Job ID = 7111256 SRX = SRX8189510 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-07-22T05:04:28 prefetch.2.10.7: 1) Downloading 'SRR11625406'... 2020-07-22T05:04:29 prefetch.2.10.7: Downloading via HTTPS... 2020-07-22T05:04:54 prefetch.2.10.7: HTTPS download succeed 2020-07-22T05:04:55 prefetch.2.10.7: 'SRR11625406' is valid 2020-07-22T05:04:55 prefetch.2.10.7: 1) 'SRR11625406' was downloaded successfully 2020-07-22T05:05:37 prefetch.2.10.7: 'SRR11625406' has 8 unresolved dependencies 2020-07-22T05:05:37 prefetch.2.10.7: 2) Downloading 'ncbi-acc:NC_001133.9?vdb-ctx=refseq'... 2020-07-22T05:05:37 prefetch.2.10.7: Downloading via HTTPS... 2020-07-22T05:05:44 prefetch.2.10.7: HTTPS download succeed 2020-07-22T05:05:44 prefetch.2.10.7: 2) 'ncbi-acc:NC_001133.9?vdb-ctx=refseq' was downloaded successfully 2020-07-22T05:05:44 prefetch.2.10.7: 3) Downloading 'ncbi-acc:NC_001134.8?vdb-ctx=refseq'... 2020-07-22T05:05:44 prefetch.2.10.7: Downloading via HTTPS... 2020-07-22T05:05:53 prefetch.2.10.7: HTTPS download succeed 2020-07-22T05:05:53 prefetch.2.10.7: 3) 'ncbi-acc:NC_001134.8?vdb-ctx=refseq' was downloaded successfully 2020-07-22T05:05:53 prefetch.2.10.7: 4) Downloading 'ncbi-acc:NC_001135.5?vdb-ctx=refseq'... 2020-07-22T05:05:53 prefetch.2.10.7: Downloading via HTTPS... 2020-07-22T05:06:00 prefetch.2.10.7: HTTPS download succeed 2020-07-22T05:06:00 prefetch.2.10.7: 4) 'ncbi-acc:NC_001135.5?vdb-ctx=refseq' was downloaded successfully 2020-07-22T05:06:00 prefetch.2.10.7: 5) Downloading 'ncbi-acc:NC_001136.10?vdb-ctx=refseq'... 2020-07-22T05:06:00 prefetch.2.10.7: Downloading via HTTPS... 2020-07-22T05:06:09 prefetch.2.10.7: HTTPS download succeed 2020-07-22T05:06:09 prefetch.2.10.7: 5) 'ncbi-acc:NC_001136.10?vdb-ctx=refseq' was downloaded successfully 2020-07-22T05:06:09 prefetch.2.10.7: 6) Downloading 'ncbi-acc:NC_001139.9?vdb-ctx=refseq'... 2020-07-22T05:06:09 prefetch.2.10.7: Downloading via HTTPS... 2020-07-22T05:06:18 prefetch.2.10.7: HTTPS download succeed 2020-07-22T05:06:18 prefetch.2.10.7: 6) 'ncbi-acc:NC_001139.9?vdb-ctx=refseq' was downloaded successfully 2020-07-22T05:06:18 prefetch.2.10.7: 7) Downloading 'ncbi-acc:NC_001144.5?vdb-ctx=refseq'... 2020-07-22T05:06:18 prefetch.2.10.7: Downloading via HTTPS... 2020-07-22T05:06:27 prefetch.2.10.7: HTTPS download succeed 2020-07-22T05:06:27 prefetch.2.10.7: 7) 'ncbi-acc:NC_001144.5?vdb-ctx=refseq' was downloaded successfully 2020-07-22T05:06:27 prefetch.2.10.7: 8) Downloading 'ncbi-acc:NC_001147.6?vdb-ctx=refseq'... 2020-07-22T05:06:27 prefetch.2.10.7: Downloading via HTTPS... 2020-07-22T05:06:34 prefetch.2.10.7: HTTPS download succeed 2020-07-22T05:06:34 prefetch.2.10.7: 8) 'ncbi-acc:NC_001147.6?vdb-ctx=refseq' was downloaded successfully 2020-07-22T05:06:34 prefetch.2.10.7: 9) Downloading 'ncbi-acc:NC_001224.1?vdb-ctx=refseq'... 2020-07-22T05:06:34 prefetch.2.10.7: Downloading via HTTPS... 2020-07-22T05:06:41 prefetch.2.10.7: HTTPS download succeed 2020-07-22T05:06:41 prefetch.2.10.7: 9) 'ncbi-acc:NC_001224.1?vdb-ctx=refseq' was downloaded successfully Read 3143419 spots for SRR11625406/SRR11625406.sra Written 3143419 spots for SRR11625406/SRR11625406.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: 00:00:22 3143419 reads; of these: 3143419 (100.00%) were unpaired; of these: 171636 (5.46%) aligned 0 times 1132459 (36.03%) aligned exactly 1 time 1839324 (58.51%) aligned >1 times 94.54% overall alignment rate Time searching: 00:00:22 Overall time: 00:00:22 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_rmdupse_core] 2230053 / 2971783 = 0.7504 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 @ Wed, 22 Jul 2020 14:08:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8189510/SRX8189510.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8189510/SRX8189510.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8189510/SRX8189510.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8189510/SRX8189510.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 @ Wed, 22 Jul 2020 14:08:18: #1 read tag files... INFO @ Wed, 22 Jul 2020 14:08:18: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 14:08:22: #1 tag size is determined as 64 bps INFO @ Wed, 22 Jul 2020 14:08:22: #1 tag size = 64 INFO @ Wed, 22 Jul 2020 14:08:22: #1 total tags in treatment: 741730 INFO @ Wed, 22 Jul 2020 14:08:22: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 14:08:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Jul 2020 14:08:22: #1 tags after filtering in treatment: 741730 INFO @ Wed, 22 Jul 2020 14:08:22: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Jul 2020 14:08:22: #1 finished! INFO @ Wed, 22 Jul 2020 14:08:22: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 14:08:22: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 14:08:22: #2 number of paired peaks: 73 WARNING @ Wed, 22 Jul 2020 14:08:22: Too few paired peaks (73) 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 @ Wed, 22 Jul 2020 14:08:22: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8189510/SRX8189510.05_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/SRX8189510/SRX8189510.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8189510/SRX8189510.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8189510/SRX8189510.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling 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 @ Wed, 22 Jul 2020 14:08:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8189510/SRX8189510.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8189510/SRX8189510.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8189510/SRX8189510.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8189510/SRX8189510.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 @ Wed, 22 Jul 2020 14:08:48: #1 read tag files... INFO @ Wed, 22 Jul 2020 14:08:48: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 14:08:53: #1 tag size is determined as 64 bps INFO @ Wed, 22 Jul 2020 14:08:53: #1 tag size = 64 INFO @ Wed, 22 Jul 2020 14:08:53: #1 total tags in treatment: 741730 INFO @ Wed, 22 Jul 2020 14:08:53: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 14:08:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Jul 2020 14:08:53: #1 tags after filtering in treatment: 741730 INFO @ Wed, 22 Jul 2020 14:08:53: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Jul 2020 14:08:53: #1 finished! INFO @ Wed, 22 Jul 2020 14:08:53: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 14:08:53: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 14:08:53: #2 number of paired peaks: 73 WARNING @ Wed, 22 Jul 2020 14:08:53: Too few paired peaks (73) 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 @ Wed, 22 Jul 2020 14:08:53: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8189510/SRX8189510.10_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/SRX8189510/SRX8189510.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8189510/SRX8189510.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8189510/SRX8189510.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling 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 @ Wed, 22 Jul 2020 14:09:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8189510/SRX8189510.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8189510/SRX8189510.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8189510/SRX8189510.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8189510/SRX8189510.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 @ Wed, 22 Jul 2020 14:09:18: #1 read tag files... INFO @ Wed, 22 Jul 2020 14:09:18: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Wed, 22 Jul 2020 14:09:23: #1 tag size is determined as 64 bps INFO @ Wed, 22 Jul 2020 14:09:23: #1 tag size = 64 INFO @ Wed, 22 Jul 2020 14:09:23: #1 total tags in treatment: 741730 INFO @ Wed, 22 Jul 2020 14:09:23: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 14:09:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Jul 2020 14:09:23: #1 tags after filtering in treatment: 741730 INFO @ Wed, 22 Jul 2020 14:09:23: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Jul 2020 14:09:23: #1 finished! INFO @ Wed, 22 Jul 2020 14:09:23: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 14:09:23: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 14:09:23: #2 number of paired peaks: 73 WARNING @ Wed, 22 Jul 2020 14:09:23: Too few paired peaks (73) 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 @ Wed, 22 Jul 2020 14:09:23: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8189510/SRX8189510.20_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/SRX8189510/SRX8189510.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8189510/SRX8189510.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8189510/SRX8189510.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling