Job ID = 14521404 SRX = SRX10828576 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 3603601 spots for SRR14480401/SRR14480401.sra Written 3603601 spots for SRR14480401/SRR14480401.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: 00:01:54 3603601 reads; of these: 3603601 (100.00%) were paired; of these: 463399 (12.86%) aligned concordantly 0 times 2819099 (78.23%) aligned concordantly exactly 1 time 321103 (8.91%) aligned concordantly >1 times ---- 463399 pairs aligned concordantly 0 times; of these: 105616 (22.79%) aligned discordantly 1 time ---- 357783 pairs aligned 0 times concordantly or discordantly; of these: 715566 mates make up the pairs; of these: 597051 (83.44%) aligned 0 times 84588 (11.82%) aligned exactly 1 time 33927 (4.74%) aligned >1 times 91.72% overall alignment rate Time searching: 00:01:54 Overall time: 00:01:54 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] 375823 / 3202233 = 0.1174 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 21:00:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX10828576/SRX10828576.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX10828576/SRX10828576.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX10828576/SRX10828576.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX10828576/SRX10828576.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 21:00:12: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:00:12: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:00:17: 1000000 INFO @ Sat, 15 Jan 2022 21:00:22: 2000000 INFO @ Sat, 15 Jan 2022 21:00:26: 3000000 INFO @ Sat, 15 Jan 2022 21:00:31: 4000000 INFO @ Sat, 15 Jan 2022 21:00:36: 5000000 INFO @ Sat, 15 Jan 2022 21:00:40: #1 tag size is determined as 51 bps INFO @ Sat, 15 Jan 2022 21:00:40: #1 tag size = 51 INFO @ Sat, 15 Jan 2022 21:00:40: #1 total tags in treatment: 2768284 INFO @ Sat, 15 Jan 2022 21:00:40: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:00:40: #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 21:00:40: #1 tags after filtering in treatment: 2059675 INFO @ Sat, 15 Jan 2022 21:00:40: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 15 Jan 2022 21:00:40: #1 finished! INFO @ Sat, 15 Jan 2022 21:00:40: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:00:40: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:00:40: #2 number of paired peaks: 17 WARNING @ Sat, 15 Jan 2022 21:00:40: 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 21:00:40: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX10828576/SRX10828576.05_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/SRX10828576/SRX10828576.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX10828576/SRX10828576.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX10828576/SRX10828576.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling 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 21:00:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX10828576/SRX10828576.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX10828576/SRX10828576.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX10828576/SRX10828576.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX10828576/SRX10828576.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 21:00:42: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:00:42: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:00:48: 1000000 INFO @ Sat, 15 Jan 2022 21:00:54: 2000000 INFO @ Sat, 15 Jan 2022 21:01:00: 3000000 INFO @ Sat, 15 Jan 2022 21:01:05: 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 21:01:11: 5000000 INFO @ Sat, 15 Jan 2022 21:01:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX10828576/SRX10828576.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX10828576/SRX10828576.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX10828576/SRX10828576.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX10828576/SRX10828576.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 21:01:12: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:01:12: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:01:16: #1 tag size is determined as 51 bps INFO @ Sat, 15 Jan 2022 21:01:16: #1 tag size = 51 INFO @ Sat, 15 Jan 2022 21:01:16: #1 total tags in treatment: 2768284 INFO @ Sat, 15 Jan 2022 21:01:16: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:01:16: #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 21:01:16: #1 tags after filtering in treatment: 2059675 INFO @ Sat, 15 Jan 2022 21:01:16: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 15 Jan 2022 21:01:16: #1 finished! INFO @ Sat, 15 Jan 2022 21:01:16: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:01:16: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:01:16: #2 number of paired peaks: 17 WARNING @ Sat, 15 Jan 2022 21:01:16: 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 21:01:16: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX10828576/SRX10828576.10_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/SRX10828576/SRX10828576.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX10828576/SRX10828576.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX10828576/SRX10828576.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 21:01:18: 1000000 INFO @ Sat, 15 Jan 2022 21:01:24: 2000000 INFO @ Sat, 15 Jan 2022 21:01:29: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 21:01:35: 4000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 21:01:41: 5000000 INFO @ Sat, 15 Jan 2022 21:01:46: #1 tag size is determined as 51 bps INFO @ Sat, 15 Jan 2022 21:01:46: #1 tag size = 51 INFO @ Sat, 15 Jan 2022 21:01:46: #1 total tags in treatment: 2768284 INFO @ Sat, 15 Jan 2022 21:01:46: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:01:46: #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 21:01:46: #1 tags after filtering in treatment: 2059675 INFO @ Sat, 15 Jan 2022 21:01:46: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 15 Jan 2022 21:01:46: #1 finished! INFO @ Sat, 15 Jan 2022 21:01:46: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:01:46: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:01:46: #2 number of paired peaks: 17 WARNING @ Sat, 15 Jan 2022 21:01:46: 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 21:01:46: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX10828576/SRX10828576.20_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/SRX10828576/SRX10828576.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX10828576/SRX10828576.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX10828576/SRX10828576.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling