Job ID = 6455831 SRX = SRX3011238 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:21:36 prefetch.2.10.7: 1) Downloading 'SRR5834715'... 2020-06-21T10:21:36 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:24:38 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:24:39 prefetch.2.10.7: 'SRR5834715' is valid 2020-06-21T10:24:39 prefetch.2.10.7: 1) 'SRR5834715' was downloaded successfully 2020-06-21T10:25:31 prefetch.2.10.7: 'SRR5834715' has 10 unresolved dependencies 2020-06-21T10:25:31 prefetch.2.10.7: 2) Downloading 'ncbi-acc:NC_004353.3?vdb-ctx=refseq'... 2020-06-21T10:25:31 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:25:43 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:25:43 prefetch.2.10.7: 2) 'ncbi-acc:NC_004353.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:25:43 prefetch.2.10.7: 3) Downloading 'ncbi-acc:NC_004354.3?vdb-ctx=refseq'... 2020-06-21T10:25:43 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:26:00 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:26:00 prefetch.2.10.7: 3) 'ncbi-acc:NC_004354.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:26:00 prefetch.2.10.7: 4) Downloading 'ncbi-acc:NS_000188.1?vdb-ctx=refseq'... 2020-06-21T10:26:00 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:26:15 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:26:15 prefetch.2.10.7: 4) 'ncbi-acc:NS_000188.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:26:15 prefetch.2.10.7: 5) Downloading 'ncbi-acc:NT_033777.2?vdb-ctx=refseq'... 2020-06-21T10:26:15 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:26:33 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:26:33 prefetch.2.10.7: 5) 'ncbi-acc:NT_033777.2?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:26:33 prefetch.2.10.7: 6) Downloading 'ncbi-acc:NT_033778.3?vdb-ctx=refseq'... 2020-06-21T10:26:33 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:26:52 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:26:52 prefetch.2.10.7: 6) 'ncbi-acc:NT_033778.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:26:52 prefetch.2.10.7: 7) Downloading 'ncbi-acc:NT_033779.4?vdb-ctx=refseq'... 2020-06-21T10:26:52 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:27:09 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:27:09 prefetch.2.10.7: 7) 'ncbi-acc:NT_033779.4?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:27:09 prefetch.2.10.7: 8) Downloading 'ncbi-acc:NT_037436.3?vdb-ctx=refseq'... 2020-06-21T10:27:09 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:27:26 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:27:26 prefetch.2.10.7: 8) 'ncbi-acc:NT_037436.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:27:26 prefetch.2.10.7: 9) Downloading 'ncbi-acc:NW_001848856.1?vdb-ctx=refseq'... 2020-06-21T10:27:26 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:27:40 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:27:40 prefetch.2.10.7: 9) 'ncbi-acc:NW_001848856.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:27:40 prefetch.2.10.7: 10) Downloading 'ncbi-acc:NW_001848857.1?vdb-ctx=refseq'... 2020-06-21T10:27:40 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:27:53 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:27:53 prefetch.2.10.7: 10) 'ncbi-acc:NW_001848857.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:27:53 prefetch.2.10.7: 11) Downloading 'ncbi-acc:NW_001848858.1?vdb-ctx=refseq'... 2020-06-21T10:27:53 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:28:05 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:28:05 prefetch.2.10.7: 11) 'ncbi-acc:NW_001848858.1?vdb-ctx=refseq' was downloaded successfully Read 16428120 spots for SRR5834715/SRR5834715.sra Written 16428120 spots for SRR5834715/SRR5834715.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: 00:04:38 16428120 reads; of these: 16428120 (100.00%) were unpaired; of these: 510193 (3.11%) aligned 0 times 13494308 (82.14%) aligned exactly 1 time 2423619 (14.75%) aligned >1 times 96.89% overall alignment rate Time searching: 00:04:38 Overall time: 00:04:38 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 8 files... [bam_rmdupse_core] 8196264 / 15917927 = 0.5149 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 19:39:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3011238/SRX3011238.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3011238/SRX3011238.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3011238/SRX3011238.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3011238/SRX3011238.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 19:39:40: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:39:40: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:39:47: 1000000 INFO @ Sun, 21 Jun 2020 19:39:55: 2000000 INFO @ Sun, 21 Jun 2020 19:40:02: 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 19:40:10: 4000000 INFO @ Sun, 21 Jun 2020 19:40:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3011238/SRX3011238.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3011238/SRX3011238.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3011238/SRX3011238.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3011238/SRX3011238.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 19:40:10: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:40:10: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:40:18: 5000000 INFO @ Sun, 21 Jun 2020 19:40:18: 1000000 INFO @ Sun, 21 Jun 2020 19:40:26: 6000000 INFO @ Sun, 21 Jun 2020 19:40:26: 2000000 INFO @ Sun, 21 Jun 2020 19:40:35: 3000000 INFO @ Sun, 21 Jun 2020 19:40:35: 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 19:40:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3011238/SRX3011238.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3011238/SRX3011238.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3011238/SRX3011238.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3011238/SRX3011238.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 19:40:40: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:40:40: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:40:41: #1 tag size is determined as 80 bps INFO @ Sun, 21 Jun 2020 19:40:41: #1 tag size = 80 INFO @ Sun, 21 Jun 2020 19:40:41: #1 total tags in treatment: 7721663 INFO @ Sun, 21 Jun 2020 19:40:41: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:40:41: #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 19:40:42: #1 tags after filtering in treatment: 7721443 INFO @ Sun, 21 Jun 2020 19:40:42: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:40:42: #1 finished! INFO @ Sun, 21 Jun 2020 19:40:42: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:40:42: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:40:43: 4000000 INFO @ Sun, 21 Jun 2020 19:40:43: #2 number of paired peaks: 5430 INFO @ Sun, 21 Jun 2020 19:40:43: start model_add_line... INFO @ Sun, 21 Jun 2020 19:40:43: start X-correlation... INFO @ Sun, 21 Jun 2020 19:40:43: end of X-cor INFO @ Sun, 21 Jun 2020 19:40:43: #2 finished! INFO @ Sun, 21 Jun 2020 19:40:43: #2 predicted fragment length is 188 bps INFO @ Sun, 21 Jun 2020 19:40:43: #2 alternative fragment length(s) may be 188 bps INFO @ Sun, 21 Jun 2020 19:40:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3011238/SRX3011238.05_model.r INFO @ Sun, 21 Jun 2020 19:40:43: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:40:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:40:48: 1000000 INFO @ Sun, 21 Jun 2020 19:40:50: 5000000 INFO @ Sun, 21 Jun 2020 19:40:55: 2000000 INFO @ Sun, 21 Jun 2020 19:40:58: 6000000 INFO @ Sun, 21 Jun 2020 19:41:03: 3000000 INFO @ Sun, 21 Jun 2020 19:41:06: 7000000 INFO @ Sun, 21 Jun 2020 19:41:07: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:41:11: 4000000 INFO @ Sun, 21 Jun 2020 19:41:12: #1 tag size is determined as 80 bps INFO @ Sun, 21 Jun 2020 19:41:12: #1 tag size = 80 INFO @ Sun, 21 Jun 2020 19:41:12: #1 total tags in treatment: 7721663 INFO @ Sun, 21 Jun 2020 19:41:12: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:41:12: #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 19:41:13: #1 tags after filtering in treatment: 7721443 INFO @ Sun, 21 Jun 2020 19:41:13: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:41:13: #1 finished! INFO @ Sun, 21 Jun 2020 19:41:13: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:41:13: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:41:14: #2 number of paired peaks: 5430 INFO @ Sun, 21 Jun 2020 19:41:14: start model_add_line... INFO @ Sun, 21 Jun 2020 19:41:14: start X-correlation... INFO @ Sun, 21 Jun 2020 19:41:14: end of X-cor INFO @ Sun, 21 Jun 2020 19:41:14: #2 finished! INFO @ Sun, 21 Jun 2020 19:41:14: #2 predicted fragment length is 188 bps INFO @ Sun, 21 Jun 2020 19:41:14: #2 alternative fragment length(s) may be 188 bps INFO @ Sun, 21 Jun 2020 19:41:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3011238/SRX3011238.10_model.r INFO @ Sun, 21 Jun 2020 19:41:14: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:41:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:41:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3011238/SRX3011238.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:41:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3011238/SRX3011238.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:41:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3011238/SRX3011238.05_summits.bed INFO @ Sun, 21 Jun 2020 19:41:18: Done! pass1 - making usageList (240 chroms): 3 millis pass2 - checking and writing primary data (8674 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:41:18: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:41:26: 6000000 INFO @ Sun, 21 Jun 2020 19:41:34: 7000000 INFO @ Sun, 21 Jun 2020 19:41:38: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:41:40: #1 tag size is determined as 80 bps INFO @ Sun, 21 Jun 2020 19:41:40: #1 tag size = 80 INFO @ Sun, 21 Jun 2020 19:41:40: #1 total tags in treatment: 7721663 INFO @ Sun, 21 Jun 2020 19:41:40: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:41:40: #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 19:41:40: #1 tags after filtering in treatment: 7721443 INFO @ Sun, 21 Jun 2020 19:41:40: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:41:40: #1 finished! INFO @ Sun, 21 Jun 2020 19:41:40: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:41:40: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:41:41: #2 number of paired peaks: 5430 INFO @ Sun, 21 Jun 2020 19:41:41: start model_add_line... INFO @ Sun, 21 Jun 2020 19:41:41: start X-correlation... INFO @ Sun, 21 Jun 2020 19:41:41: end of X-cor INFO @ Sun, 21 Jun 2020 19:41:41: #2 finished! INFO @ Sun, 21 Jun 2020 19:41:41: #2 predicted fragment length is 188 bps INFO @ Sun, 21 Jun 2020 19:41:41: #2 alternative fragment length(s) may be 188 bps INFO @ Sun, 21 Jun 2020 19:41:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3011238/SRX3011238.20_model.r INFO @ Sun, 21 Jun 2020 19:41:41: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:41:41: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:41:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3011238/SRX3011238.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:41:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3011238/SRX3011238.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:41:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3011238/SRX3011238.10_summits.bed INFO @ Sun, 21 Jun 2020 19:41:48: Done! pass1 - making usageList (207 chroms): 2 millis pass2 - checking and writing primary data (6691 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:42:06: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:42:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3011238/SRX3011238.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:42:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3011238/SRX3011238.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:42:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3011238/SRX3011238.20_summits.bed INFO @ Sun, 21 Jun 2020 19:42:16: Done! pass1 - making usageList (161 chroms): 2 millis pass2 - checking and writing primary data (4870 records, 4 fields): 15 millis CompletedMACS2peakCalling