Job ID = 14521197 SRX = SRX8245375 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 7990711 spots for SRR11684586/SRR11684586.sra Written 7990711 spots for SRR11684586/SRR11684586.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: 00:07:56 7990711 reads; of these: 7990711 (100.00%) were paired; of these: 4316766 (54.02%) aligned concordantly 0 times 2543136 (31.83%) aligned concordantly exactly 1 time 1130809 (14.15%) aligned concordantly >1 times ---- 4316766 pairs aligned concordantly 0 times; of these: 79629 (1.84%) aligned discordantly 1 time ---- 4237137 pairs aligned 0 times concordantly or discordantly; of these: 8474274 mates make up the pairs; of these: 5602695 (66.11%) aligned 0 times 1979003 (23.35%) aligned exactly 1 time 892576 (10.53%) aligned >1 times 64.94% overall alignment rate Time searching: 00:07:56 Overall time: 00:07:56 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_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] 192431 / 3752813 = 0.0513 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 20:47:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245375/SRX8245375.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245375/SRX8245375.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245375/SRX8245375.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245375/SRX8245375.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 20:47:35: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:47:35: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:47:41: 1000000 INFO @ Sat, 15 Jan 2022 20:47:47: 2000000 INFO @ Sat, 15 Jan 2022 20:47:52: 3000000 INFO @ Sat, 15 Jan 2022 20:47:57: 4000000 INFO @ Sat, 15 Jan 2022 20:48:03: 5000000 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 20:48:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245375/SRX8245375.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245375/SRX8245375.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245375/SRX8245375.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245375/SRX8245375.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 20:48:05: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:48:05: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:48:10: 6000000 INFO @ Sat, 15 Jan 2022 20:48:13: 1000000 INFO @ Sat, 15 Jan 2022 20:48:17: 7000000 INFO @ Sat, 15 Jan 2022 20:48:21: 2000000 INFO @ Sat, 15 Jan 2022 20:48:24: 8000000 INFO @ Sat, 15 Jan 2022 20:48:28: 3000000 INFO @ Sat, 15 Jan 2022 20:48:31: 9000000 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 20:48:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245375/SRX8245375.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245375/SRX8245375.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245375/SRX8245375.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245375/SRX8245375.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 20:48:35: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:48:35: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:48:36: 4000000 INFO @ Sat, 15 Jan 2022 20:48:38: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:48:38: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:48:38: #1 total tags in treatment: 3483673 INFO @ Sat, 15 Jan 2022 20:48:38: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:48:38: #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 20:48:38: #1 tags after filtering in treatment: 2334669 INFO @ Sat, 15 Jan 2022 20:48:38: #1 Redundant rate of treatment: 0.33 INFO @ Sat, 15 Jan 2022 20:48:38: #1 finished! INFO @ Sat, 15 Jan 2022 20:48:38: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:48:38: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:48:39: #2 number of paired peaks: 107 WARNING @ Sat, 15 Jan 2022 20:48:39: Fewer paired peaks (107) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 107 pairs to build model! INFO @ Sat, 15 Jan 2022 20:48:39: start model_add_line... INFO @ Sat, 15 Jan 2022 20:48:39: start X-correlation... INFO @ Sat, 15 Jan 2022 20:48:39: end of X-cor INFO @ Sat, 15 Jan 2022 20:48:39: #2 finished! INFO @ Sat, 15 Jan 2022 20:48:39: #2 predicted fragment length is 345 bps INFO @ Sat, 15 Jan 2022 20:48:39: #2 alternative fragment length(s) may be 2,312,334,340,345 bps INFO @ Sat, 15 Jan 2022 20:48:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245375/SRX8245375.05_model.r INFO @ Sat, 15 Jan 2022 20:48:39: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:48:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:48:43: 5000000 INFO @ Sat, 15 Jan 2022 20:48:43: 1000000 INFO @ Sat, 15 Jan 2022 20:48:48: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:48:50: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8245375/SRX8245375.05_peaks.xls INFO @ Sat, 15 Jan 2022 20:48:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8245375/SRX8245375.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:48:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8245375/SRX8245375.05_summits.bed INFO @ Sat, 15 Jan 2022 20:48:50: Done! pass1 - making usageList (17 chroms): 2 millis pass2 - checking and writing primary data (514 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 20:48:51: 6000000 INFO @ Sat, 15 Jan 2022 20:48:51: 2000000 INFO @ Sat, 15 Jan 2022 20:48:58: 7000000 INFO @ Sat, 15 Jan 2022 20:48:59: 3000000 INFO @ Sat, 15 Jan 2022 20:49:06: 8000000 INFO @ Sat, 15 Jan 2022 20:49:06: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 20:49:14: 9000000 INFO @ Sat, 15 Jan 2022 20:49:14: 5000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 20:49:21: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:49:21: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:49:21: #1 total tags in treatment: 3483673 INFO @ Sat, 15 Jan 2022 20:49:21: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:49:21: #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 20:49:21: #1 tags after filtering in treatment: 2334669 INFO @ Sat, 15 Jan 2022 20:49:21: #1 Redundant rate of treatment: 0.33 INFO @ Sat, 15 Jan 2022 20:49:21: #1 finished! INFO @ Sat, 15 Jan 2022 20:49:21: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:49:21: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:49:21: #2 number of paired peaks: 107 WARNING @ Sat, 15 Jan 2022 20:49:21: Fewer paired peaks (107) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 107 pairs to build model! INFO @ Sat, 15 Jan 2022 20:49:21: start model_add_line... INFO @ Sat, 15 Jan 2022 20:49:21: start X-correlation... INFO @ Sat, 15 Jan 2022 20:49:21: end of X-cor INFO @ Sat, 15 Jan 2022 20:49:21: #2 finished! INFO @ Sat, 15 Jan 2022 20:49:21: #2 predicted fragment length is 345 bps INFO @ Sat, 15 Jan 2022 20:49:21: #2 alternative fragment length(s) may be 2,312,334,340,345 bps INFO @ Sat, 15 Jan 2022 20:49:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245375/SRX8245375.10_model.r INFO @ Sat, 15 Jan 2022 20:49:21: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:49:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:49:22: 6000000 INFO @ Sat, 15 Jan 2022 20:49:28: 7000000 INFO @ Sat, 15 Jan 2022 20:49:31: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:49:33: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8245375/SRX8245375.10_peaks.xls INFO @ Sat, 15 Jan 2022 20:49:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8245375/SRX8245375.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:49:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8245375/SRX8245375.10_summits.bed INFO @ Sat, 15 Jan 2022 20:49:33: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (266 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 20:49:35: 8000000 INFO @ Sat, 15 Jan 2022 20:49:41: 9000000 INFO @ Sat, 15 Jan 2022 20:49:48: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:49:48: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:49:48: #1 total tags in treatment: 3483673 INFO @ Sat, 15 Jan 2022 20:49:48: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:49:48: #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 20:49:48: #1 tags after filtering in treatment: 2334669 INFO @ Sat, 15 Jan 2022 20:49:48: #1 Redundant rate of treatment: 0.33 INFO @ Sat, 15 Jan 2022 20:49:48: #1 finished! INFO @ Sat, 15 Jan 2022 20:49:48: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:49:48: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:49:48: #2 number of paired peaks: 107 WARNING @ Sat, 15 Jan 2022 20:49:48: Fewer paired peaks (107) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 107 pairs to build model! INFO @ Sat, 15 Jan 2022 20:49:48: start model_add_line... INFO @ Sat, 15 Jan 2022 20:49:48: start X-correlation... INFO @ Sat, 15 Jan 2022 20:49:48: end of X-cor INFO @ Sat, 15 Jan 2022 20:49:48: #2 finished! INFO @ Sat, 15 Jan 2022 20:49:48: #2 predicted fragment length is 345 bps INFO @ Sat, 15 Jan 2022 20:49:48: #2 alternative fragment length(s) may be 2,312,334,340,345 bps INFO @ Sat, 15 Jan 2022 20:49:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245375/SRX8245375.20_model.r INFO @ Sat, 15 Jan 2022 20:49:48: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:49:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:49:58: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:50:00: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8245375/SRX8245375.20_peaks.xls INFO @ Sat, 15 Jan 2022 20:50:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8245375/SRX8245375.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:50:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8245375/SRX8245375.20_summits.bed INFO @ Sat, 15 Jan 2022 20:50:00: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (101 records, 4 fields): 1 millis CompletedMACS2peakCalling