Job ID = 6527580 SRX = SRX1150354 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T13:11:21 prefetch.2.10.7: 1) Downloading 'SRR2163806'... 2020-06-29T13:11:21 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T13:13:09 prefetch.2.10.7: HTTPS download succeed 2020-06-29T13:13:09 prefetch.2.10.7: 'SRR2163806' is valid 2020-06-29T13:13:09 prefetch.2.10.7: 1) 'SRR2163806' was downloaded successfully 2020-06-29T13:14:01 prefetch.2.10.7: 'SRR2163806' has 10 unresolved dependencies 2020-06-29T13:14:01 prefetch.2.10.7: 2) Downloading 'ncbi-acc:NC_004353.3?vdb-ctx=refseq'... 2020-06-29T13:14:01 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T13:14:14 prefetch.2.10.7: HTTPS download succeed 2020-06-29T13:14:14 prefetch.2.10.7: 2) 'ncbi-acc:NC_004353.3?vdb-ctx=refseq' was downloaded successfully 2020-06-29T13:14:14 prefetch.2.10.7: 3) Downloading 'ncbi-acc:NC_004354.3?vdb-ctx=refseq'... 2020-06-29T13:14:14 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T13:14:30 prefetch.2.10.7: HTTPS download succeed 2020-06-29T13:14:30 prefetch.2.10.7: 3) 'ncbi-acc:NC_004354.3?vdb-ctx=refseq' was downloaded successfully 2020-06-29T13:14:30 prefetch.2.10.7: 4) Downloading 'ncbi-acc:NS_000188.1?vdb-ctx=refseq'... 2020-06-29T13:14:30 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T13:14:43 prefetch.2.10.7: HTTPS download succeed 2020-06-29T13:14:43 prefetch.2.10.7: 4) 'ncbi-acc:NS_000188.1?vdb-ctx=refseq' was downloaded successfully 2020-06-29T13:14:43 prefetch.2.10.7: 5) Downloading 'ncbi-acc:NT_033777.2?vdb-ctx=refseq'... 2020-06-29T13:14:43 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T13:14:59 prefetch.2.10.7: HTTPS download succeed 2020-06-29T13:14:59 prefetch.2.10.7: 5) 'ncbi-acc:NT_033777.2?vdb-ctx=refseq' was downloaded successfully 2020-06-29T13:14:59 prefetch.2.10.7: 6) Downloading 'ncbi-acc:NT_033778.3?vdb-ctx=refseq'... 2020-06-29T13:14:59 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T13:15:14 prefetch.2.10.7: HTTPS download succeed 2020-06-29T13:15:14 prefetch.2.10.7: 6) 'ncbi-acc:NT_033778.3?vdb-ctx=refseq' was downloaded successfully 2020-06-29T13:15:14 prefetch.2.10.7: 7) Downloading 'ncbi-acc:NT_033779.4?vdb-ctx=refseq'... 2020-06-29T13:15:14 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T13:15:31 prefetch.2.10.7: HTTPS download succeed 2020-06-29T13:15:31 prefetch.2.10.7: 7) 'ncbi-acc:NT_033779.4?vdb-ctx=refseq' was downloaded successfully 2020-06-29T13:15:31 prefetch.2.10.7: 8) Downloading 'ncbi-acc:NT_037436.3?vdb-ctx=refseq'... 2020-06-29T13:15:31 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T13:15:44 prefetch.2.10.7: HTTPS download succeed 2020-06-29T13:15:44 prefetch.2.10.7: 8) 'ncbi-acc:NT_037436.3?vdb-ctx=refseq' was downloaded successfully 2020-06-29T13:15:44 prefetch.2.10.7: 9) Downloading 'ncbi-acc:NW_001848856.1?vdb-ctx=refseq'... 2020-06-29T13:15:44 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T13:16:00 prefetch.2.10.7: HTTPS download succeed 2020-06-29T13:16:00 prefetch.2.10.7: 9) 'ncbi-acc:NW_001848856.1?vdb-ctx=refseq' was downloaded successfully 2020-06-29T13:16:00 prefetch.2.10.7: 10) Downloading 'ncbi-acc:NW_001848857.1?vdb-ctx=refseq'... 2020-06-29T13:16:00 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T13:16:12 prefetch.2.10.7: HTTPS download succeed 2020-06-29T13:16:12 prefetch.2.10.7: 10) 'ncbi-acc:NW_001848857.1?vdb-ctx=refseq' was downloaded successfully 2020-06-29T13:16:12 prefetch.2.10.7: 11) Downloading 'ncbi-acc:NW_001848858.1?vdb-ctx=refseq'... 2020-06-29T13:16:12 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T13:16:27 prefetch.2.10.7: HTTPS download succeed 2020-06-29T13:16:27 prefetch.2.10.7: 11) 'ncbi-acc:NW_001848858.1?vdb-ctx=refseq' was downloaded successfully Read 22406467 spots for SRR2163806/SRR2163806.sra Written 22406467 spots for SRR2163806/SRR2163806.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: 00:07:48 22406467 reads; of these: 22406467 (100.00%) were unpaired; of these: 363474 (1.62%) aligned 0 times 13125568 (58.58%) aligned exactly 1 time 8917425 (39.80%) aligned >1 times 98.38% overall alignment rate Time searching: 00:07:48 Overall time: 00:07:48 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] 2983384 / 22042993 = 0.1353 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 22:33:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1150354/SRX1150354.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1150354/SRX1150354.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1150354/SRX1150354.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1150354/SRX1150354.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 22:33:22: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:33:22: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:33:30: 1000000 INFO @ Mon, 29 Jun 2020 22:33:37: 2000000 INFO @ Mon, 29 Jun 2020 22:33:44: 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 22:33:52: 4000000 INFO @ Mon, 29 Jun 2020 22:33:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1150354/SRX1150354.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1150354/SRX1150354.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1150354/SRX1150354.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1150354/SRX1150354.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 22:33:52: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:33:52: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:33:59: 1000000 INFO @ Mon, 29 Jun 2020 22:34:00: 5000000 INFO @ Mon, 29 Jun 2020 22:34:06: 2000000 INFO @ Mon, 29 Jun 2020 22:34:08: 6000000 INFO @ Mon, 29 Jun 2020 22:34:14: 3000000 INFO @ Mon, 29 Jun 2020 22:34:16: 7000000 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 22:34:21: 4000000 INFO @ Mon, 29 Jun 2020 22:34:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1150354/SRX1150354.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1150354/SRX1150354.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1150354/SRX1150354.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1150354/SRX1150354.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 22:34:22: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:34:22: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:34:24: 8000000 INFO @ Mon, 29 Jun 2020 22:34:28: 5000000 INFO @ Mon, 29 Jun 2020 22:34:29: 1000000 INFO @ Mon, 29 Jun 2020 22:34:32: 9000000 INFO @ Mon, 29 Jun 2020 22:34:36: 6000000 INFO @ Mon, 29 Jun 2020 22:34:37: 2000000 INFO @ Mon, 29 Jun 2020 22:34:40: 10000000 INFO @ Mon, 29 Jun 2020 22:34:43: 7000000 INFO @ Mon, 29 Jun 2020 22:34:44: 3000000 INFO @ Mon, 29 Jun 2020 22:34:48: 11000000 INFO @ Mon, 29 Jun 2020 22:34:50: 8000000 INFO @ Mon, 29 Jun 2020 22:34:52: 4000000 INFO @ Mon, 29 Jun 2020 22:34:56: 12000000 INFO @ Mon, 29 Jun 2020 22:34:58: 9000000 INFO @ Mon, 29 Jun 2020 22:34:59: 5000000 INFO @ Mon, 29 Jun 2020 22:35:04: 13000000 INFO @ Mon, 29 Jun 2020 22:35:05: 10000000 INFO @ Mon, 29 Jun 2020 22:35:06: 6000000 INFO @ Mon, 29 Jun 2020 22:35:12: 14000000 INFO @ Mon, 29 Jun 2020 22:35:13: 11000000 INFO @ Mon, 29 Jun 2020 22:35:14: 7000000 INFO @ Mon, 29 Jun 2020 22:35:20: 12000000 INFO @ Mon, 29 Jun 2020 22:35:20: 15000000 INFO @ Mon, 29 Jun 2020 22:35:21: 8000000 INFO @ Mon, 29 Jun 2020 22:35:28: 13000000 INFO @ Mon, 29 Jun 2020 22:35:28: 16000000 INFO @ Mon, 29 Jun 2020 22:35:29: 9000000 INFO @ Mon, 29 Jun 2020 22:35:35: 14000000 INFO @ Mon, 29 Jun 2020 22:35:36: 10000000 INFO @ Mon, 29 Jun 2020 22:35:36: 17000000 INFO @ Mon, 29 Jun 2020 22:35:43: 15000000 INFO @ Mon, 29 Jun 2020 22:35:43: 11000000 INFO @ Mon, 29 Jun 2020 22:35:44: 18000000 INFO @ Mon, 29 Jun 2020 22:35:50: 16000000 INFO @ Mon, 29 Jun 2020 22:35:51: 12000000 INFO @ Mon, 29 Jun 2020 22:35:52: 19000000 INFO @ Mon, 29 Jun 2020 22:35:52: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 22:35:52: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 22:35:52: #1 total tags in treatment: 19059609 INFO @ Mon, 29 Jun 2020 22:35:52: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:35:52: #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 22:35:52: #1 tags after filtering in treatment: 19059609 INFO @ Mon, 29 Jun 2020 22:35:52: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:35:52: #1 finished! INFO @ Mon, 29 Jun 2020 22:35:52: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:35:52: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:35:54: #2 number of paired peaks: 47 WARNING @ Mon, 29 Jun 2020 22:35:54: Too few paired peaks (47) 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 22:35:54: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX1150354/SRX1150354.05_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/SRX1150354/SRX1150354.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX1150354/SRX1150354.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX1150354/SRX1150354.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 22:35:57: 17000000 INFO @ Mon, 29 Jun 2020 22:35:58: 13000000 INFO @ Mon, 29 Jun 2020 22:36:04: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 29 Jun 2020 22:36:04: 14000000 INFO @ Mon, 29 Jun 2020 22:36:10: 19000000 INFO @ Mon, 29 Jun 2020 22:36:10: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 22:36:10: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 22:36:10: #1 total tags in treatment: 19059609 INFO @ Mon, 29 Jun 2020 22:36:10: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:36:10: #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 22:36:11: #1 tags after filtering in treatment: 19059609 INFO @ Mon, 29 Jun 2020 22:36:11: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:36:11: #1 finished! INFO @ Mon, 29 Jun 2020 22:36:11: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:36:11: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:36:11: 15000000 INFO @ Mon, 29 Jun 2020 22:36:12: #2 number of paired peaks: 47 WARNING @ Mon, 29 Jun 2020 22:36:12: Too few paired peaks (47) 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 22:36:12: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX1150354/SRX1150354.10_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/SRX1150354/SRX1150354.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX1150354/SRX1150354.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX1150354/SRX1150354.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 22:36:17: 16000000 INFO @ Mon, 29 Jun 2020 22:36:23: 17000000 INFO @ Mon, 29 Jun 2020 22:36:29: 18000000 INFO @ Mon, 29 Jun 2020 22:36:35: 19000000 INFO @ Mon, 29 Jun 2020 22:36:35: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 22:36:35: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 22:36:35: #1 total tags in treatment: 19059609 INFO @ Mon, 29 Jun 2020 22:36:35: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:36:35: #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 22:36:35: #1 tags after filtering in treatment: 19059609 INFO @ Mon, 29 Jun 2020 22:36:35: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:36:35: #1 finished! INFO @ Mon, 29 Jun 2020 22:36:35: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:36:35: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:36:37: #2 number of paired peaks: 47 WARNING @ Mon, 29 Jun 2020 22:36:37: Too few paired peaks (47) 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 22:36:37: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX1150354/SRX1150354.20_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/SRX1150354/SRX1150354.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX1150354/SRX1150354.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX1150354/SRX1150354.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。