Job ID = 14520982 SRX = ERX4123660 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 7559739 spots for ERR4157915/ERR4157915.sra Written 7559739 spots for ERR4157915/ERR4157915.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: 00:00:01 Multiseed full-index search: 00:00:53 7559739 reads; of these: 7559739 (100.00%) were unpaired; of these: 1209898 (16.00%) aligned 0 times 5481342 (72.51%) aligned exactly 1 time 868499 (11.49%) aligned >1 times 84.00% overall alignment rate Time searching: 00:00:54 Overall time: 00:00:54 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] 2437167 / 6349841 = 0.3838 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 20:15:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4123660/ERX4123660.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4123660/ERX4123660.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4123660/ERX4123660.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4123660/ERX4123660.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 20:15:05: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:15:05: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:15:11: 1000000 INFO @ Sat, 15 Jan 2022 20:15:17: 2000000 INFO @ Sat, 15 Jan 2022 20:15:23: 3000000 INFO @ Sat, 15 Jan 2022 20:15:28: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:15:28: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:15:28: #1 total tags in treatment: 3912674 INFO @ Sat, 15 Jan 2022 20:15:28: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:15:28: #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 20:15:28: #1 tags after filtering in treatment: 3912674 INFO @ Sat, 15 Jan 2022 20:15:28: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 20:15:28: #1 finished! INFO @ Sat, 15 Jan 2022 20:15:28: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:15:28: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:15:28: #2 number of paired peaks: 136 WARNING @ Sat, 15 Jan 2022 20:15:28: Fewer paired peaks (136) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 136 pairs to build model! INFO @ Sat, 15 Jan 2022 20:15:28: start model_add_line... INFO @ Sat, 15 Jan 2022 20:15:28: start X-correlation... INFO @ Sat, 15 Jan 2022 20:15:28: end of X-cor INFO @ Sat, 15 Jan 2022 20:15:28: #2 finished! INFO @ Sat, 15 Jan 2022 20:15:28: #2 predicted fragment length is 111 bps INFO @ Sat, 15 Jan 2022 20:15:28: #2 alternative fragment length(s) may be 27,71,111,151,176,196,216,254,273,325,355,370,401,436,467,481,494,515,525,527,552,567,590 bps INFO @ Sat, 15 Jan 2022 20:15:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX4123660/ERX4123660.05_model.r INFO @ Sat, 15 Jan 2022 20:15:29: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:15:29: #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 20:15:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4123660/ERX4123660.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4123660/ERX4123660.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4123660/ERX4123660.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4123660/ERX4123660.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 20:15:34: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:15:34: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:15:35: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:15:37: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX4123660/ERX4123660.05_peaks.xls INFO @ Sat, 15 Jan 2022 20:15:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX4123660/ERX4123660.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:15:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX4123660/ERX4123660.05_summits.bed INFO @ Sat, 15 Jan 2022 20:15:37: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (28 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 20:15:40: 1000000 INFO @ Sat, 15 Jan 2022 20:15:46: 2000000 INFO @ Sat, 15 Jan 2022 20:15:52: 3000000 INFO @ Sat, 15 Jan 2022 20:15:57: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:15:57: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:15:57: #1 total tags in treatment: 3912674 INFO @ Sat, 15 Jan 2022 20:15:57: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:15:57: #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 20:15:57: #1 tags after filtering in treatment: 3912674 INFO @ Sat, 15 Jan 2022 20:15:57: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 20:15:57: #1 finished! INFO @ Sat, 15 Jan 2022 20:15:57: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:15:57: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:15:57: #2 number of paired peaks: 136 WARNING @ Sat, 15 Jan 2022 20:15:57: Fewer paired peaks (136) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 136 pairs to build model! INFO @ Sat, 15 Jan 2022 20:15:57: start model_add_line... INFO @ Sat, 15 Jan 2022 20:15:57: start X-correlation... INFO @ Sat, 15 Jan 2022 20:15:57: end of X-cor INFO @ Sat, 15 Jan 2022 20:15:57: #2 finished! INFO @ Sat, 15 Jan 2022 20:15:57: #2 predicted fragment length is 111 bps INFO @ Sat, 15 Jan 2022 20:15:57: #2 alternative fragment length(s) may be 27,71,111,151,176,196,216,254,273,325,355,370,401,436,467,481,494,515,525,527,552,567,590 bps INFO @ Sat, 15 Jan 2022 20:15:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX4123660/ERX4123660.10_model.r INFO @ Sat, 15 Jan 2022 20:15:57: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:15:57: #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 20:16:03: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:16:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4123660/ERX4123660.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4123660/ERX4123660.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4123660/ERX4123660.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4123660/ERX4123660.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 20:16:04: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:16:04: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:16:05: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX4123660/ERX4123660.10_peaks.xls INFO @ Sat, 15 Jan 2022 20:16:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX4123660/ERX4123660.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:16:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX4123660/ERX4123660.10_summits.bed INFO @ Sat, 15 Jan 2022 20:16:05: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (11 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 20:16:10: 1000000 INFO @ Sat, 15 Jan 2022 20:16:15: 2000000 INFO @ Sat, 15 Jan 2022 20:16:20: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 20:16:24: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:16:24: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:16:24: #1 total tags in treatment: 3912674 INFO @ Sat, 15 Jan 2022 20:16:24: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:16:24: #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 20:16:24: #1 tags after filtering in treatment: 3912674 INFO @ Sat, 15 Jan 2022 20:16:24: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 20:16:24: #1 finished! INFO @ Sat, 15 Jan 2022 20:16:24: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:16:24: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:16:24: #2 number of paired peaks: 136 WARNING @ Sat, 15 Jan 2022 20:16:24: Fewer paired peaks (136) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 136 pairs to build model! INFO @ Sat, 15 Jan 2022 20:16:24: start model_add_line... INFO @ Sat, 15 Jan 2022 20:16:24: start X-correlation... INFO @ Sat, 15 Jan 2022 20:16:25: end of X-cor INFO @ Sat, 15 Jan 2022 20:16:25: #2 finished! INFO @ Sat, 15 Jan 2022 20:16:25: #2 predicted fragment length is 111 bps INFO @ Sat, 15 Jan 2022 20:16:25: #2 alternative fragment length(s) may be 27,71,111,151,176,196,216,254,273,325,355,370,401,436,467,481,494,515,525,527,552,567,590 bps INFO @ Sat, 15 Jan 2022 20:16:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX4123660/ERX4123660.20_model.r INFO @ Sat, 15 Jan 2022 20:16:25: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:16:25: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 20:16:30: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:16:33: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX4123660/ERX4123660.20_peaks.xls INFO @ Sat, 15 Jan 2022 20:16:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX4123660/ERX4123660.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:16:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX4123660/ERX4123660.20_summits.bed INFO @ Sat, 15 Jan 2022 20:16:33: Done! pass1 - making usageList (3 chroms): 0 millis pass2 - checking and writing primary data (3 records, 4 fields): 1 millis CompletedMACS2peakCalling