Job ID = 10223857 SRX = ERX4439607 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-10-15T23:29:02 prefetch.2.10.7: 1) Downloading 'ERR4501536'... 2020-10-15T23:29:02 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T23:29:44 prefetch.2.10.7: HTTPS download succeed 2020-10-15T23:29:44 prefetch.2.10.7: 'ERR4501536' is valid 2020-10-15T23:29:44 prefetch.2.10.7: 1) 'ERR4501536' was downloaded successfully 2020-10-15T23:30:12 prefetch.2.10.7: 'ERR4501536' has 5 unresolved dependencies 2020-10-15T23:30:12 prefetch.2.10.7: 2) Downloading 'ncbi-acc:NC_001136.8?vdb-ctx=refseq'... 2020-10-15T23:30:12 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T23:30:24 prefetch.2.10.7: HTTPS download succeed 2020-10-15T23:30:24 prefetch.2.10.7: 2) 'ncbi-acc:NC_001136.8?vdb-ctx=refseq' was downloaded successfully 2020-10-15T23:30:24 prefetch.2.10.7: 3) Downloading 'ncbi-acc:NC_001139.7?vdb-ctx=refseq'... 2020-10-15T23:30:24 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T23:30:36 prefetch.2.10.7: HTTPS download succeed 2020-10-15T23:30:36 prefetch.2.10.7: 3) 'ncbi-acc:NC_001139.7?vdb-ctx=refseq' was downloaded successfully 2020-10-15T23:30:36 prefetch.2.10.7: 4) Downloading 'ncbi-acc:NC_001144.4?vdb-ctx=refseq'... 2020-10-15T23:30:36 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T23:30:48 prefetch.2.10.7: HTTPS download succeed 2020-10-15T23:30:48 prefetch.2.10.7: 4) 'ncbi-acc:NC_001144.4?vdb-ctx=refseq' was downloaded successfully 2020-10-15T23:30:48 prefetch.2.10.7: 5) Downloading 'ncbi-acc:NC_001147.5?vdb-ctx=refseq'... 2020-10-15T23:30:48 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T23:31:01 prefetch.2.10.7: HTTPS download succeed 2020-10-15T23:31:01 prefetch.2.10.7: 5) 'ncbi-acc:NC_001147.5?vdb-ctx=refseq' was downloaded successfully 2020-10-15T23:31:01 prefetch.2.10.7: 6) Downloading 'ncbi-acc:NC_001224.1?vdb-ctx=refseq'... 2020-10-15T23:31:01 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T23:31:07 prefetch.2.10.7: HTTPS download succeed 2020-10-15T23:31:07 prefetch.2.10.7: 6) 'ncbi-acc:NC_001224.1?vdb-ctx=refseq' was downloaded successfully Read 4421401 spots for ERR4501536/ERR4501536.sra Written 4421401 spots for ERR4501536/ERR4501536.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: 00:03:14 4421401 reads; of these: 4421401 (100.00%) were paired; of these: 1409323 (31.88%) aligned concordantly 0 times 2545017 (57.56%) aligned concordantly exactly 1 time 467061 (10.56%) aligned concordantly >1 times ---- 1409323 pairs aligned concordantly 0 times; of these: 569240 (40.39%) aligned discordantly 1 time ---- 840083 pairs aligned 0 times concordantly or discordantly; of these: 1680166 mates make up the pairs; of these: 1381581 (82.23%) aligned 0 times 76759 (4.57%) aligned exactly 1 time 221826 (13.20%) aligned >1 times 84.38% overall alignment rate Time searching: 00:03:14 Overall time: 00:03:14 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] 68865 / 3542327 = 0.0194 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 @ Fri, 16 Oct 2020 08:38:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4439607/ERX4439607.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4439607/ERX4439607.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4439607/ERX4439607.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4439607/ERX4439607.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 @ Fri, 16 Oct 2020 08:38:44: #1 read tag files... INFO @ Fri, 16 Oct 2020 08:38:44: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 08:38:50: 1000000 INFO @ Fri, 16 Oct 2020 08:38:57: 2000000 INFO @ Fri, 16 Oct 2020 08:39:03: 3000000 INFO @ Fri, 16 Oct 2020 08:39:10: 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 @ Fri, 16 Oct 2020 08:39:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4439607/ERX4439607.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4439607/ERX4439607.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4439607/ERX4439607.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4439607/ERX4439607.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 @ Fri, 16 Oct 2020 08:39:14: #1 read tag files... INFO @ Fri, 16 Oct 2020 08:39:14: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 08:39:17: 5000000 INFO @ Fri, 16 Oct 2020 08:39:22: 1000000 INFO @ Fri, 16 Oct 2020 08:39:25: 6000000 INFO @ Fri, 16 Oct 2020 08:39:31: 2000000 INFO @ Fri, 16 Oct 2020 08:39:33: 7000000 INFO @ Fri, 16 Oct 2020 08:39:36: #1 tag size is determined as 100 bps INFO @ Fri, 16 Oct 2020 08:39:36: #1 tag size = 100 INFO @ Fri, 16 Oct 2020 08:39:36: #1 total tags in treatment: 2954020 INFO @ Fri, 16 Oct 2020 08:39:36: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 08:39:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Oct 2020 08:39:36: #1 tags after filtering in treatment: 2528885 INFO @ Fri, 16 Oct 2020 08:39:36: #1 Redundant rate of treatment: 0.14 INFO @ Fri, 16 Oct 2020 08:39:36: #1 finished! INFO @ Fri, 16 Oct 2020 08:39:36: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 08:39:36: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 08:39:36: #2 number of paired peaks: 77 WARNING @ Fri, 16 Oct 2020 08:39:36: Too few paired peaks (77) 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 @ Fri, 16 Oct 2020 08:39:36: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX4439607/ERX4439607.05_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/ERX4439607/ERX4439607.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX4439607/ERX4439607.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX4439607/ERX4439607.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 16 Oct 2020 08:39:39: 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 @ Fri, 16 Oct 2020 08:39:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4439607/ERX4439607.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4439607/ERX4439607.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4439607/ERX4439607.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4439607/ERX4439607.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 @ Fri, 16 Oct 2020 08:39:44: #1 read tag files... INFO @ Fri, 16 Oct 2020 08:39:44: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 08:39:47: 4000000 INFO @ Fri, 16 Oct 2020 08:39:52: 1000000 INFO @ Fri, 16 Oct 2020 08:39:55: 5000000 INFO @ Fri, 16 Oct 2020 08:40:01: 2000000 INFO @ Fri, 16 Oct 2020 08:40:04: 6000000 INFO @ Fri, 16 Oct 2020 08:40:09: 3000000 INFO @ Fri, 16 Oct 2020 08:40:12: 7000000 INFO @ Fri, 16 Oct 2020 08:40:15: #1 tag size is determined as 100 bps INFO @ Fri, 16 Oct 2020 08:40:15: #1 tag size = 100 INFO @ Fri, 16 Oct 2020 08:40:15: #1 total tags in treatment: 2954020 INFO @ Fri, 16 Oct 2020 08:40:15: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 08:40:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Oct 2020 08:40:15: #1 tags after filtering in treatment: 2528885 INFO @ Fri, 16 Oct 2020 08:40:15: #1 Redundant rate of treatment: 0.14 INFO @ Fri, 16 Oct 2020 08:40:15: #1 finished! INFO @ Fri, 16 Oct 2020 08:40:15: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 08:40:15: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 08:40:15: #2 number of paired peaks: 77 WARNING @ Fri, 16 Oct 2020 08:40:15: Too few paired peaks (77) 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 @ Fri, 16 Oct 2020 08:40:15: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX4439607/ERX4439607.10_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/ERX4439607/ERX4439607.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX4439607/ERX4439607.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX4439607/ERX4439607.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 16 Oct 2020 08:40:17: 4000000 INFO @ Fri, 16 Oct 2020 08:40:25: 5000000 BigWig に変換しました。 INFO @ Fri, 16 Oct 2020 08:40:32: 6000000 INFO @ Fri, 16 Oct 2020 08:40:39: 7000000 INFO @ Fri, 16 Oct 2020 08:40:42: #1 tag size is determined as 100 bps INFO @ Fri, 16 Oct 2020 08:40:42: #1 tag size = 100 INFO @ Fri, 16 Oct 2020 08:40:42: #1 total tags in treatment: 2954020 INFO @ Fri, 16 Oct 2020 08:40:42: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 08:40:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Oct 2020 08:40:42: #1 tags after filtering in treatment: 2528885 INFO @ Fri, 16 Oct 2020 08:40:42: #1 Redundant rate of treatment: 0.14 INFO @ Fri, 16 Oct 2020 08:40:42: #1 finished! INFO @ Fri, 16 Oct 2020 08:40:42: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 08:40:42: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 08:40:42: #2 number of paired peaks: 77 WARNING @ Fri, 16 Oct 2020 08:40:42: Too few paired peaks (77) 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 @ Fri, 16 Oct 2020 08:40:42: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX4439607/ERX4439607.20_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/ERX4439607/ERX4439607.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX4439607/ERX4439607.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX4439607/ERX4439607.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling