Job ID = 14522100 SRX = SRX9067136 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 4030914 spots for SRR12580289/SRR12580289.sra Written 4030914 spots for SRR12580289/SRR12580289.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: 00:02:06 4030914 reads; of these: 4030914 (100.00%) were paired; of these: 582506 (14.45%) aligned concordantly 0 times 2885196 (71.58%) aligned concordantly exactly 1 time 563212 (13.97%) aligned concordantly >1 times ---- 582506 pairs aligned concordantly 0 times; of these: 178935 (30.72%) aligned discordantly 1 time ---- 403571 pairs aligned 0 times concordantly or discordantly; of these: 807142 mates make up the pairs; of these: 607610 (75.28%) aligned 0 times 120521 (14.93%) aligned exactly 1 time 79011 (9.79%) aligned >1 times 92.46% overall alignment rate Time searching: 00:02:06 Overall time: 00:02:06 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] 425450 / 3519094 = 0.1209 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 22:13:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9067136/SRX9067136.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9067136/SRX9067136.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9067136/SRX9067136.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9067136/SRX9067136.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 22:13:10: #1 read tag files... INFO @ Sat, 15 Jan 2022 22:13:10: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 22:13:15: 1000000 INFO @ Sat, 15 Jan 2022 22:13:20: 2000000 INFO @ Sat, 15 Jan 2022 22:13:25: 3000000 INFO @ Sat, 15 Jan 2022 22:13:29: 4000000 INFO @ Sat, 15 Jan 2022 22:13:34: 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 22:13:39: 6000000 INFO @ Sat, 15 Jan 2022 22:13:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9067136/SRX9067136.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9067136/SRX9067136.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9067136/SRX9067136.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9067136/SRX9067136.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 22:13:40: #1 read tag files... INFO @ Sat, 15 Jan 2022 22:13:40: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 22:13:42: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 22:13:42: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 22:13:42: #1 total tags in treatment: 3027223 INFO @ Sat, 15 Jan 2022 22:13:42: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 22:13:42: #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 22:13:42: #1 tags after filtering in treatment: 2198982 INFO @ Sat, 15 Jan 2022 22:13:42: #1 Redundant rate of treatment: 0.27 INFO @ Sat, 15 Jan 2022 22:13:42: #1 finished! INFO @ Sat, 15 Jan 2022 22:13:42: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 22:13:42: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 22:13:42: #2 number of paired peaks: 23 WARNING @ Sat, 15 Jan 2022 22:13:42: Too few paired peaks (23) 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 22:13:42: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX9067136/SRX9067136.05_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/SRX9067136/SRX9067136.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9067136/SRX9067136.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9067136/SRX9067136.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 22:13:46: 1000000 INFO @ Sat, 15 Jan 2022 22:13:52: 2000000 INFO @ Sat, 15 Jan 2022 22:13:58: 3000000 INFO @ Sat, 15 Jan 2022 22:14:04: 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 22:14:10: 5000000 INFO @ Sat, 15 Jan 2022 22:14:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9067136/SRX9067136.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9067136/SRX9067136.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9067136/SRX9067136.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9067136/SRX9067136.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 22:14:10: #1 read tag files... INFO @ Sat, 15 Jan 2022 22:14:10: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 22:14:16: 1000000 INFO @ Sat, 15 Jan 2022 22:14:17: 6000000 INFO @ Sat, 15 Jan 2022 22:14:21: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 22:14:21: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 22:14:21: #1 total tags in treatment: 3027223 INFO @ Sat, 15 Jan 2022 22:14:21: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 22:14:21: #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 22:14:21: #1 tags after filtering in treatment: 2198982 INFO @ Sat, 15 Jan 2022 22:14:21: #1 Redundant rate of treatment: 0.27 INFO @ Sat, 15 Jan 2022 22:14:21: #1 finished! INFO @ Sat, 15 Jan 2022 22:14:21: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 22:14:21: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 22:14:21: #2 number of paired peaks: 23 WARNING @ Sat, 15 Jan 2022 22:14:21: Too few paired peaks (23) 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 22:14:21: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX9067136/SRX9067136.10_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/SRX9067136/SRX9067136.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9067136/SRX9067136.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9067136/SRX9067136.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 22:14:22: 2000000 INFO @ Sat, 15 Jan 2022 22:14:27: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 22:14:31: 4000000 INFO @ Sat, 15 Jan 2022 22:14:36: 5000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 22:14:41: 6000000 INFO @ Sat, 15 Jan 2022 22:14:43: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 22:14:43: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 22:14:43: #1 total tags in treatment: 3027223 INFO @ Sat, 15 Jan 2022 22:14:43: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 22:14:43: #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 22:14:43: #1 tags after filtering in treatment: 2198982 INFO @ Sat, 15 Jan 2022 22:14:43: #1 Redundant rate of treatment: 0.27 INFO @ Sat, 15 Jan 2022 22:14:43: #1 finished! INFO @ Sat, 15 Jan 2022 22:14:43: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 22:14:43: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 22:14:44: #2 number of paired peaks: 23 WARNING @ Sat, 15 Jan 2022 22:14:44: Too few paired peaks (23) 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 22:14:44: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX9067136/SRX9067136.20_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/SRX9067136/SRX9067136.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9067136/SRX9067136.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9067136/SRX9067136.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling