Job ID = 10223895 SRX = ERX4439636 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-10-15T23:40:03 prefetch.2.10.7: 1) Downloading 'ERR4501565'... 2020-10-15T23:40:03 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T23:40:56 prefetch.2.10.7: HTTPS download succeed 2020-10-15T23:40:57 prefetch.2.10.7: 'ERR4501565' is valid 2020-10-15T23:40:57 prefetch.2.10.7: 1) 'ERR4501565' was downloaded successfully 2020-10-15T23:41:25 prefetch.2.10.7: 'ERR4501565' has 5 unresolved dependencies 2020-10-15T23:41:25 prefetch.2.10.7: 2) Downloading 'ncbi-acc:NC_001136.8?vdb-ctx=refseq'... 2020-10-15T23:41:25 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T23:41:36 prefetch.2.10.7: HTTPS download succeed 2020-10-15T23:41:36 prefetch.2.10.7: 2) 'ncbi-acc:NC_001136.8?vdb-ctx=refseq' was downloaded successfully 2020-10-15T23:41:36 prefetch.2.10.7: 3) Downloading 'ncbi-acc:NC_001139.7?vdb-ctx=refseq'... 2020-10-15T23:41:36 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T23:41:48 prefetch.2.10.7: HTTPS download succeed 2020-10-15T23:41:48 prefetch.2.10.7: 3) 'ncbi-acc:NC_001139.7?vdb-ctx=refseq' was downloaded successfully 2020-10-15T23:41:48 prefetch.2.10.7: 4) Downloading 'ncbi-acc:NC_001144.4?vdb-ctx=refseq'... 2020-10-15T23:41:48 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T23:41:55 prefetch.2.10.7: HTTPS download succeed 2020-10-15T23:41:55 prefetch.2.10.7: 4) 'ncbi-acc:NC_001144.4?vdb-ctx=refseq' was downloaded successfully 2020-10-15T23:41:55 prefetch.2.10.7: 5) Downloading 'ncbi-acc:NC_001147.5?vdb-ctx=refseq'... 2020-10-15T23:41:55 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T23:42:03 prefetch.2.10.7: HTTPS download succeed 2020-10-15T23:42:03 prefetch.2.10.7: 5) 'ncbi-acc:NC_001147.5?vdb-ctx=refseq' was downloaded successfully 2020-10-15T23:42:03 prefetch.2.10.7: 6) Downloading 'ncbi-acc:NC_001224.1?vdb-ctx=refseq'... 2020-10-15T23:42:03 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T23:42:10 prefetch.2.10.7: HTTPS download succeed 2020-10-15T23:42:10 prefetch.2.10.7: 6) 'ncbi-acc:NC_001224.1?vdb-ctx=refseq' was downloaded successfully Read 6716005 spots for ERR4501565/ERR4501565.sra Written 6716005 spots for ERR4501565/ERR4501565.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: 00:04:32 6716005 reads; of these: 6716005 (100.00%) were paired; of these: 1615941 (24.06%) aligned concordantly 0 times 4383115 (65.26%) aligned concordantly exactly 1 time 716949 (10.68%) aligned concordantly >1 times ---- 1615941 pairs aligned concordantly 0 times; of these: 699818 (43.31%) aligned discordantly 1 time ---- 916123 pairs aligned 0 times concordantly or discordantly; of these: 1832246 mates make up the pairs; of these: 1542938 (84.21%) aligned 0 times 85437 (4.66%) aligned exactly 1 time 203871 (11.13%) aligned >1 times 88.51% overall alignment rate Time searching: 00:04:32 Overall time: 00:04:32 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] 1559258 / 5743377 = 0.2715 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 08:52:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4439636/ERX4439636.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4439636/ERX4439636.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4439636/ERX4439636.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4439636/ERX4439636.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 08:52:45: #1 read tag files... INFO @ Fri, 16 Oct 2020 08:52:45: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 08:52:52: 1000000 INFO @ Fri, 16 Oct 2020 08:52:58: 2000000 INFO @ Fri, 16 Oct 2020 08:53:05: 3000000 INFO @ Fri, 16 Oct 2020 08:53:12: 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 08:53:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4439636/ERX4439636.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4439636/ERX4439636.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4439636/ERX4439636.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4439636/ERX4439636.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 08:53:15: #1 read tag files... INFO @ Fri, 16 Oct 2020 08:53:15: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 08:53:19: 5000000 INFO @ Fri, 16 Oct 2020 08:53:23: 1000000 INFO @ Fri, 16 Oct 2020 08:53:27: 6000000 INFO @ Fri, 16 Oct 2020 08:53:31: 2000000 INFO @ Fri, 16 Oct 2020 08:53:35: 7000000 INFO @ Fri, 16 Oct 2020 08:53:39: 3000000 INFO @ Fri, 16 Oct 2020 08:53:43: 8000000 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 08:53:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4439636/ERX4439636.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4439636/ERX4439636.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4439636/ERX4439636.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4439636/ERX4439636.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 08:53:45: #1 read tag files... INFO @ Fri, 16 Oct 2020 08:53:45: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 08:53:47: 4000000 INFO @ Fri, 16 Oct 2020 08:53:49: #1 tag size is determined as 100 bps INFO @ Fri, 16 Oct 2020 08:53:49: #1 tag size = 100 INFO @ Fri, 16 Oct 2020 08:53:49: #1 total tags in treatment: 3625260 INFO @ Fri, 16 Oct 2020 08:53:49: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 08:53:49: #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 08:53:49: #1 tags after filtering in treatment: 1851552 INFO @ Fri, 16 Oct 2020 08:53:49: #1 Redundant rate of treatment: 0.49 INFO @ Fri, 16 Oct 2020 08:53:49: #1 finished! INFO @ Fri, 16 Oct 2020 08:53:49: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 08:53:49: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 08:53:49: #2 number of paired peaks: 29 WARNING @ Fri, 16 Oct 2020 08:53:49: Too few paired peaks (29) 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 08:53:49: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX4439636/ERX4439636.05_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/ERX4439636/ERX4439636.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX4439636/ERX4439636.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX4439636/ERX4439636.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 16 Oct 2020 08:53:53: 1000000 INFO @ Fri, 16 Oct 2020 08:53:55: 5000000 INFO @ Fri, 16 Oct 2020 08:54:01: 2000000 INFO @ Fri, 16 Oct 2020 08:54:03: 6000000 INFO @ Fri, 16 Oct 2020 08:54:09: 3000000 INFO @ Fri, 16 Oct 2020 08:54:11: 7000000 INFO @ Fri, 16 Oct 2020 08:54:17: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 16 Oct 2020 08:54:19: 8000000 BigWig に変換しました。 INFO @ Fri, 16 Oct 2020 08:54:25: 5000000 INFO @ Fri, 16 Oct 2020 08:54:25: #1 tag size is determined as 100 bps INFO @ Fri, 16 Oct 2020 08:54:25: #1 tag size = 100 INFO @ Fri, 16 Oct 2020 08:54:25: #1 total tags in treatment: 3625260 INFO @ Fri, 16 Oct 2020 08:54:25: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 08:54:25: #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 08:54:25: #1 tags after filtering in treatment: 1851552 INFO @ Fri, 16 Oct 2020 08:54:25: #1 Redundant rate of treatment: 0.49 INFO @ Fri, 16 Oct 2020 08:54:25: #1 finished! INFO @ Fri, 16 Oct 2020 08:54:25: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 08:54:25: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 08:54:25: #2 number of paired peaks: 29 WARNING @ Fri, 16 Oct 2020 08:54:25: Too few paired peaks (29) 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 08:54:25: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX4439636/ERX4439636.10_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 3 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX4439636/ERX4439636.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX4439636/ERX4439636.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX4439636/ERX4439636.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 16 Oct 2020 08:54:32: 6000000 INFO @ Fri, 16 Oct 2020 08:54:39: 7000000 INFO @ Fri, 16 Oct 2020 08:54:47: 8000000 INFO @ Fri, 16 Oct 2020 08:54:52: #1 tag size is determined as 100 bps INFO @ Fri, 16 Oct 2020 08:54:52: #1 tag size = 100 INFO @ Fri, 16 Oct 2020 08:54:52: #1 total tags in treatment: 3625260 INFO @ Fri, 16 Oct 2020 08:54:52: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 08:54:52: #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 08:54:52: #1 tags after filtering in treatment: 1851552 INFO @ Fri, 16 Oct 2020 08:54:52: #1 Redundant rate of treatment: 0.49 INFO @ Fri, 16 Oct 2020 08:54:52: #1 finished! INFO @ Fri, 16 Oct 2020 08:54:52: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 08:54:52: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 08:54:52: #2 number of paired peaks: 29 WARNING @ Fri, 16 Oct 2020 08:54:52: Too few paired peaks (29) 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 08:54:52: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX4439636/ERX4439636.20_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/ERX4439636/ERX4439636.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX4439636/ERX4439636.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX4439636/ERX4439636.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling