Job ID = 6527579 SRX = SRX1150333 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T12:58:39 prefetch.2.10.7: 1) Downloading 'SRR2163796'... 2020-06-29T12:58:39 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T12:59:53 prefetch.2.10.7: HTTPS download succeed 2020-06-29T12:59:53 prefetch.2.10.7: 'SRR2163796' is valid 2020-06-29T12:59:53 prefetch.2.10.7: 1) 'SRR2163796' was downloaded successfully 2020-06-29T13:00:45 prefetch.2.10.7: 'SRR2163796' has 10 unresolved dependencies 2020-06-29T13:00:45 prefetch.2.10.7: 2) Downloading 'ncbi-acc:NC_004353.3?vdb-ctx=refseq'... 2020-06-29T13:00:45 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T13:00:54 prefetch.2.10.7: HTTPS download succeed 2020-06-29T13:00:54 prefetch.2.10.7: 2) 'ncbi-acc:NC_004353.3?vdb-ctx=refseq' was downloaded successfully 2020-06-29T13:00:54 prefetch.2.10.7: 3) Downloading 'ncbi-acc:NC_004354.3?vdb-ctx=refseq'... 2020-06-29T13:00:54 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T13:01:11 prefetch.2.10.7: HTTPS download succeed 2020-06-29T13:01:11 prefetch.2.10.7: 3) 'ncbi-acc:NC_004354.3?vdb-ctx=refseq' was downloaded successfully 2020-06-29T13:01:11 prefetch.2.10.7: 4) Downloading 'ncbi-acc:NS_000188.1?vdb-ctx=refseq'... 2020-06-29T13:01:11 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T13:01:28 prefetch.2.10.7: HTTPS download succeed 2020-06-29T13:01:28 prefetch.2.10.7: 4) 'ncbi-acc:NS_000188.1?vdb-ctx=refseq' was downloaded successfully 2020-06-29T13:01:28 prefetch.2.10.7: 5) Downloading 'ncbi-acc:NT_033777.2?vdb-ctx=refseq'... 2020-06-29T13:01:28 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T13:01:41 prefetch.2.10.7: HTTPS download succeed 2020-06-29T13:01:41 prefetch.2.10.7: 5) 'ncbi-acc:NT_033777.2?vdb-ctx=refseq' was downloaded successfully 2020-06-29T13:01:41 prefetch.2.10.7: 6) Downloading 'ncbi-acc:NT_033778.3?vdb-ctx=refseq'... 2020-06-29T13:01:41 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T13:01:59 prefetch.2.10.7: HTTPS download succeed 2020-06-29T13:01:59 prefetch.2.10.7: 6) 'ncbi-acc:NT_033778.3?vdb-ctx=refseq' was downloaded successfully 2020-06-29T13:01:59 prefetch.2.10.7: 7) Downloading 'ncbi-acc:NT_033779.4?vdb-ctx=refseq'... 2020-06-29T13:01:59 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T13:02:12 prefetch.2.10.7: HTTPS download succeed 2020-06-29T13:02:12 prefetch.2.10.7: 7) 'ncbi-acc:NT_033779.4?vdb-ctx=refseq' was downloaded successfully 2020-06-29T13:02:12 prefetch.2.10.7: 8) Downloading 'ncbi-acc:NT_037436.3?vdb-ctx=refseq'... 2020-06-29T13:02:12 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T13:02:27 prefetch.2.10.7: HTTPS download succeed 2020-06-29T13:02:27 prefetch.2.10.7: 8) 'ncbi-acc:NT_037436.3?vdb-ctx=refseq' was downloaded successfully 2020-06-29T13:02:27 prefetch.2.10.7: 9) Downloading 'ncbi-acc:NW_001848856.1?vdb-ctx=refseq'... 2020-06-29T13:02:27 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T13:02:40 prefetch.2.10.7: HTTPS download succeed 2020-06-29T13:02:40 prefetch.2.10.7: 9) 'ncbi-acc:NW_001848856.1?vdb-ctx=refseq' was downloaded successfully 2020-06-29T13:02:40 prefetch.2.10.7: 10) Downloading 'ncbi-acc:NW_001848857.1?vdb-ctx=refseq'... 2020-06-29T13:02:40 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T13:02:51 prefetch.2.10.7: HTTPS download succeed 2020-06-29T13:02:51 prefetch.2.10.7: 10) 'ncbi-acc:NW_001848857.1?vdb-ctx=refseq' was downloaded successfully 2020-06-29T13:02:51 prefetch.2.10.7: 11) Downloading 'ncbi-acc:NW_001848858.1?vdb-ctx=refseq'... 2020-06-29T13:02:51 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T13:03:04 prefetch.2.10.7: HTTPS download succeed 2020-06-29T13:03:04 prefetch.2.10.7: 11) 'ncbi-acc:NW_001848858.1?vdb-ctx=refseq' was downloaded successfully Read 25518805 spots for SRR2163796/SRR2163796.sra Written 25518805 spots for SRR2163796/SRR2163796.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:08:17 25518805 reads; of these: 25518805 (100.00%) were unpaired; of these: 457786 (1.79%) aligned 0 times 16348229 (64.06%) aligned exactly 1 time 8712790 (34.14%) aligned >1 times 98.21% overall alignment rate Time searching: 00:08:18 Overall time: 00:08:18 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_sort_core] merging from 12 files... [bam_rmdupse_core] 4075075 / 25061019 = 0.1626 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 22:21:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1150333/SRX1150333.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1150333/SRX1150333.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1150333/SRX1150333.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1150333/SRX1150333.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 22:21:25: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:21:25: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:21:31: 1000000 INFO @ Mon, 29 Jun 2020 22:21:36: 2000000 INFO @ Mon, 29 Jun 2020 22:21:41: 3000000 INFO @ Mon, 29 Jun 2020 22:21:46: 4000000 INFO @ Mon, 29 Jun 2020 22:21:51: 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 @ Mon, 29 Jun 2020 22:21:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1150333/SRX1150333.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1150333/SRX1150333.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1150333/SRX1150333.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1150333/SRX1150333.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 22:21:56: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:21:56: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:21:56: 6000000 INFO @ Mon, 29 Jun 2020 22:22:01: 1000000 INFO @ Mon, 29 Jun 2020 22:22:02: 7000000 INFO @ Mon, 29 Jun 2020 22:22:06: 2000000 INFO @ Mon, 29 Jun 2020 22:22:07: 8000000 INFO @ Mon, 29 Jun 2020 22:22:11: 3000000 INFO @ Mon, 29 Jun 2020 22:22:12: 9000000 INFO @ Mon, 29 Jun 2020 22:22:16: 4000000 INFO @ Mon, 29 Jun 2020 22:22:17: 10000000 INFO @ Mon, 29 Jun 2020 22:22:22: 5000000 INFO @ Mon, 29 Jun 2020 22:22:23: 11000000 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 22:22:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1150333/SRX1150333.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1150333/SRX1150333.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1150333/SRX1150333.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1150333/SRX1150333.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 22:22:25: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:22:25: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:22:27: 6000000 INFO @ Mon, 29 Jun 2020 22:22:28: 12000000 INFO @ Mon, 29 Jun 2020 22:22:31: 1000000 INFO @ Mon, 29 Jun 2020 22:22:33: 7000000 INFO @ Mon, 29 Jun 2020 22:22:33: 13000000 INFO @ Mon, 29 Jun 2020 22:22:36: 2000000 INFO @ Mon, 29 Jun 2020 22:22:38: 8000000 INFO @ Mon, 29 Jun 2020 22:22:39: 14000000 INFO @ Mon, 29 Jun 2020 22:22:42: 3000000 INFO @ Mon, 29 Jun 2020 22:22:43: 9000000 INFO @ Mon, 29 Jun 2020 22:22:44: 15000000 INFO @ Mon, 29 Jun 2020 22:22:47: 4000000 INFO @ Mon, 29 Jun 2020 22:22:49: 10000000 INFO @ Mon, 29 Jun 2020 22:22:49: 16000000 INFO @ Mon, 29 Jun 2020 22:22:52: 5000000 INFO @ Mon, 29 Jun 2020 22:22:54: 11000000 INFO @ Mon, 29 Jun 2020 22:22:55: 17000000 INFO @ Mon, 29 Jun 2020 22:22:58: 6000000 INFO @ Mon, 29 Jun 2020 22:22:59: 12000000 INFO @ Mon, 29 Jun 2020 22:23:00: 18000000 INFO @ Mon, 29 Jun 2020 22:23:03: 7000000 INFO @ Mon, 29 Jun 2020 22:23:05: 13000000 INFO @ Mon, 29 Jun 2020 22:23:06: 19000000 INFO @ Mon, 29 Jun 2020 22:23:09: 8000000 INFO @ Mon, 29 Jun 2020 22:23:10: 14000000 INFO @ Mon, 29 Jun 2020 22:23:11: 20000000 INFO @ Mon, 29 Jun 2020 22:23:14: 9000000 INFO @ Mon, 29 Jun 2020 22:23:16: 15000000 INFO @ Mon, 29 Jun 2020 22:23:16: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 22:23:16: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 22:23:16: #1 total tags in treatment: 20985944 INFO @ Mon, 29 Jun 2020 22:23:16: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:23:16: #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 22:23:16: #1 tags after filtering in treatment: 20985944 INFO @ Mon, 29 Jun 2020 22:23:16: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:23:16: #1 finished! INFO @ Mon, 29 Jun 2020 22:23:16: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:23:17: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:23:18: #2 number of paired peaks: 35 WARNING @ Mon, 29 Jun 2020 22:23:18: Too few paired peaks (35) 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 22:23:18: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX1150333/SRX1150333.05_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/dm3/SRX1150333/SRX1150333.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX1150333/SRX1150333.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX1150333/SRX1150333.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 22:23:19: 10000000 INFO @ Mon, 29 Jun 2020 22:23:21: 16000000 INFO @ Mon, 29 Jun 2020 22:23:25: 11000000 INFO @ Mon, 29 Jun 2020 22:23:26: 17000000 INFO @ Mon, 29 Jun 2020 22:23:30: 12000000 INFO @ Mon, 29 Jun 2020 22:23:32: 18000000 INFO @ Mon, 29 Jun 2020 22:23:36: 13000000 INFO @ Mon, 29 Jun 2020 22:23:37: 19000000 INFO @ Mon, 29 Jun 2020 22:23:41: 14000000 INFO @ Mon, 29 Jun 2020 22:23:42: 20000000 INFO @ Mon, 29 Jun 2020 22:23:46: 15000000 INFO @ Mon, 29 Jun 2020 22:23:47: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 22:23:47: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 22:23:47: #1 total tags in treatment: 20985944 INFO @ Mon, 29 Jun 2020 22:23:47: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:23:47: #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 22:23:48: #1 tags after filtering in treatment: 20985944 INFO @ Mon, 29 Jun 2020 22:23:48: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:23:48: #1 finished! INFO @ Mon, 29 Jun 2020 22:23:48: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:23:48: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:23:49: #2 number of paired peaks: 35 WARNING @ Mon, 29 Jun 2020 22:23:49: Too few paired peaks (35) 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 22:23:49: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX1150333/SRX1150333.10_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/dm3/SRX1150333/SRX1150333.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX1150333/SRX1150333.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX1150333/SRX1150333.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 22:23:51: 16000000 INFO @ Mon, 29 Jun 2020 22:23:57: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 29 Jun 2020 22:24:02: 18000000 INFO @ Mon, 29 Jun 2020 22:24:07: 19000000 INFO @ Mon, 29 Jun 2020 22:24:12: 20000000 INFO @ Mon, 29 Jun 2020 22:24:17: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 22:24:17: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 22:24:17: #1 total tags in treatment: 20985944 INFO @ Mon, 29 Jun 2020 22:24:17: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:24:17: #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 22:24:17: #1 tags after filtering in treatment: 20985944 INFO @ Mon, 29 Jun 2020 22:24:17: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:24:17: #1 finished! INFO @ Mon, 29 Jun 2020 22:24:17: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:24:17: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:24:18: #2 number of paired peaks: 35 WARNING @ Mon, 29 Jun 2020 22:24:18: Too few paired peaks (35) 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 22:24:18: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX1150333/SRX1150333.20_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/SRX1150333/SRX1150333.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX1150333/SRX1150333.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX1150333/SRX1150333.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。