Job ID = 6455835 SRX = SRX3011242 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:19:36 prefetch.2.10.7: 1) Downloading 'SRR5834719'... 2020-06-21T10:19:36 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:21:50 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:21:51 prefetch.2.10.7: 'SRR5834719' is valid 2020-06-21T10:21:51 prefetch.2.10.7: 1) 'SRR5834719' was downloaded successfully 2020-06-21T10:22:43 prefetch.2.10.7: 'SRR5834719' has 10 unresolved dependencies 2020-06-21T10:22:43 prefetch.2.10.7: 2) Downloading 'ncbi-acc:NC_004353.3?vdb-ctx=refseq'... 2020-06-21T10:22:43 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:22:56 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:22:56 prefetch.2.10.7: 2) 'ncbi-acc:NC_004353.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:22:56 prefetch.2.10.7: 3) Downloading 'ncbi-acc:NC_004354.3?vdb-ctx=refseq'... 2020-06-21T10:22:56 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:23:12 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:23:12 prefetch.2.10.7: 3) 'ncbi-acc:NC_004354.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:23:12 prefetch.2.10.7: 4) Downloading 'ncbi-acc:NS_000188.1?vdb-ctx=refseq'... 2020-06-21T10:23:12 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:23:27 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:23:27 prefetch.2.10.7: 4) 'ncbi-acc:NS_000188.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:23:27 prefetch.2.10.7: 5) Downloading 'ncbi-acc:NT_033777.2?vdb-ctx=refseq'... 2020-06-21T10:23:27 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:23:45 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:23:45 prefetch.2.10.7: 5) 'ncbi-acc:NT_033777.2?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:23:45 prefetch.2.10.7: 6) Downloading 'ncbi-acc:NT_033778.3?vdb-ctx=refseq'... 2020-06-21T10:23:45 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:24:01 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:24:01 prefetch.2.10.7: 6) 'ncbi-acc:NT_033778.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:24:01 prefetch.2.10.7: 7) Downloading 'ncbi-acc:NT_033779.4?vdb-ctx=refseq'... 2020-06-21T10:24:01 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:24:18 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:24:18 prefetch.2.10.7: 7) 'ncbi-acc:NT_033779.4?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:24:18 prefetch.2.10.7: 8) Downloading 'ncbi-acc:NT_037436.3?vdb-ctx=refseq'... 2020-06-21T10:24:18 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:24:34 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:24:34 prefetch.2.10.7: 8) 'ncbi-acc:NT_037436.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:24:34 prefetch.2.10.7: 9) Downloading 'ncbi-acc:NW_001848856.1?vdb-ctx=refseq'... 2020-06-21T10:24:34 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:24:49 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:24:49 prefetch.2.10.7: 9) 'ncbi-acc:NW_001848856.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:24:49 prefetch.2.10.7: 10) Downloading 'ncbi-acc:NW_001848857.1?vdb-ctx=refseq'... 2020-06-21T10:24:49 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:25:02 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:25:02 prefetch.2.10.7: 10) 'ncbi-acc:NW_001848857.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:25:02 prefetch.2.10.7: 11) Downloading 'ncbi-acc:NW_001848858.1?vdb-ctx=refseq'... 2020-06-21T10:25:02 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:25:15 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:25:15 prefetch.2.10.7: 11) 'ncbi-acc:NW_001848858.1?vdb-ctx=refseq' was downloaded successfully Read 16691306 spots for SRR5834719/SRR5834719.sra Written 16691306 spots for SRR5834719/SRR5834719.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: 00:04:35 16691306 reads; of these: 16691306 (100.00%) were unpaired; of these: 272879 (1.63%) aligned 0 times 12575200 (75.34%) aligned exactly 1 time 3843227 (23.03%) aligned >1 times 98.37% overall alignment rate Time searching: 00:04:35 Overall time: 00:04:35 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] 9622555 / 16418427 = 0.5861 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 19:34:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3011242/SRX3011242.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3011242/SRX3011242.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3011242/SRX3011242.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3011242/SRX3011242.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 19:34:53: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:34:53: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:35:00: 1000000 INFO @ Sun, 21 Jun 2020 19:35:06: 2000000 INFO @ Sun, 21 Jun 2020 19:35:13: 3000000 INFO @ Sun, 21 Jun 2020 19:35:20: 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 19:35:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3011242/SRX3011242.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3011242/SRX3011242.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3011242/SRX3011242.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3011242/SRX3011242.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 19:35:23: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:35:23: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:35:26: 5000000 INFO @ Sun, 21 Jun 2020 19:35:30: 1000000 INFO @ Sun, 21 Jun 2020 19:35:33: 6000000 INFO @ Sun, 21 Jun 2020 19:35:37: 2000000 INFO @ Sun, 21 Jun 2020 19:35:39: #1 tag size is determined as 80 bps INFO @ Sun, 21 Jun 2020 19:35:39: #1 tag size = 80 INFO @ Sun, 21 Jun 2020 19:35:39: #1 total tags in treatment: 6795872 INFO @ Sun, 21 Jun 2020 19:35:39: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:35:39: #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 19:35:39: #1 tags after filtering in treatment: 6795515 INFO @ Sun, 21 Jun 2020 19:35:39: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:35:39: #1 finished! INFO @ Sun, 21 Jun 2020 19:35:39: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:35:39: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:35:40: #2 number of paired peaks: 9031 INFO @ Sun, 21 Jun 2020 19:35:40: start model_add_line... INFO @ Sun, 21 Jun 2020 19:35:40: start X-correlation... INFO @ Sun, 21 Jun 2020 19:35:40: end of X-cor INFO @ Sun, 21 Jun 2020 19:35:40: #2 finished! INFO @ Sun, 21 Jun 2020 19:35:40: #2 predicted fragment length is 183 bps INFO @ Sun, 21 Jun 2020 19:35:40: #2 alternative fragment length(s) may be 183 bps INFO @ Sun, 21 Jun 2020 19:35:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3011242/SRX3011242.05_model.r INFO @ Sun, 21 Jun 2020 19:35:40: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:35:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:35:44: 3000000 INFO @ Sun, 21 Jun 2020 19:35:50: 4000000 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 19:35:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3011242/SRX3011242.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3011242/SRX3011242.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3011242/SRX3011242.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3011242/SRX3011242.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 19:35:53: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:35:53: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:35:57: 5000000 INFO @ Sun, 21 Jun 2020 19:36:00: 1000000 INFO @ Sun, 21 Jun 2020 19:36:04: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:36:04: 6000000 INFO @ Sun, 21 Jun 2020 19:36:06: 2000000 INFO @ Sun, 21 Jun 2020 19:36:10: #1 tag size is determined as 80 bps INFO @ Sun, 21 Jun 2020 19:36:10: #1 tag size = 80 INFO @ Sun, 21 Jun 2020 19:36:10: #1 total tags in treatment: 6795872 INFO @ Sun, 21 Jun 2020 19:36:10: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:36:10: #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 19:36:11: #1 tags after filtering in treatment: 6795515 INFO @ Sun, 21 Jun 2020 19:36:11: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:36:11: #1 finished! INFO @ Sun, 21 Jun 2020 19:36:11: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:36:11: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:36:12: #2 number of paired peaks: 9031 INFO @ Sun, 21 Jun 2020 19:36:12: start model_add_line... INFO @ Sun, 21 Jun 2020 19:36:12: start X-correlation... INFO @ Sun, 21 Jun 2020 19:36:12: end of X-cor INFO @ Sun, 21 Jun 2020 19:36:12: #2 finished! INFO @ Sun, 21 Jun 2020 19:36:12: #2 predicted fragment length is 183 bps INFO @ Sun, 21 Jun 2020 19:36:12: #2 alternative fragment length(s) may be 183 bps INFO @ Sun, 21 Jun 2020 19:36:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3011242/SRX3011242.10_model.r INFO @ Sun, 21 Jun 2020 19:36:12: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:36:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:36:12: 3000000 INFO @ Sun, 21 Jun 2020 19:36:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3011242/SRX3011242.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:36:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3011242/SRX3011242.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:36:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3011242/SRX3011242.05_summits.bed INFO @ Sun, 21 Jun 2020 19:36:13: Done! pass1 - making usageList (216 chroms): 2 millis pass2 - checking and writing primary data (8988 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:36:18: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:36:24: 5000000 INFO @ Sun, 21 Jun 2020 19:36:30: 6000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:36:35: #1 tag size is determined as 80 bps INFO @ Sun, 21 Jun 2020 19:36:35: #1 tag size = 80 INFO @ Sun, 21 Jun 2020 19:36:35: #1 total tags in treatment: 6795872 INFO @ Sun, 21 Jun 2020 19:36:35: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:36:35: #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 19:36:35: #1 tags after filtering in treatment: 6795515 INFO @ Sun, 21 Jun 2020 19:36:35: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:36:35: #1 finished! INFO @ Sun, 21 Jun 2020 19:36:35: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:36:35: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:36:36: #2 number of paired peaks: 9031 INFO @ Sun, 21 Jun 2020 19:36:36: start model_add_line... INFO @ Sun, 21 Jun 2020 19:36:36: start X-correlation... INFO @ Sun, 21 Jun 2020 19:36:36: end of X-cor INFO @ Sun, 21 Jun 2020 19:36:36: #2 finished! INFO @ Sun, 21 Jun 2020 19:36:36: #2 predicted fragment length is 183 bps INFO @ Sun, 21 Jun 2020 19:36:36: #2 alternative fragment length(s) may be 183 bps INFO @ Sun, 21 Jun 2020 19:36:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3011242/SRX3011242.20_model.r INFO @ Sun, 21 Jun 2020 19:36:36: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:36:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:36:37: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:36:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3011242/SRX3011242.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:36:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3011242/SRX3011242.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:36:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3011242/SRX3011242.10_summits.bed INFO @ Sun, 21 Jun 2020 19:36:46: Done! pass1 - making usageList (194 chroms): 2 millis pass2 - checking and writing primary data (7529 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:37:01: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:37:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3011242/SRX3011242.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:37:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3011242/SRX3011242.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:37:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3011242/SRX3011242.20_summits.bed INFO @ Sun, 21 Jun 2020 19:37:10: Done! pass1 - making usageList (156 chroms): 2 millis pass2 - checking and writing primary data (6033 records, 4 fields): 12 millis CompletedMACS2peakCalling