Job ID = 14521059 SRX = ERX4123678 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 12932691 spots for ERR4157933/ERR4157933.sra Written 12932691 spots for ERR4157933/ERR4157933.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: 00:02:12 12932691 reads; of these: 12932691 (100.00%) were unpaired; of these: 2508320 (19.40%) aligned 0 times 5890050 (45.54%) aligned exactly 1 time 4534321 (35.06%) aligned >1 times 80.60% overall alignment rate Time searching: 00:02:12 Overall time: 00:02:12 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] 8309995 / 10424371 = 0.7972 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 20:25:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4123678/ERX4123678.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4123678/ERX4123678.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4123678/ERX4123678.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4123678/ERX4123678.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 20:25:49: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:25:49: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:25:53: 1000000 INFO @ Sat, 15 Jan 2022 20:25:58: 2000000 INFO @ Sat, 15 Jan 2022 20:25:58: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:25:58: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:25:58: #1 total tags in treatment: 2114376 INFO @ Sat, 15 Jan 2022 20:25:58: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:25:58: #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 20:25:58: #1 tags after filtering in treatment: 2114376 INFO @ Sat, 15 Jan 2022 20:25:58: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 20:25:58: #1 finished! INFO @ Sat, 15 Jan 2022 20:25:58: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:25:58: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:25:58: #2 number of paired peaks: 171 WARNING @ Sat, 15 Jan 2022 20:25:58: Fewer paired peaks (171) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 171 pairs to build model! INFO @ Sat, 15 Jan 2022 20:25:58: start model_add_line... INFO @ Sat, 15 Jan 2022 20:25:58: start X-correlation... INFO @ Sat, 15 Jan 2022 20:25:58: end of X-cor INFO @ Sat, 15 Jan 2022 20:25:58: #2 finished! INFO @ Sat, 15 Jan 2022 20:25:58: #2 predicted fragment length is 180 bps INFO @ Sat, 15 Jan 2022 20:25:58: #2 alternative fragment length(s) may be 180 bps INFO @ Sat, 15 Jan 2022 20:25:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX4123678/ERX4123678.05_model.r INFO @ Sat, 15 Jan 2022 20:25:58: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:25:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:26:04: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:26:06: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX4123678/ERX4123678.05_peaks.xls INFO @ Sat, 15 Jan 2022 20:26:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX4123678/ERX4123678.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:26:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX4123678/ERX4123678.05_summits.bed INFO @ Sat, 15 Jan 2022 20:26:06: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (676 records, 4 fields): 3 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 20:26:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4123678/ERX4123678.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4123678/ERX4123678.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4123678/ERX4123678.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4123678/ERX4123678.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 20:26:19: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:26:19: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:26:24: 1000000 INFO @ Sat, 15 Jan 2022 20:26:29: 2000000 INFO @ Sat, 15 Jan 2022 20:26:30: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:26:30: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:26:30: #1 total tags in treatment: 2114376 INFO @ Sat, 15 Jan 2022 20:26:30: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:26:30: #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 20:26:30: #1 tags after filtering in treatment: 2114376 INFO @ Sat, 15 Jan 2022 20:26:30: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 20:26:30: #1 finished! INFO @ Sat, 15 Jan 2022 20:26:30: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:26:30: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:26:30: #2 number of paired peaks: 171 WARNING @ Sat, 15 Jan 2022 20:26:30: Fewer paired peaks (171) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 171 pairs to build model! INFO @ Sat, 15 Jan 2022 20:26:30: start model_add_line... INFO @ Sat, 15 Jan 2022 20:26:30: start X-correlation... INFO @ Sat, 15 Jan 2022 20:26:30: end of X-cor INFO @ Sat, 15 Jan 2022 20:26:30: #2 finished! INFO @ Sat, 15 Jan 2022 20:26:30: #2 predicted fragment length is 180 bps INFO @ Sat, 15 Jan 2022 20:26:30: #2 alternative fragment length(s) may be 180 bps INFO @ Sat, 15 Jan 2022 20:26:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX4123678/ERX4123678.10_model.r INFO @ Sat, 15 Jan 2022 20:26:30: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:26:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:26:36: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:26:38: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX4123678/ERX4123678.10_peaks.xls INFO @ Sat, 15 Jan 2022 20:26:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX4123678/ERX4123678.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:26:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX4123678/ERX4123678.10_summits.bed INFO @ Sat, 15 Jan 2022 20:26:38: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (499 records, 4 fields): 4 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 20:26:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4123678/ERX4123678.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4123678/ERX4123678.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4123678/ERX4123678.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4123678/ERX4123678.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 20:26:49: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:26:49: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:26:54: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 20:26:59: 2000000 INFO @ Sat, 15 Jan 2022 20:27:00: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:27:00: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:27:00: #1 total tags in treatment: 2114376 INFO @ Sat, 15 Jan 2022 20:27:00: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:27:00: #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 20:27:00: #1 tags after filtering in treatment: 2114376 INFO @ Sat, 15 Jan 2022 20:27:00: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 20:27:00: #1 finished! INFO @ Sat, 15 Jan 2022 20:27:00: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:27:00: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:27:00: #2 number of paired peaks: 171 WARNING @ Sat, 15 Jan 2022 20:27:00: Fewer paired peaks (171) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 171 pairs to build model! INFO @ Sat, 15 Jan 2022 20:27:00: start model_add_line... INFO @ Sat, 15 Jan 2022 20:27:00: start X-correlation... INFO @ Sat, 15 Jan 2022 20:27:00: end of X-cor INFO @ Sat, 15 Jan 2022 20:27:00: #2 finished! INFO @ Sat, 15 Jan 2022 20:27:00: #2 predicted fragment length is 180 bps INFO @ Sat, 15 Jan 2022 20:27:00: #2 alternative fragment length(s) may be 180 bps INFO @ Sat, 15 Jan 2022 20:27:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX4123678/ERX4123678.20_model.r INFO @ Sat, 15 Jan 2022 20:27:00: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:27:00: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 20:27:06: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:27:08: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX4123678/ERX4123678.20_peaks.xls INFO @ Sat, 15 Jan 2022 20:27:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX4123678/ERX4123678.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:27:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX4123678/ERX4123678.20_summits.bed INFO @ Sat, 15 Jan 2022 20:27:08: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (394 records, 4 fields): 2 millis CompletedMACS2peakCalling