Job ID = 6455821 SRX = SRX3011231 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:16:51 prefetch.2.10.7: 1) Downloading 'SRR5834708'... 2020-06-21T10:16:51 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:18:48 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:18:48 prefetch.2.10.7: 'SRR5834708' is valid 2020-06-21T10:18:48 prefetch.2.10.7: 1) 'SRR5834708' was downloaded successfully 2020-06-21T10:19:40 prefetch.2.10.7: 'SRR5834708' has 10 unresolved dependencies 2020-06-21T10:19:40 prefetch.2.10.7: 2) Downloading 'ncbi-acc:NC_004353.3?vdb-ctx=refseq'... 2020-06-21T10:19:40 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:19:52 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:19:52 prefetch.2.10.7: 2) 'ncbi-acc:NC_004353.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:19:52 prefetch.2.10.7: 3) Downloading 'ncbi-acc:NC_004354.3?vdb-ctx=refseq'... 2020-06-21T10:19:52 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:20:08 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:20:08 prefetch.2.10.7: 3) 'ncbi-acc:NC_004354.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:20:08 prefetch.2.10.7: 4) Downloading 'ncbi-acc:NS_000188.1?vdb-ctx=refseq'... 2020-06-21T10:20:08 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:20:23 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:20:23 prefetch.2.10.7: 4) 'ncbi-acc:NS_000188.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:20:23 prefetch.2.10.7: 5) Downloading 'ncbi-acc:NT_033777.2?vdb-ctx=refseq'... 2020-06-21T10:20:23 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:20:39 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:20:39 prefetch.2.10.7: 5) 'ncbi-acc:NT_033777.2?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:20:39 prefetch.2.10.7: 6) Downloading 'ncbi-acc:NT_033778.3?vdb-ctx=refseq'... 2020-06-21T10:20:39 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:20:57 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:20:57 prefetch.2.10.7: 6) 'ncbi-acc:NT_033778.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:20:57 prefetch.2.10.7: 7) Downloading 'ncbi-acc:NT_033779.4?vdb-ctx=refseq'... 2020-06-21T10:20:57 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:21:14 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:21:14 prefetch.2.10.7: 7) 'ncbi-acc:NT_033779.4?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:21:14 prefetch.2.10.7: 8) Downloading 'ncbi-acc:NT_037436.3?vdb-ctx=refseq'... 2020-06-21T10:21:14 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:21:29 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:21:29 prefetch.2.10.7: 8) 'ncbi-acc:NT_037436.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:21:29 prefetch.2.10.7: 9) Downloading 'ncbi-acc:NW_001848856.1?vdb-ctx=refseq'... 2020-06-21T10:21:29 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:21:42 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:21:42 prefetch.2.10.7: 9) 'ncbi-acc:NW_001848856.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:21:42 prefetch.2.10.7: 10) Downloading 'ncbi-acc:NW_001848857.1?vdb-ctx=refseq'... 2020-06-21T10:21:42 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:21:54 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:21:54 prefetch.2.10.7: 10) 'ncbi-acc:NW_001848857.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:21:54 prefetch.2.10.7: 11) Downloading 'ncbi-acc:NW_001848858.1?vdb-ctx=refseq'... 2020-06-21T10:21:54 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: 11) 'ncbi-acc:NW_001848858.1?vdb-ctx=refseq' was downloaded successfully Read 16203007 spots for SRR5834708/SRR5834708.sra Written 16203007 spots for SRR5834708/SRR5834708.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: 00:02:08 16203007 reads; of these: 16203007 (100.00%) were unpaired; of these: 151125 (0.93%) aligned 0 times 15802153 (97.53%) aligned exactly 1 time 249729 (1.54%) aligned >1 times 99.07% overall alignment rate Time searching: 00:02:08 Overall time: 00:02:08 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 8 files... [bam_rmdupse_core] 5510055 / 16051882 = 0.3433 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 19:29:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3011231/SRX3011231.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3011231/SRX3011231.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3011231/SRX3011231.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3011231/SRX3011231.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 19:29:05: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:29:05: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:29:12: 1000000 INFO @ Sun, 21 Jun 2020 19:29:18: 2000000 INFO @ Sun, 21 Jun 2020 19:29:25: 3000000 INFO @ Sun, 21 Jun 2020 19:29:32: 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 @ Sun, 21 Jun 2020 19:29:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3011231/SRX3011231.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3011231/SRX3011231.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3011231/SRX3011231.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3011231/SRX3011231.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 19:29:35: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:29:35: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:29:38: 5000000 INFO @ Sun, 21 Jun 2020 19:29:42: 1000000 INFO @ Sun, 21 Jun 2020 19:29:45: 6000000 INFO @ Sun, 21 Jun 2020 19:29:50: 2000000 INFO @ Sun, 21 Jun 2020 19:29:53: 7000000 INFO @ Sun, 21 Jun 2020 19:29:57: 3000000 INFO @ Sun, 21 Jun 2020 19:30:00: 8000000 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 19:30:04: 4000000 INFO @ Sun, 21 Jun 2020 19:30:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3011231/SRX3011231.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3011231/SRX3011231.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3011231/SRX3011231.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3011231/SRX3011231.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 19:30:05: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:30:05: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:30:07: 9000000 INFO @ Sun, 21 Jun 2020 19:30:11: 5000000 INFO @ Sun, 21 Jun 2020 19:30:12: 1000000 INFO @ Sun, 21 Jun 2020 19:30:14: 10000000 INFO @ Sun, 21 Jun 2020 19:30:18: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:30:18: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:30:18: #1 total tags in treatment: 10541827 INFO @ Sun, 21 Jun 2020 19:30:18: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:30:18: #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 19:30:18: #1 tags after filtering in treatment: 10541192 INFO @ Sun, 21 Jun 2020 19:30:18: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:30:18: #1 finished! INFO @ Sun, 21 Jun 2020 19:30:18: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:30:18: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:30:18: 6000000 INFO @ Sun, 21 Jun 2020 19:30:19: #2 number of paired peaks: 6096 INFO @ Sun, 21 Jun 2020 19:30:19: start model_add_line... INFO @ Sun, 21 Jun 2020 19:30:19: start X-correlation... INFO @ Sun, 21 Jun 2020 19:30:19: 2000000 INFO @ Sun, 21 Jun 2020 19:30:19: end of X-cor INFO @ Sun, 21 Jun 2020 19:30:19: #2 finished! INFO @ Sun, 21 Jun 2020 19:30:19: #2 predicted fragment length is 189 bps INFO @ Sun, 21 Jun 2020 19:30:19: #2 alternative fragment length(s) may be 189 bps INFO @ Sun, 21 Jun 2020 19:30:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3011231/SRX3011231.05_model.r INFO @ Sun, 21 Jun 2020 19:30:19: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:30:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:30:25: 7000000 INFO @ Sun, 21 Jun 2020 19:30:26: 3000000 INFO @ Sun, 21 Jun 2020 19:30:32: 8000000 INFO @ Sun, 21 Jun 2020 19:30:33: 4000000 INFO @ Sun, 21 Jun 2020 19:30:39: 9000000 INFO @ Sun, 21 Jun 2020 19:30:39: 5000000 INFO @ Sun, 21 Jun 2020 19:30:46: 6000000 INFO @ Sun, 21 Jun 2020 19:30:47: 10000000 INFO @ Sun, 21 Jun 2020 19:30:50: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:30:51: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:30:51: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:30:51: #1 total tags in treatment: 10541827 INFO @ Sun, 21 Jun 2020 19:30:51: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:30:51: #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 19:30:51: #1 tags after filtering in treatment: 10541192 INFO @ Sun, 21 Jun 2020 19:30:51: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:30:51: #1 finished! INFO @ Sun, 21 Jun 2020 19:30:51: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:30:51: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:30:52: #2 number of paired peaks: 6096 INFO @ Sun, 21 Jun 2020 19:30:52: start model_add_line... INFO @ Sun, 21 Jun 2020 19:30:52: start X-correlation... INFO @ Sun, 21 Jun 2020 19:30:52: end of X-cor INFO @ Sun, 21 Jun 2020 19:30:52: #2 finished! INFO @ Sun, 21 Jun 2020 19:30:52: #2 predicted fragment length is 189 bps INFO @ Sun, 21 Jun 2020 19:30:52: #2 alternative fragment length(s) may be 189 bps INFO @ Sun, 21 Jun 2020 19:30:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3011231/SRX3011231.10_model.r INFO @ Sun, 21 Jun 2020 19:30:52: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:30:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:30:53: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:30:59: 8000000 INFO @ Sun, 21 Jun 2020 19:31:05: 9000000 INFO @ Sun, 21 Jun 2020 19:31:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3011231/SRX3011231.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:31:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3011231/SRX3011231.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:31:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3011231/SRX3011231.05_summits.bed INFO @ Sun, 21 Jun 2020 19:31:05: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (9715 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:31:10: 10000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:31:13: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:31:13: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:31:13: #1 total tags in treatment: 10541827 INFO @ Sun, 21 Jun 2020 19:31:13: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:31:13: #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 19:31:13: #1 tags after filtering in treatment: 10541192 INFO @ Sun, 21 Jun 2020 19:31:13: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:31:13: #1 finished! INFO @ Sun, 21 Jun 2020 19:31:13: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:31:13: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:31:15: #2 number of paired peaks: 6096 INFO @ Sun, 21 Jun 2020 19:31:15: start model_add_line... INFO @ Sun, 21 Jun 2020 19:31:15: start X-correlation... INFO @ Sun, 21 Jun 2020 19:31:15: end of X-cor INFO @ Sun, 21 Jun 2020 19:31:15: #2 finished! INFO @ Sun, 21 Jun 2020 19:31:15: #2 predicted fragment length is 189 bps INFO @ Sun, 21 Jun 2020 19:31:15: #2 alternative fragment length(s) may be 189 bps INFO @ Sun, 21 Jun 2020 19:31:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3011231/SRX3011231.20_model.r INFO @ Sun, 21 Jun 2020 19:31:15: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:31:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:31:24: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:31:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3011231/SRX3011231.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:31:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3011231/SRX3011231.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:31:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3011231/SRX3011231.10_summits.bed INFO @ Sun, 21 Jun 2020 19:31:38: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (7460 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:31:48: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:32:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3011231/SRX3011231.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:32:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3011231/SRX3011231.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:32:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3011231/SRX3011231.20_summits.bed INFO @ Sun, 21 Jun 2020 19:32:02: Done! pass1 - making usageList (11 chroms): 2 millis pass2 - checking and writing primary data (5386 records, 4 fields): 7 millis CompletedMACS2peakCalling