Job ID = 10223846 SRX = ERX4439599 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-10-15T23:23:02 prefetch.2.10.7: 1) Downloading 'ERR4501528'... 2020-10-15T23:23:02 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T23:23:38 prefetch.2.10.7: HTTPS download succeed 2020-10-15T23:23:38 prefetch.2.10.7: 'ERR4501528' is valid 2020-10-15T23:23:38 prefetch.2.10.7: 1) 'ERR4501528' was downloaded successfully 2020-10-15T23:24:06 prefetch.2.10.7: 'ERR4501528' has 5 unresolved dependencies 2020-10-15T23:24:06 prefetch.2.10.7: 2) Downloading 'ncbi-acc:NC_001136.8?vdb-ctx=refseq'... 2020-10-15T23:24:06 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T23:24:19 prefetch.2.10.7: HTTPS download succeed 2020-10-15T23:24:19 prefetch.2.10.7: 2) 'ncbi-acc:NC_001136.8?vdb-ctx=refseq' was downloaded successfully 2020-10-15T23:24:19 prefetch.2.10.7: 3) Downloading 'ncbi-acc:NC_001139.7?vdb-ctx=refseq'... 2020-10-15T23:24:19 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T23:24:30 prefetch.2.10.7: HTTPS download succeed 2020-10-15T23:24:30 prefetch.2.10.7: 3) 'ncbi-acc:NC_001139.7?vdb-ctx=refseq' was downloaded successfully 2020-10-15T23:24:30 prefetch.2.10.7: 4) Downloading 'ncbi-acc:NC_001144.4?vdb-ctx=refseq'... 2020-10-15T23:24:30 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T23:24:38 prefetch.2.10.7: HTTPS download succeed 2020-10-15T23:24:38 prefetch.2.10.7: 4) 'ncbi-acc:NC_001144.4?vdb-ctx=refseq' was downloaded successfully 2020-10-15T23:24:38 prefetch.2.10.7: 5) Downloading 'ncbi-acc:NC_001147.5?vdb-ctx=refseq'... 2020-10-15T23:24:38 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T23:24:51 prefetch.2.10.7: HTTPS download succeed 2020-10-15T23:24:51 prefetch.2.10.7: 5) 'ncbi-acc:NC_001147.5?vdb-ctx=refseq' was downloaded successfully 2020-10-15T23:24:51 prefetch.2.10.7: 6) Downloading 'ncbi-acc:NC_001224.1?vdb-ctx=refseq'... 2020-10-15T23:24:51 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T23:25:01 prefetch.2.10.7: HTTPS download succeed 2020-10-15T23:25:01 prefetch.2.10.7: 6) 'ncbi-acc:NC_001224.1?vdb-ctx=refseq' was downloaded successfully Read 3366643 spots for ERR4501528/ERR4501528.sra Written 3366643 spots for ERR4501528/ERR4501528.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: 00:02:32 3366643 reads; of these: 3366643 (100.00%) were paired; of these: 967301 (28.73%) aligned concordantly 0 times 2025770 (60.17%) aligned concordantly exactly 1 time 373572 (11.10%) aligned concordantly >1 times ---- 967301 pairs aligned concordantly 0 times; of these: 431120 (44.57%) aligned discordantly 1 time ---- 536181 pairs aligned 0 times concordantly or discordantly; of these: 1072362 mates make up the pairs; of these: 847366 (79.02%) aligned 0 times 62092 (5.79%) aligned exactly 1 time 162904 (15.19%) aligned >1 times 87.42% overall alignment rate Time searching: 00:02:32 Overall time: 00:02:32 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_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] 44870 / 2800928 = 0.0160 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 08:31:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4439599/ERX4439599.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4439599/ERX4439599.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4439599/ERX4439599.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4439599/ERX4439599.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 08:31:05: #1 read tag files... INFO @ Fri, 16 Oct 2020 08:31:05: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 08:31:11: 1000000 INFO @ Fri, 16 Oct 2020 08:31:16: 2000000 INFO @ Fri, 16 Oct 2020 08:31:22: 3000000 INFO @ Fri, 16 Oct 2020 08:31:27: 4000000 INFO @ Fri, 16 Oct 2020 08:31:32: 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 08:31:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4439599/ERX4439599.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4439599/ERX4439599.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4439599/ERX4439599.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4439599/ERX4439599.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 08:31:35: #1 read tag files... INFO @ Fri, 16 Oct 2020 08:31:35: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 08:31:37: #1 tag size is determined as 100 bps INFO @ Fri, 16 Oct 2020 08:31:37: #1 tag size = 100 INFO @ Fri, 16 Oct 2020 08:31:37: #1 total tags in treatment: 2361647 INFO @ Fri, 16 Oct 2020 08:31:37: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 08:31:37: #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 08:31:37: #1 tags after filtering in treatment: 2056252 INFO @ Fri, 16 Oct 2020 08:31:37: #1 Redundant rate of treatment: 0.13 INFO @ Fri, 16 Oct 2020 08:31:37: #1 finished! INFO @ Fri, 16 Oct 2020 08:31:37: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 08:31:37: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 08:31:37: #2 number of paired peaks: 55 WARNING @ Fri, 16 Oct 2020 08:31:37: Too few paired peaks (55) 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 08:31:37: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX4439599/ERX4439599.05_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/ERX4439599/ERX4439599.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX4439599/ERX4439599.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX4439599/ERX4439599.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 16 Oct 2020 08:31:42: 1000000 INFO @ Fri, 16 Oct 2020 08:31:48: 2000000 INFO @ Fri, 16 Oct 2020 08:31:54: 3000000 INFO @ Fri, 16 Oct 2020 08:31:59: 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 08:32:04: 5000000 INFO @ Fri, 16 Oct 2020 08:32:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4439599/ERX4439599.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4439599/ERX4439599.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4439599/ERX4439599.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4439599/ERX4439599.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 08:32:05: #1 read tag files... INFO @ Fri, 16 Oct 2020 08:32:05: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 08:32:09: #1 tag size is determined as 100 bps INFO @ Fri, 16 Oct 2020 08:32:09: #1 tag size = 100 INFO @ Fri, 16 Oct 2020 08:32:09: #1 total tags in treatment: 2361647 INFO @ Fri, 16 Oct 2020 08:32:09: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 08:32:09: #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 08:32:09: #1 tags after filtering in treatment: 2056252 INFO @ Fri, 16 Oct 2020 08:32:09: #1 Redundant rate of treatment: 0.13 INFO @ Fri, 16 Oct 2020 08:32:09: #1 finished! INFO @ Fri, 16 Oct 2020 08:32:09: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 08:32:09: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 08:32:09: #2 number of paired peaks: 55 WARNING @ Fri, 16 Oct 2020 08:32:09: Too few paired peaks (55) 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 08:32:09: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX4439599/ERX4439599.10_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/ERX4439599/ERX4439599.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX4439599/ERX4439599.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX4439599/ERX4439599.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 16 Oct 2020 08:32:12: 1000000 INFO @ Fri, 16 Oct 2020 08:32:17: 2000000 INFO @ Fri, 16 Oct 2020 08:32:24: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 16 Oct 2020 08:32:30: 4000000 INFO @ Fri, 16 Oct 2020 08:32:37: 5000000 BigWig に変換しました。 INFO @ Fri, 16 Oct 2020 08:32:42: #1 tag size is determined as 100 bps INFO @ Fri, 16 Oct 2020 08:32:42: #1 tag size = 100 INFO @ Fri, 16 Oct 2020 08:32:42: #1 total tags in treatment: 2361647 INFO @ Fri, 16 Oct 2020 08:32:42: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 08:32:42: #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 08:32:42: #1 tags after filtering in treatment: 2056252 INFO @ Fri, 16 Oct 2020 08:32:42: #1 Redundant rate of treatment: 0.13 INFO @ Fri, 16 Oct 2020 08:32:42: #1 finished! INFO @ Fri, 16 Oct 2020 08:32:42: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 08:32:42: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 08:32:42: #2 number of paired peaks: 55 WARNING @ Fri, 16 Oct 2020 08:32:42: Too few paired peaks (55) 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 08:32:42: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX4439599/ERX4439599.20_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/ERX4439599/ERX4439599.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX4439599/ERX4439599.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX4439599/ERX4439599.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling