Job ID = 6527973 SRX = SRX3511962 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T13:50:03 prefetch.2.10.7: 1) Downloading 'SRR6418947'... 2020-06-29T13:50:03 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T13:50:58 prefetch.2.10.7: HTTPS download succeed 2020-06-29T13:50:58 prefetch.2.10.7: 'SRR6418947' is valid 2020-06-29T13:50:58 prefetch.2.10.7: 1) 'SRR6418947' was downloaded successfully 2020-06-29T13:50:58 prefetch.2.10.7: 'SRR6418947' has 0 unresolved dependencies Read 4676767 spots for SRR6418947/SRR6418947.sra Written 4676767 spots for SRR6418947/SRR6418947.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: 00:02:58 4676767 reads; of these: 4676767 (100.00%) were unpaired; of these: 406573 (8.69%) aligned 0 times 3013012 (64.43%) aligned exactly 1 time 1257182 (26.88%) aligned >1 times 91.31% overall alignment rate Time searching: 00:02:58 Overall time: 00:02:58 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_rmdupse_core] 347342 / 4270194 = 0.0813 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 @ Mon, 29 Jun 2020 22:58:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3511962/SRX3511962.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3511962/SRX3511962.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3511962/SRX3511962.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3511962/SRX3511962.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Mon, 29 Jun 2020 22:58:21: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:58:21: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:58:29: 1000000 INFO @ Mon, 29 Jun 2020 22:58:37: 2000000 INFO @ Mon, 29 Jun 2020 22:58:44: 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 @ Mon, 29 Jun 2020 22:58:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3511962/SRX3511962.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3511962/SRX3511962.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3511962/SRX3511962.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3511962/SRX3511962.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Mon, 29 Jun 2020 22:58:51: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:58:51: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:58:52: #1 tag size is determined as 89 bps INFO @ Mon, 29 Jun 2020 22:58:52: #1 tag size = 89 INFO @ Mon, 29 Jun 2020 22:58:52: #1 total tags in treatment: 3922852 INFO @ Mon, 29 Jun 2020 22:58:52: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:58:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 22:58:52: #1 tags after filtering in treatment: 3922852 INFO @ Mon, 29 Jun 2020 22:58:52: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:58:52: #1 finished! INFO @ Mon, 29 Jun 2020 22:58:52: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:58:52: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:58:52: #2 number of paired peaks: 66 WARNING @ Mon, 29 Jun 2020 22:58:52: Too few paired peaks (66) 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 @ Mon, 29 Jun 2020 22:58:52: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX3511962/SRX3511962.05_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX3511962/SRX3511962.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX3511962/SRX3511962.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX3511962/SRX3511962.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 22:58:59: 1000000 INFO @ Mon, 29 Jun 2020 22:59:08: 2000000 INFO @ Mon, 29 Jun 2020 22:59:16: 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 @ Mon, 29 Jun 2020 22:59:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3511962/SRX3511962.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3511962/SRX3511962.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3511962/SRX3511962.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3511962/SRX3511962.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Mon, 29 Jun 2020 22:59:21: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:59:21: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:59:24: #1 tag size is determined as 89 bps INFO @ Mon, 29 Jun 2020 22:59:24: #1 tag size = 89 INFO @ Mon, 29 Jun 2020 22:59:24: #1 total tags in treatment: 3922852 INFO @ Mon, 29 Jun 2020 22:59:24: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:59:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 22:59:24: #1 tags after filtering in treatment: 3922852 INFO @ Mon, 29 Jun 2020 22:59:24: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:59:24: #1 finished! INFO @ Mon, 29 Jun 2020 22:59:24: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:59:24: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:59:24: #2 number of paired peaks: 66 WARNING @ Mon, 29 Jun 2020 22:59:24: Too few paired peaks (66) 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 @ Mon, 29 Jun 2020 22:59:24: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX3511962/SRX3511962.10_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX3511962/SRX3511962.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX3511962/SRX3511962.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX3511962/SRX3511962.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 22:59:29: 1000000 INFO @ Mon, 29 Jun 2020 22:59:38: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 29 Jun 2020 22:59:46: 3000000 INFO @ Mon, 29 Jun 2020 22:59:54: #1 tag size is determined as 89 bps INFO @ Mon, 29 Jun 2020 22:59:54: #1 tag size = 89 INFO @ Mon, 29 Jun 2020 22:59:54: #1 total tags in treatment: 3922852 INFO @ Mon, 29 Jun 2020 22:59:54: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:59:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 22:59:54: #1 tags after filtering in treatment: 3922852 INFO @ Mon, 29 Jun 2020 22:59:54: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:59:54: #1 finished! INFO @ Mon, 29 Jun 2020 22:59:54: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:59:54: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:59:54: #2 number of paired peaks: 66 WARNING @ Mon, 29 Jun 2020 22:59:54: Too few paired peaks (66) 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 @ Mon, 29 Jun 2020 22:59:54: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX3511962/SRX3511962.20_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/dm3/SRX3511962/SRX3511962.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX3511962/SRX3511962.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX3511962/SRX3511962.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。