2022 20:27:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4123672/ERX4123672.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4123672/ERX4123672.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4123672/ERX4123672.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4123672/ERX4123672.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 @ Sat, 15 Jan 2022 20:27:17: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:27:17: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:27:23: 1000000 INFO @ Sat, 15 Jan 2022 20:27:28: 2000000 INFO @ Sat, 15 Jan 2022 20:27:31: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:27:31: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:27:31: #1 total tags in treatment: 2400361 INFO @ Sat, 15 Jan 2022 20:27:31: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:27:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Jan 2022 20:27:31: #1 tags after filtering in treatment: 2400361 INFO @ Sat, 15 Jan 2022 20:27:31: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 20:27:31: #1 finished! INFO @ Sat, 15 Jan 2022 20:27:31: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:27:31: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:27:31: #2 number of paired peaks: 232 WARNING @ Sat, 15 Jan 2022 20:27:31: Fewer paired peaks (232) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 232 pairs to build model! INFO @ Sat, 15 Jan 2022 20:27:31: start model_add_line... INFO @ Sat, 15 Jan 2022 20:27:31: start X-correlation... INFO @ Sat, 15 Jan 2022 20:27:31: end of X-cor INFO @ Sat, 15 Jan 2022 20:27:31: #2 finished! INFO @ Sat, 15 Jan 2022 20:27:31: #2 predicted fragment length is 188 bps INFO @ Sat, 15 Jan 2022 20:27:31: #2 alternative fragment length(s) may be 188 bps INFO @ Sat, 15 Jan 2022 20:27:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX4123672/ERX4123672.10_model.r INFO @ Sat, 15 Jan 2022 20:27:31: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:27:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:27:40: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:27:43: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX4123672/ERX4123672.10_peaks.xls INFO @ Sat, 15 Jan 2022 20:27:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX4123672/ERX4123672.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:27:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX4123672/ERX4123672.10_summits.bed INFO @ Sat, 15 Jan 2022 20:27:43: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (687 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 15 Jan 2022 20:27:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4123672/ERX4123672.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4123672/ERX4123672.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4123672/ERX4123672.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4123672/ERX4123672.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 @ Sat, 15 Jan 2022 20:27:47: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:27:47: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:27:53: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 20:27:59: 2000000 INFO @ Sat, 15 Jan 2022 20:28:01: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:28:01: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:28:01: #1 total tags in treatment: 2400361 INFO @ Sat, 15 Jan 2022 20:28:01: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:28:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Jan 2022 20:28:01: #1 tags after filtering in treatment: 2400361 INFO @ Sat, 15 Jan 2022 20:28:01: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 20:28:01: #1 finished! INFO @ Sat, 15 Jan 2022 20:28:01: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:28:01: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:28:01: #2 number of paired peaks: 232 WARNING @ Sat, 15 Jan 2022 20:28:01: Fewer paired peaks (232) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 232 pairs to build model! INFO @ Sat, 15 Jan 2022 20:28:01: start model_add_line... INFO @ Sat, 15 Jan 2022 20:28:01: start X-correlation... INFO @ Sat, 15 Jan 2022 20:28:01: end of X-cor INFO @ Sat, 15 Jan 2022 20:28:01: #2 finished! INFO @ Sat, 15 Jan 2022 20:28:01: #2 predicted fragment length is 188 bps INFO @ Sat, 15 Jan 2022 20:28:01: #2 alternative fragment length(s) may be 188 bps INFO @ Sat, 15 Jan 2022 20:28:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX4123672/ERX4123672.20_model.r INFO @ Sat, 15 Jan 2022 20:28:01: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:28:01: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 20:28:11: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:28:13: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX4123672/ERX4123672.20_peaks.xls INFO @ Sat, 15 Jan 2022 20:28:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX4123672/ERX4123672.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:28:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX4123672/ERX4123672.20_summits.bed INFO @ Sat, 15 Jan 2022 20:28:13: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (493 records, 4 fields): 4 millis CompletedMACS2peakCalling