Job ID = 14521453 SRX = SRX10468477 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 5089486 spots for SRR14094889/SRR14094889.sra Written 5089486 spots for SRR14094889/SRR14094889.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: 00:01:44 5089486 reads; of these: 5089486 (100.00%) were paired; of these: 743323 (14.61%) aligned concordantly 0 times 3490296 (68.58%) aligned concordantly exactly 1 time 855867 (16.82%) aligned concordantly >1 times ---- 743323 pairs aligned concordantly 0 times; of these: 43575 (5.86%) aligned discordantly 1 time ---- 699748 pairs aligned 0 times concordantly or discordantly; of these: 1399496 mates make up the pairs; of these: 1291182 (92.26%) aligned 0 times 65010 (4.65%) aligned exactly 1 time 43304 (3.09%) aligned >1 times 87.32% overall alignment rate Time searching: 00:01:44 Overall time: 00:01:44 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] 123949 / 4349518 = 0.0285 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 21:03:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX10468477/SRX10468477.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX10468477/SRX10468477.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX10468477/SRX10468477.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX10468477/SRX10468477.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 21:03:37: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:03:37: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:03:42: 1000000 INFO @ Sat, 15 Jan 2022 21:03:46: 2000000 INFO @ Sat, 15 Jan 2022 21:03:50: 3000000 INFO @ Sat, 15 Jan 2022 21:03:54: 4000000 INFO @ Sat, 15 Jan 2022 21:03:58: 5000000 INFO @ Sat, 15 Jan 2022 21:04:02: 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 21:04:06: 7000000 INFO @ Sat, 15 Jan 2022 21:04:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX10468477/SRX10468477.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX10468477/SRX10468477.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX10468477/SRX10468477.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX10468477/SRX10468477.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 21:04:07: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:04:07: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:04:10: 8000000 INFO @ Sat, 15 Jan 2022 21:04:12: 1000000 INFO @ Sat, 15 Jan 2022 21:04:13: #1 tag size is determined as 25 bps INFO @ Sat, 15 Jan 2022 21:04:13: #1 tag size = 25 INFO @ Sat, 15 Jan 2022 21:04:13: #1 total tags in treatment: 4222264 INFO @ Sat, 15 Jan 2022 21:04:13: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:04:13: #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 21:04:13: #1 tags after filtering in treatment: 3420538 INFO @ Sat, 15 Jan 2022 21:04:13: #1 Redundant rate of treatment: 0.19 INFO @ Sat, 15 Jan 2022 21:04:13: #1 finished! INFO @ Sat, 15 Jan 2022 21:04:13: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:04:13: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:04:14: #2 number of paired peaks: 29 WARNING @ Sat, 15 Jan 2022 21:04:14: Too few paired peaks (29) 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 21:04:14: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX10468477/SRX10468477.05_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/SRX10468477/SRX10468477.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX10468477/SRX10468477.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX10468477/SRX10468477.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 21:04:17: 2000000 INFO @ Sat, 15 Jan 2022 21:04:21: 3000000 INFO @ Sat, 15 Jan 2022 21:04:25: 4000000 INFO @ Sat, 15 Jan 2022 21:04:30: 5000000 INFO @ Sat, 15 Jan 2022 21:04:34: 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 21:04:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX10468477/SRX10468477.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX10468477/SRX10468477.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX10468477/SRX10468477.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX10468477/SRX10468477.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 21:04:37: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:04:37: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:04:38: 7000000 INFO @ Sat, 15 Jan 2022 21:04:43: 1000000 INFO @ Sat, 15 Jan 2022 21:04:43: 8000000 INFO @ Sat, 15 Jan 2022 21:04:46: #1 tag size is determined as 25 bps INFO @ Sat, 15 Jan 2022 21:04:46: #1 tag size = 25 INFO @ Sat, 15 Jan 2022 21:04:46: #1 total tags in treatment: 4222264 INFO @ Sat, 15 Jan 2022 21:04:46: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:04:46: #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 21:04:46: #1 tags after filtering in treatment: 3420538 INFO @ Sat, 15 Jan 2022 21:04:46: #1 Redundant rate of treatment: 0.19 INFO @ Sat, 15 Jan 2022 21:04:46: #1 finished! INFO @ Sat, 15 Jan 2022 21:04:46: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:04:46: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:04:47: #2 number of paired peaks: 29 WARNING @ Sat, 15 Jan 2022 21:04:47: Too few paired peaks (29) 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 21:04:47: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX10468477/SRX10468477.10_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/SRX10468477/SRX10468477.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX10468477/SRX10468477.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX10468477/SRX10468477.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 21:04:48: 2000000 INFO @ Sat, 15 Jan 2022 21:04:53: 3000000 INFO @ Sat, 15 Jan 2022 21:04:58: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 21:05:03: 5000000 INFO @ Sat, 15 Jan 2022 21:05:08: 6000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 21:05:13: 7000000 INFO @ Sat, 15 Jan 2022 21:05:18: 8000000 INFO @ Sat, 15 Jan 2022 21:05:22: #1 tag size is determined as 25 bps INFO @ Sat, 15 Jan 2022 21:05:22: #1 tag size = 25 INFO @ Sat, 15 Jan 2022 21:05:22: #1 total tags in treatment: 4222264 INFO @ Sat, 15 Jan 2022 21:05:22: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:05:22: #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 21:05:22: #1 tags after filtering in treatment: 3420538 INFO @ Sat, 15 Jan 2022 21:05:22: #1 Redundant rate of treatment: 0.19 INFO @ Sat, 15 Jan 2022 21:05:22: #1 finished! INFO @ Sat, 15 Jan 2022 21:05:22: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:05:22: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:05:22: #2 number of paired peaks: 29 WARNING @ Sat, 15 Jan 2022 21:05:22: Too few paired peaks (29) 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 21:05:22: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX10468477/SRX10468477.20_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/SRX10468477/SRX10468477.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX10468477/SRX10468477.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX10468477/SRX10468477.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling