Job ID = 7111829 SRX = SRX8357670 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-07-22T05:13:27 prefetch.2.10.7: 1) Downloading 'SRR11806258'... 2020-07-22T05:13:27 prefetch.2.10.7: Downloading via HTTPS... 2020-07-22T05:14:05 prefetch.2.10.7: HTTPS download succeed 2020-07-22T05:14:05 prefetch.2.10.7: 'SRR11806258' is valid 2020-07-22T05:14:05 prefetch.2.10.7: 1) 'SRR11806258' was downloaded successfully 2020-07-22T05:14:05 prefetch.2.10.7: 'SRR11806258' has 0 unresolved dependencies Read 12404412 spots for SRR11806258/SRR11806258.sra Written 12404412 spots for SRR11806258/SRR11806258.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: 00:06:00 12404412 reads; of these: 12404412 (100.00%) were paired; of these: 3183761 (25.67%) aligned concordantly 0 times 6796572 (54.79%) aligned concordantly exactly 1 time 2424079 (19.54%) aligned concordantly >1 times ---- 3183761 pairs aligned concordantly 0 times; of these: 79391 (2.49%) aligned discordantly 1 time ---- 3104370 pairs aligned 0 times concordantly or discordantly; of these: 6208740 mates make up the pairs; of these: 5878261 (94.68%) aligned 0 times 107265 (1.73%) aligned exactly 1 time 223214 (3.60%) aligned >1 times 76.31% overall alignment rate Time searching: 00:06:00 Overall time: 00:06:00 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] 3881616 / 9276083 = 0.4185 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 14:24:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8357670/SRX8357670.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8357670/SRX8357670.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8357670/SRX8357670.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8357670/SRX8357670.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 14:24:22: #1 read tag files... INFO @ Wed, 22 Jul 2020 14:24:22: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 14:24:28: 1000000 INFO @ Wed, 22 Jul 2020 14:24:34: 2000000 INFO @ Wed, 22 Jul 2020 14:24:40: 3000000 INFO @ Wed, 22 Jul 2020 14:24:46: 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 14:24:52: 5000000 INFO @ Wed, 22 Jul 2020 14:24:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8357670/SRX8357670.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8357670/SRX8357670.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8357670/SRX8357670.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8357670/SRX8357670.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 14:24:52: #1 read tag files... INFO @ Wed, 22 Jul 2020 14:24:52: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 14:24:58: 1000000 INFO @ Wed, 22 Jul 2020 14:24:59: 6000000 INFO @ Wed, 22 Jul 2020 14:25:04: 2000000 INFO @ Wed, 22 Jul 2020 14:25:05: 7000000 INFO @ Wed, 22 Jul 2020 14:25:10: 3000000 INFO @ Wed, 22 Jul 2020 14:25:12: 8000000 INFO @ Wed, 22 Jul 2020 14:25:16: 4000000 INFO @ Wed, 22 Jul 2020 14:25:18: 9000000 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 14:25:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8357670/SRX8357670.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8357670/SRX8357670.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8357670/SRX8357670.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8357670/SRX8357670.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 14:25:22: #1 read tag files... INFO @ Wed, 22 Jul 2020 14:25:22: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 14:25:22: 5000000 INFO @ Wed, 22 Jul 2020 14:25:25: 10000000 INFO @ Wed, 22 Jul 2020 14:25:28: 1000000 INFO @ Wed, 22 Jul 2020 14:25:28: 6000000 INFO @ Wed, 22 Jul 2020 14:25:32: 11000000 INFO @ Wed, 22 Jul 2020 14:25:33: #1 tag size is determined as 51 bps INFO @ Wed, 22 Jul 2020 14:25:33: #1 tag size = 51 INFO @ Wed, 22 Jul 2020 14:25:33: #1 total tags in treatment: 5370854 INFO @ Wed, 22 Jul 2020 14:25:33: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 14:25:33: #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 14:25:33: #1 tags after filtering in treatment: 3216222 INFO @ Wed, 22 Jul 2020 14:25:33: #1 Redundant rate of treatment: 0.40 INFO @ Wed, 22 Jul 2020 14:25:33: #1 finished! INFO @ Wed, 22 Jul 2020 14:25:33: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 14:25:33: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 14:25:33: #2 number of paired peaks: 26 WARNING @ Wed, 22 Jul 2020 14:25:33: Too few paired peaks (26) 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 14:25:33: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8357670/SRX8357670.05_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/SRX8357670/SRX8357670.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8357670/SRX8357670.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8357670/SRX8357670.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Jul 2020 14:25:34: 2000000 INFO @ Wed, 22 Jul 2020 14:25:34: 7000000 INFO @ Wed, 22 Jul 2020 14:25:40: 3000000 INFO @ Wed, 22 Jul 2020 14:25:40: 8000000 INFO @ Wed, 22 Jul 2020 14:25:46: 4000000 INFO @ Wed, 22 Jul 2020 14:25:47: 9000000 INFO @ Wed, 22 Jul 2020 14:25:51: 5000000 INFO @ Wed, 22 Jul 2020 14:25:54: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Jul 2020 14:25:57: 6000000 INFO @ Wed, 22 Jul 2020 14:26:00: 11000000 INFO @ Wed, 22 Jul 2020 14:26:01: #1 tag size is determined as 51 bps INFO @ Wed, 22 Jul 2020 14:26:01: #1 tag size = 51 INFO @ Wed, 22 Jul 2020 14:26:01: #1 total tags in treatment: 5370854 INFO @ Wed, 22 Jul 2020 14:26:01: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 14:26:01: #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 14:26:01: #1 tags after filtering in treatment: 3216222 INFO @ Wed, 22 Jul 2020 14:26:01: #1 Redundant rate of treatment: 0.40 INFO @ Wed, 22 Jul 2020 14:26:01: #1 finished! INFO @ Wed, 22 Jul 2020 14:26:01: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 14:26:01: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 14:26:01: #2 number of paired peaks: 26 WARNING @ Wed, 22 Jul 2020 14:26:01: Too few paired peaks (26) 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 14:26:01: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8357670/SRX8357670.10_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/SRX8357670/SRX8357670.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8357670/SRX8357670.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8357670/SRX8357670.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Jul 2020 14:26:03: 7000000 BigWig に変換しました。 INFO @ Wed, 22 Jul 2020 14:26:08: 8000000 INFO @ Wed, 22 Jul 2020 14:26:14: 9000000 INFO @ Wed, 22 Jul 2020 14:26:19: 10000000 INFO @ Wed, 22 Jul 2020 14:26:25: 11000000 INFO @ Wed, 22 Jul 2020 14:26:25: #1 tag size is determined as 51 bps INFO @ Wed, 22 Jul 2020 14:26:25: #1 tag size = 51 INFO @ Wed, 22 Jul 2020 14:26:25: #1 total tags in treatment: 5370854 INFO @ Wed, 22 Jul 2020 14:26:25: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 14:26:25: #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 14:26:26: #1 tags after filtering in treatment: 3216222 INFO @ Wed, 22 Jul 2020 14:26:26: #1 Redundant rate of treatment: 0.40 INFO @ Wed, 22 Jul 2020 14:26:26: #1 finished! INFO @ Wed, 22 Jul 2020 14:26:26: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 14:26:26: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 14:26:26: #2 number of paired peaks: 26 WARNING @ Wed, 22 Jul 2020 14:26:26: Too few paired peaks (26) 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 14:26:26: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8357670/SRX8357670.20_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/SRX8357670/SRX8357670.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8357670/SRX8357670.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8357670/SRX8357670.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling