Job ID = 14521796 SRX = SRX9399067 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 4448046 spots for SRR12935348/SRR12935348.sra Written 4448046 spots for SRR12935348/SRR12935348.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: 00:02:53 4448046 reads; of these: 4448046 (100.00%) were paired; of these: 482639 (10.85%) aligned concordantly 0 times 3505300 (78.81%) aligned concordantly exactly 1 time 460107 (10.34%) aligned concordantly >1 times ---- 482639 pairs aligned concordantly 0 times; of these: 93655 (19.40%) aligned discordantly 1 time ---- 388984 pairs aligned 0 times concordantly or discordantly; of these: 777968 mates make up the pairs; of these: 608891 (78.27%) aligned 0 times 128958 (16.58%) aligned exactly 1 time 40119 (5.16%) aligned >1 times 93.16% overall alignment rate Time searching: 00:02:53 Overall time: 00:02:53 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] 284543 / 4003909 = 0.0711 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 21:41:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9399067/SRX9399067.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9399067/SRX9399067.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9399067/SRX9399067.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9399067/SRX9399067.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 21:41:50: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:41:50: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:41:56: 1000000 INFO @ Sat, 15 Jan 2022 21:42:01: 2000000 INFO @ Sat, 15 Jan 2022 21:42:06: 3000000 INFO @ Sat, 15 Jan 2022 21:42:12: 4000000 INFO @ Sat, 15 Jan 2022 21:42:17: 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 21:42:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9399067/SRX9399067.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9399067/SRX9399067.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9399067/SRX9399067.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9399067/SRX9399067.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 21:42:20: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:42:20: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:42:22: 6000000 INFO @ Sat, 15 Jan 2022 21:42:26: 1000000 INFO @ Sat, 15 Jan 2022 21:42:28: 7000000 INFO @ Sat, 15 Jan 2022 21:42:32: #1 tag size is determined as 37 bps INFO @ Sat, 15 Jan 2022 21:42:32: #1 tag size = 37 INFO @ Sat, 15 Jan 2022 21:42:32: #1 total tags in treatment: 3681616 INFO @ Sat, 15 Jan 2022 21:42:32: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:42:32: #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 21:42:32: 2000000 INFO @ Sat, 15 Jan 2022 21:42:32: #1 tags after filtering in treatment: 2700297 INFO @ Sat, 15 Jan 2022 21:42:32: #1 Redundant rate of treatment: 0.27 INFO @ Sat, 15 Jan 2022 21:42:32: #1 finished! INFO @ Sat, 15 Jan 2022 21:42:32: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:42:32: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:42:32: #2 number of paired peaks: 3 WARNING @ Sat, 15 Jan 2022 21:42:32: Too few paired peaks (3) 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 21:42:32: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX9399067/SRX9399067.05_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/SRX9399067/SRX9399067.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399067/SRX9399067.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399067/SRX9399067.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 21:42:38: 3000000 INFO @ Sat, 15 Jan 2022 21:42:44: 4000000 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 21:42:50: 5000000 INFO @ Sat, 15 Jan 2022 21:42:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9399067/SRX9399067.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9399067/SRX9399067.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9399067/SRX9399067.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9399067/SRX9399067.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 21:42:51: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:42:51: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:42:55: 6000000 INFO @ Sat, 15 Jan 2022 21:42:56: 1000000 INFO @ Sat, 15 Jan 2022 21:43:01: 7000000 INFO @ Sat, 15 Jan 2022 21:43:02: 2000000 INFO @ Sat, 15 Jan 2022 21:43:05: #1 tag size is determined as 37 bps INFO @ Sat, 15 Jan 2022 21:43:05: #1 tag size = 37 INFO @ Sat, 15 Jan 2022 21:43:05: #1 total tags in treatment: 3681616 INFO @ Sat, 15 Jan 2022 21:43:05: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:43:05: #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 21:43:06: #1 tags after filtering in treatment: 2700297 INFO @ Sat, 15 Jan 2022 21:43:06: #1 Redundant rate of treatment: 0.27 INFO @ Sat, 15 Jan 2022 21:43:06: #1 finished! INFO @ Sat, 15 Jan 2022 21:43:06: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:43:06: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:43:06: #2 number of paired peaks: 3 WARNING @ Sat, 15 Jan 2022 21:43:06: Too few paired peaks (3) 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 21:43:06: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX9399067/SRX9399067.10_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/SRX9399067/SRX9399067.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399067/SRX9399067.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399067/SRX9399067.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 21:43:07: 3000000 INFO @ Sat, 15 Jan 2022 21:43:12: 4000000 INFO @ Sat, 15 Jan 2022 21:43:18: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 21:43:23: 6000000 INFO @ Sat, 15 Jan 2022 21:43:29: 7000000 INFO @ Sat, 15 Jan 2022 21:43:32: #1 tag size is determined as 37 bps INFO @ Sat, 15 Jan 2022 21:43:32: #1 tag size = 37 INFO @ Sat, 15 Jan 2022 21:43:32: #1 total tags in treatment: 3681616 INFO @ Sat, 15 Jan 2022 21:43:32: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:43:32: #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 21:43:33: #1 tags after filtering in treatment: 2700297 INFO @ Sat, 15 Jan 2022 21:43:33: #1 Redundant rate of treatment: 0.27 INFO @ Sat, 15 Jan 2022 21:43:33: #1 finished! INFO @ Sat, 15 Jan 2022 21:43:33: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:43:33: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:43:33: #2 number of paired peaks: 3 WARNING @ Sat, 15 Jan 2022 21:43:33: Too few paired peaks (3) 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 21:43:33: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX9399067/SRX9399067.20_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/SRX9399067/SRX9399067.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399067/SRX9399067.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399067/SRX9399067.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。