Job ID = 6527582 SRX = SRX1166563 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T13:04:24 prefetch.2.10.7: 1) Downloading 'SRR2188970'... 2020-06-29T13:04:24 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T13:05:36 prefetch.2.10.7: HTTPS download succeed 2020-06-29T13:05:36 prefetch.2.10.7: 'SRR2188970' is valid 2020-06-29T13:05:36 prefetch.2.10.7: 1) 'SRR2188970' was downloaded successfully 2020-06-29T13:06:28 prefetch.2.10.7: 'SRR2188970' has 10 unresolved dependencies 2020-06-29T13:06:28 prefetch.2.10.7: 2) Downloading 'ncbi-acc:NC_004353.3?vdb-ctx=refseq'... 2020-06-29T13:06:28 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T13:06:36 prefetch.2.10.7: HTTPS download succeed 2020-06-29T13:06:36 prefetch.2.10.7: 2) 'ncbi-acc:NC_004353.3?vdb-ctx=refseq' was downloaded successfully 2020-06-29T13:06:36 prefetch.2.10.7: 3) Downloading 'ncbi-acc:NC_004354.3?vdb-ctx=refseq'... 2020-06-29T13:06:36 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T13:06:53 prefetch.2.10.7: HTTPS download succeed 2020-06-29T13:06:53 prefetch.2.10.7: 3) 'ncbi-acc:NC_004354.3?vdb-ctx=refseq' was downloaded successfully 2020-06-29T13:06:53 prefetch.2.10.7: 4) Downloading 'ncbi-acc:NS_000188.1?vdb-ctx=refseq'... 2020-06-29T13:06:53 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T13:07:12 prefetch.2.10.7: HTTPS download succeed 2020-06-29T13:07:12 prefetch.2.10.7: 4) 'ncbi-acc:NS_000188.1?vdb-ctx=refseq' was downloaded successfully 2020-06-29T13:07:12 prefetch.2.10.7: 5) Downloading 'ncbi-acc:NT_033777.2?vdb-ctx=refseq'... 2020-06-29T13:07:12 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T13:07:29 prefetch.2.10.7: HTTPS download succeed 2020-06-29T13:07:29 prefetch.2.10.7: 5) 'ncbi-acc:NT_033777.2?vdb-ctx=refseq' was downloaded successfully 2020-06-29T13:07:29 prefetch.2.10.7: 6) Downloading 'ncbi-acc:NT_033778.3?vdb-ctx=refseq'... 2020-06-29T13:07:29 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T13:07:46 prefetch.2.10.7: HTTPS download succeed 2020-06-29T13:07:46 prefetch.2.10.7: 6) 'ncbi-acc:NT_033778.3?vdb-ctx=refseq' was downloaded successfully 2020-06-29T13:07:46 prefetch.2.10.7: 7) Downloading 'ncbi-acc:NT_033779.4?vdb-ctx=refseq'... 2020-06-29T13:07:46 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T13:07:59 prefetch.2.10.7: HTTPS download succeed 2020-06-29T13:07:59 prefetch.2.10.7: 7) 'ncbi-acc:NT_033779.4?vdb-ctx=refseq' was downloaded successfully 2020-06-29T13:07:59 prefetch.2.10.7: 8) Downloading 'ncbi-acc:NT_037436.3?vdb-ctx=refseq'... 2020-06-29T13:07:59 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T13:08:13 prefetch.2.10.7: HTTPS download succeed 2020-06-29T13:08:13 prefetch.2.10.7: 8) 'ncbi-acc:NT_037436.3?vdb-ctx=refseq' was downloaded successfully 2020-06-29T13:08:13 prefetch.2.10.7: 9) Downloading 'ncbi-acc:NW_001848856.1?vdb-ctx=refseq'... 2020-06-29T13:08:13 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T13:08:22 prefetch.2.10.7: HTTPS download succeed 2020-06-29T13:08:22 prefetch.2.10.7: 9) 'ncbi-acc:NW_001848856.1?vdb-ctx=refseq' was downloaded successfully 2020-06-29T13:08:22 prefetch.2.10.7: 10) Downloading 'ncbi-acc:NW_001848857.1?vdb-ctx=refseq'... 2020-06-29T13:08:22 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T13:08:31 prefetch.2.10.7: HTTPS download succeed 2020-06-29T13:08:31 prefetch.2.10.7: 10) 'ncbi-acc:NW_001848857.1?vdb-ctx=refseq' was downloaded successfully 2020-06-29T13:08:31 prefetch.2.10.7: 11) Downloading 'ncbi-acc:NW_001848858.1?vdb-ctx=refseq'... 2020-06-29T13:08:31 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T13:08:44 prefetch.2.10.7: HTTPS download succeed 2020-06-29T13:08:44 prefetch.2.10.7: 11) 'ncbi-acc:NW_001848858.1?vdb-ctx=refseq' was downloaded successfully Read 25353483 spots for SRR2188970/SRR2188970.sra Written 25353483 spots for SRR2188970/SRR2188970.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: 00:07:12 25353483 reads; of these: 25353483 (100.00%) were unpaired; of these: 490771 (1.94%) aligned 0 times 19784832 (78.04%) aligned exactly 1 time 5077880 (20.03%) aligned >1 times 98.06% overall alignment rate Time searching: 00:07:12 Overall time: 00:07:12 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] 5939576 / 24862712 = 0.2389 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 22:27:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1166563/SRX1166563.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1166563/SRX1166563.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1166563/SRX1166563.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1166563/SRX1166563.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 22:27:18: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:27:18: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:27:24: 1000000 INFO @ Mon, 29 Jun 2020 22:27:30: 2000000 INFO @ Mon, 29 Jun 2020 22:27:36: 3000000 INFO @ Mon, 29 Jun 2020 22:27:42: 4000000 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 22:27:48: 5000000 INFO @ Mon, 29 Jun 2020 22:27:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1166563/SRX1166563.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1166563/SRX1166563.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1166563/SRX1166563.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1166563/SRX1166563.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 22:27:48: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:27:48: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:27:54: 1000000 INFO @ Mon, 29 Jun 2020 22:27:54: 6000000 INFO @ Mon, 29 Jun 2020 22:28:00: 2000000 INFO @ Mon, 29 Jun 2020 22:28:00: 7000000 INFO @ Mon, 29 Jun 2020 22:28:06: 3000000 INFO @ Mon, 29 Jun 2020 22:28:06: 8000000 INFO @ Mon, 29 Jun 2020 22:28:12: 4000000 INFO @ Mon, 29 Jun 2020 22:28:12: 9000000 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 22:28:18: 5000000 INFO @ Mon, 29 Jun 2020 22:28:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1166563/SRX1166563.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1166563/SRX1166563.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1166563/SRX1166563.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1166563/SRX1166563.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 22:28:18: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:28:18: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:28:19: 10000000 INFO @ Mon, 29 Jun 2020 22:28:24: 6000000 INFO @ Mon, 29 Jun 2020 22:28:25: 1000000 INFO @ Mon, 29 Jun 2020 22:28:26: 11000000 INFO @ Mon, 29 Jun 2020 22:28:30: 7000000 INFO @ Mon, 29 Jun 2020 22:28:32: 2000000 INFO @ Mon, 29 Jun 2020 22:28:33: 12000000 INFO @ Mon, 29 Jun 2020 22:28:36: 8000000 INFO @ Mon, 29 Jun 2020 22:28:39: 3000000 INFO @ Mon, 29 Jun 2020 22:28:40: 13000000 INFO @ Mon, 29 Jun 2020 22:28:42: 9000000 INFO @ Mon, 29 Jun 2020 22:28:46: 4000000 INFO @ Mon, 29 Jun 2020 22:28:47: 14000000 INFO @ Mon, 29 Jun 2020 22:28:47: 10000000 INFO @ Mon, 29 Jun 2020 22:28:53: 5000000 INFO @ Mon, 29 Jun 2020 22:28:53: 11000000 INFO @ Mon, 29 Jun 2020 22:28:54: 15000000 INFO @ Mon, 29 Jun 2020 22:28:59: 12000000 INFO @ Mon, 29 Jun 2020 22:29:00: 6000000 INFO @ Mon, 29 Jun 2020 22:29:01: 16000000 INFO @ Mon, 29 Jun 2020 22:29:05: 13000000 INFO @ Mon, 29 Jun 2020 22:29:07: 7000000 INFO @ Mon, 29 Jun 2020 22:29:08: 17000000 INFO @ Mon, 29 Jun 2020 22:29:11: 14000000 INFO @ Mon, 29 Jun 2020 22:29:14: 8000000 INFO @ Mon, 29 Jun 2020 22:29:15: 18000000 INFO @ Mon, 29 Jun 2020 22:29:17: 15000000 INFO @ Mon, 29 Jun 2020 22:29:21: 9000000 INFO @ Mon, 29 Jun 2020 22:29:22: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 22:29:22: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 22:29:22: #1 total tags in treatment: 18923136 INFO @ Mon, 29 Jun 2020 22:29:22: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:29:22: #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 22:29:22: #1 tags after filtering in treatment: 18923136 INFO @ Mon, 29 Jun 2020 22:29:22: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:29:22: #1 finished! INFO @ Mon, 29 Jun 2020 22:29:22: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:29:22: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:29:22: 16000000 INFO @ Mon, 29 Jun 2020 22:29:24: #2 number of paired peaks: 60 WARNING @ Mon, 29 Jun 2020 22:29:24: Too few paired peaks (60) 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 22:29:24: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX1166563/SRX1166563.05_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/SRX1166563/SRX1166563.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX1166563/SRX1166563.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX1166563/SRX1166563.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 22:29:28: 10000000 INFO @ Mon, 29 Jun 2020 22:29:28: 17000000 INFO @ Mon, 29 Jun 2020 22:29:34: 11000000 INFO @ Mon, 29 Jun 2020 22:29:34: 18000000 INFO @ Mon, 29 Jun 2020 22:29:40: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 22:29:40: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 22:29:40: #1 total tags in treatment: 18923136 INFO @ Mon, 29 Jun 2020 22:29:40: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:29:40: #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 22:29:40: 12000000 INFO @ Mon, 29 Jun 2020 22:29:40: #1 tags after filtering in treatment: 18923136 INFO @ Mon, 29 Jun 2020 22:29:40: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:29:40: #1 finished! INFO @ Mon, 29 Jun 2020 22:29:40: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:29:40: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:29:41: #2 number of paired peaks: 60 WARNING @ Mon, 29 Jun 2020 22:29:41: Too few paired peaks (60) 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 22:29:41: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX1166563/SRX1166563.10_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/SRX1166563/SRX1166563.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX1166563/SRX1166563.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX1166563/SRX1166563.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 22:29:46: 13000000 INFO @ Mon, 29 Jun 2020 22:29:52: 14000000 INFO @ Mon, 29 Jun 2020 22:29:58: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 29 Jun 2020 22:30:04: 16000000 INFO @ Mon, 29 Jun 2020 22:30:10: 17000000 INFO @ Mon, 29 Jun 2020 22:30:16: 18000000 INFO @ Mon, 29 Jun 2020 22:30:22: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 22:30:22: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 22:30:22: #1 total tags in treatment: 18923136 INFO @ Mon, 29 Jun 2020 22:30:22: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:30:22: #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 22:30:22: #1 tags after filtering in treatment: 18923136 INFO @ Mon, 29 Jun 2020 22:30:22: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:30:22: #1 finished! INFO @ Mon, 29 Jun 2020 22:30:22: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:30:22: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:30:23: #2 number of paired peaks: 60 WARNING @ Mon, 29 Jun 2020 22:30:23: Too few paired peaks (60) 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 22:30:23: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX1166563/SRX1166563.20_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/SRX1166563/SRX1166563.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX1166563/SRX1166563.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX1166563/SRX1166563.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。