Job ID = 14520255 SRX = SRX8398438 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 1896408 spots for SRR11848026/SRR11848026.sra Written 1896408 spots for SRR11848026/SRR11848026.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: 00:01:02 1896408 reads; of these: 1896408 (100.00%) were paired; of these: 526771 (27.78%) aligned concordantly 0 times 1167978 (61.59%) aligned concordantly exactly 1 time 201659 (10.63%) aligned concordantly >1 times ---- 526771 pairs aligned concordantly 0 times; of these: 15458 (2.93%) aligned discordantly 1 time ---- 511313 pairs aligned 0 times concordantly or discordantly; of these: 1022626 mates make up the pairs; of these: 1008631 (98.63%) aligned 0 times 6790 (0.66%) aligned exactly 1 time 7205 (0.70%) aligned >1 times 73.41% overall alignment rate Time searching: 00:01:02 Overall time: 00:01:02 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] 85865 / 1384480 = 0.0620 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 18:48:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8398438/SRX8398438.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8398438/SRX8398438.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8398438/SRX8398438.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8398438/SRX8398438.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 18:48:27: #1 read tag files... INFO @ Sat, 15 Jan 2022 18:48:27: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 18:48:32: 1000000 INFO @ Sat, 15 Jan 2022 18:48:37: 2000000 INFO @ Sat, 15 Jan 2022 18:48:39: #1 tag size is determined as 38 bps INFO @ Sat, 15 Jan 2022 18:48:39: #1 tag size = 38 INFO @ Sat, 15 Jan 2022 18:48:39: #1 total tags in treatment: 1284063 INFO @ Sat, 15 Jan 2022 18:48:39: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 18:48:39: #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 18:48:39: #1 tags after filtering in treatment: 991690 INFO @ Sat, 15 Jan 2022 18:48:39: #1 Redundant rate of treatment: 0.23 INFO @ Sat, 15 Jan 2022 18:48:39: #1 finished! INFO @ Sat, 15 Jan 2022 18:48:39: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 18:48:39: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 18:48:39: #2 number of paired peaks: 268 WARNING @ Sat, 15 Jan 2022 18:48:39: Fewer paired peaks (268) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 268 pairs to build model! INFO @ Sat, 15 Jan 2022 18:48:39: start model_add_line... INFO @ Sat, 15 Jan 2022 18:48:39: start X-correlation... INFO @ Sat, 15 Jan 2022 18:48:39: end of X-cor INFO @ Sat, 15 Jan 2022 18:48:39: #2 finished! INFO @ Sat, 15 Jan 2022 18:48:39: #2 predicted fragment length is 83 bps INFO @ Sat, 15 Jan 2022 18:48:39: #2 alternative fragment length(s) may be 4,36,83,583 bps INFO @ Sat, 15 Jan 2022 18:48:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8398438/SRX8398438.05_model.r INFO @ Sat, 15 Jan 2022 18:48:39: #3 Call peaks... INFO @ Sat, 15 Jan 2022 18:48:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 18:48:42: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 18:48:43: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8398438/SRX8398438.05_peaks.xls INFO @ Sat, 15 Jan 2022 18:48:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8398438/SRX8398438.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 18:48:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8398438/SRX8398438.05_summits.bed INFO @ Sat, 15 Jan 2022 18:48:43: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (200 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 18:48:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8398438/SRX8398438.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8398438/SRX8398438.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8398438/SRX8398438.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8398438/SRX8398438.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 18:48:58: #1 read tag files... INFO @ Sat, 15 Jan 2022 18:48:58: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 18:49:03: 1000000 INFO @ Sat, 15 Jan 2022 18:49:09: 2000000 INFO @ Sat, 15 Jan 2022 18:49:13: #1 tag size is determined as 38 bps INFO @ Sat, 15 Jan 2022 18:49:13: #1 tag size = 38 INFO @ Sat, 15 Jan 2022 18:49:13: #1 total tags in treatment: 1284063 INFO @ Sat, 15 Jan 2022 18:49:13: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 18:49:13: #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 18:49:13: #1 tags after filtering in treatment: 991690 INFO @ Sat, 15 Jan 2022 18:49:13: #1 Redundant rate of treatment: 0.23 INFO @ Sat, 15 Jan 2022 18:49:13: #1 finished! INFO @ Sat, 15 Jan 2022 18:49:13: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 18:49:13: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 18:49:13: #2 number of paired peaks: 268 WARNING @ Sat, 15 Jan 2022 18:49:13: Fewer paired peaks (268) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 268 pairs to build model! INFO @ Sat, 15 Jan 2022 18:49:13: start model_add_line... INFO @ Sat, 15 Jan 2022 18:49:13: start X-correlation... INFO @ Sat, 15 Jan 2022 18:49:13: end of X-cor INFO @ Sat, 15 Jan 2022 18:49:13: #2 finished! INFO @ Sat, 15 Jan 2022 18:49:13: #2 predicted fragment length is 83 bps INFO @ Sat, 15 Jan 2022 18:49:13: #2 alternative fragment length(s) may be 4,36,83,583 bps INFO @ Sat, 15 Jan 2022 18:49:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8398438/SRX8398438.10_model.r INFO @ Sat, 15 Jan 2022 18:49:13: #3 Call peaks... INFO @ Sat, 15 Jan 2022 18:49:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 18:49:15: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 18:49:16: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8398438/SRX8398438.10_peaks.xls INFO @ Sat, 15 Jan 2022 18:49:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8398438/SRX8398438.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 18:49:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8398438/SRX8398438.10_summits.bed INFO @ Sat, 15 Jan 2022 18:49:16: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (56 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 18:49:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8398438/SRX8398438.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8398438/SRX8398438.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8398438/SRX8398438.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8398438/SRX8398438.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 18:49:27: #1 read tag files... INFO @ Sat, 15 Jan 2022 18:49:27: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 18:49:32: 1000000 INFO @ Sat, 15 Jan 2022 18:49:37: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 18:49:40: #1 tag size is determined as 38 bps INFO @ Sat, 15 Jan 2022 18:49:40: #1 tag size = 38 INFO @ Sat, 15 Jan 2022 18:49:40: #1 total tags in treatment: 1284063 INFO @ Sat, 15 Jan 2022 18:49:40: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 18:49:40: #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 18:49:40: #1 tags after filtering in treatment: 991690 INFO @ Sat, 15 Jan 2022 18:49:40: #1 Redundant rate of treatment: 0.23 INFO @ Sat, 15 Jan 2022 18:49:40: #1 finished! INFO @ Sat, 15 Jan 2022 18:49:40: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 18:49:40: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 18:49:40: #2 number of paired peaks: 268 WARNING @ Sat, 15 Jan 2022 18:49:40: Fewer paired peaks (268) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 268 pairs to build model! INFO @ Sat, 15 Jan 2022 18:49:40: start model_add_line... INFO @ Sat, 15 Jan 2022 18:49:40: start X-correlation... INFO @ Sat, 15 Jan 2022 18:49:40: end of X-cor INFO @ Sat, 15 Jan 2022 18:49:40: #2 finished! INFO @ Sat, 15 Jan 2022 18:49:40: #2 predicted fragment length is 83 bps INFO @ Sat, 15 Jan 2022 18:49:40: #2 alternative fragment length(s) may be 4,36,83,583 bps INFO @ Sat, 15 Jan 2022 18:49:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8398438/SRX8398438.20_model.r INFO @ Sat, 15 Jan 2022 18:49:40: #3 Call peaks... INFO @ Sat, 15 Jan 2022 18:49:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 18:49:42: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 18:49:43: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8398438/SRX8398438.20_peaks.xls INFO @ Sat, 15 Jan 2022 18:49:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8398438/SRX8398438.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 18:49:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8398438/SRX8398438.20_summits.bed INFO @ Sat, 15 Jan 2022 18:49:43: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (3 records, 4 fields): 1 millis CompletedMACS2peakCalling