Job ID = 14521355 SRX = SRX8952641 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 4370526 spots for SRR12458245/SRR12458245.sra Written 4370526 spots for SRR12458245/SRR12458245.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: 00:01:09 4370526 reads; of these: 4370526 (100.00%) were paired; of these: 3674145 (84.07%) aligned concordantly 0 times 603113 (13.80%) aligned concordantly exactly 1 time 93268 (2.13%) aligned concordantly >1 times ---- 3674145 pairs aligned concordantly 0 times; of these: 106251 (2.89%) aligned discordantly 1 time ---- 3567894 pairs aligned 0 times concordantly or discordantly; of these: 7135788 mates make up the pairs; of these: 6657307 (93.29%) aligned 0 times 383515 (5.37%) aligned exactly 1 time 94966 (1.33%) aligned >1 times 23.84% overall alignment rate Time searching: 00:01:09 Overall time: 00:01:09 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] 330321 / 797273 = 0.4143 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 20:54:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8952641/SRX8952641.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8952641/SRX8952641.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8952641/SRX8952641.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8952641/SRX8952641.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 20:54:26: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:54:26: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:54:33: 1000000 INFO @ Sat, 15 Jan 2022 20:54:36: #1 tag size is determined as 43 bps INFO @ Sat, 15 Jan 2022 20:54:36: #1 tag size = 43 INFO @ Sat, 15 Jan 2022 20:54:36: #1 total tags in treatment: 423437 INFO @ Sat, 15 Jan 2022 20:54:36: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:54:36: #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 20:54:36: #1 tags after filtering in treatment: 387636 INFO @ Sat, 15 Jan 2022 20:54:36: #1 Redundant rate of treatment: 0.08 INFO @ Sat, 15 Jan 2022 20:54:36: #1 finished! INFO @ Sat, 15 Jan 2022 20:54:36: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:54:36: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:54:36: #2 number of paired peaks: 116 WARNING @ Sat, 15 Jan 2022 20:54:36: Fewer paired peaks (116) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 116 pairs to build model! INFO @ Sat, 15 Jan 2022 20:54:36: start model_add_line... INFO @ Sat, 15 Jan 2022 20:54:36: start X-correlation... INFO @ Sat, 15 Jan 2022 20:54:36: end of X-cor INFO @ Sat, 15 Jan 2022 20:54:36: #2 finished! INFO @ Sat, 15 Jan 2022 20:54:36: #2 predicted fragment length is 251 bps INFO @ Sat, 15 Jan 2022 20:54:36: #2 alternative fragment length(s) may be 4,225,251,598 bps INFO @ Sat, 15 Jan 2022 20:54:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8952641/SRX8952641.05_model.r INFO @ Sat, 15 Jan 2022 20:54:36: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:54:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:54:37: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:54:37: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8952641/SRX8952641.05_peaks.xls INFO @ Sat, 15 Jan 2022 20:54:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8952641/SRX8952641.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:54:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8952641/SRX8952641.05_summits.bed INFO @ Sat, 15 Jan 2022 20:54:37: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (169 records, 4 fields): 2 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 20:54:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8952641/SRX8952641.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8952641/SRX8952641.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8952641/SRX8952641.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8952641/SRX8952641.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 20:54:56: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:54:56: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:55:03: 1000000 INFO @ Sat, 15 Jan 2022 20:55:06: #1 tag size is determined as 43 bps INFO @ Sat, 15 Jan 2022 20:55:06: #1 tag size = 43 INFO @ Sat, 15 Jan 2022 20:55:06: #1 total tags in treatment: 423437 INFO @ Sat, 15 Jan 2022 20:55:06: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:55:06: #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 20:55:06: #1 tags after filtering in treatment: 387636 INFO @ Sat, 15 Jan 2022 20:55:06: #1 Redundant rate of treatment: 0.08 INFO @ Sat, 15 Jan 2022 20:55:06: #1 finished! INFO @ Sat, 15 Jan 2022 20:55:06: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:55:06: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:55:06: #2 number of paired peaks: 116 WARNING @ Sat, 15 Jan 2022 20:55:06: Fewer paired peaks (116) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 116 pairs to build model! INFO @ Sat, 15 Jan 2022 20:55:06: start model_add_line... INFO @ Sat, 15 Jan 2022 20:55:06: start X-correlation... INFO @ Sat, 15 Jan 2022 20:55:06: end of X-cor INFO @ Sat, 15 Jan 2022 20:55:06: #2 finished! INFO @ Sat, 15 Jan 2022 20:55:06: #2 predicted fragment length is 251 bps INFO @ Sat, 15 Jan 2022 20:55:06: #2 alternative fragment length(s) may be 4,225,251,598 bps INFO @ Sat, 15 Jan 2022 20:55:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8952641/SRX8952641.10_model.r INFO @ Sat, 15 Jan 2022 20:55:06: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:55:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:55:07: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:55:08: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8952641/SRX8952641.10_peaks.xls INFO @ Sat, 15 Jan 2022 20:55:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8952641/SRX8952641.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:55:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8952641/SRX8952641.10_summits.bed INFO @ Sat, 15 Jan 2022 20:55:08: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (89 records, 4 fields): 2 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 20:55:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8952641/SRX8952641.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8952641/SRX8952641.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8952641/SRX8952641.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8952641/SRX8952641.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 20:55:26: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:55:26: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 20:55:32: 1000000 INFO @ Sat, 15 Jan 2022 20:55:34: #1 tag size is determined as 43 bps INFO @ Sat, 15 Jan 2022 20:55:34: #1 tag size = 43 INFO @ Sat, 15 Jan 2022 20:55:34: #1 total tags in treatment: 423437 INFO @ Sat, 15 Jan 2022 20:55:34: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:55:34: #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 20:55:34: #1 tags after filtering in treatment: 387636 INFO @ Sat, 15 Jan 2022 20:55:34: #1 Redundant rate of treatment: 0.08 INFO @ Sat, 15 Jan 2022 20:55:34: #1 finished! INFO @ Sat, 15 Jan 2022 20:55:34: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:55:34: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:55:34: #2 number of paired peaks: 116 WARNING @ Sat, 15 Jan 2022 20:55:34: Fewer paired peaks (116) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 116 pairs to build model! INFO @ Sat, 15 Jan 2022 20:55:34: start model_add_line... INFO @ Sat, 15 Jan 2022 20:55:34: start X-correlation... INFO @ Sat, 15 Jan 2022 20:55:34: end of X-cor INFO @ Sat, 15 Jan 2022 20:55:34: #2 finished! INFO @ Sat, 15 Jan 2022 20:55:34: #2 predicted fragment length is 251 bps INFO @ Sat, 15 Jan 2022 20:55:34: #2 alternative fragment length(s) may be 4,225,251,598 bps INFO @ Sat, 15 Jan 2022 20:55:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8952641/SRX8952641.20_model.r INFO @ Sat, 15 Jan 2022 20:55:34: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:55:34: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 20:55:35: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:55:36: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8952641/SRX8952641.20_peaks.xls INFO @ Sat, 15 Jan 2022 20:55:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8952641/SRX8952641.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:55:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8952641/SRX8952641.20_summits.bed INFO @ Sat, 15 Jan 2022 20:55:36: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (38 records, 4 fields): 2 millis CompletedMACS2peakCalling