Job ID = 14521393 SRX = SRX8952655 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 3127904 spots for SRR12458231/SRR12458231.sra Written 3127904 spots for SRR12458231/SRR12458231.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: 00:01:05 3127904 reads; of these: 3127904 (100.00%) were paired; of these: 2292475 (73.29%) aligned concordantly 0 times 674842 (21.57%) aligned concordantly exactly 1 time 160587 (5.13%) aligned concordantly >1 times ---- 2292475 pairs aligned concordantly 0 times; of these: 209021 (9.12%) aligned discordantly 1 time ---- 2083454 pairs aligned 0 times concordantly or discordantly; of these: 4166908 mates make up the pairs; of these: 3241674 (77.80%) aligned 0 times 790188 (18.96%) aligned exactly 1 time 135046 (3.24%) aligned >1 times 48.18% overall alignment rate Time searching: 00:01:05 Overall time: 00:01:05 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_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrIX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrVI... [bam_rmdup_core] processing reference chrVII... [bam_rmdup_core] processing reference chrVIII... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXI... [bam_rmdup_core] processing reference chrXII... [bam_rmdup_core] processing reference chrXIII... [bam_rmdup_core] processing reference chrXIV... [bam_rmdup_core] processing reference chrXV... [bam_rmdup_core] processing reference chrXVI... [bam_rmdup_core] 176387 / 1016675 = 0.1735 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 20:58:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8952655/SRX8952655.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8952655/SRX8952655.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8952655/SRX8952655.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8952655/SRX8952655.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 20:58:20: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:58:20: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:58:25: 1000000 INFO @ Sat, 15 Jan 2022 20:58:31: 2000000 INFO @ Sat, 15 Jan 2022 20:58:34: #1 tag size is determined as 41 bps INFO @ Sat, 15 Jan 2022 20:58:34: #1 tag size = 41 INFO @ Sat, 15 Jan 2022 20:58:34: #1 total tags in treatment: 767022 INFO @ Sat, 15 Jan 2022 20:58:34: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:58:34: #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 20:58:34: #1 tags after filtering in treatment: 673351 INFO @ Sat, 15 Jan 2022 20:58:34: #1 Redundant rate of treatment: 0.12 INFO @ Sat, 15 Jan 2022 20:58:34: #1 finished! INFO @ Sat, 15 Jan 2022 20:58:34: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:58:34: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:58:34: #2 number of paired peaks: 173 WARNING @ Sat, 15 Jan 2022 20:58:34: Fewer paired peaks (173) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 173 pairs to build model! INFO @ Sat, 15 Jan 2022 20:58:34: start model_add_line... INFO @ Sat, 15 Jan 2022 20:58:34: start X-correlation... INFO @ Sat, 15 Jan 2022 20:58:34: end of X-cor INFO @ Sat, 15 Jan 2022 20:58:34: #2 finished! INFO @ Sat, 15 Jan 2022 20:58:34: #2 predicted fragment length is 283 bps INFO @ Sat, 15 Jan 2022 20:58:34: #2 alternative fragment length(s) may be 1,19,73,125,148,265,283,322,507,593 bps INFO @ Sat, 15 Jan 2022 20:58:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8952655/SRX8952655.05_model.r INFO @ Sat, 15 Jan 2022 20:58:34: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:58:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:58:36: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:58:37: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8952655/SRX8952655.05_peaks.xls INFO @ Sat, 15 Jan 2022 20:58:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8952655/SRX8952655.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:58:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8952655/SRX8952655.05_summits.bed INFO @ Sat, 15 Jan 2022 20:58:37: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (48 records, 4 fields): 1 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 20:58:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8952655/SRX8952655.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8952655/SRX8952655.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8952655/SRX8952655.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8952655/SRX8952655.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 20:58:50: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:58:50: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:58:55: 1000000 INFO @ Sat, 15 Jan 2022 20:59:00: 2000000 INFO @ Sat, 15 Jan 2022 20:59:04: #1 tag size is determined as 41 bps INFO @ Sat, 15 Jan 2022 20:59:04: #1 tag size = 41 INFO @ Sat, 15 Jan 2022 20:59:04: #1 total tags in treatment: 767022 INFO @ Sat, 15 Jan 2022 20:59:04: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:59:04: #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 20:59:04: #1 tags after filtering in treatment: 673351 INFO @ Sat, 15 Jan 2022 20:59:04: #1 Redundant rate of treatment: 0.12 INFO @ Sat, 15 Jan 2022 20:59:04: #1 finished! INFO @ Sat, 15 Jan 2022 20:59:04: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:59:04: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:59:04: #2 number of paired peaks: 173 WARNING @ Sat, 15 Jan 2022 20:59:04: Fewer paired peaks (173) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 173 pairs to build model! INFO @ Sat, 15 Jan 2022 20:59:04: start model_add_line... INFO @ Sat, 15 Jan 2022 20:59:04: start X-correlation... INFO @ Sat, 15 Jan 2022 20:59:04: end of X-cor INFO @ Sat, 15 Jan 2022 20:59:04: #2 finished! INFO @ Sat, 15 Jan 2022 20:59:04: #2 predicted fragment length is 283 bps INFO @ Sat, 15 Jan 2022 20:59:04: #2 alternative fragment length(s) may be 1,19,73,125,148,265,283,322,507,593 bps INFO @ Sat, 15 Jan 2022 20:59:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8952655/SRX8952655.10_model.r INFO @ Sat, 15 Jan 2022 20:59:04: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:59:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:59:06: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:59:06: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8952655/SRX8952655.10_peaks.xls INFO @ Sat, 15 Jan 2022 20:59:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8952655/SRX8952655.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:59:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8952655/SRX8952655.10_summits.bed INFO @ Sat, 15 Jan 2022 20:59:06: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (16 records, 4 fields): 51 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 20:59:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8952655/SRX8952655.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8952655/SRX8952655.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8952655/SRX8952655.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8952655/SRX8952655.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 20:59:20: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:59:20: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:59:25: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 20:59:31: 2000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 20:59:34: #1 tag size is determined as 41 bps INFO @ Sat, 15 Jan 2022 20:59:34: #1 tag size = 41 INFO @ Sat, 15 Jan 2022 20:59:34: #1 total tags in treatment: 767022 INFO @ Sat, 15 Jan 2022 20:59:34: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:59:34: #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 20:59:34: #1 tags after filtering in treatment: 673351 INFO @ Sat, 15 Jan 2022 20:59:34: #1 Redundant rate of treatment: 0.12 INFO @ Sat, 15 Jan 2022 20:59:34: #1 finished! INFO @ Sat, 15 Jan 2022 20:59:34: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:59:34: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:59:34: #2 number of paired peaks: 173 WARNING @ Sat, 15 Jan 2022 20:59:34: Fewer paired peaks (173) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 173 pairs to build model! INFO @ Sat, 15 Jan 2022 20:59:34: start model_add_line... INFO @ Sat, 15 Jan 2022 20:59:34: start X-correlation... INFO @ Sat, 15 Jan 2022 20:59:34: end of X-cor INFO @ Sat, 15 Jan 2022 20:59:34: #2 finished! INFO @ Sat, 15 Jan 2022 20:59:34: #2 predicted fragment length is 283 bps INFO @ Sat, 15 Jan 2022 20:59:34: #2 alternative fragment length(s) may be 1,19,73,125,148,265,283,322,507,593 bps INFO @ Sat, 15 Jan 2022 20:59:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8952655/SRX8952655.20_model.r INFO @ Sat, 15 Jan 2022 20:59:34: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:59:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:59:36: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:59:36: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8952655/SRX8952655.20_peaks.xls INFO @ Sat, 15 Jan 2022 20:59:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8952655/SRX8952655.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:59:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8952655/SRX8952655.20_summits.bed INFO @ Sat, 15 Jan 2022 20:59:37: Done! pass1 - making usageList (2 chroms): 0 millis pass2 - checking and writing primary data (4 records, 4 fields): 1 millis CompletedMACS2peakCalling