Job ID = 6455819 SRX = SRX3011229 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:36:29 prefetch.2.10.7: 1) Downloading 'SRR5834706'... 2020-06-21T10:36:29 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:38:24 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:38:24 prefetch.2.10.7: 'SRR5834706' is valid 2020-06-21T10:38:24 prefetch.2.10.7: 1) 'SRR5834706' was downloaded successfully 2020-06-21T10:39:16 prefetch.2.10.7: 'SRR5834706' has 10 unresolved dependencies 2020-06-21T10:39:16 prefetch.2.10.7: 2) Downloading 'ncbi-acc:NC_004353.3?vdb-ctx=refseq'... 2020-06-21T10:39:16 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:39:29 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:39:29 prefetch.2.10.7: 2) 'ncbi-acc:NC_004353.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:39:29 prefetch.2.10.7: 3) Downloading 'ncbi-acc:NC_004354.3?vdb-ctx=refseq'... 2020-06-21T10:39:29 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:39:45 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:39:45 prefetch.2.10.7: 3) 'ncbi-acc:NC_004354.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:39:45 prefetch.2.10.7: 4) Downloading 'ncbi-acc:NS_000188.1?vdb-ctx=refseq'... 2020-06-21T10:39:45 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:40:01 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:40:01 prefetch.2.10.7: 4) 'ncbi-acc:NS_000188.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:40:01 prefetch.2.10.7: 5) Downloading 'ncbi-acc:NT_033777.2?vdb-ctx=refseq'... 2020-06-21T10:40:01 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:40:20 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:40:20 prefetch.2.10.7: 5) 'ncbi-acc:NT_033777.2?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:40:20 prefetch.2.10.7: 6) Downloading 'ncbi-acc:NT_033778.3?vdb-ctx=refseq'... 2020-06-21T10:40:20 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:40:35 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:40:35 prefetch.2.10.7: 6) 'ncbi-acc:NT_033778.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:40:35 prefetch.2.10.7: 7) Downloading 'ncbi-acc:NT_033779.4?vdb-ctx=refseq'... 2020-06-21T10:40:35 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:40:54 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:40:54 prefetch.2.10.7: 7) 'ncbi-acc:NT_033779.4?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:40:54 prefetch.2.10.7: 8) Downloading 'ncbi-acc:NT_037436.3?vdb-ctx=refseq'... 2020-06-21T10:40:54 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:41:10 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:41:10 prefetch.2.10.7: 8) 'ncbi-acc:NT_037436.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:41:10 prefetch.2.10.7: 9) Downloading 'ncbi-acc:NW_001848856.1?vdb-ctx=refseq'... 2020-06-21T10:41:10 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:41:23 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:41:23 prefetch.2.10.7: 9) 'ncbi-acc:NW_001848856.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:41:23 prefetch.2.10.7: 10) Downloading 'ncbi-acc:NW_001848857.1?vdb-ctx=refseq'... 2020-06-21T10:41:23 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:41:35 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:41:35 prefetch.2.10.7: 10) 'ncbi-acc:NW_001848857.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:41:35 prefetch.2.10.7: 11) Downloading 'ncbi-acc:NW_001848858.1?vdb-ctx=refseq'... 2020-06-21T10:41:35 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:41:48 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:41:48 prefetch.2.10.7: 11) 'ncbi-acc:NW_001848858.1?vdb-ctx=refseq' was downloaded successfully Read 19846217 spots for SRR5834706/SRR5834706.sra Written 19846217 spots for SRR5834706/SRR5834706.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: 00:02:27 19846217 reads; of these: 19846217 (100.00%) were unpaired; of these: 189405 (0.95%) aligned 0 times 19383121 (97.67%) aligned exactly 1 time 273691 (1.38%) aligned >1 times 99.05% overall alignment rate Time searching: 00:02:27 Overall time: 00:02:27 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] 8342178 / 19656812 = 0.4244 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 19:49:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3011229/SRX3011229.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3011229/SRX3011229.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3011229/SRX3011229.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3011229/SRX3011229.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 19:49:28: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:49:28: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:49:35: 1000000 INFO @ Sun, 21 Jun 2020 19:49:42: 2000000 INFO @ Sun, 21 Jun 2020 19:49:49: 3000000 INFO @ Sun, 21 Jun 2020 19:49:56: 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 19:49:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3011229/SRX3011229.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3011229/SRX3011229.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3011229/SRX3011229.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3011229/SRX3011229.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 19:49:58: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:49:58: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:50:03: 5000000 INFO @ Sun, 21 Jun 2020 19:50:05: 1000000 INFO @ Sun, 21 Jun 2020 19:50:10: 6000000 INFO @ Sun, 21 Jun 2020 19:50:12: 2000000 INFO @ Sun, 21 Jun 2020 19:50:18: 7000000 INFO @ Sun, 21 Jun 2020 19:50:18: 3000000 INFO @ Sun, 21 Jun 2020 19:50:25: 4000000 INFO @ Sun, 21 Jun 2020 19:50:25: 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 19:50:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3011229/SRX3011229.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3011229/SRX3011229.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3011229/SRX3011229.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3011229/SRX3011229.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 19:50:28: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:50:28: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:50:31: 5000000 INFO @ Sun, 21 Jun 2020 19:50:32: 9000000 INFO @ Sun, 21 Jun 2020 19:50:35: 1000000 INFO @ Sun, 21 Jun 2020 19:50:38: 6000000 INFO @ Sun, 21 Jun 2020 19:50:40: 10000000 INFO @ Sun, 21 Jun 2020 19:50:42: 2000000 INFO @ Sun, 21 Jun 2020 19:50:44: 7000000 INFO @ Sun, 21 Jun 2020 19:50:47: 11000000 INFO @ Sun, 21 Jun 2020 19:50:48: 3000000 INFO @ Sun, 21 Jun 2020 19:50:50: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:50:50: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:50:50: #1 total tags in treatment: 11314634 INFO @ Sun, 21 Jun 2020 19:50:50: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:50:50: #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 19:50:50: #1 tags after filtering in treatment: 11314031 INFO @ Sun, 21 Jun 2020 19:50:50: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:50:50: #1 finished! INFO @ Sun, 21 Jun 2020 19:50:50: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:50:50: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:50:51: 8000000 INFO @ Sun, 21 Jun 2020 19:50:51: #2 number of paired peaks: 8175 INFO @ Sun, 21 Jun 2020 19:50:51: start model_add_line... INFO @ Sun, 21 Jun 2020 19:50:51: start X-correlation... INFO @ Sun, 21 Jun 2020 19:50:51: end of X-cor INFO @ Sun, 21 Jun 2020 19:50:51: #2 finished! INFO @ Sun, 21 Jun 2020 19:50:51: #2 predicted fragment length is 208 bps INFO @ Sun, 21 Jun 2020 19:50:51: #2 alternative fragment length(s) may be 208 bps INFO @ Sun, 21 Jun 2020 19:50:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3011229/SRX3011229.05_model.r INFO @ Sun, 21 Jun 2020 19:50:51: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:50:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:50:55: 4000000 INFO @ Sun, 21 Jun 2020 19:50:57: 9000000 INFO @ Sun, 21 Jun 2020 19:51:01: 5000000 INFO @ Sun, 21 Jun 2020 19:51:04: 10000000 INFO @ Sun, 21 Jun 2020 19:51:07: 6000000 INFO @ Sun, 21 Jun 2020 19:51:10: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:51:12: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:51:12: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:51:12: #1 total tags in treatment: 11314634 INFO @ Sun, 21 Jun 2020 19:51:12: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:51:12: #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 19:51:12: #1 tags after filtering in treatment: 11314031 INFO @ Sun, 21 Jun 2020 19:51:12: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:51:12: #1 finished! INFO @ Sun, 21 Jun 2020 19:51:12: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:51:12: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:51:14: #2 number of paired peaks: 8175 INFO @ Sun, 21 Jun 2020 19:51:14: start model_add_line... INFO @ Sun, 21 Jun 2020 19:51:14: 7000000 INFO @ Sun, 21 Jun 2020 19:51:14: start X-correlation... INFO @ Sun, 21 Jun 2020 19:51:14: end of X-cor INFO @ Sun, 21 Jun 2020 19:51:14: #2 finished! INFO @ Sun, 21 Jun 2020 19:51:14: #2 predicted fragment length is 208 bps INFO @ Sun, 21 Jun 2020 19:51:14: #2 alternative fragment length(s) may be 208 bps INFO @ Sun, 21 Jun 2020 19:51:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3011229/SRX3011229.10_model.r INFO @ Sun, 21 Jun 2020 19:51:14: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:51:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:51:20: 8000000 INFO @ Sun, 21 Jun 2020 19:51:26: 9000000 INFO @ Sun, 21 Jun 2020 19:51:28: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:51:31: 10000000 INFO @ Sun, 21 Jun 2020 19:51:37: 11000000 INFO @ Sun, 21 Jun 2020 19:51:39: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:51:39: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:51:39: #1 total tags in treatment: 11314634 INFO @ Sun, 21 Jun 2020 19:51:39: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:51:39: #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 19:51:39: #1 tags after filtering in treatment: 11314031 INFO @ Sun, 21 Jun 2020 19:51:39: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:51:39: #1 finished! INFO @ Sun, 21 Jun 2020 19:51:39: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:51:39: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:51:40: #2 number of paired peaks: 8175 INFO @ Sun, 21 Jun 2020 19:51:40: start model_add_line... INFO @ Sun, 21 Jun 2020 19:51:40: start X-correlation... INFO @ Sun, 21 Jun 2020 19:51:41: end of X-cor INFO @ Sun, 21 Jun 2020 19:51:41: #2 finished! INFO @ Sun, 21 Jun 2020 19:51:41: #2 predicted fragment length is 208 bps INFO @ Sun, 21 Jun 2020 19:51:41: #2 alternative fragment length(s) may be 208 bps INFO @ Sun, 21 Jun 2020 19:51:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3011229/SRX3011229.20_model.r INFO @ Sun, 21 Jun 2020 19:51:41: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:51:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:51:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3011229/SRX3011229.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:51:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3011229/SRX3011229.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:51:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3011229/SRX3011229.05_summits.bed INFO @ Sun, 21 Jun 2020 19:51:44: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (10056 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:51:50: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:52:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3011229/SRX3011229.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:52:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3011229/SRX3011229.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:52:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3011229/SRX3011229.10_summits.bed INFO @ Sun, 21 Jun 2020 19:52:05: Done! pass1 - making usageList (12 chroms): 2 millis pass2 - checking and writing primary data (8114 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:52:17: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:52:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3011229/SRX3011229.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:52:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3011229/SRX3011229.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:52:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3011229/SRX3011229.20_summits.bed INFO @ Sun, 21 Jun 2020 19:52:32: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (6155 records, 4 fields): 7 millis CompletedMACS2peakCalling