Job ID = 10223830 SRX = ERX4439587 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-10-15T23:18:32 prefetch.2.10.7: 1) Downloading 'ERR4501516'... 2020-10-15T23:18:32 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T23:19:12 prefetch.2.10.7: HTTPS download succeed 2020-10-15T23:19:12 prefetch.2.10.7: 'ERR4501516' is valid 2020-10-15T23:19:12 prefetch.2.10.7: 1) 'ERR4501516' was downloaded successfully 2020-10-15T23:19:40 prefetch.2.10.7: 'ERR4501516' has 5 unresolved dependencies 2020-10-15T23:19:40 prefetch.2.10.7: 2) Downloading 'ncbi-acc:NC_001136.8?vdb-ctx=refseq'... 2020-10-15T23:19:40 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T23:19:52 prefetch.2.10.7: HTTPS download succeed 2020-10-15T23:19:52 prefetch.2.10.7: 2) 'ncbi-acc:NC_001136.8?vdb-ctx=refseq' was downloaded successfully 2020-10-15T23:19:52 prefetch.2.10.7: 3) Downloading 'ncbi-acc:NC_001139.7?vdb-ctx=refseq'... 2020-10-15T23:19:52 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T23:20:01 prefetch.2.10.7: HTTPS download succeed 2020-10-15T23:20:01 prefetch.2.10.7: 3) 'ncbi-acc:NC_001139.7?vdb-ctx=refseq' was downloaded successfully 2020-10-15T23:20:01 prefetch.2.10.7: 4) Downloading 'ncbi-acc:NC_001144.4?vdb-ctx=refseq'... 2020-10-15T23:20:01 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T23:20:12 prefetch.2.10.7: HTTPS download succeed 2020-10-15T23:20:12 prefetch.2.10.7: 4) 'ncbi-acc:NC_001144.4?vdb-ctx=refseq' was downloaded successfully 2020-10-15T23:20:12 prefetch.2.10.7: 5) Downloading 'ncbi-acc:NC_001147.5?vdb-ctx=refseq'... 2020-10-15T23:20:12 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T23:20:24 prefetch.2.10.7: HTTPS download succeed 2020-10-15T23:20:24 prefetch.2.10.7: 5) 'ncbi-acc:NC_001147.5?vdb-ctx=refseq' was downloaded successfully 2020-10-15T23:20:24 prefetch.2.10.7: 6) Downloading 'ncbi-acc:NC_001224.1?vdb-ctx=refseq'... 2020-10-15T23:20:24 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T23:20:34 prefetch.2.10.7: HTTPS download succeed 2020-10-15T23:20:34 prefetch.2.10.7: 6) 'ncbi-acc:NC_001224.1?vdb-ctx=refseq' was downloaded successfully Read 3647354 spots for ERR4501516/ERR4501516.sra Written 3647354 spots for ERR4501516/ERR4501516.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: 00:02:42 3647354 reads; of these: 3647354 (100.00%) were paired; of these: 906884 (24.86%) aligned concordantly 0 times 2295215 (62.93%) aligned concordantly exactly 1 time 445255 (12.21%) aligned concordantly >1 times ---- 906884 pairs aligned concordantly 0 times; of these: 367370 (40.51%) aligned discordantly 1 time ---- 539514 pairs aligned 0 times concordantly or discordantly; of these: 1079028 mates make up the pairs; of these: 851530 (78.92%) aligned 0 times 54282 (5.03%) aligned exactly 1 time 173216 (16.05%) aligned >1 times 88.33% overall alignment rate Time searching: 00:02:42 Overall time: 00:02:42 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] 58555 / 3080046 = 0.0190 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 08:27:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4439587/ERX4439587.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4439587/ERX4439587.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4439587/ERX4439587.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4439587/ERX4439587.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 08:27:01: #1 read tag files... INFO @ Fri, 16 Oct 2020 08:27:01: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 08:27:06: 1000000 INFO @ Fri, 16 Oct 2020 08:27:12: 2000000 INFO @ Fri, 16 Oct 2020 08:27:18: 3000000 INFO @ Fri, 16 Oct 2020 08:27:23: 4000000 INFO @ Fri, 16 Oct 2020 08:27:29: 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 @ Fri, 16 Oct 2020 08:27:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4439587/ERX4439587.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4439587/ERX4439587.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4439587/ERX4439587.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4439587/ERX4439587.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 08:27:31: #1 read tag files... INFO @ Fri, 16 Oct 2020 08:27:31: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 08:27:34: 6000000 INFO @ Fri, 16 Oct 2020 08:27:36: #1 tag size is determined as 100 bps INFO @ Fri, 16 Oct 2020 08:27:36: #1 tag size = 100 INFO @ Fri, 16 Oct 2020 08:27:36: #1 total tags in treatment: 2688581 INFO @ Fri, 16 Oct 2020 08:27:36: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 08:27:36: #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 08:27:36: #1 tags after filtering in treatment: 2298757 INFO @ Fri, 16 Oct 2020 08:27:36: #1 Redundant rate of treatment: 0.14 INFO @ Fri, 16 Oct 2020 08:27:36: #1 finished! INFO @ Fri, 16 Oct 2020 08:27:36: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 08:27:36: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 08:27:37: #2 number of paired peaks: 51 WARNING @ Fri, 16 Oct 2020 08:27:37: Too few paired peaks (51) 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 08:27:37: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX4439587/ERX4439587.05_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/ERX4439587/ERX4439587.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX4439587/ERX4439587.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX4439587/ERX4439587.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 16 Oct 2020 08:27:37: 1000000 INFO @ Fri, 16 Oct 2020 08:27:43: 2000000 INFO @ Fri, 16 Oct 2020 08:27:48: 3000000 INFO @ Fri, 16 Oct 2020 08:27:54: 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 @ Fri, 16 Oct 2020 08:28:00: 5000000 INFO @ Fri, 16 Oct 2020 08:28:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4439587/ERX4439587.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4439587/ERX4439587.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4439587/ERX4439587.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4439587/ERX4439587.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 08:28:01: #1 read tag files... INFO @ Fri, 16 Oct 2020 08:28:01: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 08:28:06: 6000000 INFO @ Fri, 16 Oct 2020 08:28:07: 1000000 INFO @ Fri, 16 Oct 2020 08:28:08: #1 tag size is determined as 100 bps INFO @ Fri, 16 Oct 2020 08:28:08: #1 tag size = 100 INFO @ Fri, 16 Oct 2020 08:28:08: #1 total tags in treatment: 2688581 INFO @ Fri, 16 Oct 2020 08:28:08: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 08:28:08: #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 08:28:08: #1 tags after filtering in treatment: 2298757 INFO @ Fri, 16 Oct 2020 08:28:08: #1 Redundant rate of treatment: 0.14 INFO @ Fri, 16 Oct 2020 08:28:08: #1 finished! INFO @ Fri, 16 Oct 2020 08:28:08: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 08:28:08: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 08:28:08: #2 number of paired peaks: 51 WARNING @ Fri, 16 Oct 2020 08:28:08: Too few paired peaks (51) 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 08:28:08: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX4439587/ERX4439587.10_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/ERX4439587/ERX4439587.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX4439587/ERX4439587.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX4439587/ERX4439587.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 16 Oct 2020 08:28:13: 2000000 INFO @ Fri, 16 Oct 2020 08:28:18: 3000000 INFO @ Fri, 16 Oct 2020 08:28:24: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 16 Oct 2020 08:28:30: 5000000 INFO @ Fri, 16 Oct 2020 08:28:36: 6000000 BigWig に変換しました。 INFO @ Fri, 16 Oct 2020 08:28:37: #1 tag size is determined as 100 bps INFO @ Fri, 16 Oct 2020 08:28:37: #1 tag size = 100 INFO @ Fri, 16 Oct 2020 08:28:37: #1 total tags in treatment: 2688581 INFO @ Fri, 16 Oct 2020 08:28:37: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 08:28:37: #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 08:28:38: #1 tags after filtering in treatment: 2298757 INFO @ Fri, 16 Oct 2020 08:28:38: #1 Redundant rate of treatment: 0.14 INFO @ Fri, 16 Oct 2020 08:28:38: #1 finished! INFO @ Fri, 16 Oct 2020 08:28:38: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 08:28:38: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 08:28:38: #2 number of paired peaks: 51 WARNING @ Fri, 16 Oct 2020 08:28:38: Too few paired peaks (51) 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 08:28:38: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX4439587/ERX4439587.20_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/ERX4439587/ERX4439587.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX4439587/ERX4439587.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX4439587/ERX4439587.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling