Job ID = 6527584 SRX = SRX1166571 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T12:31:37 prefetch.2.10.7: 1) Downloading 'SRR2189058'... 2020-06-29T12:31:37 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T12:33:18 prefetch.2.10.7: HTTPS download succeed 2020-06-29T12:33:18 prefetch.2.10.7: 'SRR2189058' is valid 2020-06-29T12:33:18 prefetch.2.10.7: 1) 'SRR2189058' was downloaded successfully 2020-06-29T12:34:10 prefetch.2.10.7: 'SRR2189058' has 10 unresolved dependencies 2020-06-29T12:34:10 prefetch.2.10.7: 2) Downloading 'ncbi-acc:NC_004353.3?vdb-ctx=refseq'... 2020-06-29T12:34:10 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T12:34:22 prefetch.2.10.7: HTTPS download succeed 2020-06-29T12:34:22 prefetch.2.10.7: 2) 'ncbi-acc:NC_004353.3?vdb-ctx=refseq' was downloaded successfully 2020-06-29T12:34:22 prefetch.2.10.7: 3) Downloading 'ncbi-acc:NC_004354.3?vdb-ctx=refseq'... 2020-06-29T12:34:22 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T12:34:35 prefetch.2.10.7: HTTPS download succeed 2020-06-29T12:34:35 prefetch.2.10.7: 3) 'ncbi-acc:NC_004354.3?vdb-ctx=refseq' was downloaded successfully 2020-06-29T12:34:35 prefetch.2.10.7: 4) Downloading 'ncbi-acc:NS_000188.1?vdb-ctx=refseq'... 2020-06-29T12:34:35 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T12:34:46 prefetch.2.10.7: HTTPS download succeed 2020-06-29T12:34:46 prefetch.2.10.7: 4) 'ncbi-acc:NS_000188.1?vdb-ctx=refseq' was downloaded successfully 2020-06-29T12:34:46 prefetch.2.10.7: 5) Downloading 'ncbi-acc:NT_033777.2?vdb-ctx=refseq'... 2020-06-29T12:34:46 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T12:35:01 prefetch.2.10.7: HTTPS download succeed 2020-06-29T12:35:01 prefetch.2.10.7: 5) 'ncbi-acc:NT_033777.2?vdb-ctx=refseq' was downloaded successfully 2020-06-29T12:35:01 prefetch.2.10.7: 6) Downloading 'ncbi-acc:NT_033778.3?vdb-ctx=refseq'... 2020-06-29T12:35:01 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T12:35:14 prefetch.2.10.7: HTTPS download succeed 2020-06-29T12:35:14 prefetch.2.10.7: 6) 'ncbi-acc:NT_033778.3?vdb-ctx=refseq' was downloaded successfully 2020-06-29T12:35:14 prefetch.2.10.7: 7) Downloading 'ncbi-acc:NT_033779.4?vdb-ctx=refseq'... 2020-06-29T12:35:14 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T12:35:26 prefetch.2.10.7: HTTPS download succeed 2020-06-29T12:35:26 prefetch.2.10.7: 7) 'ncbi-acc:NT_033779.4?vdb-ctx=refseq' was downloaded successfully 2020-06-29T12:35:26 prefetch.2.10.7: 8) Downloading 'ncbi-acc:NT_037436.3?vdb-ctx=refseq'... 2020-06-29T12:35:26 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T12:35:38 prefetch.2.10.7: HTTPS download succeed 2020-06-29T12:35:38 prefetch.2.10.7: 8) 'ncbi-acc:NT_037436.3?vdb-ctx=refseq' was downloaded successfully 2020-06-29T12:35:38 prefetch.2.10.7: 9) Downloading 'ncbi-acc:NW_001848856.1?vdb-ctx=refseq'... 2020-06-29T12:35:38 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T12:35:51 prefetch.2.10.7: HTTPS download succeed 2020-06-29T12:35:51 prefetch.2.10.7: 9) 'ncbi-acc:NW_001848856.1?vdb-ctx=refseq' was downloaded successfully 2020-06-29T12:35:51 prefetch.2.10.7: 10) Downloading 'ncbi-acc:NW_001848857.1?vdb-ctx=refseq'... 2020-06-29T12:35:51 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T12:35:59 prefetch.2.10.7: HTTPS download succeed 2020-06-29T12:35:59 prefetch.2.10.7: 10) 'ncbi-acc:NW_001848857.1?vdb-ctx=refseq' was downloaded successfully 2020-06-29T12:35:59 prefetch.2.10.7: 11) Downloading 'ncbi-acc:NW_001848858.1?vdb-ctx=refseq'... 2020-06-29T12:35:59 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T12:36:08 prefetch.2.10.7: HTTPS download succeed 2020-06-29T12:36:08 prefetch.2.10.7: 11) 'ncbi-acc:NW_001848858.1?vdb-ctx=refseq' was downloaded successfully Read 25367465 spots for SRR2189058/SRR2189058.sra Written 25367465 spots for SRR2189058/SRR2189058.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: 00:06:45 25367465 reads; of these: 25367465 (100.00%) were unpaired; of these: 478737 (1.89%) aligned 0 times 19750704 (77.86%) aligned exactly 1 time 5138024 (20.25%) aligned >1 times 98.11% overall alignment rate Time searching: 00:06:45 Overall time: 00:06:45 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] 7711737 / 24888728 = 0.3098 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 21:54:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1166571/SRX1166571.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1166571/SRX1166571.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1166571/SRX1166571.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1166571/SRX1166571.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 21:54:45: #1 read tag files... INFO @ Mon, 29 Jun 2020 21:54:45: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 21:54:52: 1000000 INFO @ Mon, 29 Jun 2020 21:54:59: 2000000 INFO @ Mon, 29 Jun 2020 21:55:07: 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 21:55:13: 4000000 INFO @ Mon, 29 Jun 2020 21:55:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1166571/SRX1166571.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1166571/SRX1166571.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1166571/SRX1166571.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1166571/SRX1166571.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 21:55:15: #1 read tag files... INFO @ Mon, 29 Jun 2020 21:55:15: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 21:55:21: 5000000 INFO @ Mon, 29 Jun 2020 21:55:23: 1000000 INFO @ Mon, 29 Jun 2020 21:55:28: 6000000 INFO @ Mon, 29 Jun 2020 21:55:30: 2000000 INFO @ Mon, 29 Jun 2020 21:55:36: 7000000 INFO @ Mon, 29 Jun 2020 21:55:38: 3000000 INFO @ Mon, 29 Jun 2020 21:55:43: 8000000 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 21:55:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1166571/SRX1166571.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1166571/SRX1166571.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1166571/SRX1166571.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1166571/SRX1166571.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 21:55:45: #1 read tag files... INFO @ Mon, 29 Jun 2020 21:55:45: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 21:55:46: 4000000 INFO @ Mon, 29 Jun 2020 21:55:50: 9000000 INFO @ Mon, 29 Jun 2020 21:55:53: 5000000 INFO @ Mon, 29 Jun 2020 21:55:53: 1000000 INFO @ Mon, 29 Jun 2020 21:55:58: 10000000 INFO @ Mon, 29 Jun 2020 21:56:01: 6000000 INFO @ Mon, 29 Jun 2020 21:56:01: 2000000 INFO @ Mon, 29 Jun 2020 21:56:06: 11000000 INFO @ Mon, 29 Jun 2020 21:56:09: 7000000 INFO @ Mon, 29 Jun 2020 21:56:09: 3000000 INFO @ Mon, 29 Jun 2020 21:56:13: 12000000 INFO @ Mon, 29 Jun 2020 21:56:16: 8000000 INFO @ Mon, 29 Jun 2020 21:56:17: 4000000 INFO @ Mon, 29 Jun 2020 21:56:21: 13000000 INFO @ Mon, 29 Jun 2020 21:56:24: 9000000 INFO @ Mon, 29 Jun 2020 21:56:24: 5000000 INFO @ Mon, 29 Jun 2020 21:56:29: 14000000 INFO @ Mon, 29 Jun 2020 21:56:32: 10000000 INFO @ Mon, 29 Jun 2020 21:56:32: 6000000 INFO @ Mon, 29 Jun 2020 21:56:37: 15000000 INFO @ Mon, 29 Jun 2020 21:56:39: 11000000 INFO @ Mon, 29 Jun 2020 21:56:40: 7000000 INFO @ Mon, 29 Jun 2020 21:56:44: 16000000 INFO @ Mon, 29 Jun 2020 21:56:47: 12000000 INFO @ Mon, 29 Jun 2020 21:56:48: 8000000 INFO @ Mon, 29 Jun 2020 21:56:52: 17000000 INFO @ Mon, 29 Jun 2020 21:56:53: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 21:56:53: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 21:56:53: #1 total tags in treatment: 17176991 INFO @ Mon, 29 Jun 2020 21:56:53: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 21:56:53: #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 21:56:54: #1 tags after filtering in treatment: 17176991 INFO @ Mon, 29 Jun 2020 21:56:54: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 21:56:54: #1 finished! INFO @ Mon, 29 Jun 2020 21:56:54: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 21:56:54: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 21:56:55: 13000000 INFO @ Mon, 29 Jun 2020 21:56:55: #2 number of paired peaks: 50 WARNING @ Mon, 29 Jun 2020 21:56:55: Too few paired peaks (50) 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 21:56:55: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX1166571/SRX1166571.05_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/SRX1166571/SRX1166571.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX1166571/SRX1166571.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX1166571/SRX1166571.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 21:56:55: 9000000 INFO @ Mon, 29 Jun 2020 21:57:02: 14000000 INFO @ Mon, 29 Jun 2020 21:57:03: 10000000 INFO @ Mon, 29 Jun 2020 21:57:09: 15000000 INFO @ Mon, 29 Jun 2020 21:57:10: 11000000 INFO @ Mon, 29 Jun 2020 21:57:17: 16000000 INFO @ Mon, 29 Jun 2020 21:57:17: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 29 Jun 2020 21:57:24: 17000000 INFO @ Mon, 29 Jun 2020 21:57:25: 13000000 INFO @ Mon, 29 Jun 2020 21:57:25: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 21:57:25: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 21:57:25: #1 total tags in treatment: 17176991 INFO @ Mon, 29 Jun 2020 21:57:25: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 21:57:25: #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 21:57:25: #1 tags after filtering in treatment: 17176991 INFO @ Mon, 29 Jun 2020 21:57:25: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 21:57:25: #1 finished! INFO @ Mon, 29 Jun 2020 21:57:25: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 21:57:25: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 21:57:27: #2 number of paired peaks: 50 WARNING @ Mon, 29 Jun 2020 21:57:27: Too few paired peaks (50) 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 21:57:27: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX1166571/SRX1166571.10_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/SRX1166571/SRX1166571.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX1166571/SRX1166571.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX1166571/SRX1166571.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 21:57:32: 14000000 INFO @ Mon, 29 Jun 2020 21:57:38: 15000000 INFO @ Mon, 29 Jun 2020 21:57:45: 16000000 INFO @ Mon, 29 Jun 2020 21:57:52: 17000000 INFO @ Mon, 29 Jun 2020 21:57:53: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 21:57:53: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 21:57:53: #1 total tags in treatment: 17176991 INFO @ Mon, 29 Jun 2020 21:57:53: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 21:57:53: #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 21:57:54: #1 tags after filtering in treatment: 17176991 INFO @ Mon, 29 Jun 2020 21:57:54: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 21:57:54: #1 finished! INFO @ Mon, 29 Jun 2020 21:57:54: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 21:57:54: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 21:57:55: #2 number of paired peaks: 50 WARNING @ Mon, 29 Jun 2020 21:57:55: Too few paired peaks (50) 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 21:57:55: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX1166571/SRX1166571.20_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/SRX1166571/SRX1166571.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX1166571/SRX1166571.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX1166571/SRX1166571.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。