Job ID = 7111814 SRX = SRX8357669 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-07-22T05:11:58 prefetch.2.10.7: 1) Downloading 'SRR11806257'... 2020-07-22T05:11:58 prefetch.2.10.7: Downloading via HTTPS... 2020-07-22T05:12:54 prefetch.2.10.7: HTTPS download succeed 2020-07-22T05:12:54 prefetch.2.10.7: 'SRR11806257' is valid 2020-07-22T05:12:54 prefetch.2.10.7: 1) 'SRR11806257' was downloaded successfully 2020-07-22T05:12:54 prefetch.2.10.7: 'SRR11806257' has 0 unresolved dependencies Read 10970427 spots for SRR11806257/SRR11806257.sra Written 10970427 spots for SRR11806257/SRR11806257.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: 00:05:12 10970427 reads; of these: 10970427 (100.00%) were paired; of these: 3872841 (35.30%) aligned concordantly 0 times 5882145 (53.62%) aligned concordantly exactly 1 time 1215441 (11.08%) aligned concordantly >1 times ---- 3872841 pairs aligned concordantly 0 times; of these: 60302 (1.56%) aligned discordantly 1 time ---- 3812539 pairs aligned 0 times concordantly or discordantly; of these: 7625078 mates make up the pairs; of these: 7302426 (95.77%) aligned 0 times 123131 (1.61%) aligned exactly 1 time 199521 (2.62%) aligned >1 times 66.72% overall alignment rate Time searching: 00:05:12 Overall time: 00:05:12 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] 2491710 / 7140124 = 0.3490 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 14:21:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8357669/SRX8357669.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8357669/SRX8357669.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8357669/SRX8357669.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8357669/SRX8357669.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 14:21:51: #1 read tag files... INFO @ Wed, 22 Jul 2020 14:21:51: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 14:21:57: 1000000 INFO @ Wed, 22 Jul 2020 14:22:03: 2000000 INFO @ Wed, 22 Jul 2020 14:22:10: 3000000 INFO @ Wed, 22 Jul 2020 14:22:16: 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 14:22:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8357669/SRX8357669.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8357669/SRX8357669.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8357669/SRX8357669.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8357669/SRX8357669.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 14:22:21: #1 read tag files... INFO @ Wed, 22 Jul 2020 14:22:21: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 14:22:23: 5000000 INFO @ Wed, 22 Jul 2020 14:22:28: 1000000 INFO @ Wed, 22 Jul 2020 14:22:30: 6000000 INFO @ Wed, 22 Jul 2020 14:22:34: 2000000 INFO @ Wed, 22 Jul 2020 14:22:37: 7000000 INFO @ Wed, 22 Jul 2020 14:22:40: 3000000 INFO @ Wed, 22 Jul 2020 14:22:45: 8000000 INFO @ Wed, 22 Jul 2020 14:22:47: 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 14:22:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8357669/SRX8357669.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8357669/SRX8357669.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8357669/SRX8357669.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8357669/SRX8357669.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 14:22:51: #1 read tag files... INFO @ Wed, 22 Jul 2020 14:22:51: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 14:22:52: 9000000 INFO @ Wed, 22 Jul 2020 14:22:53: 5000000 INFO @ Wed, 22 Jul 2020 14:22:56: #1 tag size is determined as 51 bps INFO @ Wed, 22 Jul 2020 14:22:56: #1 tag size = 51 INFO @ Wed, 22 Jul 2020 14:22:56: #1 total tags in treatment: 4626613 INFO @ Wed, 22 Jul 2020 14:22:56: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 14:22:56: #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 14:22:56: #1 tags after filtering in treatment: 3004496 INFO @ Wed, 22 Jul 2020 14:22:56: #1 Redundant rate of treatment: 0.35 INFO @ Wed, 22 Jul 2020 14:22:56: #1 finished! INFO @ Wed, 22 Jul 2020 14:22:56: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 14:22:56: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 14:22:56: #2 number of paired peaks: 22 WARNING @ Wed, 22 Jul 2020 14:22:56: Too few paired peaks (22) 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 14:22:56: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8357669/SRX8357669.05_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/SRX8357669/SRX8357669.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8357669/SRX8357669.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8357669/SRX8357669.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Jul 2020 14:22:58: 1000000 INFO @ Wed, 22 Jul 2020 14:23:00: 6000000 INFO @ Wed, 22 Jul 2020 14:23:04: 2000000 INFO @ Wed, 22 Jul 2020 14:23:07: 7000000 INFO @ Wed, 22 Jul 2020 14:23:10: 3000000 INFO @ Wed, 22 Jul 2020 14:23:14: 8000000 INFO @ Wed, 22 Jul 2020 14:23:16: 4000000 INFO @ Wed, 22 Jul 2020 14:23:21: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Jul 2020 14:23:22: 5000000 INFO @ Wed, 22 Jul 2020 14:23:25: #1 tag size is determined as 51 bps INFO @ Wed, 22 Jul 2020 14:23:25: #1 tag size = 51 INFO @ Wed, 22 Jul 2020 14:23:25: #1 total tags in treatment: 4626613 INFO @ Wed, 22 Jul 2020 14:23:25: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 14:23:25: #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 14:23:25: #1 tags after filtering in treatment: 3004496 INFO @ Wed, 22 Jul 2020 14:23:25: #1 Redundant rate of treatment: 0.35 INFO @ Wed, 22 Jul 2020 14:23:25: #1 finished! INFO @ Wed, 22 Jul 2020 14:23:25: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 14:23:25: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 14:23:25: #2 number of paired peaks: 22 WARNING @ Wed, 22 Jul 2020 14:23:25: Too few paired peaks (22) 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 14:23:25: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8357669/SRX8357669.10_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/SRX8357669/SRX8357669.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8357669/SRX8357669.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8357669/SRX8357669.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Jul 2020 14:23:28: 6000000 BigWig に変換しました。 INFO @ Wed, 22 Jul 2020 14:23:34: 7000000 INFO @ Wed, 22 Jul 2020 14:23:39: 8000000 INFO @ Wed, 22 Jul 2020 14:23:45: 9000000 INFO @ Wed, 22 Jul 2020 14:23:49: #1 tag size is determined as 51 bps INFO @ Wed, 22 Jul 2020 14:23:49: #1 tag size = 51 INFO @ Wed, 22 Jul 2020 14:23:49: #1 total tags in treatment: 4626613 INFO @ Wed, 22 Jul 2020 14:23:49: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 14:23:49: #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 14:23:49: #1 tags after filtering in treatment: 3004496 INFO @ Wed, 22 Jul 2020 14:23:49: #1 Redundant rate of treatment: 0.35 INFO @ Wed, 22 Jul 2020 14:23:49: #1 finished! INFO @ Wed, 22 Jul 2020 14:23:49: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 14:23:49: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 14:23:49: #2 number of paired peaks: 22 WARNING @ Wed, 22 Jul 2020 14:23:49: Too few paired peaks (22) 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 14:23:49: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8357669/SRX8357669.20_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/SRX8357669/SRX8357669.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8357669/SRX8357669.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8357669/SRX8357669.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling