Job ID = 7111525 SRX = SRX8357660 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-07-22T05:07:13 prefetch.2.10.7: 1) Downloading 'SRR11806248'... 2020-07-22T05:07:13 prefetch.2.10.7: Downloading via HTTPS... 2020-07-22T05:07:45 prefetch.2.10.7: HTTPS download succeed 2020-07-22T05:07:45 prefetch.2.10.7: 'SRR11806248' is valid 2020-07-22T05:07:45 prefetch.2.10.7: 1) 'SRR11806248' was downloaded successfully 2020-07-22T05:07:46 prefetch.2.10.7: 'SRR11806248' has 0 unresolved dependencies Read 5998823 spots for SRR11806248/SRR11806248.sra Written 5998823 spots for SRR11806248/SRR11806248.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: 00:02:59 5998823 reads; of these: 5998823 (100.00%) were paired; of these: 1481347 (24.69%) aligned concordantly 0 times 3671739 (61.21%) aligned concordantly exactly 1 time 845737 (14.10%) aligned concordantly >1 times ---- 1481347 pairs aligned concordantly 0 times; of these: 22892 (1.55%) aligned discordantly 1 time ---- 1458455 pairs aligned 0 times concordantly or discordantly; of these: 2916910 mates make up the pairs; of these: 2786145 (95.52%) aligned 0 times 61227 (2.10%) aligned exactly 1 time 69538 (2.38%) aligned >1 times 76.78% overall alignment rate Time searching: 00:02:59 Overall time: 00:02:59 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] 675664 / 4532820 = 0.1491 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 14:13:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8357660/SRX8357660.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8357660/SRX8357660.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8357660/SRX8357660.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8357660/SRX8357660.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 14:13:51: #1 read tag files... INFO @ Wed, 22 Jul 2020 14:13:51: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 14:13:56: 1000000 INFO @ Wed, 22 Jul 2020 14:14:01: 2000000 INFO @ Wed, 22 Jul 2020 14:14:06: 3000000 INFO @ Wed, 22 Jul 2020 14:14:10: 4000000 INFO @ Wed, 22 Jul 2020 14:14:15: 5000000 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 14:14:20: 6000000 INFO @ Wed, 22 Jul 2020 14:14:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8357660/SRX8357660.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8357660/SRX8357660.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8357660/SRX8357660.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8357660/SRX8357660.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 14:14:21: #1 read tag files... INFO @ Wed, 22 Jul 2020 14:14:21: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 14:14:25: 7000000 INFO @ Wed, 22 Jul 2020 14:14:26: 1000000 INFO @ Wed, 22 Jul 2020 14:14:29: #1 tag size is determined as 51 bps INFO @ Wed, 22 Jul 2020 14:14:29: #1 tag size = 51 INFO @ Wed, 22 Jul 2020 14:14:29: #1 total tags in treatment: 3843558 INFO @ Wed, 22 Jul 2020 14:14:29: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 14:14:29: #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 14:14:29: #1 tags after filtering in treatment: 2639449 INFO @ Wed, 22 Jul 2020 14:14:29: #1 Redundant rate of treatment: 0.31 INFO @ Wed, 22 Jul 2020 14:14:29: #1 finished! INFO @ Wed, 22 Jul 2020 14:14:29: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 14:14:29: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 14:14:29: #2 number of paired peaks: 27 WARNING @ Wed, 22 Jul 2020 14:14:29: Too few paired peaks (27) 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 14:14:29: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8357660/SRX8357660.05_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/SRX8357660/SRX8357660.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8357660/SRX8357660.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8357660/SRX8357660.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Jul 2020 14:14:32: 2000000 INFO @ Wed, 22 Jul 2020 14:14:36: 3000000 INFO @ Wed, 22 Jul 2020 14:14:41: 4000000 INFO @ Wed, 22 Jul 2020 14:14:46: 5000000 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 14:14:51: 6000000 INFO @ Wed, 22 Jul 2020 14:14:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8357660/SRX8357660.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8357660/SRX8357660.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8357660/SRX8357660.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8357660/SRX8357660.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 14:14:51: #1 read tag files... INFO @ Wed, 22 Jul 2020 14:14:51: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 14:14:56: 7000000 INFO @ Wed, 22 Jul 2020 14:14:57: 1000000 INFO @ Wed, 22 Jul 2020 14:15:01: #1 tag size is determined as 51 bps INFO @ Wed, 22 Jul 2020 14:15:01: #1 tag size = 51 INFO @ Wed, 22 Jul 2020 14:15:01: #1 total tags in treatment: 3843558 INFO @ Wed, 22 Jul 2020 14:15:01: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 14:15:01: #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 14:15:01: #1 tags after filtering in treatment: 2639449 INFO @ Wed, 22 Jul 2020 14:15:01: #1 Redundant rate of treatment: 0.31 INFO @ Wed, 22 Jul 2020 14:15:01: #1 finished! INFO @ Wed, 22 Jul 2020 14:15:01: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 14:15:01: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 14:15:01: #2 number of paired peaks: 27 WARNING @ Wed, 22 Jul 2020 14:15:01: Too few paired peaks (27) 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 14:15:01: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8357660/SRX8357660.10_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/SRX8357660/SRX8357660.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8357660/SRX8357660.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8357660/SRX8357660.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Jul 2020 14:15:02: 2000000 INFO @ Wed, 22 Jul 2020 14:15:07: 3000000 INFO @ Wed, 22 Jul 2020 14:15:11: 4000000 INFO @ Wed, 22 Jul 2020 14:15:16: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Jul 2020 14:15:21: 6000000 INFO @ Wed, 22 Jul 2020 14:15:26: 7000000 BigWig に変換しました。 INFO @ Wed, 22 Jul 2020 14:15:30: #1 tag size is determined as 51 bps INFO @ Wed, 22 Jul 2020 14:15:30: #1 tag size = 51 INFO @ Wed, 22 Jul 2020 14:15:30: #1 total tags in treatment: 3843558 INFO @ Wed, 22 Jul 2020 14:15:30: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 14:15:30: #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 14:15:30: #1 tags after filtering in treatment: 2639449 INFO @ Wed, 22 Jul 2020 14:15:30: #1 Redundant rate of treatment: 0.31 INFO @ Wed, 22 Jul 2020 14:15:30: #1 finished! INFO @ Wed, 22 Jul 2020 14:15:30: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 14:15:30: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 14:15:30: #2 number of paired peaks: 27 WARNING @ Wed, 22 Jul 2020 14:15:30: Too few paired peaks (27) 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 14:15:30: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8357660/SRX8357660.20_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/SRX8357660/SRX8357660.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8357660/SRX8357660.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8357660/SRX8357660.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling