Job ID = 10223821 SRX = ERX4439581 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-10-15T23:15:20 prefetch.2.10.7: 1) Downloading 'ERR4501510'... 2020-10-15T23:15:20 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T23:16:09 prefetch.2.10.7: HTTPS download succeed 2020-10-15T23:16:10 prefetch.2.10.7: 'ERR4501510' is valid 2020-10-15T23:16:10 prefetch.2.10.7: 1) 'ERR4501510' was downloaded successfully 2020-10-15T23:16:38 prefetch.2.10.7: 'ERR4501510' has 5 unresolved dependencies 2020-10-15T23:16:38 prefetch.2.10.7: 2) Downloading 'ncbi-acc:NC_001136.8?vdb-ctx=refseq'... 2020-10-15T23:16:38 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T23:16:50 prefetch.2.10.7: HTTPS download succeed 2020-10-15T23:16:50 prefetch.2.10.7: 2) 'ncbi-acc:NC_001136.8?vdb-ctx=refseq' was downloaded successfully 2020-10-15T23:16:50 prefetch.2.10.7: 3) Downloading 'ncbi-acc:NC_001139.7?vdb-ctx=refseq'... 2020-10-15T23:16:50 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T23:16:58 prefetch.2.10.7: HTTPS download succeed 2020-10-15T23:16:58 prefetch.2.10.7: 3) 'ncbi-acc:NC_001139.7?vdb-ctx=refseq' was downloaded successfully 2020-10-15T23:16:58 prefetch.2.10.7: 4) Downloading 'ncbi-acc:NC_001144.4?vdb-ctx=refseq'... 2020-10-15T23:16:58 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T23:17:10 prefetch.2.10.7: HTTPS download succeed 2020-10-15T23:17:10 prefetch.2.10.7: 4) 'ncbi-acc:NC_001144.4?vdb-ctx=refseq' was downloaded successfully 2020-10-15T23:17:10 prefetch.2.10.7: 5) Downloading 'ncbi-acc:NC_001147.5?vdb-ctx=refseq'... 2020-10-15T23:17:10 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T23:17:23 prefetch.2.10.7: HTTPS download succeed 2020-10-15T23:17:23 prefetch.2.10.7: 5) 'ncbi-acc:NC_001147.5?vdb-ctx=refseq' was downloaded successfully 2020-10-15T23:17:23 prefetch.2.10.7: 6) Downloading 'ncbi-acc:NC_001224.1?vdb-ctx=refseq'... 2020-10-15T23:17:23 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T23:17:33 prefetch.2.10.7: HTTPS download succeed 2020-10-15T23:17:33 prefetch.2.10.7: 6) 'ncbi-acc:NC_001224.1?vdb-ctx=refseq' was downloaded successfully Read 7525335 spots for ERR4501510/ERR4501510.sra Written 7525335 spots for ERR4501510/ERR4501510.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: 00:05:08 7525335 reads; of these: 7525335 (100.00%) were paired; of these: 995958 (13.23%) aligned concordantly 0 times 6003103 (79.77%) aligned concordantly exactly 1 time 526274 (6.99%) aligned concordantly >1 times ---- 995958 pairs aligned concordantly 0 times; of these: 409796 (41.15%) aligned discordantly 1 time ---- 586162 pairs aligned 0 times concordantly or discordantly; of these: 1172324 mates make up the pairs; of these: 1027198 (87.62%) aligned 0 times 69821 (5.96%) aligned exactly 1 time 75305 (6.42%) aligned >1 times 93.18% overall alignment rate Time searching: 00:05:08 Overall time: 00:05:08 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] 575160 / 6903954 = 0.0833 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 08:29:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4439581/ERX4439581.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4439581/ERX4439581.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4439581/ERX4439581.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4439581/ERX4439581.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 08:29:57: #1 read tag files... INFO @ Fri, 16 Oct 2020 08:29:57: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 08:30:06: 1000000 INFO @ Fri, 16 Oct 2020 08:30:14: 2000000 INFO @ Fri, 16 Oct 2020 08:30:23: 3000000 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 08:30:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4439581/ERX4439581.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4439581/ERX4439581.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4439581/ERX4439581.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4439581/ERX4439581.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 08:30:27: #1 read tag files... INFO @ Fri, 16 Oct 2020 08:30:27: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 08:30:32: 4000000 INFO @ Fri, 16 Oct 2020 08:30:35: 1000000 INFO @ Fri, 16 Oct 2020 08:30:41: 5000000 INFO @ Fri, 16 Oct 2020 08:30:44: 2000000 INFO @ Fri, 16 Oct 2020 08:30:51: 6000000 INFO @ Fri, 16 Oct 2020 08:30:52: 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 08:30:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4439581/ERX4439581.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4439581/ERX4439581.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4439581/ERX4439581.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4439581/ERX4439581.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 08:30:57: #1 read tag files... INFO @ Fri, 16 Oct 2020 08:30:57: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 08:31:01: 7000000 INFO @ Fri, 16 Oct 2020 08:31:01: 4000000 INFO @ Fri, 16 Oct 2020 08:31:06: 1000000 INFO @ Fri, 16 Oct 2020 08:31:10: 5000000 INFO @ Fri, 16 Oct 2020 08:31:11: 8000000 INFO @ Fri, 16 Oct 2020 08:31:15: 2000000 INFO @ Fri, 16 Oct 2020 08:31:19: 6000000 INFO @ Fri, 16 Oct 2020 08:31:21: 9000000 INFO @ Fri, 16 Oct 2020 08:31:23: 3000000 INFO @ Fri, 16 Oct 2020 08:31:27: 7000000 INFO @ Fri, 16 Oct 2020 08:31:31: 10000000 INFO @ Fri, 16 Oct 2020 08:31:32: 4000000 INFO @ Fri, 16 Oct 2020 08:31:36: 8000000 INFO @ Fri, 16 Oct 2020 08:31:41: 5000000 INFO @ Fri, 16 Oct 2020 08:31:41: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 16 Oct 2020 08:31:45: 9000000 INFO @ Fri, 16 Oct 2020 08:31:49: 6000000 INFO @ Fri, 16 Oct 2020 08:31:52: 12000000 INFO @ Fri, 16 Oct 2020 08:31:54: 10000000 BigWig に変換しました。 INFO @ Fri, 16 Oct 2020 08:31:58: 7000000 INFO @ Fri, 16 Oct 2020 08:32:00: #1 tag size is determined as 100 bps INFO @ Fri, 16 Oct 2020 08:32:00: #1 tag size = 100 INFO @ Fri, 16 Oct 2020 08:32:00: #1 total tags in treatment: 5959950 INFO @ Fri, 16 Oct 2020 08:32:00: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 08:32:00: #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 08:32:00: #1 tags after filtering in treatment: 3831398 INFO @ Fri, 16 Oct 2020 08:32:00: #1 Redundant rate of treatment: 0.36 INFO @ Fri, 16 Oct 2020 08:32:00: #1 finished! INFO @ Fri, 16 Oct 2020 08:32:00: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 08:32:00: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 08:32:01: #2 number of paired peaks: 0 WARNING @ Fri, 16 Oct 2020 08:32:01: Too few paired peaks (0) 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 08:32:01: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX4439581/ERX4439581.05_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/ERX4439581/ERX4439581.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX4439581/ERX4439581.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX4439581/ERX4439581.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 16 Oct 2020 08:32:03: 11000000 INFO @ Fri, 16 Oct 2020 08:32:07: 8000000 INFO @ Fri, 16 Oct 2020 08:32:11: 12000000 INFO @ Fri, 16 Oct 2020 08:32:16: 9000000 INFO @ Fri, 16 Oct 2020 08:32:18: #1 tag size is determined as 100 bps INFO @ Fri, 16 Oct 2020 08:32:18: #1 tag size = 100 INFO @ Fri, 16 Oct 2020 08:32:18: #1 total tags in treatment: 5959950 INFO @ Fri, 16 Oct 2020 08:32:18: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 08:32:18: #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 08:32:18: #1 tags after filtering in treatment: 3831398 INFO @ Fri, 16 Oct 2020 08:32:18: #1 Redundant rate of treatment: 0.36 INFO @ Fri, 16 Oct 2020 08:32:18: #1 finished! INFO @ Fri, 16 Oct 2020 08:32:18: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 08:32:18: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 08:32:19: #2 number of paired peaks: 0 WARNING @ Fri, 16 Oct 2020 08:32:19: Too few paired peaks (0) 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 08:32:19: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX4439581/ERX4439581.10_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/ERX4439581/ERX4439581.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX4439581/ERX4439581.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX4439581/ERX4439581.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 16 Oct 2020 08:32:24: 10000000 INFO @ Fri, 16 Oct 2020 08:32:31: 11000000 INFO @ Fri, 16 Oct 2020 08:32:39: 12000000 INFO @ Fri, 16 Oct 2020 08:32:45: #1 tag size is determined as 100 bps INFO @ Fri, 16 Oct 2020 08:32:45: #1 tag size = 100 INFO @ Fri, 16 Oct 2020 08:32:45: #1 total tags in treatment: 5959950 INFO @ Fri, 16 Oct 2020 08:32:45: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 08:32:45: #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 08:32:45: #1 tags after filtering in treatment: 3831398 INFO @ Fri, 16 Oct 2020 08:32:45: #1 Redundant rate of treatment: 0.36 INFO @ Fri, 16 Oct 2020 08:32:45: #1 finished! INFO @ Fri, 16 Oct 2020 08:32:45: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 08:32:45: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 08:32:45: #2 number of paired peaks: 0 WARNING @ Fri, 16 Oct 2020 08:32:45: Too few paired peaks (0) 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 08:32:45: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX4439581/ERX4439581.20_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/ERX4439581/ERX4439581.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX4439581/ERX4439581.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX4439581/ERX4439581.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling