Job ID = 14519823 SRX = ERX4107473 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 15640924 spots for ERR4140182/ERR4140182.sra Written 15640924 spots for ERR4140182/ERR4140182.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: 00:01:48 15640924 reads; of these: 15640924 (100.00%) were unpaired; of these: 5459856 (34.91%) aligned 0 times 8992370 (57.49%) aligned exactly 1 time 1188698 (7.60%) aligned >1 times 65.09% overall alignment rate Time searching: 00:01:48 Overall time: 00:01:48 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] 8087723 / 10181068 = 0.7944 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 17:52:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4107473/ERX4107473.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4107473/ERX4107473.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4107473/ERX4107473.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4107473/ERX4107473.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 17:52:29: #1 read tag files... INFO @ Sat, 15 Jan 2022 17:52:29: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 17:52:34: 1000000 INFO @ Sat, 15 Jan 2022 17:52:40: 2000000 INFO @ Sat, 15 Jan 2022 17:52:40: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 17:52:40: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 17:52:40: #1 total tags in treatment: 2093345 INFO @ Sat, 15 Jan 2022 17:52:40: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 17:52:40: #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 17:52:40: #1 tags after filtering in treatment: 2093345 INFO @ Sat, 15 Jan 2022 17:52:40: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 17:52:40: #1 finished! INFO @ Sat, 15 Jan 2022 17:52:40: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 17:52:40: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 17:52:40: #2 number of paired peaks: 227 WARNING @ Sat, 15 Jan 2022 17:52:40: Fewer paired peaks (227) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 227 pairs to build model! INFO @ Sat, 15 Jan 2022 17:52:40: start model_add_line... INFO @ Sat, 15 Jan 2022 17:52:40: start X-correlation... INFO @ Sat, 15 Jan 2022 17:52:40: end of X-cor INFO @ Sat, 15 Jan 2022 17:52:40: #2 finished! INFO @ Sat, 15 Jan 2022 17:52:40: #2 predicted fragment length is 161 bps INFO @ Sat, 15 Jan 2022 17:52:40: #2 alternative fragment length(s) may be 1,41,61,68,103,124,141,161,184,203,218,233,254,299,325,365,387,503,559 bps INFO @ Sat, 15 Jan 2022 17:52:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX4107473/ERX4107473.05_model.r INFO @ Sat, 15 Jan 2022 17:52:40: #3 Call peaks... INFO @ Sat, 15 Jan 2022 17:52:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 17:52:46: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 17:52:47: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX4107473/ERX4107473.05_peaks.xls INFO @ Sat, 15 Jan 2022 17:52:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX4107473/ERX4107473.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 17:52:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX4107473/ERX4107473.05_summits.bed INFO @ Sat, 15 Jan 2022 17:52:47: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (281 records, 4 fields): 1 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 17:52:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4107473/ERX4107473.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4107473/ERX4107473.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4107473/ERX4107473.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4107473/ERX4107473.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 17:52:59: #1 read tag files... INFO @ Sat, 15 Jan 2022 17:52:59: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 17:53:04: 1000000 INFO @ Sat, 15 Jan 2022 17:53:10: 2000000 INFO @ Sat, 15 Jan 2022 17:53:10: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 17:53:10: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 17:53:10: #1 total tags in treatment: 2093345 INFO @ Sat, 15 Jan 2022 17:53:10: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 17:53:10: #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 17:53:10: #1 tags after filtering in treatment: 2093345 INFO @ Sat, 15 Jan 2022 17:53:10: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 17:53:10: #1 finished! INFO @ Sat, 15 Jan 2022 17:53:10: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 17:53:10: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 17:53:10: #2 number of paired peaks: 227 WARNING @ Sat, 15 Jan 2022 17:53:10: Fewer paired peaks (227) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 227 pairs to build model! INFO @ Sat, 15 Jan 2022 17:53:10: start model_add_line... INFO @ Sat, 15 Jan 2022 17:53:10: start X-correlation... INFO @ Sat, 15 Jan 2022 17:53:11: end of X-cor INFO @ Sat, 15 Jan 2022 17:53:11: #2 finished! INFO @ Sat, 15 Jan 2022 17:53:11: #2 predicted fragment length is 161 bps INFO @ Sat, 15 Jan 2022 17:53:11: #2 alternative fragment length(s) may be 1,41,61,68,103,124,141,161,184,203,218,233,254,299,325,365,387,503,559 bps INFO @ Sat, 15 Jan 2022 17:53:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX4107473/ERX4107473.10_model.r INFO @ Sat, 15 Jan 2022 17:53:11: #3 Call peaks... INFO @ Sat, 15 Jan 2022 17:53:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 17:53:16: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 17:53:17: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX4107473/ERX4107473.10_peaks.xls INFO @ Sat, 15 Jan 2022 17:53:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX4107473/ERX4107473.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 17:53:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX4107473/ERX4107473.10_summits.bed INFO @ Sat, 15 Jan 2022 17:53:18: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (188 records, 4 fields): 1 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 17:53:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4107473/ERX4107473.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4107473/ERX4107473.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4107473/ERX4107473.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4107473/ERX4107473.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 17:53:29: #1 read tag files... INFO @ Sat, 15 Jan 2022 17:53:29: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 17:53:34: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 17:53:39: 2000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 17:53:40: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 17:53:40: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 17:53:40: #1 total tags in treatment: 2093345 INFO @ Sat, 15 Jan 2022 17:53:40: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 17:53:40: #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 17:53:40: #1 tags after filtering in treatment: 2093345 INFO @ Sat, 15 Jan 2022 17:53:40: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 17:53:40: #1 finished! INFO @ Sat, 15 Jan 2022 17:53:40: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 17:53:40: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 17:53:40: #2 number of paired peaks: 227 WARNING @ Sat, 15 Jan 2022 17:53:40: Fewer paired peaks (227) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 227 pairs to build model! INFO @ Sat, 15 Jan 2022 17:53:40: start model_add_line... INFO @ Sat, 15 Jan 2022 17:53:40: start X-correlation... INFO @ Sat, 15 Jan 2022 17:53:40: end of X-cor INFO @ Sat, 15 Jan 2022 17:53:40: #2 finished! INFO @ Sat, 15 Jan 2022 17:53:40: #2 predicted fragment length is 161 bps INFO @ Sat, 15 Jan 2022 17:53:40: #2 alternative fragment length(s) may be 1,41,61,68,103,124,141,161,184,203,218,233,254,299,325,365,387,503,559 bps INFO @ Sat, 15 Jan 2022 17:53:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX4107473/ERX4107473.20_model.r INFO @ Sat, 15 Jan 2022 17:53:40: #3 Call peaks... INFO @ Sat, 15 Jan 2022 17:53:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 17:53:45: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 17:53:47: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX4107473/ERX4107473.20_peaks.xls INFO @ Sat, 15 Jan 2022 17:53:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX4107473/ERX4107473.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 17:53:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX4107473/ERX4107473.20_summits.bed INFO @ Sat, 15 Jan 2022 17:53:47: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (54 records, 4 fields): 1 millis CompletedMACS2peakCalling