Job ID = 14519820 SRX = ERX4107470 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 21858263 spots for ERR4140179/ERR4140179.sra Written 21858263 spots for ERR4140179/ERR4140179.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: 00:03:38 21858263 reads; of these: 21858263 (100.00%) were unpaired; of these: 3465407 (15.85%) aligned 0 times 14873271 (68.04%) aligned exactly 1 time 3519585 (16.10%) aligned >1 times 84.15% overall alignment rate Time searching: 00:03:38 Overall time: 00:03:38 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] 15798502 / 18392856 = 0.8589 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 17:55:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4107470/ERX4107470.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4107470/ERX4107470.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4107470/ERX4107470.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4107470/ERX4107470.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 17:55:46: #1 read tag files... INFO @ Sat, 15 Jan 2022 17:55:46: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 17:55:54: 1000000 INFO @ Sat, 15 Jan 2022 17:56:01: 2000000 INFO @ Sat, 15 Jan 2022 17:56:05: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 17:56:05: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 17:56:05: #1 total tags in treatment: 2594354 INFO @ Sat, 15 Jan 2022 17:56:05: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 17:56:05: #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 17:56:06: #1 tags after filtering in treatment: 2594354 INFO @ Sat, 15 Jan 2022 17:56:06: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 17:56:06: #1 finished! INFO @ Sat, 15 Jan 2022 17:56:06: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 17:56:06: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 17:56:06: #2 number of paired peaks: 193 WARNING @ Sat, 15 Jan 2022 17:56:06: Fewer paired peaks (193) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 193 pairs to build model! INFO @ Sat, 15 Jan 2022 17:56:06: start model_add_line... INFO @ Sat, 15 Jan 2022 17:56:06: start X-correlation... INFO @ Sat, 15 Jan 2022 17:56:06: end of X-cor INFO @ Sat, 15 Jan 2022 17:56:06: #2 finished! INFO @ Sat, 15 Jan 2022 17:56:06: #2 predicted fragment length is 313 bps INFO @ Sat, 15 Jan 2022 17:56:06: #2 alternative fragment length(s) may be 0,264,297,313 bps INFO @ Sat, 15 Jan 2022 17:56:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX4107470/ERX4107470.05_model.r INFO @ Sat, 15 Jan 2022 17:56:06: #3 Call peaks... INFO @ Sat, 15 Jan 2022 17:56:06: #3 Pre-compute pvalue-qvalue table... 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 17:56:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4107470/ERX4107470.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4107470/ERX4107470.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4107470/ERX4107470.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4107470/ERX4107470.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 17:56:16: #1 read tag files... INFO @ Sat, 15 Jan 2022 17:56:16: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 17:56:17: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 17:56:19: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX4107470/ERX4107470.05_peaks.xls INFO @ Sat, 15 Jan 2022 17:56:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX4107470/ERX4107470.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 17:56:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX4107470/ERX4107470.05_summits.bed INFO @ Sat, 15 Jan 2022 17:56:19: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (249 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 17:56:23: 1000000 INFO @ Sat, 15 Jan 2022 17:56:30: 2000000 INFO @ Sat, 15 Jan 2022 17:56:33: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 17:56:33: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 17:56:33: #1 total tags in treatment: 2594354 INFO @ Sat, 15 Jan 2022 17:56:33: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 17:56:33: #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 17:56:33: #1 tags after filtering in treatment: 2594354 INFO @ Sat, 15 Jan 2022 17:56:33: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 17:56:33: #1 finished! INFO @ Sat, 15 Jan 2022 17:56:33: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 17:56:33: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 17:56:33: #2 number of paired peaks: 193 WARNING @ Sat, 15 Jan 2022 17:56:33: Fewer paired peaks (193) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 193 pairs to build model! INFO @ Sat, 15 Jan 2022 17:56:33: start model_add_line... INFO @ Sat, 15 Jan 2022 17:56:33: start X-correlation... INFO @ Sat, 15 Jan 2022 17:56:33: end of X-cor INFO @ Sat, 15 Jan 2022 17:56:33: #2 finished! INFO @ Sat, 15 Jan 2022 17:56:33: #2 predicted fragment length is 313 bps INFO @ Sat, 15 Jan 2022 17:56:33: #2 alternative fragment length(s) may be 0,264,297,313 bps INFO @ Sat, 15 Jan 2022 17:56:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX4107470/ERX4107470.10_model.r INFO @ Sat, 15 Jan 2022 17:56:33: #3 Call peaks... INFO @ Sat, 15 Jan 2022 17:56:33: #3 Pre-compute pvalue-qvalue table... 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 17:56:45: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 17:56:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4107470/ERX4107470.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4107470/ERX4107470.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4107470/ERX4107470.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4107470/ERX4107470.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 17:56:46: #1 read tag files... INFO @ Sat, 15 Jan 2022 17:56:46: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 17:56:47: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX4107470/ERX4107470.10_peaks.xls INFO @ Sat, 15 Jan 2022 17:56:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX4107470/ERX4107470.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 17:56:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX4107470/ERX4107470.10_summits.bed INFO @ Sat, 15 Jan 2022 17:56:47: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (167 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 17:56:54: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 17:57:02: 2000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 17:57:06: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 17:57:06: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 17:57:06: #1 total tags in treatment: 2594354 INFO @ Sat, 15 Jan 2022 17:57:06: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 17:57:06: #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 17:57:06: #1 tags after filtering in treatment: 2594354 INFO @ Sat, 15 Jan 2022 17:57:06: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 17:57:06: #1 finished! INFO @ Sat, 15 Jan 2022 17:57:06: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 17:57:06: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 17:57:06: #2 number of paired peaks: 193 WARNING @ Sat, 15 Jan 2022 17:57:06: Fewer paired peaks (193) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 193 pairs to build model! INFO @ Sat, 15 Jan 2022 17:57:06: start model_add_line... INFO @ Sat, 15 Jan 2022 17:57:06: start X-correlation... INFO @ Sat, 15 Jan 2022 17:57:06: end of X-cor INFO @ Sat, 15 Jan 2022 17:57:06: #2 finished! INFO @ Sat, 15 Jan 2022 17:57:06: #2 predicted fragment length is 313 bps INFO @ Sat, 15 Jan 2022 17:57:06: #2 alternative fragment length(s) may be 0,264,297,313 bps INFO @ Sat, 15 Jan 2022 17:57:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX4107470/ERX4107470.20_model.r INFO @ Sat, 15 Jan 2022 17:57:06: #3 Call peaks... INFO @ Sat, 15 Jan 2022 17:57:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 17:57:17: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 17:57:19: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX4107470/ERX4107470.20_peaks.xls INFO @ Sat, 15 Jan 2022 17:57:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX4107470/ERX4107470.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 17:57:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX4107470/ERX4107470.20_summits.bed INFO @ Sat, 15 Jan 2022 17:57:19: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (38 records, 4 fields): 2 millis CompletedMACS2peakCalling