Job ID = 14521057 SRX = ERX4123677 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 13420878 spots for ERR4157932/ERR4157932.sra Written 13420878 spots for ERR4157932/ERR4157932.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: 00:02:38 13420878 reads; of these: 13420878 (100.00%) were unpaired; of these: 2598718 (19.36%) aligned 0 times 5368497 (40.00%) aligned exactly 1 time 5453663 (40.64%) aligned >1 times 80.64% overall alignment rate Time searching: 00:02:38 Overall time: 00:02:38 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] 9117550 / 10822160 = 0.8425 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 20:27:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4123677/ERX4123677.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4123677/ERX4123677.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4123677/ERX4123677.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4123677/ERX4123677.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 20:27:00: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:27:00: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:27:08: 1000000 INFO @ Sat, 15 Jan 2022 20:27:13: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:27:13: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:27:13: #1 total tags in treatment: 1704610 INFO @ Sat, 15 Jan 2022 20:27:13: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:27:13: #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 20:27:13: #1 tags after filtering in treatment: 1704610 INFO @ Sat, 15 Jan 2022 20:27:13: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 20:27:13: #1 finished! INFO @ Sat, 15 Jan 2022 20:27:13: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:27:13: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:27:14: #2 number of paired peaks: 360 WARNING @ Sat, 15 Jan 2022 20:27:14: Fewer paired peaks (360) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 360 pairs to build model! INFO @ Sat, 15 Jan 2022 20:27:14: start model_add_line... INFO @ Sat, 15 Jan 2022 20:27:14: start X-correlation... INFO @ Sat, 15 Jan 2022 20:27:14: end of X-cor INFO @ Sat, 15 Jan 2022 20:27:14: #2 finished! INFO @ Sat, 15 Jan 2022 20:27:14: #2 predicted fragment length is 186 bps INFO @ Sat, 15 Jan 2022 20:27:14: #2 alternative fragment length(s) may be 186 bps INFO @ Sat, 15 Jan 2022 20:27:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX4123677/ERX4123677.05_model.r INFO @ Sat, 15 Jan 2022 20:27:14: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:27:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:27:21: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:27:24: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX4123677/ERX4123677.05_peaks.xls INFO @ Sat, 15 Jan 2022 20:27:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX4123677/ERX4123677.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:27:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX4123677/ERX4123677.05_summits.bed INFO @ Sat, 15 Jan 2022 20:27:24: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (835 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 20:27:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4123677/ERX4123677.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4123677/ERX4123677.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4123677/ERX4123677.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4123677/ERX4123677.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 20:27:31: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:27:31: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:27:39: 1000000 INFO @ Sat, 15 Jan 2022 20:27:44: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:27:44: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:27:44: #1 total tags in treatment: 1704610 INFO @ Sat, 15 Jan 2022 20:27:44: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:27:44: #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 20:27:44: #1 tags after filtering in treatment: 1704610 INFO @ Sat, 15 Jan 2022 20:27:44: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 20:27:44: #1 finished! INFO @ Sat, 15 Jan 2022 20:27:44: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:27:44: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:27:44: #2 number of paired peaks: 360 WARNING @ Sat, 15 Jan 2022 20:27:44: Fewer paired peaks (360) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 360 pairs to build model! INFO @ Sat, 15 Jan 2022 20:27:44: start model_add_line... INFO @ Sat, 15 Jan 2022 20:27:44: start X-correlation... INFO @ Sat, 15 Jan 2022 20:27:44: end of X-cor INFO @ Sat, 15 Jan 2022 20:27:44: #2 finished! INFO @ Sat, 15 Jan 2022 20:27:44: #2 predicted fragment length is 186 bps INFO @ Sat, 15 Jan 2022 20:27:44: #2 alternative fragment length(s) may be 186 bps INFO @ Sat, 15 Jan 2022 20:27:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX4123677/ERX4123677.10_model.r INFO @ Sat, 15 Jan 2022 20:27:44: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:27:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:27:52: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:27:55: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX4123677/ERX4123677.10_peaks.xls INFO @ Sat, 15 Jan 2022 20:27:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX4123677/ERX4123677.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:27:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX4123677/ERX4123677.10_summits.bed INFO @ Sat, 15 Jan 2022 20:27:55: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (628 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 20:28:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4123677/ERX4123677.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4123677/ERX4123677.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4123677/ERX4123677.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4123677/ERX4123677.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 20:28:00: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:28:00: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 20:28:08: 1000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 20:28:13: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:28:13: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:28:13: #1 total tags in treatment: 1704610 INFO @ Sat, 15 Jan 2022 20:28:13: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:28:13: #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 20:28:13: #1 tags after filtering in treatment: 1704610 INFO @ Sat, 15 Jan 2022 20:28:13: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 20:28:13: #1 finished! INFO @ Sat, 15 Jan 2022 20:28:13: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:28:13: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:28:13: #2 number of paired peaks: 360 WARNING @ Sat, 15 Jan 2022 20:28:13: Fewer paired peaks (360) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 360 pairs to build model! INFO @ Sat, 15 Jan 2022 20:28:13: start model_add_line... INFO @ Sat, 15 Jan 2022 20:28:13: start X-correlation... INFO @ Sat, 15 Jan 2022 20:28:13: end of X-cor INFO @ Sat, 15 Jan 2022 20:28:13: #2 finished! INFO @ Sat, 15 Jan 2022 20:28:13: #2 predicted fragment length is 186 bps INFO @ Sat, 15 Jan 2022 20:28:13: #2 alternative fragment length(s) may be 186 bps INFO @ Sat, 15 Jan 2022 20:28:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX4123677/ERX4123677.20_model.r INFO @ Sat, 15 Jan 2022 20:28:13: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:28:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:28:21: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:28:23: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX4123677/ERX4123677.20_peaks.xls INFO @ Sat, 15 Jan 2022 20:28:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX4123677/ERX4123677.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:28:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX4123677/ERX4123677.20_summits.bed INFO @ Sat, 15 Jan 2022 20:28:23: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (451 records, 4 fields): 2 millis CompletedMACS2peakCalling