Job ID = 6455817 SRX = SRX3011227 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:16:06 prefetch.2.10.7: 1) Downloading 'SRR5834704'... 2020-06-21T10:16:06 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:19:28 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:19:28 prefetch.2.10.7: 1) 'SRR5834704' was downloaded successfully 2020-06-21T10:20:20 prefetch.2.10.7: 'SRR5834704' has 10 unresolved dependencies 2020-06-21T10:20:20 prefetch.2.10.7: 2) Downloading 'ncbi-acc:NC_004353.3?vdb-ctx=refseq'... 2020-06-21T10:20:20 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:20:31 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:20:31 prefetch.2.10.7: 2) 'ncbi-acc:NC_004353.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:20:31 prefetch.2.10.7: 3) Downloading 'ncbi-acc:NC_004354.3?vdb-ctx=refseq'... 2020-06-21T10:20:31 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:20:46 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:20:46 prefetch.2.10.7: 3) 'ncbi-acc:NC_004354.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:20:46 prefetch.2.10.7: 4) Downloading 'ncbi-acc:NS_000188.1?vdb-ctx=refseq'... 2020-06-21T10:20:46 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:21:01 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:21:01 prefetch.2.10.7: 4) 'ncbi-acc:NS_000188.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:21:01 prefetch.2.10.7: 5) Downloading 'ncbi-acc:NT_033777.2?vdb-ctx=refseq'... 2020-06-21T10:21:01 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:21:18 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:21:18 prefetch.2.10.7: 5) 'ncbi-acc:NT_033777.2?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:21:18 prefetch.2.10.7: 6) Downloading 'ncbi-acc:NT_033778.3?vdb-ctx=refseq'... 2020-06-21T10:21:18 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:21:35 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:21:35 prefetch.2.10.7: 6) 'ncbi-acc:NT_033778.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:21:35 prefetch.2.10.7: 7) Downloading 'ncbi-acc:NT_033779.4?vdb-ctx=refseq'... 2020-06-21T10:21:35 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:21:52 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:21:52 prefetch.2.10.7: 7) 'ncbi-acc:NT_033779.4?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:21:52 prefetch.2.10.7: 8) Downloading 'ncbi-acc:NT_037436.3?vdb-ctx=refseq'... 2020-06-21T10:21:52 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:22:09 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:22:09 prefetch.2.10.7: 8) 'ncbi-acc:NT_037436.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:22:09 prefetch.2.10.7: 9) Downloading 'ncbi-acc:NW_001848856.1?vdb-ctx=refseq'... 2020-06-21T10:22:09 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:22:22 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:22:22 prefetch.2.10.7: 9) 'ncbi-acc:NW_001848856.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:22:22 prefetch.2.10.7: 10) Downloading 'ncbi-acc:NW_001848857.1?vdb-ctx=refseq'... 2020-06-21T10:22:22 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:22:35 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:22:35 prefetch.2.10.7: 10) 'ncbi-acc:NW_001848857.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:22:35 prefetch.2.10.7: 11) Downloading 'ncbi-acc:NW_001848858.1?vdb-ctx=refseq'... 2020-06-21T10:22:35 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:22:49 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:22:49 prefetch.2.10.7: 11) 'ncbi-acc:NW_001848858.1?vdb-ctx=refseq' was downloaded successfully Read 28824750 spots for SRR5834704/SRR5834704.sra Written 28824750 spots for SRR5834704/SRR5834704.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: 00:03:51 28824750 reads; of these: 28824750 (100.00%) were unpaired; of these: 370915 (1.29%) aligned 0 times 28006291 (97.16%) aligned exactly 1 time 447544 (1.55%) aligned >1 times 98.71% overall alignment rate Time searching: 00:03:51 Overall time: 00:03:51 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] 9542855 / 28453835 = 0.3354 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 19:34:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3011227/SRX3011227.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3011227/SRX3011227.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3011227/SRX3011227.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3011227/SRX3011227.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 19:34:12: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:34:12: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:34:19: 1000000 INFO @ Sun, 21 Jun 2020 19:34:27: 2000000 INFO @ Sun, 21 Jun 2020 19:34:34: 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 @ Sun, 21 Jun 2020 19:34:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3011227/SRX3011227.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3011227/SRX3011227.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3011227/SRX3011227.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3011227/SRX3011227.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 19:34:42: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:34:42: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:34:42: 4000000 INFO @ Sun, 21 Jun 2020 19:34:49: 1000000 INFO @ Sun, 21 Jun 2020 19:34:50: 5000000 INFO @ Sun, 21 Jun 2020 19:34:56: 2000000 INFO @ Sun, 21 Jun 2020 19:34:58: 6000000 INFO @ Sun, 21 Jun 2020 19:35:04: 3000000 INFO @ Sun, 21 Jun 2020 19:35:07: 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 @ Sun, 21 Jun 2020 19:35:11: 4000000 INFO @ Sun, 21 Jun 2020 19:35:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3011227/SRX3011227.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3011227/SRX3011227.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3011227/SRX3011227.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3011227/SRX3011227.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 19:35:12: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:35:12: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:35:15: 8000000 INFO @ Sun, 21 Jun 2020 19:35:18: 5000000 INFO @ Sun, 21 Jun 2020 19:35:19: 1000000 INFO @ Sun, 21 Jun 2020 19:35:23: 9000000 INFO @ Sun, 21 Jun 2020 19:35:26: 6000000 INFO @ Sun, 21 Jun 2020 19:35:26: 2000000 INFO @ Sun, 21 Jun 2020 19:35:31: 10000000 INFO @ Sun, 21 Jun 2020 19:35:33: 7000000 INFO @ Sun, 21 Jun 2020 19:35:34: 3000000 INFO @ Sun, 21 Jun 2020 19:35:40: 11000000 INFO @ Sun, 21 Jun 2020 19:35:40: 8000000 INFO @ Sun, 21 Jun 2020 19:35:41: 4000000 INFO @ Sun, 21 Jun 2020 19:35:48: 9000000 INFO @ Sun, 21 Jun 2020 19:35:48: 12000000 INFO @ Sun, 21 Jun 2020 19:35:48: 5000000 INFO @ Sun, 21 Jun 2020 19:35:55: 10000000 INFO @ Sun, 21 Jun 2020 19:35:56: 6000000 INFO @ Sun, 21 Jun 2020 19:35:56: 13000000 INFO @ Sun, 21 Jun 2020 19:36:03: 11000000 INFO @ Sun, 21 Jun 2020 19:36:03: 7000000 INFO @ Sun, 21 Jun 2020 19:36:05: 14000000 INFO @ Sun, 21 Jun 2020 19:36:10: 12000000 INFO @ Sun, 21 Jun 2020 19:36:11: 8000000 INFO @ Sun, 21 Jun 2020 19:36:13: 15000000 INFO @ Sun, 21 Jun 2020 19:36:17: 13000000 INFO @ Sun, 21 Jun 2020 19:36:18: 9000000 INFO @ Sun, 21 Jun 2020 19:36:21: 16000000 INFO @ Sun, 21 Jun 2020 19:36:25: 14000000 INFO @ Sun, 21 Jun 2020 19:36:25: 10000000 INFO @ Sun, 21 Jun 2020 19:36:30: 17000000 INFO @ Sun, 21 Jun 2020 19:36:32: 15000000 INFO @ Sun, 21 Jun 2020 19:36:33: 11000000 INFO @ Sun, 21 Jun 2020 19:36:38: 18000000 INFO @ Sun, 21 Jun 2020 19:36:40: 16000000 INFO @ Sun, 21 Jun 2020 19:36:40: 12000000 INFO @ Sun, 21 Jun 2020 19:36:46: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:36:46: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:36:46: #1 total tags in treatment: 18910980 INFO @ Sun, 21 Jun 2020 19:36:46: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:36:46: #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 19:36:46: #1 tags after filtering in treatment: 18910475 INFO @ Sun, 21 Jun 2020 19:36:46: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:36:46: #1 finished! INFO @ Sun, 21 Jun 2020 19:36:46: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:36:46: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:36:47: 13000000 INFO @ Sun, 21 Jun 2020 19:36:47: 17000000 INFO @ Sun, 21 Jun 2020 19:36:48: #2 number of paired peaks: 3375 INFO @ Sun, 21 Jun 2020 19:36:48: start model_add_line... INFO @ Sun, 21 Jun 2020 19:36:48: start X-correlation... INFO @ Sun, 21 Jun 2020 19:36:48: end of X-cor INFO @ Sun, 21 Jun 2020 19:36:48: #2 finished! INFO @ Sun, 21 Jun 2020 19:36:48: #2 predicted fragment length is 279 bps INFO @ Sun, 21 Jun 2020 19:36:48: #2 alternative fragment length(s) may be 279 bps INFO @ Sun, 21 Jun 2020 19:36:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3011227/SRX3011227.05_model.r INFO @ Sun, 21 Jun 2020 19:36:48: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:36:48: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:36:54: 14000000 INFO @ Sun, 21 Jun 2020 19:36:55: 18000000 INFO @ Sun, 21 Jun 2020 19:37:01: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:37:01: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:37:01: #1 total tags in treatment: 18910980 INFO @ Sun, 21 Jun 2020 19:37:01: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:37:01: #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 19:37:01: 15000000 INFO @ Sun, 21 Jun 2020 19:37:02: #1 tags after filtering in treatment: 18910475 INFO @ Sun, 21 Jun 2020 19:37:02: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:37:02: #1 finished! INFO @ Sun, 21 Jun 2020 19:37:02: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:37:02: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:37:03: #2 number of paired peaks: 3375 INFO @ Sun, 21 Jun 2020 19:37:03: start model_add_line... INFO @ Sun, 21 Jun 2020 19:37:03: start X-correlation... INFO @ Sun, 21 Jun 2020 19:37:03: end of X-cor INFO @ Sun, 21 Jun 2020 19:37:03: #2 finished! INFO @ Sun, 21 Jun 2020 19:37:03: #2 predicted fragment length is 279 bps INFO @ Sun, 21 Jun 2020 19:37:03: #2 alternative fragment length(s) may be 279 bps INFO @ Sun, 21 Jun 2020 19:37:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3011227/SRX3011227.10_model.r INFO @ Sun, 21 Jun 2020 19:37:03: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:37:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:37:07: 16000000 INFO @ Sun, 21 Jun 2020 19:37:14: 17000000 INFO @ Sun, 21 Jun 2020 19:37:20: 18000000 INFO @ Sun, 21 Jun 2020 19:37:26: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:37:26: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:37:26: #1 total tags in treatment: 18910980 INFO @ Sun, 21 Jun 2020 19:37:26: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:37:26: #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 19:37:26: #1 tags after filtering in treatment: 18910475 INFO @ Sun, 21 Jun 2020 19:37:26: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:37:26: #1 finished! INFO @ Sun, 21 Jun 2020 19:37:26: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:37:26: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:37:28: #2 number of paired peaks: 3375 INFO @ Sun, 21 Jun 2020 19:37:28: start model_add_line... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:37:28: start X-correlation... INFO @ Sun, 21 Jun 2020 19:37:28: end of X-cor INFO @ Sun, 21 Jun 2020 19:37:28: #2 finished! INFO @ Sun, 21 Jun 2020 19:37:28: #2 predicted fragment length is 279 bps INFO @ Sun, 21 Jun 2020 19:37:28: #2 alternative fragment length(s) may be 279 bps INFO @ Sun, 21 Jun 2020 19:37:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3011227/SRX3011227.20_model.r INFO @ Sun, 21 Jun 2020 19:37:28: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:37:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:37:50: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:38:02: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:38:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3011227/SRX3011227.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:38:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3011227/SRX3011227.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:38:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3011227/SRX3011227.05_summits.bed INFO @ Sun, 21 Jun 2020 19:38:15: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (13369 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:38:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3011227/SRX3011227.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:38:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3011227/SRX3011227.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:38:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3011227/SRX3011227.10_summits.bed INFO @ Sun, 21 Jun 2020 19:38:27: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (10039 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:38:29: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:38:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3011227/SRX3011227.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:38:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3011227/SRX3011227.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:38:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3011227/SRX3011227.20_summits.bed INFO @ Sun, 21 Jun 2020 19:38:53: Done! pass1 - making usageList (12 chroms): 2 millis pass2 - checking and writing primary data (6324 records, 4 fields): 7 millis CompletedMACS2peakCalling