Job ID = 7115484 SRX = SRX8462235 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-07-22T06:08:35 prefetch.2.10.7: 1) Downloading 'SRR11915694'... 2020-07-22T06:08:35 prefetch.2.10.7: Downloading via HTTPS... 2020-07-22T06:09:20 prefetch.2.10.7: HTTPS download succeed 2020-07-22T06:09:20 prefetch.2.10.7: 'SRR11915694' is valid 2020-07-22T06:09:20 prefetch.2.10.7: 1) 'SRR11915694' was downloaded successfully 2020-07-22T06:09:20 prefetch.2.10.7: 'SRR11915694' has 0 unresolved dependencies Read 3377043 spots for SRR11915694/SRR11915694.sra Written 3377043 spots for SRR11915694/SRR11915694.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: 00:02:56 3377043 reads; of these: 3377043 (100.00%) were paired; of these: 169189 (5.01%) aligned concordantly 0 times 2781592 (82.37%) aligned concordantly exactly 1 time 426262 (12.62%) aligned concordantly >1 times ---- 169189 pairs aligned concordantly 0 times; of these: 11381 (6.73%) aligned discordantly 1 time ---- 157808 pairs aligned 0 times concordantly or discordantly; of these: 315616 mates make up the pairs; of these: 243989 (77.31%) aligned 0 times 57209 (18.13%) aligned exactly 1 time 14418 (4.57%) aligned >1 times 96.39% overall alignment rate Time searching: 00:02:56 Overall time: 00:02:56 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] 579961 / 3213345 = 0.1805 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 22 Jul 2020 15:15:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8462235/SRX8462235.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8462235/SRX8462235.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8462235/SRX8462235.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8462235/SRX8462235.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 @ Wed, 22 Jul 2020 15:15:07: #1 read tag files... INFO @ Wed, 22 Jul 2020 15:15:07: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 15:15:13: 1000000 INFO @ Wed, 22 Jul 2020 15:15:20: 2000000 INFO @ Wed, 22 Jul 2020 15:15:28: 3000000 INFO @ Wed, 22 Jul 2020 15:15:35: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 22 Jul 2020 15:15:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8462235/SRX8462235.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8462235/SRX8462235.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8462235/SRX8462235.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8462235/SRX8462235.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 @ Wed, 22 Jul 2020 15:15:37: #1 read tag files... INFO @ Wed, 22 Jul 2020 15:15:37: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 15:15:43: 5000000 INFO @ Wed, 22 Jul 2020 15:15:44: 1000000 INFO @ Wed, 22 Jul 2020 15:15:45: #1 tag size is determined as 75 bps INFO @ Wed, 22 Jul 2020 15:15:45: #1 tag size = 75 INFO @ Wed, 22 Jul 2020 15:15:45: #1 total tags in treatment: 2628341 INFO @ Wed, 22 Jul 2020 15:15:45: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 15:15:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Jul 2020 15:15:45: #1 tags after filtering in treatment: 2269015 INFO @ Wed, 22 Jul 2020 15:15:45: #1 Redundant rate of treatment: 0.14 INFO @ Wed, 22 Jul 2020 15:15:45: #1 finished! INFO @ Wed, 22 Jul 2020 15:15:45: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 15:15:45: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 15:15:45: #2 number of paired peaks: 69 WARNING @ Wed, 22 Jul 2020 15:15:45: Too few paired peaks (69) 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 @ Wed, 22 Jul 2020 15:15:45: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8462235/SRX8462235.05_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/SRX8462235/SRX8462235.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8462235/SRX8462235.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8462235/SRX8462235.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Jul 2020 15:15:51: 2000000 INFO @ Wed, 22 Jul 2020 15:15:58: 3000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 22 Jul 2020 15:16:06: 4000000 INFO @ Wed, 22 Jul 2020 15:16:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8462235/SRX8462235.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8462235/SRX8462235.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8462235/SRX8462235.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8462235/SRX8462235.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 @ Wed, 22 Jul 2020 15:16:07: #1 read tag files... INFO @ Wed, 22 Jul 2020 15:16:07: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 15:16:13: 5000000 INFO @ Wed, 22 Jul 2020 15:16:15: 1000000 INFO @ Wed, 22 Jul 2020 15:16:16: #1 tag size is determined as 75 bps INFO @ Wed, 22 Jul 2020 15:16:16: #1 tag size = 75 INFO @ Wed, 22 Jul 2020 15:16:16: #1 total tags in treatment: 2628341 INFO @ Wed, 22 Jul 2020 15:16:16: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 15:16:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Jul 2020 15:16:16: #1 tags after filtering in treatment: 2269015 INFO @ Wed, 22 Jul 2020 15:16:16: #1 Redundant rate of treatment: 0.14 INFO @ Wed, 22 Jul 2020 15:16:16: #1 finished! INFO @ Wed, 22 Jul 2020 15:16:16: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 15:16:16: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 15:16:16: #2 number of paired peaks: 69 WARNING @ Wed, 22 Jul 2020 15:16:16: Too few paired peaks (69) 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 @ Wed, 22 Jul 2020 15:16:16: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8462235/SRX8462235.10_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/SRX8462235/SRX8462235.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8462235/SRX8462235.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8462235/SRX8462235.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Jul 2020 15:16:23: 2000000 INFO @ Wed, 22 Jul 2020 15:16:30: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Jul 2020 15:16:38: 4000000 BigWig に変換しました。 INFO @ Wed, 22 Jul 2020 15:16:46: 5000000 INFO @ Wed, 22 Jul 2020 15:16:48: #1 tag size is determined as 75 bps INFO @ Wed, 22 Jul 2020 15:16:48: #1 tag size = 75 INFO @ Wed, 22 Jul 2020 15:16:48: #1 total tags in treatment: 2628341 INFO @ Wed, 22 Jul 2020 15:16:48: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 15:16:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Jul 2020 15:16:48: #1 tags after filtering in treatment: 2269015 INFO @ Wed, 22 Jul 2020 15:16:48: #1 Redundant rate of treatment: 0.14 INFO @ Wed, 22 Jul 2020 15:16:48: #1 finished! INFO @ Wed, 22 Jul 2020 15:16:48: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 15:16:48: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 15:16:48: #2 number of paired peaks: 69 WARNING @ Wed, 22 Jul 2020 15:16:48: Too few paired peaks (69) 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 @ Wed, 22 Jul 2020 15:16:48: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8462235/SRX8462235.20_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/SRX8462235/SRX8462235.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8462235/SRX8462235.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8462235/SRX8462235.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling