Job ID = 6455134 SRX = SRX2779384 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:49:55 prefetch.2.10.7: 1) Downloading 'SRR5499065'... 2020-06-21T09:49:55 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:50:45 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:50:45 prefetch.2.10.7: 'SRR5499065' is valid 2020-06-21T09:50:45 prefetch.2.10.7: 1) 'SRR5499065' was downloaded successfully 2020-06-21T09:51:37 prefetch.2.10.7: 'SRR5499065' has 10 unresolved dependencies 2020-06-21T09:51:37 prefetch.2.10.7: 2) Downloading 'ncbi-acc:NC_004353.3?vdb-ctx=refseq'... 2020-06-21T09:51:37 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:51:50 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:51:50 prefetch.2.10.7: 2) 'ncbi-acc:NC_004353.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T09:51:50 prefetch.2.10.7: 3) Downloading 'ncbi-acc:NC_004354.3?vdb-ctx=refseq'... 2020-06-21T09:51:50 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:52:06 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:52:06 prefetch.2.10.7: 3) 'ncbi-acc:NC_004354.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T09:52:06 prefetch.2.10.7: 4) Downloading 'ncbi-acc:NS_000188.1?vdb-ctx=refseq'... 2020-06-21T09:52:06 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:52:21 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:52:21 prefetch.2.10.7: 4) 'ncbi-acc:NS_000188.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T09:52:21 prefetch.2.10.7: 5) Downloading 'ncbi-acc:NT_033777.2?vdb-ctx=refseq'... 2020-06-21T09:52:21 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:52:42 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:52:42 prefetch.2.10.7: 5) 'ncbi-acc:NT_033777.2?vdb-ctx=refseq' was downloaded successfully 2020-06-21T09:52:42 prefetch.2.10.7: 6) Downloading 'ncbi-acc:NT_033778.3?vdb-ctx=refseq'... 2020-06-21T09:52:42 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:52:58 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:52:58 prefetch.2.10.7: 6) 'ncbi-acc:NT_033778.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T09:52:58 prefetch.2.10.7: 7) Downloading 'ncbi-acc:NT_033779.4?vdb-ctx=refseq'... 2020-06-21T09:52:58 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:53:15 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:53:15 prefetch.2.10.7: 7) 'ncbi-acc:NT_033779.4?vdb-ctx=refseq' was downloaded successfully 2020-06-21T09:53:15 prefetch.2.10.7: 8) Downloading 'ncbi-acc:NT_037436.3?vdb-ctx=refseq'... 2020-06-21T09:53:15 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:53:33 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:53:33 prefetch.2.10.7: 8) 'ncbi-acc:NT_037436.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T09:53:33 prefetch.2.10.7: 9) Downloading 'ncbi-acc:NW_001848856.1?vdb-ctx=refseq'... 2020-06-21T09:53:33 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:53:46 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:53:46 prefetch.2.10.7: 9) 'ncbi-acc:NW_001848856.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T09:53:46 prefetch.2.10.7: 10) Downloading 'ncbi-acc:NW_001848857.1?vdb-ctx=refseq'... 2020-06-21T09:53:46 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:54:00 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:54:00 prefetch.2.10.7: 10) 'ncbi-acc:NW_001848857.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T09:54:00 prefetch.2.10.7: 11) Downloading 'ncbi-acc:NW_001848858.1?vdb-ctx=refseq'... 2020-06-21T09:54:00 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:54:13 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:54:13 prefetch.2.10.7: 11) 'ncbi-acc:NW_001848858.1?vdb-ctx=refseq' was downloaded successfully Read 5165839 spots for SRR5499065/SRR5499065.sra Written 5165839 spots for SRR5499065/SRR5499065.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: 00:00:53 5165839 reads; of these: 5165839 (100.00%) were unpaired; of these: 102926 (1.99%) aligned 0 times 4976366 (96.33%) aligned exactly 1 time 86547 (1.68%) aligned >1 times 98.01% overall alignment rate Time searching: 00:00:53 Overall time: 00:00:53 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_rmdupse_core] 855243 / 5062913 = 0.1689 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 18:56:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2779384/SRX2779384.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2779384/SRX2779384.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2779384/SRX2779384.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2779384/SRX2779384.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 18:56:55: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:56:55: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:57:00: 1000000 INFO @ Sun, 21 Jun 2020 18:57:06: 2000000 INFO @ Sun, 21 Jun 2020 18:57:11: 3000000 INFO @ Sun, 21 Jun 2020 18:57:17: 4000000 INFO @ Sun, 21 Jun 2020 18:57:18: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:57:18: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:57:18: #1 total tags in treatment: 4207670 INFO @ Sun, 21 Jun 2020 18:57:18: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:57:18: #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 18:57:18: #1 tags after filtering in treatment: 4207157 INFO @ Sun, 21 Jun 2020 18:57:18: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:57:18: #1 finished! INFO @ Sun, 21 Jun 2020 18:57:18: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:57:18: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:57:19: #2 number of paired peaks: 3570 INFO @ Sun, 21 Jun 2020 18:57:19: start model_add_line... INFO @ Sun, 21 Jun 2020 18:57:19: start X-correlation... INFO @ Sun, 21 Jun 2020 18:57:19: end of X-cor INFO @ Sun, 21 Jun 2020 18:57:19: #2 finished! INFO @ Sun, 21 Jun 2020 18:57:19: #2 predicted fragment length is 322 bps INFO @ Sun, 21 Jun 2020 18:57:19: #2 alternative fragment length(s) may be 322 bps INFO @ Sun, 21 Jun 2020 18:57:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2779384/SRX2779384.05_model.r INFO @ Sun, 21 Jun 2020 18:57:19: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:57:19: #3 Pre-compute pvalue-qvalue table... 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 18:57:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2779384/SRX2779384.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2779384/SRX2779384.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2779384/SRX2779384.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2779384/SRX2779384.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 18:57:26: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:57:26: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:57:30: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:57:31: 1000000 INFO @ Sun, 21 Jun 2020 18:57:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2779384/SRX2779384.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:57:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2779384/SRX2779384.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:57:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2779384/SRX2779384.05_summits.bed INFO @ Sun, 21 Jun 2020 18:57:36: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (4806 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:57:37: 2000000 INFO @ Sun, 21 Jun 2020 18:57:42: 3000000 INFO @ Sun, 21 Jun 2020 18:57:48: 4000000 INFO @ Sun, 21 Jun 2020 18:57:49: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:57:49: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:57:49: #1 total tags in treatment: 4207670 INFO @ Sun, 21 Jun 2020 18:57:49: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:57:49: #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 18:57:49: #1 tags after filtering in treatment: 4207157 INFO @ Sun, 21 Jun 2020 18:57:49: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:57:49: #1 finished! INFO @ Sun, 21 Jun 2020 18:57:49: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:57:49: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:57:49: #2 number of paired peaks: 3570 INFO @ Sun, 21 Jun 2020 18:57:49: start model_add_line... INFO @ Sun, 21 Jun 2020 18:57:49: start X-correlation... INFO @ Sun, 21 Jun 2020 18:57:49: end of X-cor INFO @ Sun, 21 Jun 2020 18:57:49: #2 finished! INFO @ Sun, 21 Jun 2020 18:57:49: #2 predicted fragment length is 322 bps INFO @ Sun, 21 Jun 2020 18:57:49: #2 alternative fragment length(s) may be 322 bps INFO @ Sun, 21 Jun 2020 18:57:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2779384/SRX2779384.10_model.r INFO @ Sun, 21 Jun 2020 18:57:49: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:57:49: #3 Pre-compute pvalue-qvalue table... 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 18:57:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2779384/SRX2779384.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2779384/SRX2779384.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2779384/SRX2779384.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2779384/SRX2779384.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 18:57:55: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:57:55: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:58:00: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:58:00: 1000000 INFO @ Sun, 21 Jun 2020 18:58:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2779384/SRX2779384.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:58:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2779384/SRX2779384.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:58:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2779384/SRX2779384.10_summits.bed INFO @ Sun, 21 Jun 2020 18:58:05: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (3243 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:58:06: 2000000 INFO @ Sun, 21 Jun 2020 18:58:11: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:58:17: 4000000 INFO @ Sun, 21 Jun 2020 18:58:18: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:58:18: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:58:18: #1 total tags in treatment: 4207670 INFO @ Sun, 21 Jun 2020 18:58:18: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:58:18: #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 18:58:18: #1 tags after filtering in treatment: 4207157 INFO @ Sun, 21 Jun 2020 18:58:18: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:58:18: #1 finished! INFO @ Sun, 21 Jun 2020 18:58:18: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:58:18: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:58:19: #2 number of paired peaks: 3570 INFO @ Sun, 21 Jun 2020 18:58:19: start model_add_line... INFO @ Sun, 21 Jun 2020 18:58:19: start X-correlation... INFO @ Sun, 21 Jun 2020 18:58:19: end of X-cor INFO @ Sun, 21 Jun 2020 18:58:19: #2 finished! INFO @ Sun, 21 Jun 2020 18:58:19: #2 predicted fragment length is 322 bps INFO @ Sun, 21 Jun 2020 18:58:19: #2 alternative fragment length(s) may be 322 bps INFO @ Sun, 21 Jun 2020 18:58:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2779384/SRX2779384.20_model.r INFO @ Sun, 21 Jun 2020 18:58:19: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:58:19: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:58:30: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:58:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2779384/SRX2779384.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:58:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2779384/SRX2779384.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:58:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2779384/SRX2779384.20_summits.bed INFO @ Sun, 21 Jun 2020 18:58:36: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1693 records, 4 fields): 3 millis CompletedMACS2peakCalling