Job ID = 14521371 SRX = SRX10468567 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 3690503 spots for SRR14094877/SRR14094877.sra Written 3690503 spots for SRR14094877/SRR14094877.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: 00:01:18 3690503 reads; of these: 3690503 (100.00%) were paired; of these: 305805 (8.29%) aligned concordantly 0 times 2892222 (78.37%) aligned concordantly exactly 1 time 492476 (13.34%) aligned concordantly >1 times ---- 305805 pairs aligned concordantly 0 times; of these: 47347 (15.48%) aligned discordantly 1 time ---- 258458 pairs aligned 0 times concordantly or discordantly; of these: 516916 mates make up the pairs; of these: 440987 (85.31%) aligned 0 times 47590 (9.21%) aligned exactly 1 time 28339 (5.48%) aligned >1 times 94.03% overall alignment rate Time searching: 00:01:18 Overall time: 00:01:18 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] 74124 / 3388806 = 0.0219 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 20:56:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX10468567/SRX10468567.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX10468567/SRX10468567.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX10468567/SRX10468567.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX10468567/SRX10468567.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 20:56:49: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:56:49: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:56:53: 1000000 INFO @ Sat, 15 Jan 2022 20:56:58: 2000000 INFO @ Sat, 15 Jan 2022 20:57:02: 3000000 INFO @ Sat, 15 Jan 2022 20:57:06: 4000000 INFO @ Sat, 15 Jan 2022 20:57:10: 5000000 INFO @ Sat, 15 Jan 2022 20:57:15: 6000000 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 20:57:18: #1 tag size is determined as 25 bps INFO @ Sat, 15 Jan 2022 20:57:18: #1 tag size = 25 INFO @ Sat, 15 Jan 2022 20:57:18: #1 total tags in treatment: 3310627 INFO @ Sat, 15 Jan 2022 20:57:18: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:57:18: #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 20:57:18: #1 tags after filtering in treatment: 2867132 INFO @ Sat, 15 Jan 2022 20:57:18: #1 Redundant rate of treatment: 0.13 INFO @ Sat, 15 Jan 2022 20:57:18: #1 finished! INFO @ Sat, 15 Jan 2022 20:57:18: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:57:18: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:57:18: #2 number of paired peaks: 30 WARNING @ Sat, 15 Jan 2022 20:57:18: 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 20:57:18: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX10468567/SRX10468567.05_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/SRX10468567/SRX10468567.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX10468567/SRX10468567.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX10468567/SRX10468567.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 20:57:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX10468567/SRX10468567.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX10468567/SRX10468567.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX10468567/SRX10468567.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX10468567/SRX10468567.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 20:57:19: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:57:19: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:57:23: 1000000 INFO @ Sat, 15 Jan 2022 20:57:27: 2000000 INFO @ Sat, 15 Jan 2022 20:57:32: 3000000 INFO @ Sat, 15 Jan 2022 20:57:36: 4000000 INFO @ Sat, 15 Jan 2022 20:57:40: 5000000 INFO @ Sat, 15 Jan 2022 20:57:45: 6000000 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 20:57:48: #1 tag size is determined as 25 bps INFO @ Sat, 15 Jan 2022 20:57:48: #1 tag size = 25 INFO @ Sat, 15 Jan 2022 20:57:48: #1 total tags in treatment: 3310627 INFO @ Sat, 15 Jan 2022 20:57:48: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:57:48: #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 20:57:48: #1 tags after filtering in treatment: 2867132 INFO @ Sat, 15 Jan 2022 20:57:48: #1 Redundant rate of treatment: 0.13 INFO @ Sat, 15 Jan 2022 20:57:48: #1 finished! INFO @ Sat, 15 Jan 2022 20:57:48: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:57:48: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:57:48: #2 number of paired peaks: 30 WARNING @ Sat, 15 Jan 2022 20:57:48: 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 20:57:48: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX10468567/SRX10468567.10_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/SRX10468567/SRX10468567.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX10468567/SRX10468567.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX10468567/SRX10468567.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 20:57:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX10468567/SRX10468567.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX10468567/SRX10468567.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX10468567/SRX10468567.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX10468567/SRX10468567.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 20:57:49: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:57:49: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:57:54: 1000000 INFO @ Sat, 15 Jan 2022 20:57:59: 2000000 INFO @ Sat, 15 Jan 2022 20:58:05: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 20:58:10: 4000000 INFO @ Sat, 15 Jan 2022 20:58:16: 5000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 20:58:21: 6000000 INFO @ Sat, 15 Jan 2022 20:58:25: #1 tag size is determined as 25 bps INFO @ Sat, 15 Jan 2022 20:58:25: #1 tag size = 25 INFO @ Sat, 15 Jan 2022 20:58:25: #1 total tags in treatment: 3310627 INFO @ Sat, 15 Jan 2022 20:58:25: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:58:25: #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 20:58:25: #1 tags after filtering in treatment: 2867132 INFO @ Sat, 15 Jan 2022 20:58:25: #1 Redundant rate of treatment: 0.13 INFO @ Sat, 15 Jan 2022 20:58:25: #1 finished! INFO @ Sat, 15 Jan 2022 20:58:25: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:58:25: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:58:25: #2 number of paired peaks: 30 WARNING @ Sat, 15 Jan 2022 20:58:25: 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 20:58:25: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX10468567/SRX10468567.20_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/SRX10468567/SRX10468567.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX10468567/SRX10468567.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX10468567/SRX10468567.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling