Job ID = 14521660 SRX = SRX9399021 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 5062692 spots for SRR12935303/SRR12935303.sra Written 5062692 spots for SRR12935303/SRR12935303.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: 00:02:03 5062692 reads; of these: 5062692 (100.00%) were paired; of these: 669958 (13.23%) aligned concordantly 0 times 3751286 (74.10%) aligned concordantly exactly 1 time 641448 (12.67%) aligned concordantly >1 times ---- 669958 pairs aligned concordantly 0 times; of these: 247431 (36.93%) aligned discordantly 1 time ---- 422527 pairs aligned 0 times concordantly or discordantly; of these: 845054 mates make up the pairs; of these: 522452 (61.82%) aligned 0 times 208717 (24.70%) aligned exactly 1 time 113885 (13.48%) aligned >1 times 94.84% overall alignment rate Time searching: 00:02:03 Overall time: 00:02:03 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] 477151 / 4446810 = 0.1073 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 21:26:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9399021/SRX9399021.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9399021/SRX9399021.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9399021/SRX9399021.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9399021/SRX9399021.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 21:26:24: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:26:24: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:26:30: 1000000 INFO @ Sat, 15 Jan 2022 21:26:36: 2000000 INFO @ Sat, 15 Jan 2022 21:26:43: 3000000 INFO @ Sat, 15 Jan 2022 21:26:50: 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 21:26:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9399021/SRX9399021.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9399021/SRX9399021.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9399021/SRX9399021.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9399021/SRX9399021.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 21:26:54: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:26:54: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:26:56: 5000000 INFO @ Sat, 15 Jan 2022 21:27:00: 1000000 INFO @ Sat, 15 Jan 2022 21:27:04: 6000000 INFO @ Sat, 15 Jan 2022 21:27:06: 2000000 INFO @ Sat, 15 Jan 2022 21:27:11: 7000000 INFO @ Sat, 15 Jan 2022 21:27:13: 3000000 INFO @ Sat, 15 Jan 2022 21:27:18: 8000000 INFO @ Sat, 15 Jan 2022 21:27:19: 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 21:27:23: #1 tag size is determined as 40 bps INFO @ Sat, 15 Jan 2022 21:27:23: #1 tag size = 40 INFO @ Sat, 15 Jan 2022 21:27:23: #1 total tags in treatment: 3916913 INFO @ Sat, 15 Jan 2022 21:27:23: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:27:23: #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 21:27:23: #1 tags after filtering in treatment: 2717781 INFO @ Sat, 15 Jan 2022 21:27:23: #1 Redundant rate of treatment: 0.31 INFO @ Sat, 15 Jan 2022 21:27:23: #1 finished! INFO @ Sat, 15 Jan 2022 21:27:23: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:27:23: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:27:23: #2 number of paired peaks: 17 WARNING @ Sat, 15 Jan 2022 21:27:23: Too few paired peaks (17) 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 21:27:23: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX9399021/SRX9399021.05_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/SRX9399021/SRX9399021.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399021/SRX9399021.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399021/SRX9399021.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 21:27:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9399021/SRX9399021.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9399021/SRX9399021.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9399021/SRX9399021.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9399021/SRX9399021.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 21:27:24: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:27:24: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:27:25: 5000000 INFO @ Sat, 15 Jan 2022 21:27:30: 1000000 INFO @ Sat, 15 Jan 2022 21:27:31: 6000000 INFO @ Sat, 15 Jan 2022 21:27:36: 2000000 INFO @ Sat, 15 Jan 2022 21:27:38: 7000000 INFO @ Sat, 15 Jan 2022 21:27:42: 3000000 INFO @ Sat, 15 Jan 2022 21:27:44: 8000000 INFO @ Sat, 15 Jan 2022 21:27:47: #1 tag size is determined as 40 bps INFO @ Sat, 15 Jan 2022 21:27:47: #1 tag size = 40 INFO @ Sat, 15 Jan 2022 21:27:47: #1 total tags in treatment: 3916913 INFO @ Sat, 15 Jan 2022 21:27:47: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:27:47: #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 21:27:47: #1 tags after filtering in treatment: 2717781 INFO @ Sat, 15 Jan 2022 21:27:47: #1 Redundant rate of treatment: 0.31 INFO @ Sat, 15 Jan 2022 21:27:47: #1 finished! INFO @ Sat, 15 Jan 2022 21:27:47: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:27:47: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:27:48: #2 number of paired peaks: 17 WARNING @ Sat, 15 Jan 2022 21:27:48: Too few paired peaks (17) 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 21:27:48: Process for pairing-model is terminated! INFO @ Sat, 15 Jan 2022 21:27:48: 4000000 cut: /home/okishinya/chipatlas/results/sacCer3/SRX9399021/SRX9399021.10_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/SRX9399021/SRX9399021.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399021/SRX9399021.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399021/SRX9399021.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 21:27:54: 5000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 21:27:59: 6000000 INFO @ Sat, 15 Jan 2022 21:28:04: 7000000 INFO @ Sat, 15 Jan 2022 21:28:09: 8000000 INFO @ Sat, 15 Jan 2022 21:28:12: #1 tag size is determined as 40 bps INFO @ Sat, 15 Jan 2022 21:28:12: #1 tag size = 40 INFO @ Sat, 15 Jan 2022 21:28:12: #1 total tags in treatment: 3916913 INFO @ Sat, 15 Jan 2022 21:28:12: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:28:12: #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 21:28:12: #1 tags after filtering in treatment: 2717781 INFO @ Sat, 15 Jan 2022 21:28:12: #1 Redundant rate of treatment: 0.31 INFO @ Sat, 15 Jan 2022 21:28:12: #1 finished! INFO @ Sat, 15 Jan 2022 21:28:12: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:28:12: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:28:12: #2 number of paired peaks: 17 WARNING @ Sat, 15 Jan 2022 21:28:12: Too few paired peaks (17) 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 21:28:12: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX9399021/SRX9399021.20_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 3 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399021/SRX9399021.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399021/SRX9399021.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399021/SRX9399021.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling