Job ID = 14520607 SRX = SRX3659096 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 3063242 spots for SRR6682811/SRR6682811.sra Written 3063242 spots for SRR6682811/SRR6682811.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: 00:03:06 3063242 reads; of these: 3063242 (100.00%) were paired; of these: 233609 (7.63%) aligned concordantly 0 times 2280630 (74.45%) aligned concordantly exactly 1 time 549003 (17.92%) aligned concordantly >1 times ---- 233609 pairs aligned concordantly 0 times; of these: 47289 (20.24%) aligned discordantly 1 time ---- 186320 pairs aligned 0 times concordantly or discordantly; of these: 372640 mates make up the pairs; of these: 309725 (83.12%) aligned 0 times 30662 (8.23%) aligned exactly 1 time 32253 (8.66%) aligned >1 times 94.94% overall alignment rate Time searching: 00:03:06 Overall time: 00:03:06 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] 87716 / 2871486 = 0.0305 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 19:33:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3659096/SRX3659096.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3659096/SRX3659096.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3659096/SRX3659096.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3659096/SRX3659096.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 19:33:52: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:33:52: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:33:58: 1000000 INFO @ Sat, 15 Jan 2022 19:34:04: 2000000 INFO @ Sat, 15 Jan 2022 19:34:10: 3000000 INFO @ Sat, 15 Jan 2022 19:34:16: 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 19:34:22: 5000000 INFO @ Sat, 15 Jan 2022 19:34:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3659096/SRX3659096.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3659096/SRX3659096.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3659096/SRX3659096.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3659096/SRX3659096.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 19:34:22: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:34:22: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:34:26: #1 tag size is determined as 100 bps INFO @ Sat, 15 Jan 2022 19:34:26: #1 tag size = 100 INFO @ Sat, 15 Jan 2022 19:34:26: #1 total tags in treatment: 2742391 INFO @ Sat, 15 Jan 2022 19:34:26: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:34:26: #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 19:34:26: #1 tags after filtering in treatment: 2233704 INFO @ Sat, 15 Jan 2022 19:34:26: #1 Redundant rate of treatment: 0.19 INFO @ Sat, 15 Jan 2022 19:34:26: #1 finished! INFO @ Sat, 15 Jan 2022 19:34:26: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:34:26: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:34:26: #2 number of paired peaks: 75 WARNING @ Sat, 15 Jan 2022 19:34:26: Too few paired peaks (75) 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 19:34:26: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX3659096/SRX3659096.05_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/SRX3659096/SRX3659096.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3659096/SRX3659096.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3659096/SRX3659096.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 19:34:30: 1000000 INFO @ Sat, 15 Jan 2022 19:34:38: 2000000 INFO @ Sat, 15 Jan 2022 19:34:46: 3000000 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 19:34:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3659096/SRX3659096.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3659096/SRX3659096.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3659096/SRX3659096.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3659096/SRX3659096.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 19:34:52: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:34:52: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:34:54: 4000000 INFO @ Sat, 15 Jan 2022 19:35:00: 1000000 INFO @ Sat, 15 Jan 2022 19:35:02: 5000000 INFO @ Sat, 15 Jan 2022 19:35:07: #1 tag size is determined as 100 bps INFO @ Sat, 15 Jan 2022 19:35:07: #1 tag size = 100 INFO @ Sat, 15 Jan 2022 19:35:07: #1 total tags in treatment: 2742391 INFO @ Sat, 15 Jan 2022 19:35:07: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:35:07: #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 19:35:07: #1 tags after filtering in treatment: 2233704 INFO @ Sat, 15 Jan 2022 19:35:07: #1 Redundant rate of treatment: 0.19 INFO @ Sat, 15 Jan 2022 19:35:07: #1 finished! INFO @ Sat, 15 Jan 2022 19:35:07: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:35:07: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:35:07: #2 number of paired peaks: 75 WARNING @ Sat, 15 Jan 2022 19:35:07: Too few paired peaks (75) 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 19:35:07: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX3659096/SRX3659096.10_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/SRX3659096/SRX3659096.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3659096/SRX3659096.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3659096/SRX3659096.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 19:35:08: 2000000 INFO @ Sat, 15 Jan 2022 19:35:16: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 19:35:23: 4000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 19:35:31: 5000000 INFO @ Sat, 15 Jan 2022 19:35:35: #1 tag size is determined as 100 bps INFO @ Sat, 15 Jan 2022 19:35:35: #1 tag size = 100 INFO @ Sat, 15 Jan 2022 19:35:35: #1 total tags in treatment: 2742391 INFO @ Sat, 15 Jan 2022 19:35:35: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:35:35: #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 19:35:35: #1 tags after filtering in treatment: 2233704 INFO @ Sat, 15 Jan 2022 19:35:35: #1 Redundant rate of treatment: 0.19 INFO @ Sat, 15 Jan 2022 19:35:35: #1 finished! INFO @ Sat, 15 Jan 2022 19:35:35: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:35:35: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:35:36: #2 number of paired peaks: 75 WARNING @ Sat, 15 Jan 2022 19:35:36: Too few paired peaks (75) 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 19:35:36: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX3659096/SRX3659096.20_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/SRX3659096/SRX3659096.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3659096/SRX3659096.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3659096/SRX3659096.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling