Job ID = 14520988 SRX = ERX4123666 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 5287668 spots for ERR4157921/ERR4157921.sra Written 5287668 spots for ERR4157921/ERR4157921.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: 00:00:58 5287668 reads; of these: 5287668 (100.00%) were unpaired; of these: 847984 (16.04%) aligned 0 times 3729872 (70.54%) aligned exactly 1 time 709812 (13.42%) aligned >1 times 83.96% overall alignment rate Time searching: 00:00:58 Overall time: 00:00:58 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_rmdupse_core] 1502750 / 4439684 = 0.3385 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 20:15:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4123666/ERX4123666.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4123666/ERX4123666.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4123666/ERX4123666.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4123666/ERX4123666.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 20:15:10: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:15:10: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:15:17: 1000000 INFO @ Sat, 15 Jan 2022 20:15:25: 2000000 INFO @ Sat, 15 Jan 2022 20:15:32: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:15:32: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:15:32: #1 total tags in treatment: 2936934 INFO @ Sat, 15 Jan 2022 20:15:32: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:15:32: #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 20:15:32: #1 tags after filtering in treatment: 2936934 INFO @ Sat, 15 Jan 2022 20:15:32: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 20:15:32: #1 finished! INFO @ Sat, 15 Jan 2022 20:15:32: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:15:32: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:15:32: #2 number of paired peaks: 172 WARNING @ Sat, 15 Jan 2022 20:15:32: Fewer paired peaks (172) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 172 pairs to build model! INFO @ Sat, 15 Jan 2022 20:15:32: start model_add_line... INFO @ Sat, 15 Jan 2022 20:15:32: start X-correlation... INFO @ Sat, 15 Jan 2022 20:15:32: end of X-cor INFO @ Sat, 15 Jan 2022 20:15:32: #2 finished! INFO @ Sat, 15 Jan 2022 20:15:32: #2 predicted fragment length is 235 bps INFO @ Sat, 15 Jan 2022 20:15:32: #2 alternative fragment length(s) may be 0,26,46,83,148,186,235,273,293,347,369,390,487,519,536,593,598 bps INFO @ Sat, 15 Jan 2022 20:15:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX4123666/ERX4123666.05_model.r INFO @ Sat, 15 Jan 2022 20:15:32: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:15:32: #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 20:15:39: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:15:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4123666/ERX4123666.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4123666/ERX4123666.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4123666/ERX4123666.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4123666/ERX4123666.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 20:15:40: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:15:40: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:15:41: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX4123666/ERX4123666.05_peaks.xls INFO @ Sat, 15 Jan 2022 20:15:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX4123666/ERX4123666.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:15:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX4123666/ERX4123666.05_summits.bed INFO @ Sat, 15 Jan 2022 20:15:42: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (19 records, 4 fields): 94 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 20:15:47: 1000000 INFO @ Sat, 15 Jan 2022 20:15:55: 2000000 INFO @ Sat, 15 Jan 2022 20:16:02: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:16:02: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:16:02: #1 total tags in treatment: 2936934 INFO @ Sat, 15 Jan 2022 20:16:02: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:16:02: #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 20:16:02: #1 tags after filtering in treatment: 2936934 INFO @ Sat, 15 Jan 2022 20:16:02: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 20:16:02: #1 finished! INFO @ Sat, 15 Jan 2022 20:16:02: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:16:02: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:16:02: #2 number of paired peaks: 172 WARNING @ Sat, 15 Jan 2022 20:16:02: Fewer paired peaks (172) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 172 pairs to build model! INFO @ Sat, 15 Jan 2022 20:16:02: start model_add_line... INFO @ Sat, 15 Jan 2022 20:16:02: start X-correlation... INFO @ Sat, 15 Jan 2022 20:16:03: end of X-cor INFO @ Sat, 15 Jan 2022 20:16:03: #2 finished! INFO @ Sat, 15 Jan 2022 20:16:03: #2 predicted fragment length is 235 bps INFO @ Sat, 15 Jan 2022 20:16:03: #2 alternative fragment length(s) may be 0,26,46,83,148,186,235,273,293,347,369,390,487,519,536,593,598 bps INFO @ Sat, 15 Jan 2022 20:16:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX4123666/ERX4123666.10_model.r INFO @ Sat, 15 Jan 2022 20:16:03: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:16:03: #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 20:16:09: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:16:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4123666/ERX4123666.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4123666/ERX4123666.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4123666/ERX4123666.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4123666/ERX4123666.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 20:16:10: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:16:10: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:16:11: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX4123666/ERX4123666.10_peaks.xls INFO @ Sat, 15 Jan 2022 20:16:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX4123666/ERX4123666.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:16:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX4123666/ERX4123666.10_summits.bed INFO @ Sat, 15 Jan 2022 20:16:12: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (14 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 20:16:20: 1000000 INFO @ Sat, 15 Jan 2022 20:16:30: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 20:16:38: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:16:38: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:16:38: #1 total tags in treatment: 2936934 INFO @ Sat, 15 Jan 2022 20:16:38: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:16:38: #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 20:16:38: #1 tags after filtering in treatment: 2936934 INFO @ Sat, 15 Jan 2022 20:16:38: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 20:16:38: #1 finished! INFO @ Sat, 15 Jan 2022 20:16:38: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:16:38: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:16:39: #2 number of paired peaks: 172 WARNING @ Sat, 15 Jan 2022 20:16:39: Fewer paired peaks (172) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 172 pairs to build model! INFO @ Sat, 15 Jan 2022 20:16:39: start model_add_line... INFO @ Sat, 15 Jan 2022 20:16:39: start X-correlation... INFO @ Sat, 15 Jan 2022 20:16:39: end of X-cor INFO @ Sat, 15 Jan 2022 20:16:39: #2 finished! INFO @ Sat, 15 Jan 2022 20:16:39: #2 predicted fragment length is 235 bps INFO @ Sat, 15 Jan 2022 20:16:39: #2 alternative fragment length(s) may be 0,26,46,83,148,186,235,273,293,347,369,390,487,519,536,593,598 bps INFO @ Sat, 15 Jan 2022 20:16:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX4123666/ERX4123666.20_model.r INFO @ Sat, 15 Jan 2022 20:16:39: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:16:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:16:45: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:16:47: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX4123666/ERX4123666.20_peaks.xls INFO @ Sat, 15 Jan 2022 20:16:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX4123666/ERX4123666.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:16:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX4123666/ERX4123666.20_summits.bed INFO @ Sat, 15 Jan 2022 20:16:48: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (12 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。