Job ID = 14521595 SRX = SRX9399107 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 6635417 spots for SRR12935388/SRR12935388.sra Written 6635417 spots for SRR12935388/SRR12935388.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: 00:04:06 6635417 reads; of these: 6635417 (100.00%) were paired; of these: 374061 (5.64%) aligned concordantly 0 times 4794549 (72.26%) aligned concordantly exactly 1 time 1466807 (22.11%) aligned concordantly >1 times ---- 374061 pairs aligned concordantly 0 times; of these: 40911 (10.94%) aligned discordantly 1 time ---- 333150 pairs aligned 0 times concordantly or discordantly; of these: 666300 mates make up the pairs; of these: 528300 (79.29%) aligned 0 times 91236 (13.69%) aligned exactly 1 time 46764 (7.02%) aligned >1 times 96.02% overall alignment rate Time searching: 00:04:06 Overall time: 00:04:06 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] 1516045 / 6291452 = 0.2410 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 21:38:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9399107/SRX9399107.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9399107/SRX9399107.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9399107/SRX9399107.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9399107/SRX9399107.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 21:38:14: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:38:14: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:38:20: 1000000 INFO @ Sat, 15 Jan 2022 21:38:26: 2000000 INFO @ Sat, 15 Jan 2022 21:38:31: 3000000 INFO @ Sat, 15 Jan 2022 21:38:37: 4000000 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 21:38:44: 5000000 INFO @ Sat, 15 Jan 2022 21:38:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9399107/SRX9399107.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9399107/SRX9399107.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9399107/SRX9399107.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9399107/SRX9399107.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 21:38:44: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:38:44: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:38:49: 1000000 INFO @ Sat, 15 Jan 2022 21:38:50: 6000000 INFO @ Sat, 15 Jan 2022 21:38:55: 2000000 INFO @ Sat, 15 Jan 2022 21:38:56: 7000000 INFO @ Sat, 15 Jan 2022 21:39:00: 3000000 INFO @ Sat, 15 Jan 2022 21:39:02: 8000000 INFO @ Sat, 15 Jan 2022 21:39:06: 4000000 INFO @ Sat, 15 Jan 2022 21:39:09: 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 21:39:12: 5000000 INFO @ Sat, 15 Jan 2022 21:39:14: #1 tag size is determined as 42 bps INFO @ Sat, 15 Jan 2022 21:39:14: #1 tag size = 42 INFO @ Sat, 15 Jan 2022 21:39:14: #1 total tags in treatment: 4747206 INFO @ Sat, 15 Jan 2022 21:39:14: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:39:14: #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 21:39:14: #1 tags after filtering in treatment: 3087833 INFO @ Sat, 15 Jan 2022 21:39:14: #1 Redundant rate of treatment: 0.35 INFO @ Sat, 15 Jan 2022 21:39:14: #1 finished! INFO @ Sat, 15 Jan 2022 21:39:14: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:39:14: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:39:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9399107/SRX9399107.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9399107/SRX9399107.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9399107/SRX9399107.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9399107/SRX9399107.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 21:39:14: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:39:14: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:39:14: #2 number of paired peaks: 27 WARNING @ Sat, 15 Jan 2022 21:39:14: Too few paired peaks (27) so I can not build the model! Broader your MFOLD range parameter may erase this error. If it still can't build the model, we suggest to use --nomodel and --extsize 147 or other fixed number instead. WARNING @ Sat, 15 Jan 2022 21:39:14: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX9399107/SRX9399107.05_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399107/SRX9399107.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399107/SRX9399107.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399107/SRX9399107.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 21:39:17: 6000000 INFO @ Sat, 15 Jan 2022 21:39:20: 1000000 INFO @ Sat, 15 Jan 2022 21:39:23: 7000000 INFO @ Sat, 15 Jan 2022 21:39:27: 2000000 INFO @ Sat, 15 Jan 2022 21:39:28: 8000000 INFO @ Sat, 15 Jan 2022 21:39:33: 3000000 INFO @ Sat, 15 Jan 2022 21:39:34: 9000000 INFO @ Sat, 15 Jan 2022 21:39:38: #1 tag size is determined as 42 bps INFO @ Sat, 15 Jan 2022 21:39:38: #1 tag size = 42 INFO @ Sat, 15 Jan 2022 21:39:38: #1 total tags in treatment: 4747206 INFO @ Sat, 15 Jan 2022 21:39:38: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:39:38: #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 21:39:38: #1 tags after filtering in treatment: 3087833 INFO @ Sat, 15 Jan 2022 21:39:38: #1 Redundant rate of treatment: 0.35 INFO @ Sat, 15 Jan 2022 21:39:38: #1 finished! INFO @ Sat, 15 Jan 2022 21:39:38: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:39:38: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:39:38: #2 number of paired peaks: 27 WARNING @ Sat, 15 Jan 2022 21:39:38: Too few paired peaks (27) so I can not build the model! Broader your MFOLD range parameter may erase this error. If it still can't build the model, we suggest to use --nomodel and --extsize 147 or other fixed number instead. WARNING @ Sat, 15 Jan 2022 21:39:38: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX9399107/SRX9399107.10_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399107/SRX9399107.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399107/SRX9399107.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399107/SRX9399107.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 21:39:40: 4000000 INFO @ Sat, 15 Jan 2022 21:39:46: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 21:39:53: 6000000 INFO @ Sat, 15 Jan 2022 21:39:59: 7000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 21:40:05: 8000000 INFO @ Sat, 15 Jan 2022 21:40:12: 9000000 INFO @ Sat, 15 Jan 2022 21:40:16: #1 tag size is determined as 42 bps INFO @ Sat, 15 Jan 2022 21:40:16: #1 tag size = 42 INFO @ Sat, 15 Jan 2022 21:40:16: #1 total tags in treatment: 4747206 INFO @ Sat, 15 Jan 2022 21:40:16: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:40:16: #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 21:40:17: #1 tags after filtering in treatment: 3087833 INFO @ Sat, 15 Jan 2022 21:40:17: #1 Redundant rate of treatment: 0.35 INFO @ Sat, 15 Jan 2022 21:40:17: #1 finished! INFO @ Sat, 15 Jan 2022 21:40:17: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:40:17: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:40:17: #2 number of paired peaks: 27 WARNING @ Sat, 15 Jan 2022 21:40:17: Too few paired peaks (27) so I can not build the model! Broader your MFOLD range parameter may erase this error. If it still can't build the model, we suggest to use --nomodel and --extsize 147 or other fixed number instead. WARNING @ Sat, 15 Jan 2022 21:40:17: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX9399107/SRX9399107.20_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399107/SRX9399107.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399107/SRX9399107.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399107/SRX9399107.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling