Job ID = 14519827 SRX = ERX4107476 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 30060115 spots for ERR4140185/ERR4140185.sra Written 30060115 spots for ERR4140185/ERR4140185.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: 00:05:08 30060115 reads; of these: 30060115 (100.00%) were unpaired; of these: 3617094 (12.03%) aligned 0 times 21735986 (72.31%) aligned exactly 1 time 4707035 (15.66%) aligned >1 times 87.97% overall alignment rate Time searching: 00:05:08 Overall time: 00:05:08 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 17 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 23111641 / 26443021 = 0.8740 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 18:00:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4107476/ERX4107476.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4107476/ERX4107476.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4107476/ERX4107476.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4107476/ERX4107476.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 18:00:00: #1 read tag files... INFO @ Sat, 15 Jan 2022 18:00:00: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 18:00:09: 1000000 INFO @ Sat, 15 Jan 2022 18:00:17: 2000000 INFO @ Sat, 15 Jan 2022 18:00:26: 3000000 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 18:00:28: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 18:00:28: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 18:00:28: #1 total tags in treatment: 3331380 INFO @ Sat, 15 Jan 2022 18:00:28: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 18:00:28: #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 18:00:28: #1 tags after filtering in treatment: 3331380 INFO @ Sat, 15 Jan 2022 18:00:28: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 18:00:28: #1 finished! INFO @ Sat, 15 Jan 2022 18:00:28: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 18:00:28: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 18:00:28: #2 number of paired peaks: 176 WARNING @ Sat, 15 Jan 2022 18:00:28: Fewer paired peaks (176) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 176 pairs to build model! INFO @ Sat, 15 Jan 2022 18:00:28: start model_add_line... INFO @ Sat, 15 Jan 2022 18:00:28: start X-correlation... INFO @ Sat, 15 Jan 2022 18:00:29: end of X-cor INFO @ Sat, 15 Jan 2022 18:00:29: #2 finished! INFO @ Sat, 15 Jan 2022 18:00:29: #2 predicted fragment length is 291 bps INFO @ Sat, 15 Jan 2022 18:00:29: #2 alternative fragment length(s) may be 53,130,231,247,291,330,391,434,436 bps INFO @ Sat, 15 Jan 2022 18:00:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX4107476/ERX4107476.05_model.r INFO @ Sat, 15 Jan 2022 18:00:29: #3 Call peaks... INFO @ Sat, 15 Jan 2022 18:00:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 18:00:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4107476/ERX4107476.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4107476/ERX4107476.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4107476/ERX4107476.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4107476/ERX4107476.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 18:00:30: #1 read tag files... INFO @ Sat, 15 Jan 2022 18:00:30: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 18:00:39: 1000000 INFO @ Sat, 15 Jan 2022 18:00:42: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 18:00:44: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX4107476/ERX4107476.05_peaks.xls INFO @ Sat, 15 Jan 2022 18:00:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX4107476/ERX4107476.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 18:00:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX4107476/ERX4107476.05_summits.bed INFO @ Sat, 15 Jan 2022 18:00:45: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (267 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 18:00:47: 2000000 INFO @ Sat, 15 Jan 2022 18:00:56: 3000000 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 18:00:58: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 18:00:58: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 18:00:58: #1 total tags in treatment: 3331380 INFO @ Sat, 15 Jan 2022 18:00:58: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 18:00:58: #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 18:00:58: #1 tags after filtering in treatment: 3331380 INFO @ Sat, 15 Jan 2022 18:00:58: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 18:00:58: #1 finished! INFO @ Sat, 15 Jan 2022 18:00:58: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 18:00:58: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 18:00:58: #2 number of paired peaks: 176 WARNING @ Sat, 15 Jan 2022 18:00:58: Fewer paired peaks (176) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 176 pairs to build model! INFO @ Sat, 15 Jan 2022 18:00:58: start model_add_line... INFO @ Sat, 15 Jan 2022 18:00:58: start X-correlation... INFO @ Sat, 15 Jan 2022 18:00:58: end of X-cor INFO @ Sat, 15 Jan 2022 18:00:58: #2 finished! INFO @ Sat, 15 Jan 2022 18:00:58: #2 predicted fragment length is 291 bps INFO @ Sat, 15 Jan 2022 18:00:58: #2 alternative fragment length(s) may be 53,130,231,247,291,330,391,434,436 bps INFO @ Sat, 15 Jan 2022 18:00:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX4107476/ERX4107476.10_model.r INFO @ Sat, 15 Jan 2022 18:00:59: #3 Call peaks... INFO @ Sat, 15 Jan 2022 18:00:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 18:01:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4107476/ERX4107476.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4107476/ERX4107476.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4107476/ERX4107476.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4107476/ERX4107476.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 18:01:00: #1 read tag files... INFO @ Sat, 15 Jan 2022 18:01:00: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 18:01:09: 1000000 INFO @ Sat, 15 Jan 2022 18:01:12: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 18:01:14: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX4107476/ERX4107476.10_peaks.xls INFO @ Sat, 15 Jan 2022 18:01:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX4107476/ERX4107476.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 18:01:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX4107476/ERX4107476.10_summits.bed INFO @ Sat, 15 Jan 2022 18:01:14: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (197 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 18:01:17: 2000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 18:01:25: 3000000 INFO @ Sat, 15 Jan 2022 18:01:28: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 18:01:28: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 18:01:28: #1 total tags in treatment: 3331380 INFO @ Sat, 15 Jan 2022 18:01:28: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 18:01:28: #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 18:01:28: #1 tags after filtering in treatment: 3331380 INFO @ Sat, 15 Jan 2022 18:01:28: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 18:01:28: #1 finished! INFO @ Sat, 15 Jan 2022 18:01:28: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 18:01:28: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 18:01:28: #2 number of paired peaks: 176 WARNING @ Sat, 15 Jan 2022 18:01:28: Fewer paired peaks (176) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 176 pairs to build model! INFO @ Sat, 15 Jan 2022 18:01:28: start model_add_line... INFO @ Sat, 15 Jan 2022 18:01:28: start X-correlation... INFO @ Sat, 15 Jan 2022 18:01:28: end of X-cor INFO @ Sat, 15 Jan 2022 18:01:28: #2 finished! INFO @ Sat, 15 Jan 2022 18:01:28: #2 predicted fragment length is 291 bps INFO @ Sat, 15 Jan 2022 18:01:28: #2 alternative fragment length(s) may be 53,130,231,247,291,330,391,434,436 bps INFO @ Sat, 15 Jan 2022 18:01:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX4107476/ERX4107476.20_model.r INFO @ Sat, 15 Jan 2022 18:01:28: #3 Call peaks... INFO @ Sat, 15 Jan 2022 18:01:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 18:01:41: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 18:01:44: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX4107476/ERX4107476.20_peaks.xls INFO @ Sat, 15 Jan 2022 18:01:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX4107476/ERX4107476.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 18:01:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX4107476/ERX4107476.20_summits.bed INFO @ Sat, 15 Jan 2022 18:01:44: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (59 records, 4 fields): 2 millis CompletedMACS2peakCalling