Job ID = 7114046 SRX = SRX8462188 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-07-22T05:49:07 prefetch.2.10.7: 1) Downloading 'SRR11915647'... 2020-07-22T05:49:07 prefetch.2.10.7: Downloading via HTTPS... 2020-07-22T05:50:31 prefetch.2.10.7: HTTPS download succeed 2020-07-22T05:50:31 prefetch.2.10.7: 'SRR11915647' is valid 2020-07-22T05:50:31 prefetch.2.10.7: 1) 'SRR11915647' was downloaded successfully 2020-07-22T05:50:31 prefetch.2.10.7: 'SRR11915647' has 0 unresolved dependencies Read 6621541 spots for SRR11915647/SRR11915647.sra Written 6621541 spots for SRR11915647/SRR11915647.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: 00:05:38 6621541 reads; of these: 6621541 (100.00%) were paired; of these: 1060737 (16.02%) aligned concordantly 0 times 4585619 (69.25%) aligned concordantly exactly 1 time 975185 (14.73%) aligned concordantly >1 times ---- 1060737 pairs aligned concordantly 0 times; of these: 12116 (1.14%) aligned discordantly 1 time ---- 1048621 pairs aligned 0 times concordantly or discordantly; of these: 2097242 mates make up the pairs; of these: 1974777 (94.16%) aligned 0 times 93224 (4.45%) aligned exactly 1 time 29241 (1.39%) aligned >1 times 85.09% overall alignment rate Time searching: 00:05:39 Overall time: 00:05:39 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_sort_core] merging from 8 files... [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] 2699742 / 5568969 = 0.4848 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 15:00:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8462188/SRX8462188.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8462188/SRX8462188.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8462188/SRX8462188.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8462188/SRX8462188.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 15:00:29: #1 read tag files... INFO @ Wed, 22 Jul 2020 15:00:29: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 15:00:36: 1000000 INFO @ Wed, 22 Jul 2020 15:00:43: 2000000 INFO @ Wed, 22 Jul 2020 15:00:50: 3000000 INFO @ Wed, 22 Jul 2020 15:00:56: 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 15:00:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8462188/SRX8462188.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8462188/SRX8462188.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8462188/SRX8462188.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8462188/SRX8462188.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 15:00:59: #1 read tag files... INFO @ Wed, 22 Jul 2020 15:00:59: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 15:01:03: 5000000 INFO @ Wed, 22 Jul 2020 15:01:06: 1000000 INFO @ Wed, 22 Jul 2020 15:01:09: #1 tag size is determined as 75 bps INFO @ Wed, 22 Jul 2020 15:01:09: #1 tag size = 75 INFO @ Wed, 22 Jul 2020 15:01:09: #1 total tags in treatment: 2862589 INFO @ Wed, 22 Jul 2020 15:01:09: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 15:01:09: #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 15:01:09: #1 tags after filtering in treatment: 2235340 INFO @ Wed, 22 Jul 2020 15:01:09: #1 Redundant rate of treatment: 0.22 INFO @ Wed, 22 Jul 2020 15:01:09: #1 finished! INFO @ Wed, 22 Jul 2020 15:01:09: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 15:01:09: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 15:01:09: #2 number of paired peaks: 33 WARNING @ Wed, 22 Jul 2020 15:01:09: Too few paired peaks (33) 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 15:01:09: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8462188/SRX8462188.05_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/SRX8462188/SRX8462188.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8462188/SRX8462188.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8462188/SRX8462188.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Jul 2020 15:01:13: 2000000 INFO @ Wed, 22 Jul 2020 15:01:20: 3000000 INFO @ Wed, 22 Jul 2020 15:01:27: 4000000 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 15:01:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8462188/SRX8462188.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8462188/SRX8462188.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8462188/SRX8462188.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8462188/SRX8462188.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 15:01:29: #1 read tag files... INFO @ Wed, 22 Jul 2020 15:01:29: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 15:01:34: 5000000 INFO @ Wed, 22 Jul 2020 15:01:37: 1000000 INFO @ Wed, 22 Jul 2020 15:01:40: #1 tag size is determined as 75 bps INFO @ Wed, 22 Jul 2020 15:01:40: #1 tag size = 75 INFO @ Wed, 22 Jul 2020 15:01:40: #1 total tags in treatment: 2862589 INFO @ Wed, 22 Jul 2020 15:01:40: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 15:01:40: #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 15:01:40: #1 tags after filtering in treatment: 2235340 INFO @ Wed, 22 Jul 2020 15:01:40: #1 Redundant rate of treatment: 0.22 INFO @ Wed, 22 Jul 2020 15:01:40: #1 finished! INFO @ Wed, 22 Jul 2020 15:01:40: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 15:01:40: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 15:01:41: #2 number of paired peaks: 33 WARNING @ Wed, 22 Jul 2020 15:01:41: Too few paired peaks (33) 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 15:01:41: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8462188/SRX8462188.10_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/SRX8462188/SRX8462188.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8462188/SRX8462188.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8462188/SRX8462188.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Jul 2020 15:01:44: 2000000 INFO @ Wed, 22 Jul 2020 15:01:51: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Jul 2020 15:01:58: 4000000 BigWig に変換しました。 INFO @ Wed, 22 Jul 2020 15:02:05: 5000000 INFO @ Wed, 22 Jul 2020 15:02:10: #1 tag size is determined as 75 bps INFO @ Wed, 22 Jul 2020 15:02:10: #1 tag size = 75 INFO @ Wed, 22 Jul 2020 15:02:10: #1 total tags in treatment: 2862589 INFO @ Wed, 22 Jul 2020 15:02:10: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 15:02:10: #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 15:02:10: #1 tags after filtering in treatment: 2235340 INFO @ Wed, 22 Jul 2020 15:02:10: #1 Redundant rate of treatment: 0.22 INFO @ Wed, 22 Jul 2020 15:02:10: #1 finished! INFO @ Wed, 22 Jul 2020 15:02:10: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 15:02:10: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 15:02:10: #2 number of paired peaks: 33 WARNING @ Wed, 22 Jul 2020 15:02:10: Too few paired peaks (33) 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 15:02:10: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8462188/SRX8462188.20_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/SRX8462188/SRX8462188.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8462188/SRX8462188.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8462188/SRX8462188.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling