Job ID = 6455820 SRX = SRX3011230 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:16:36 prefetch.2.10.7: 1) Downloading 'SRR5834707'... 2020-06-21T10:16:36 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:19:45 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:19:46 prefetch.2.10.7: 'SRR5834707' is valid 2020-06-21T10:19:46 prefetch.2.10.7: 1) 'SRR5834707' was downloaded successfully 2020-06-21T10:20:37 prefetch.2.10.7: 'SRR5834707' has 10 unresolved dependencies 2020-06-21T10:20:37 prefetch.2.10.7: 2) Downloading 'ncbi-acc:NC_004353.3?vdb-ctx=refseq'... 2020-06-21T10:20:37 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:20:50 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:20:50 prefetch.2.10.7: 2) 'ncbi-acc:NC_004353.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:20:50 prefetch.2.10.7: 3) Downloading 'ncbi-acc:NC_004354.3?vdb-ctx=refseq'... 2020-06-21T10:20:50 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:21:08 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:21:08 prefetch.2.10.7: 3) 'ncbi-acc:NC_004354.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:21:08 prefetch.2.10.7: 4) Downloading 'ncbi-acc:NS_000188.1?vdb-ctx=refseq'... 2020-06-21T10:21:08 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:21:24 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:21:24 prefetch.2.10.7: 4) 'ncbi-acc:NS_000188.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:21:24 prefetch.2.10.7: 5) Downloading 'ncbi-acc:NT_033777.2?vdb-ctx=refseq'... 2020-06-21T10:21:24 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:21:40 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:21:40 prefetch.2.10.7: 5) 'ncbi-acc:NT_033777.2?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:21:40 prefetch.2.10.7: 6) Downloading 'ncbi-acc:NT_033778.3?vdb-ctx=refseq'... 2020-06-21T10:21:40 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:21:57 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:21:57 prefetch.2.10.7: 6) 'ncbi-acc:NT_033778.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:21:57 prefetch.2.10.7: 7) Downloading 'ncbi-acc:NT_033779.4?vdb-ctx=refseq'... 2020-06-21T10:21:57 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:22:14 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:22:14 prefetch.2.10.7: 7) 'ncbi-acc:NT_033779.4?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:22:14 prefetch.2.10.7: 8) Downloading 'ncbi-acc:NT_037436.3?vdb-ctx=refseq'... 2020-06-21T10:22:14 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:22:32 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:22:32 prefetch.2.10.7: 8) 'ncbi-acc:NT_037436.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:22:32 prefetch.2.10.7: 9) Downloading 'ncbi-acc:NW_001848856.1?vdb-ctx=refseq'... 2020-06-21T10:22:32 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:22:46 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:22:46 prefetch.2.10.7: 9) 'ncbi-acc:NW_001848856.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:22:46 prefetch.2.10.7: 10) Downloading 'ncbi-acc:NW_001848857.1?vdb-ctx=refseq'... 2020-06-21T10:22:46 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:22:58 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:22:58 prefetch.2.10.7: 10) 'ncbi-acc:NW_001848857.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:22:58 prefetch.2.10.7: 11) Downloading 'ncbi-acc:NW_001848858.1?vdb-ctx=refseq'... 2020-06-21T10:22:58 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:23:11 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:23:11 prefetch.2.10.7: 11) 'ncbi-acc:NW_001848858.1?vdb-ctx=refseq' was downloaded successfully Read 21893597 spots for SRR5834707/SRR5834707.sra Written 21893597 spots for SRR5834707/SRR5834707.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: 00:02:36 21893597 reads; of these: 21893597 (100.00%) were unpaired; of these: 200072 (0.91%) aligned 0 times 21411346 (97.80%) aligned exactly 1 time 282179 (1.29%) aligned >1 times 99.09% overall alignment rate Time searching: 00:02:36 Overall time: 00:02:36 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] 9507404 / 21693525 = 0.4383 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 19:31:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3011230/SRX3011230.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3011230/SRX3011230.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3011230/SRX3011230.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3011230/SRX3011230.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 19:31:25: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:31:25: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:31:30: 1000000 INFO @ Sun, 21 Jun 2020 19:31:34: 2000000 INFO @ Sun, 21 Jun 2020 19:31:39: 3000000 INFO @ Sun, 21 Jun 2020 19:31:44: 4000000 INFO @ Sun, 21 Jun 2020 19:31:49: 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 19:31:54: 6000000 INFO @ Sun, 21 Jun 2020 19:31:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3011230/SRX3011230.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3011230/SRX3011230.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3011230/SRX3011230.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3011230/SRX3011230.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 19:31:55: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:31:55: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:31:59: 7000000 INFO @ Sun, 21 Jun 2020 19:32:00: 1000000 INFO @ Sun, 21 Jun 2020 19:32:04: 8000000 INFO @ Sun, 21 Jun 2020 19:32:05: 2000000 INFO @ Sun, 21 Jun 2020 19:32:09: 9000000 INFO @ Sun, 21 Jun 2020 19:32:10: 3000000 INFO @ Sun, 21 Jun 2020 19:32:14: 10000000 INFO @ Sun, 21 Jun 2020 19:32:15: 4000000 INFO @ Sun, 21 Jun 2020 19:32:19: 11000000 INFO @ Sun, 21 Jun 2020 19:32:20: 5000000 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 19:32:24: 12000000 INFO @ Sun, 21 Jun 2020 19:32:25: 6000000 INFO @ Sun, 21 Jun 2020 19:32:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3011230/SRX3011230.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3011230/SRX3011230.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3011230/SRX3011230.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3011230/SRX3011230.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 19:32:25: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:32:25: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:32:25: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:32:25: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:32:25: #1 total tags in treatment: 12186121 INFO @ Sun, 21 Jun 2020 19:32:25: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:32:25: #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 19:32:25: #1 tags after filtering in treatment: 12185546 INFO @ Sun, 21 Jun 2020 19:32:25: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:32:25: #1 finished! INFO @ Sun, 21 Jun 2020 19:32:25: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:32:25: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:32:26: #2 number of paired peaks: 8348 INFO @ Sun, 21 Jun 2020 19:32:26: start model_add_line... INFO @ Sun, 21 Jun 2020 19:32:27: start X-correlation... INFO @ Sun, 21 Jun 2020 19:32:27: end of X-cor INFO @ Sun, 21 Jun 2020 19:32:27: #2 finished! INFO @ Sun, 21 Jun 2020 19:32:27: #2 predicted fragment length is 210 bps INFO @ Sun, 21 Jun 2020 19:32:27: #2 alternative fragment length(s) may be 210 bps INFO @ Sun, 21 Jun 2020 19:32:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3011230/SRX3011230.05_model.r INFO @ Sun, 21 Jun 2020 19:32:27: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:32:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:32:30: 7000000 INFO @ Sun, 21 Jun 2020 19:32:31: 1000000 INFO @ Sun, 21 Jun 2020 19:32:35: 8000000 INFO @ Sun, 21 Jun 2020 19:32:36: 2000000 INFO @ Sun, 21 Jun 2020 19:32:40: 9000000 INFO @ Sun, 21 Jun 2020 19:32:42: 3000000 INFO @ Sun, 21 Jun 2020 19:32:45: 10000000 INFO @ Sun, 21 Jun 2020 19:32:48: 4000000 INFO @ Sun, 21 Jun 2020 19:32:50: 11000000 INFO @ Sun, 21 Jun 2020 19:32:54: 5000000 INFO @ Sun, 21 Jun 2020 19:32:55: 12000000 INFO @ Sun, 21 Jun 2020 19:32:57: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:32:57: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:32:57: #1 total tags in treatment: 12186121 INFO @ Sun, 21 Jun 2020 19:32:57: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:32:57: #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 19:32:57: #1 tags after filtering in treatment: 12185546 INFO @ Sun, 21 Jun 2020 19:32:57: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:32:57: #1 finished! INFO @ Sun, 21 Jun 2020 19:32:57: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:32:57: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:32:58: #2 number of paired peaks: 8348 INFO @ Sun, 21 Jun 2020 19:32:58: start model_add_line... INFO @ Sun, 21 Jun 2020 19:32:58: start X-correlation... INFO @ Sun, 21 Jun 2020 19:32:58: end of X-cor INFO @ Sun, 21 Jun 2020 19:32:58: #2 finished! INFO @ Sun, 21 Jun 2020 19:32:58: #2 predicted fragment length is 210 bps INFO @ Sun, 21 Jun 2020 19:32:58: #2 alternative fragment length(s) may be 210 bps INFO @ Sun, 21 Jun 2020 19:32:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3011230/SRX3011230.10_model.r INFO @ Sun, 21 Jun 2020 19:32:58: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:32:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:33:00: 6000000 INFO @ Sun, 21 Jun 2020 19:33:06: 7000000 INFO @ Sun, 21 Jun 2020 19:33:06: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:33:12: 8000000 INFO @ Sun, 21 Jun 2020 19:33:17: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:33:23: 10000000 INFO @ Sun, 21 Jun 2020 19:33:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3011230/SRX3011230.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:33:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3011230/SRX3011230.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:33:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3011230/SRX3011230.05_summits.bed INFO @ Sun, 21 Jun 2020 19:33:24: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (10430 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:33:29: 11000000 INFO @ Sun, 21 Jun 2020 19:33:34: 12000000 INFO @ Sun, 21 Jun 2020 19:33:36: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:33:36: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:33:36: #1 total tags in treatment: 12186121 INFO @ Sun, 21 Jun 2020 19:33:36: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:33:36: #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 19:33:36: #1 tags after filtering in treatment: 12185546 INFO @ Sun, 21 Jun 2020 19:33:36: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:33:36: #1 finished! INFO @ Sun, 21 Jun 2020 19:33:36: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:33:36: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:33:37: #2 number of paired peaks: 8348 INFO @ Sun, 21 Jun 2020 19:33:37: start model_add_line... INFO @ Sun, 21 Jun 2020 19:33:38: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:33:38: start X-correlation... INFO @ Sun, 21 Jun 2020 19:33:38: end of X-cor INFO @ Sun, 21 Jun 2020 19:33:38: #2 finished! INFO @ Sun, 21 Jun 2020 19:33:38: #2 predicted fragment length is 210 bps INFO @ Sun, 21 Jun 2020 19:33:38: #2 alternative fragment length(s) may be 210 bps INFO @ Sun, 21 Jun 2020 19:33:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3011230/SRX3011230.20_model.r INFO @ Sun, 21 Jun 2020 19:33:38: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:33:38: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:33:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3011230/SRX3011230.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:33:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3011230/SRX3011230.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:33:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3011230/SRX3011230.10_summits.bed INFO @ Sun, 21 Jun 2020 19:33:54: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (8463 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:34:18: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:34:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3011230/SRX3011230.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:34:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3011230/SRX3011230.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:34:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3011230/SRX3011230.20_summits.bed INFO @ Sun, 21 Jun 2020 19:34:35: Done! pass1 - making usageList (11 chroms): 2 millis pass2 - checking and writing primary data (6521 records, 4 fields): 7 millis CompletedMACS2peakCalling