Job ID = 6455850 SRX = SRX3011254 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:26:21 prefetch.2.10.7: 1) Downloading 'SRR5834731'... 2020-06-21T10:26:21 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:28:32 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:28:33 prefetch.2.10.7: 'SRR5834731' is valid 2020-06-21T10:28:33 prefetch.2.10.7: 1) 'SRR5834731' was downloaded successfully 2020-06-21T10:29:24 prefetch.2.10.7: 'SRR5834731' has 10 unresolved dependencies 2020-06-21T10:29:24 prefetch.2.10.7: 2) Downloading 'ncbi-acc:NC_004353.3?vdb-ctx=refseq'... 2020-06-21T10:29:24 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:29:36 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:29:36 prefetch.2.10.7: 2) 'ncbi-acc:NC_004353.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:29:36 prefetch.2.10.7: 3) Downloading 'ncbi-acc:NC_004354.3?vdb-ctx=refseq'... 2020-06-21T10:29:36 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:29:56 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:29:56 prefetch.2.10.7: 3) 'ncbi-acc:NC_004354.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:29:56 prefetch.2.10.7: 4) Downloading 'ncbi-acc:NS_000188.1?vdb-ctx=refseq'... 2020-06-21T10:29:56 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:30:11 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:30:11 prefetch.2.10.7: 4) 'ncbi-acc:NS_000188.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:30:11 prefetch.2.10.7: 5) Downloading 'ncbi-acc:NT_033777.2?vdb-ctx=refseq'... 2020-06-21T10:30:11 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:30:34 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:30:34 prefetch.2.10.7: 5) 'ncbi-acc:NT_033777.2?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:30:34 prefetch.2.10.7: 6) Downloading 'ncbi-acc:NT_033778.3?vdb-ctx=refseq'... 2020-06-21T10:30:34 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:31:42 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:31:42 prefetch.2.10.7: 6) 'ncbi-acc:NT_033778.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:31:42 prefetch.2.10.7: 7) Downloading 'ncbi-acc:NT_033779.4?vdb-ctx=refseq'... 2020-06-21T10:31:42 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:32:01 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:32:01 prefetch.2.10.7: 7) 'ncbi-acc:NT_033779.4?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:32:01 prefetch.2.10.7: 8) Downloading 'ncbi-acc:NT_037436.3?vdb-ctx=refseq'... 2020-06-21T10:32:01 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:32:18 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:32:18 prefetch.2.10.7: 8) 'ncbi-acc:NT_037436.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:32:18 prefetch.2.10.7: 9) Downloading 'ncbi-acc:NW_001848856.1?vdb-ctx=refseq'... 2020-06-21T10:32:18 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:32:32 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:32:32 prefetch.2.10.7: 9) 'ncbi-acc:NW_001848856.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:32:32 prefetch.2.10.7: 10) Downloading 'ncbi-acc:NW_001848857.1?vdb-ctx=refseq'... 2020-06-21T10:32:32 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:32:46 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:32:46 prefetch.2.10.7: 10) 'ncbi-acc:NW_001848857.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:32:46 prefetch.2.10.7: 11) Downloading 'ncbi-acc:NW_001848858.1?vdb-ctx=refseq'... 2020-06-21T10:32:46 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:32:59 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:32:59 prefetch.2.10.7: 11) 'ncbi-acc:NW_001848858.1?vdb-ctx=refseq' was downloaded successfully Read 20762234 spots for SRR5834731/SRR5834731.sra Written 20762234 spots for SRR5834731/SRR5834731.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: 00:03:07 20762234 reads; of these: 20762234 (100.00%) were unpaired; of these: 269193 (1.30%) aligned 0 times 20009327 (96.37%) aligned exactly 1 time 483714 (2.33%) aligned >1 times 98.70% overall alignment rate Time searching: 00:03:08 Overall time: 00:03:08 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 2579634 / 20493041 = 0.1259 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 @ Sun, 21 Jun 2020 19:42:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3011254/SRX3011254.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3011254/SRX3011254.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3011254/SRX3011254.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3011254/SRX3011254.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 @ Sun, 21 Jun 2020 19:42:32: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:42:32: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:42:38: 1000000 INFO @ Sun, 21 Jun 2020 19:42:43: 2000000 INFO @ Sun, 21 Jun 2020 19:42:49: 3000000 INFO @ Sun, 21 Jun 2020 19:42:54: 4000000 INFO @ Sun, 21 Jun 2020 19:42:59: 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 @ Sun, 21 Jun 2020 19:43:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3011254/SRX3011254.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3011254/SRX3011254.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3011254/SRX3011254.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3011254/SRX3011254.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 @ Sun, 21 Jun 2020 19:43:02: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:43:02: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:43:05: 6000000 INFO @ Sun, 21 Jun 2020 19:43:08: 1000000 INFO @ Sun, 21 Jun 2020 19:43:11: 7000000 INFO @ Sun, 21 Jun 2020 19:43:14: 2000000 INFO @ Sun, 21 Jun 2020 19:43:17: 8000000 INFO @ Sun, 21 Jun 2020 19:43:20: 3000000 INFO @ Sun, 21 Jun 2020 19:43:23: 9000000 INFO @ Sun, 21 Jun 2020 19:43:26: 4000000 INFO @ Sun, 21 Jun 2020 19:43:29: 10000000 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 @ Sun, 21 Jun 2020 19:43:32: 5000000 INFO @ Sun, 21 Jun 2020 19:43:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3011254/SRX3011254.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3011254/SRX3011254.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3011254/SRX3011254.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3011254/SRX3011254.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 @ Sun, 21 Jun 2020 19:43:32: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:43:32: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:43:35: 11000000 INFO @ Sun, 21 Jun 2020 19:43:38: 6000000 INFO @ Sun, 21 Jun 2020 19:43:38: 1000000 INFO @ Sun, 21 Jun 2020 19:43:41: 12000000 INFO @ Sun, 21 Jun 2020 19:43:44: 7000000 INFO @ Sun, 21 Jun 2020 19:43:45: 2000000 INFO @ Sun, 21 Jun 2020 19:43:47: 13000000 INFO @ Sun, 21 Jun 2020 19:43:50: 8000000 INFO @ Sun, 21 Jun 2020 19:43:51: 3000000 INFO @ Sun, 21 Jun 2020 19:43:53: 14000000 INFO @ Sun, 21 Jun 2020 19:43:56: 9000000 INFO @ Sun, 21 Jun 2020 19:43:57: 4000000 INFO @ Sun, 21 Jun 2020 19:43:59: 15000000 INFO @ Sun, 21 Jun 2020 19:44:02: 10000000 INFO @ Sun, 21 Jun 2020 19:44:03: 5000000 INFO @ Sun, 21 Jun 2020 19:44:06: 16000000 INFO @ Sun, 21 Jun 2020 19:44:08: 11000000 INFO @ Sun, 21 Jun 2020 19:44:09: 6000000 INFO @ Sun, 21 Jun 2020 19:44:12: 17000000 INFO @ Sun, 21 Jun 2020 19:44:14: 12000000 INFO @ Sun, 21 Jun 2020 19:44:15: 7000000 INFO @ Sun, 21 Jun 2020 19:44:18: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:44:18: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:44:18: #1 total tags in treatment: 17913407 INFO @ Sun, 21 Jun 2020 19:44:18: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:44:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 19:44:18: #1 tags after filtering in treatment: 17913025 INFO @ Sun, 21 Jun 2020 19:44:18: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:44:18: #1 finished! INFO @ Sun, 21 Jun 2020 19:44:18: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:44:18: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:44:20: #2 number of paired peaks: 160 WARNING @ Sun, 21 Jun 2020 19:44:20: Fewer paired peaks (160) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 160 pairs to build model! INFO @ Sun, 21 Jun 2020 19:44:20: start model_add_line... INFO @ Sun, 21 Jun 2020 19:44:20: start X-correlation... INFO @ Sun, 21 Jun 2020 19:44:20: end of X-cor INFO @ Sun, 21 Jun 2020 19:44:20: #2 finished! INFO @ Sun, 21 Jun 2020 19:44:20: #2 predicted fragment length is 161 bps INFO @ Sun, 21 Jun 2020 19:44:20: #2 alternative fragment length(s) may be 3,161,174,195,208 bps INFO @ Sun, 21 Jun 2020 19:44:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3011254/SRX3011254.05_model.r INFO @ Sun, 21 Jun 2020 19:44:20: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:44:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:44:20: 13000000 INFO @ Sun, 21 Jun 2020 19:44:22: 8000000 INFO @ Sun, 21 Jun 2020 19:44:26: 14000000 INFO @ Sun, 21 Jun 2020 19:44:28: 9000000 INFO @ Sun, 21 Jun 2020 19:44:32: 15000000 INFO @ Sun, 21 Jun 2020 19:44:34: 10000000 INFO @ Sun, 21 Jun 2020 19:44:38: 16000000 INFO @ Sun, 21 Jun 2020 19:44:40: 11000000 INFO @ Sun, 21 Jun 2020 19:44:44: 17000000 INFO @ Sun, 21 Jun 2020 19:44:46: 12000000 INFO @ Sun, 21 Jun 2020 19:44:50: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:44:50: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:44:50: #1 total tags in treatment: 17913407 INFO @ Sun, 21 Jun 2020 19:44:50: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:44:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 19:44:50: #1 tags after filtering in treatment: 17913025 INFO @ Sun, 21 Jun 2020 19:44:50: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:44:50: #1 finished! INFO @ Sun, 21 Jun 2020 19:44:50: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:44:50: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:44:51: #2 number of paired peaks: 160 WARNING @ Sun, 21 Jun 2020 19:44:51: Fewer paired peaks (160) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 160 pairs to build model! INFO @ Sun, 21 Jun 2020 19:44:51: start model_add_line... INFO @ Sun, 21 Jun 2020 19:44:51: start X-correlation... INFO @ Sun, 21 Jun 2020 19:44:51: end of X-cor INFO @ Sun, 21 Jun 2020 19:44:51: #2 finished! INFO @ Sun, 21 Jun 2020 19:44:51: #2 predicted fragment length is 161 bps INFO @ Sun, 21 Jun 2020 19:44:51: #2 alternative fragment length(s) may be 3,161,174,195,208 bps INFO @ Sun, 21 Jun 2020 19:44:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3011254/SRX3011254.10_model.r INFO @ Sun, 21 Jun 2020 19:44:51: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:44:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:44:52: 13000000 INFO @ Sun, 21 Jun 2020 19:44:58: 14000000 INFO @ Sun, 21 Jun 2020 19:44:58: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:45:04: 15000000 INFO @ Sun, 21 Jun 2020 19:45:09: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:45:15: 17000000 INFO @ Sun, 21 Jun 2020 19:45:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3011254/SRX3011254.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:45:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3011254/SRX3011254.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:45:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3011254/SRX3011254.05_summits.bed INFO @ Sun, 21 Jun 2020 19:45:17: Done! pass1 - making usageList (17 chroms): 2 millis pass2 - checking and writing primary data (2906 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:45:20: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:45:20: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:45:20: #1 total tags in treatment: 17913407 INFO @ Sun, 21 Jun 2020 19:45:20: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:45:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 19:45:21: #1 tags after filtering in treatment: 17913025 INFO @ Sun, 21 Jun 2020 19:45:21: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:45:21: #1 finished! INFO @ Sun, 21 Jun 2020 19:45:21: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:45:21: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:45:22: #2 number of paired peaks: 160 WARNING @ Sun, 21 Jun 2020 19:45:22: Fewer paired peaks (160) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 160 pairs to build model! INFO @ Sun, 21 Jun 2020 19:45:22: start model_add_line... INFO @ Sun, 21 Jun 2020 19:45:22: start X-correlation... INFO @ Sun, 21 Jun 2020 19:45:22: end of X-cor INFO @ Sun, 21 Jun 2020 19:45:22: #2 finished! INFO @ Sun, 21 Jun 2020 19:45:22: #2 predicted fragment length is 161 bps INFO @ Sun, 21 Jun 2020 19:45:22: #2 alternative fragment length(s) may be 3,161,174,195,208 bps INFO @ Sun, 21 Jun 2020 19:45:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3011254/SRX3011254.20_model.r INFO @ Sun, 21 Jun 2020 19:45:22: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:45:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:45:31: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:45:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3011254/SRX3011254.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:45:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3011254/SRX3011254.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:45:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3011254/SRX3011254.10_summits.bed INFO @ Sun, 21 Jun 2020 19:45:51: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (454 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:46:00: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:46:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3011254/SRX3011254.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:46:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3011254/SRX3011254.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:46:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3011254/SRX3011254.20_summits.bed INFO @ Sun, 21 Jun 2020 19:46:18: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (31 records, 4 fields): 2 millis CompletedMACS2peakCalling