Job ID = 14519832 SRX = SRX9369655 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 3234222 spots for SRR12904752/SRR12904752.sra Written 3234222 spots for SRR12904752/SRR12904752.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: 00:00:01 Multiseed full-index search: 00:02:31 3234222 reads; of these: 3234222 (100.00%) were paired; of these: 457959 (14.16%) aligned concordantly 0 times 2323393 (71.84%) aligned concordantly exactly 1 time 452870 (14.00%) aligned concordantly >1 times ---- 457959 pairs aligned concordantly 0 times; of these: 77834 (17.00%) aligned discordantly 1 time ---- 380125 pairs aligned 0 times concordantly or discordantly; of these: 760250 mates make up the pairs; of these: 710433 (93.45%) aligned 0 times 16839 (2.21%) aligned exactly 1 time 32978 (4.34%) aligned >1 times 89.02% overall alignment rate Time searching: 00:02:32 Overall time: 00:02:32 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] 284131 / 2845596 = 0.0998 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 17:54:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9369655/SRX9369655.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9369655/SRX9369655.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9369655/SRX9369655.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9369655/SRX9369655.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 17:54:13: #1 read tag files... INFO @ Sat, 15 Jan 2022 17:54:13: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 17:54:21: 1000000 INFO @ Sat, 15 Jan 2022 17:54:28: 2000000 INFO @ Sat, 15 Jan 2022 17:54:36: 3000000 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 17:54:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9369655/SRX9369655.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9369655/SRX9369655.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9369655/SRX9369655.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9369655/SRX9369655.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 17:54:42: #1 read tag files... INFO @ Sat, 15 Jan 2022 17:54:42: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 17:54:44: 4000000 INFO @ Sat, 15 Jan 2022 17:54:48: 1000000 INFO @ Sat, 15 Jan 2022 17:54:51: 5000000 INFO @ Sat, 15 Jan 2022 17:54:53: #1 tag size is determined as 51 bps INFO @ Sat, 15 Jan 2022 17:54:53: #1 tag size = 51 INFO @ Sat, 15 Jan 2022 17:54:53: #1 total tags in treatment: 2496705 INFO @ Sat, 15 Jan 2022 17:54:53: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 17:54:53: #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 17:54:53: #1 tags after filtering in treatment: 1965762 INFO @ Sat, 15 Jan 2022 17:54:53: #1 Redundant rate of treatment: 0.21 INFO @ Sat, 15 Jan 2022 17:54:53: #1 finished! INFO @ Sat, 15 Jan 2022 17:54:53: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 17:54:53: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 17:54:53: #2 number of paired peaks: 30 WARNING @ Sat, 15 Jan 2022 17:54:53: Too few paired peaks (30) 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 17:54:53: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX9369655/SRX9369655.05_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/SRX9369655/SRX9369655.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9369655/SRX9369655.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9369655/SRX9369655.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 17:54:54: 2000000 INFO @ Sat, 15 Jan 2022 17:55:00: 3000000 INFO @ Sat, 15 Jan 2022 17:55:06: 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 17:55:11: 5000000 INFO @ Sat, 15 Jan 2022 17:55:12: #1 tag size is determined as 51 bps INFO @ Sat, 15 Jan 2022 17:55:12: #1 tag size = 51 INFO @ Sat, 15 Jan 2022 17:55:12: #1 total tags in treatment: 2496705 INFO @ Sat, 15 Jan 2022 17:55:12: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 17:55:12: #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 17:55:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9369655/SRX9369655.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9369655/SRX9369655.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9369655/SRX9369655.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9369655/SRX9369655.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 17:55:12: #1 read tag files... INFO @ Sat, 15 Jan 2022 17:55:12: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 17:55:12: #1 tags after filtering in treatment: 1965762 INFO @ Sat, 15 Jan 2022 17:55:12: #1 Redundant rate of treatment: 0.21 INFO @ Sat, 15 Jan 2022 17:55:12: #1 finished! INFO @ Sat, 15 Jan 2022 17:55:12: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 17:55:12: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 17:55:12: #2 number of paired peaks: 30 WARNING @ Sat, 15 Jan 2022 17:55:12: Too few paired peaks (30) 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 17:55:12: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX9369655/SRX9369655.10_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/SRX9369655/SRX9369655.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9369655/SRX9369655.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9369655/SRX9369655.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 17:55:18: 1000000 INFO @ Sat, 15 Jan 2022 17:55:24: 2000000 INFO @ Sat, 15 Jan 2022 17:55:30: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 17:55:36: 4000000 INFO @ Sat, 15 Jan 2022 17:55:41: 5000000 INFO @ Sat, 15 Jan 2022 17:55:42: #1 tag size is determined as 51 bps INFO @ Sat, 15 Jan 2022 17:55:42: #1 tag size = 51 INFO @ Sat, 15 Jan 2022 17:55:42: #1 total tags in treatment: 2496705 INFO @ Sat, 15 Jan 2022 17:55:42: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 17:55:42: #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 17:55:42: #1 tags after filtering in treatment: 1965762 INFO @ Sat, 15 Jan 2022 17:55:42: #1 Redundant rate of treatment: 0.21 INFO @ Sat, 15 Jan 2022 17:55:42: #1 finished! INFO @ Sat, 15 Jan 2022 17:55:42: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 17:55:42: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 17:55:42: #2 number of paired peaks: 30 WARNING @ Sat, 15 Jan 2022 17:55:42: Too few paired peaks (30) 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 17:55:42: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX9369655/SRX9369655.20_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9369655/SRX9369655.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9369655/SRX9369655.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9369655/SRX9369655.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。