Job ID = 6455837 SRX = SRX3011244 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:51:16 prefetch.2.10.7: 1) Downloading 'SRR5834721'... 2020-06-21T10:51:16 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:56:22 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:56:22 prefetch.2.10.7: 1) 'SRR5834721' was downloaded successfully 2020-06-21T10:57:14 prefetch.2.10.7: 'SRR5834721' has 10 unresolved dependencies 2020-06-21T10:57:14 prefetch.2.10.7: 2) Downloading 'ncbi-acc:NC_004353.3?vdb-ctx=refseq'... 2020-06-21T10:57:14 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:57:26 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:57:26 prefetch.2.10.7: 2) 'ncbi-acc:NC_004353.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:57:26 prefetch.2.10.7: 3) Downloading 'ncbi-acc:NC_004354.3?vdb-ctx=refseq'... 2020-06-21T10:57:26 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:57:42 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:57:42 prefetch.2.10.7: 3) 'ncbi-acc:NC_004354.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:57:42 prefetch.2.10.7: 4) Downloading 'ncbi-acc:NS_000188.1?vdb-ctx=refseq'... 2020-06-21T10:57:42 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:57:57 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:57:57 prefetch.2.10.7: 4) 'ncbi-acc:NS_000188.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:57:57 prefetch.2.10.7: 5) Downloading 'ncbi-acc:NT_033777.2?vdb-ctx=refseq'... 2020-06-21T10:57:57 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:58:15 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:58:15 prefetch.2.10.7: 5) 'ncbi-acc:NT_033777.2?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:58:15 prefetch.2.10.7: 6) Downloading 'ncbi-acc:NT_033778.3?vdb-ctx=refseq'... 2020-06-21T10:58:15 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:58:32 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:58:32 prefetch.2.10.7: 6) 'ncbi-acc:NT_033778.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:58:32 prefetch.2.10.7: 7) Downloading 'ncbi-acc:NT_033779.4?vdb-ctx=refseq'... 2020-06-21T10:58:32 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:58:49 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:58:49 prefetch.2.10.7: 7) 'ncbi-acc:NT_033779.4?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:58:49 prefetch.2.10.7: 8) Downloading 'ncbi-acc:NT_037436.3?vdb-ctx=refseq'... 2020-06-21T10:58:49 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:59:06 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:59:06 prefetch.2.10.7: 8) 'ncbi-acc:NT_037436.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:59:06 prefetch.2.10.7: 9) Downloading 'ncbi-acc:NW_001848856.1?vdb-ctx=refseq'... 2020-06-21T10:59:06 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:59:20 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:59:20 prefetch.2.10.7: 9) 'ncbi-acc:NW_001848856.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:59:20 prefetch.2.10.7: 10) Downloading 'ncbi-acc:NW_001848857.1?vdb-ctx=refseq'... 2020-06-21T10:59:20 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:59:32 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:59:32 prefetch.2.10.7: 10) 'ncbi-acc:NW_001848857.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:59:32 prefetch.2.10.7: 11) Downloading 'ncbi-acc:NW_001848858.1?vdb-ctx=refseq'... 2020-06-21T10:59:32 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:59:46 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:59:46 prefetch.2.10.7: 11) 'ncbi-acc:NW_001848858.1?vdb-ctx=refseq' was downloaded successfully Read 54047251 spots for SRR5834721/SRR5834721.sra Written 54047251 spots for SRR5834721/SRR5834721.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:06:25 54047251 reads; of these: 54047251 (100.00%) were unpaired; of these: 405428 (0.75%) aligned 0 times 52605880 (97.33%) aligned exactly 1 time 1035943 (1.92%) aligned >1 times 99.25% overall alignment rate Time searching: 00:06:26 Overall time: 00:06:26 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 24 files... [bam_rmdupse_core] 40349716 / 53641823 = 0.7522 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 20:18:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3011244/SRX3011244.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3011244/SRX3011244.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3011244/SRX3011244.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3011244/SRX3011244.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 20:18:52: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:18:52: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:18:58: 1000000 INFO @ Sun, 21 Jun 2020 20:19:04: 2000000 INFO @ Sun, 21 Jun 2020 20:19:10: 3000000 INFO @ Sun, 21 Jun 2020 20:19:16: 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 20:19:22: 5000000 INFO @ Sun, 21 Jun 2020 20:19:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3011244/SRX3011244.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3011244/SRX3011244.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3011244/SRX3011244.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3011244/SRX3011244.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 20:19:22: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:19:22: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:19:27: 6000000 INFO @ Sun, 21 Jun 2020 20:19:28: 1000000 INFO @ Sun, 21 Jun 2020 20:19:33: 7000000 INFO @ Sun, 21 Jun 2020 20:19:34: 2000000 INFO @ Sun, 21 Jun 2020 20:19:39: 8000000 INFO @ Sun, 21 Jun 2020 20:19:40: 3000000 INFO @ Sun, 21 Jun 2020 20:19:45: 9000000 INFO @ Sun, 21 Jun 2020 20:19:45: 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 20:19:51: 10000000 INFO @ Sun, 21 Jun 2020 20:19:51: 5000000 INFO @ Sun, 21 Jun 2020 20:19:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3011244/SRX3011244.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3011244/SRX3011244.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3011244/SRX3011244.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3011244/SRX3011244.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 20:19:52: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:19:52: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:19:57: 11000000 INFO @ Sun, 21 Jun 2020 20:19:58: 6000000 INFO @ Sun, 21 Jun 2020 20:19:58: 1000000 INFO @ Sun, 21 Jun 2020 20:20:03: 7000000 INFO @ Sun, 21 Jun 2020 20:20:04: 12000000 INFO @ Sun, 21 Jun 2020 20:20:04: 2000000 INFO @ Sun, 21 Jun 2020 20:20:09: 8000000 INFO @ Sun, 21 Jun 2020 20:20:10: 3000000 INFO @ Sun, 21 Jun 2020 20:20:10: 13000000 INFO @ Sun, 21 Jun 2020 20:20:12: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:20:12: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:20:12: #1 total tags in treatment: 13292107 INFO @ Sun, 21 Jun 2020 20:20:12: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:20:12: #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 20:20:12: #1 tags after filtering in treatment: 13291591 INFO @ Sun, 21 Jun 2020 20:20:12: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:20:12: #1 finished! INFO @ Sun, 21 Jun 2020 20:20:12: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:20:12: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:20:14: #2 number of paired peaks: 8626 INFO @ Sun, 21 Jun 2020 20:20:14: start model_add_line... INFO @ Sun, 21 Jun 2020 20:20:14: start X-correlation... INFO @ Sun, 21 Jun 2020 20:20:14: end of X-cor INFO @ Sun, 21 Jun 2020 20:20:14: #2 finished! INFO @ Sun, 21 Jun 2020 20:20:14: #2 predicted fragment length is 201 bps INFO @ Sun, 21 Jun 2020 20:20:14: #2 alternative fragment length(s) may be 201 bps INFO @ Sun, 21 Jun 2020 20:20:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3011244/SRX3011244.05_model.r INFO @ Sun, 21 Jun 2020 20:20:14: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:20:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:20:15: 9000000 INFO @ Sun, 21 Jun 2020 20:20:15: 4000000 INFO @ Sun, 21 Jun 2020 20:20:21: 10000000 INFO @ Sun, 21 Jun 2020 20:20:21: 5000000 INFO @ Sun, 21 Jun 2020 20:20:26: 11000000 INFO @ Sun, 21 Jun 2020 20:20:27: 6000000 INFO @ Sun, 21 Jun 2020 20:20:32: 7000000 INFO @ Sun, 21 Jun 2020 20:20:32: 12000000 INFO @ Sun, 21 Jun 2020 20:20:38: 8000000 INFO @ Sun, 21 Jun 2020 20:20:38: 13000000 INFO @ Sun, 21 Jun 2020 20:20:40: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:20:40: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:20:40: #1 total tags in treatment: 13292107 INFO @ Sun, 21 Jun 2020 20:20:40: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:20:40: #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 20:20:40: #1 tags after filtering in treatment: 13291591 INFO @ Sun, 21 Jun 2020 20:20:40: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:20:40: #1 finished! INFO @ Sun, 21 Jun 2020 20:20:40: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:20:40: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:20:42: #2 number of paired peaks: 8626 INFO @ Sun, 21 Jun 2020 20:20:42: start model_add_line... INFO @ Sun, 21 Jun 2020 20:20:42: start X-correlation... INFO @ Sun, 21 Jun 2020 20:20:42: end of X-cor INFO @ Sun, 21 Jun 2020 20:20:42: #2 finished! INFO @ Sun, 21 Jun 2020 20:20:42: #2 predicted fragment length is 201 bps INFO @ Sun, 21 Jun 2020 20:20:42: #2 alternative fragment length(s) may be 201 bps INFO @ Sun, 21 Jun 2020 20:20:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3011244/SRX3011244.10_model.r INFO @ Sun, 21 Jun 2020 20:20:42: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:20:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:20:43: 9000000 INFO @ Sun, 21 Jun 2020 20:20:48: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:20:53: 11000000 INFO @ Sun, 21 Jun 2020 20:20:58: 12000000 INFO @ Sun, 21 Jun 2020 20:21:03: 13000000 INFO @ Sun, 21 Jun 2020 20:21:05: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:21:05: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:21:05: #1 total tags in treatment: 13292107 INFO @ Sun, 21 Jun 2020 20:21:05: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:21:05: #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 20:21:06: #1 tags after filtering in treatment: 13291591 INFO @ Sun, 21 Jun 2020 20:21:06: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:21:06: #1 finished! INFO @ Sun, 21 Jun 2020 20:21:06: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:21:06: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:21:06: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:21:07: #2 number of paired peaks: 8626 INFO @ Sun, 21 Jun 2020 20:21:07: start model_add_line... INFO @ Sun, 21 Jun 2020 20:21:08: start X-correlation... INFO @ Sun, 21 Jun 2020 20:21:08: end of X-cor INFO @ Sun, 21 Jun 2020 20:21:08: #2 finished! INFO @ Sun, 21 Jun 2020 20:21:08: #2 predicted fragment length is 201 bps INFO @ Sun, 21 Jun 2020 20:21:08: #2 alternative fragment length(s) may be 201 bps INFO @ Sun, 21 Jun 2020 20:21:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3011244/SRX3011244.20_model.r INFO @ Sun, 21 Jun 2020 20:21:08: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:21:08: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:21:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3011244/SRX3011244.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:21:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3011244/SRX3011244.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:21:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3011244/SRX3011244.05_summits.bed INFO @ Sun, 21 Jun 2020 20:21:22: Done! pass1 - making usageList (19 chroms): 3 millis pass2 - checking and writing primary data (11603 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:21:34: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:21:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3011244/SRX3011244.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:21:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3011244/SRX3011244.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:21:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3011244/SRX3011244.10_summits.bed INFO @ Sun, 21 Jun 2020 20:21:51: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (9715 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:22:00: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:22:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3011244/SRX3011244.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:22:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3011244/SRX3011244.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:22:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3011244/SRX3011244.20_summits.bed INFO @ Sun, 21 Jun 2020 20:22:16: Done! pass1 - making usageList (13 chroms): 3 millis pass2 - checking and writing primary data (7829 records, 4 fields): 11 millis CompletedMACS2peakCalling