Job ID = 14520995 SRX = SRX9158103 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 13256735 spots for SRR12677938/SRR12677938.sra Written 13256735 spots for SRR12677938/SRR12677938.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:08:22 13256735 reads; of these: 13256735 (100.00%) were paired; of these: 5128157 (38.68%) aligned concordantly 0 times 5340582 (40.29%) aligned concordantly exactly 1 time 2787996 (21.03%) aligned concordantly >1 times ---- 5128157 pairs aligned concordantly 0 times; of these: 111707 (2.18%) aligned discordantly 1 time ---- 5016450 pairs aligned 0 times concordantly or discordantly; of these: 10032900 mates make up the pairs; of these: 9804544 (97.72%) aligned 0 times 126286 (1.26%) aligned exactly 1 time 102070 (1.02%) aligned >1 times 63.02% overall alignment rate Time searching: 00:08:24 Overall time: 00:08:26 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] 3761632 / 8215889 = 0.4578 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 20:26:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9158103/SRX9158103.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9158103/SRX9158103.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9158103/SRX9158103.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9158103/SRX9158103.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 20:26:42: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:26:42: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:26:46: 1000000 INFO @ Sat, 15 Jan 2022 20:26:50: 2000000 INFO @ Sat, 15 Jan 2022 20:26:54: 3000000 INFO @ Sat, 15 Jan 2022 20:26:58: 4000000 INFO @ Sat, 15 Jan 2022 20:27:02: 5000000 INFO @ Sat, 15 Jan 2022 20:27:06: 6000000 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 20:27:10: 7000000 INFO @ Sat, 15 Jan 2022 20:27:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9158103/SRX9158103.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9158103/SRX9158103.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9158103/SRX9158103.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9158103/SRX9158103.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 20:27:11: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:27:11: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:27:13: 8000000 INFO @ Sat, 15 Jan 2022 20:27:15: 1000000 INFO @ Sat, 15 Jan 2022 20:27:17: 9000000 INFO @ Sat, 15 Jan 2022 20:27:18: #1 tag size is determined as 42 bps INFO @ Sat, 15 Jan 2022 20:27:18: #1 tag size = 42 INFO @ Sat, 15 Jan 2022 20:27:18: #1 total tags in treatment: 4372909 INFO @ Sat, 15 Jan 2022 20:27:18: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:27:18: #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 20:27:18: #1 tags after filtering in treatment: 2511213 INFO @ Sat, 15 Jan 2022 20:27:18: #1 Redundant rate of treatment: 0.43 INFO @ Sat, 15 Jan 2022 20:27:18: #1 finished! INFO @ Sat, 15 Jan 2022 20:27:18: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:27:18: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:27:18: #2 number of paired peaks: 317 WARNING @ Sat, 15 Jan 2022 20:27:18: Fewer paired peaks (317) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 317 pairs to build model! INFO @ Sat, 15 Jan 2022 20:27:18: start model_add_line... INFO @ Sat, 15 Jan 2022 20:27:18: start X-correlation... INFO @ Sat, 15 Jan 2022 20:27:19: end of X-cor INFO @ Sat, 15 Jan 2022 20:27:19: #2 finished! INFO @ Sat, 15 Jan 2022 20:27:19: #2 predicted fragment length is 258 bps INFO @ Sat, 15 Jan 2022 20:27:19: #2 alternative fragment length(s) may be 107,115,154,240,258 bps INFO @ Sat, 15 Jan 2022 20:27:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX9158103/SRX9158103.05_model.r INFO @ Sat, 15 Jan 2022 20:27:19: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:27:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:27:19: 2000000 INFO @ Sat, 15 Jan 2022 20:27:23: 3000000 INFO @ Sat, 15 Jan 2022 20:27:27: 4000000 INFO @ Sat, 15 Jan 2022 20:27:31: 5000000 INFO @ Sat, 15 Jan 2022 20:27:32: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:27:34: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX9158103/SRX9158103.05_peaks.xls INFO @ Sat, 15 Jan 2022 20:27:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX9158103/SRX9158103.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:27:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX9158103/SRX9158103.05_summits.bed INFO @ Sat, 15 Jan 2022 20:27:34: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (740 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 20:27:35: 6000000 INFO @ Sat, 15 Jan 2022 20:27:39: 7000000 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 20:27:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9158103/SRX9158103.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9158103/SRX9158103.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9158103/SRX9158103.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9158103/SRX9158103.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 20:27:41: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:27:41: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:27:43: 8000000 INFO @ Sat, 15 Jan 2022 20:27:45: 1000000 INFO @ Sat, 15 Jan 2022 20:27:47: 9000000 INFO @ Sat, 15 Jan 2022 20:27:47: #1 tag size is determined as 42 bps INFO @ Sat, 15 Jan 2022 20:27:48: #1 tag size = 42 INFO @ Sat, 15 Jan 2022 20:27:48: #1 total tags in treatment: 4372909 INFO @ Sat, 15 Jan 2022 20:27:48: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:27:48: #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 20:27:48: #1 tags after filtering in treatment: 2511213 INFO @ Sat, 15 Jan 2022 20:27:48: #1 Redundant rate of treatment: 0.43 INFO @ Sat, 15 Jan 2022 20:27:48: #1 finished! INFO @ Sat, 15 Jan 2022 20:27:48: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:27:48: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:27:48: #2 number of paired peaks: 317 WARNING @ Sat, 15 Jan 2022 20:27:48: Fewer paired peaks (317) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 317 pairs to build model! INFO @ Sat, 15 Jan 2022 20:27:48: start model_add_line... INFO @ Sat, 15 Jan 2022 20:27:48: start X-correlation... INFO @ Sat, 15 Jan 2022 20:27:48: end of X-cor INFO @ Sat, 15 Jan 2022 20:27:48: #2 finished! INFO @ Sat, 15 Jan 2022 20:27:48: #2 predicted fragment length is 258 bps INFO @ Sat, 15 Jan 2022 20:27:48: #2 alternative fragment length(s) may be 107,115,154,240,258 bps INFO @ Sat, 15 Jan 2022 20:27:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX9158103/SRX9158103.10_model.r INFO @ Sat, 15 Jan 2022 20:27:48: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:27:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:27:49: 2000000 INFO @ Sat, 15 Jan 2022 20:27:53: 3000000 INFO @ Sat, 15 Jan 2022 20:27:57: 4000000 INFO @ Sat, 15 Jan 2022 20:28:01: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:28:01: 5000000 INFO @ Sat, 15 Jan 2022 20:28:03: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX9158103/SRX9158103.10_peaks.xls INFO @ Sat, 15 Jan 2022 20:28:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX9158103/SRX9158103.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:28:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX9158103/SRX9158103.10_summits.bed INFO @ Sat, 15 Jan 2022 20:28:03: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (691 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 20:28:05: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 20:28:08: 7000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 20:28:12: 8000000 INFO @ Sat, 15 Jan 2022 20:28:16: 9000000 INFO @ Sat, 15 Jan 2022 20:28:17: #1 tag size is determined as 42 bps INFO @ Sat, 15 Jan 2022 20:28:17: #1 tag size = 42 INFO @ Sat, 15 Jan 2022 20:28:17: #1 total tags in treatment: 4372909 INFO @ Sat, 15 Jan 2022 20:28:17: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:28:17: #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 20:28:17: #1 tags after filtering in treatment: 2511213 INFO @ Sat, 15 Jan 2022 20:28:17: #1 Redundant rate of treatment: 0.43 INFO @ Sat, 15 Jan 2022 20:28:17: #1 finished! INFO @ Sat, 15 Jan 2022 20:28:17: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:28:17: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:28:17: #2 number of paired peaks: 317 WARNING @ Sat, 15 Jan 2022 20:28:17: Fewer paired peaks (317) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 317 pairs to build model! INFO @ Sat, 15 Jan 2022 20:28:17: start model_add_line... INFO @ Sat, 15 Jan 2022 20:28:17: start X-correlation... INFO @ Sat, 15 Jan 2022 20:28:17: end of X-cor INFO @ Sat, 15 Jan 2022 20:28:17: #2 finished! INFO @ Sat, 15 Jan 2022 20:28:17: #2 predicted fragment length is 258 bps INFO @ Sat, 15 Jan 2022 20:28:17: #2 alternative fragment length(s) may be 107,115,154,240,258 bps INFO @ Sat, 15 Jan 2022 20:28:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX9158103/SRX9158103.20_model.r INFO @ Sat, 15 Jan 2022 20:28:17: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:28:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:28:30: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:28:32: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX9158103/SRX9158103.20_peaks.xls INFO @ Sat, 15 Jan 2022 20:28:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX9158103/SRX9158103.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:28:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX9158103/SRX9158103.20_summits.bed INFO @ Sat, 15 Jan 2022 20:28:32: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (505 records, 4 fields): 2 millis CompletedMACS2peakCalling