Job ID = 6455824 SRX = SRX3011232 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:17:21 prefetch.2.10.7: 1) Downloading 'SRR5834709'... 2020-06-21T10:17:21 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:19:24 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:19:24 prefetch.2.10.7: 'SRR5834709' is valid 2020-06-21T10:19:24 prefetch.2.10.7: 1) 'SRR5834709' was downloaded successfully 2020-06-21T10:20:16 prefetch.2.10.7: 'SRR5834709' has 10 unresolved dependencies 2020-06-21T10:20:16 prefetch.2.10.7: 2) Downloading 'ncbi-acc:NC_004353.3?vdb-ctx=refseq'... 2020-06-21T10:20:16 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:20:29 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:20:29 prefetch.2.10.7: 2) 'ncbi-acc:NC_004353.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:20:29 prefetch.2.10.7: 3) Downloading 'ncbi-acc:NC_004354.3?vdb-ctx=refseq'... 2020-06-21T10:20:29 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:21:56 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:21:56 prefetch.2.10.7: 3) 'ncbi-acc:NC_004354.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:21:56 prefetch.2.10.7: 4) Downloading 'ncbi-acc:NS_000188.1?vdb-ctx=refseq'... 2020-06-21T10:21:56 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:22:11 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:22:11 prefetch.2.10.7: 4) 'ncbi-acc:NS_000188.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:22:11 prefetch.2.10.7: 5) Downloading 'ncbi-acc:NT_033777.2?vdb-ctx=refseq'... 2020-06-21T10:22:11 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:22:30 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:22:30 prefetch.2.10.7: 5) 'ncbi-acc:NT_033777.2?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:22:30 prefetch.2.10.7: 6) Downloading 'ncbi-acc:NT_033778.3?vdb-ctx=refseq'... 2020-06-21T10:22:30 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:22:46 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:22:46 prefetch.2.10.7: 6) 'ncbi-acc:NT_033778.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:22:46 prefetch.2.10.7: 7) Downloading 'ncbi-acc:NT_033779.4?vdb-ctx=refseq'... 2020-06-21T10:22:46 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:23:03 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:23:03 prefetch.2.10.7: 7) 'ncbi-acc:NT_033779.4?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:23:03 prefetch.2.10.7: 8) Downloading 'ncbi-acc:NT_037436.3?vdb-ctx=refseq'... 2020-06-21T10:23:03 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:23:23 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:23:23 prefetch.2.10.7: 8) 'ncbi-acc:NT_037436.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:23:23 prefetch.2.10.7: 9) Downloading 'ncbi-acc:NW_001848856.1?vdb-ctx=refseq'... 2020-06-21T10:23:23 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:23:36 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:23:36 prefetch.2.10.7: 9) 'ncbi-acc:NW_001848856.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:23:36 prefetch.2.10.7: 10) Downloading 'ncbi-acc:NW_001848857.1?vdb-ctx=refseq'... 2020-06-21T10:23:36 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:23:49 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:23:49 prefetch.2.10.7: 10) 'ncbi-acc:NW_001848857.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:23:49 prefetch.2.10.7: 11) Downloading 'ncbi-acc:NW_001848858.1?vdb-ctx=refseq'... 2020-06-21T10:23:49 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:24:02 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:24:02 prefetch.2.10.7: 11) 'ncbi-acc:NW_001848858.1?vdb-ctx=refseq' was downloaded successfully Read 17851707 spots for SRR5834709/SRR5834709.sra Written 17851707 spots for SRR5834709/SRR5834709.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: 00:02:21 17851707 reads; of these: 17851707 (100.00%) were unpaired; of these: 169386 (0.95%) aligned 0 times 17381915 (97.37%) aligned exactly 1 time 300406 (1.68%) aligned >1 times 99.05% overall alignment rate Time searching: 00:02:21 Overall time: 00:02:21 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] 6961609 / 17682321 = 0.3937 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 19:31:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3011232/SRX3011232.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3011232/SRX3011232.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3011232/SRX3011232.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3011232/SRX3011232.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 19:31:17: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:31:17: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:31:22: 1000000 INFO @ Sun, 21 Jun 2020 19:31:27: 2000000 INFO @ Sun, 21 Jun 2020 19:31:31: 3000000 INFO @ Sun, 21 Jun 2020 19:31:36: 4000000 INFO @ Sun, 21 Jun 2020 19:31:41: 5000000 INFO @ Sun, 21 Jun 2020 19:31:45: 6000000 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 19:31:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3011232/SRX3011232.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3011232/SRX3011232.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3011232/SRX3011232.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3011232/SRX3011232.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 19:31:47: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:31:47: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:31:50: 7000000 INFO @ Sun, 21 Jun 2020 19:31:52: 1000000 INFO @ Sun, 21 Jun 2020 19:31:55: 8000000 INFO @ Sun, 21 Jun 2020 19:31:57: 2000000 INFO @ Sun, 21 Jun 2020 19:31:59: 9000000 INFO @ Sun, 21 Jun 2020 19:32:02: 3000000 INFO @ Sun, 21 Jun 2020 19:32:04: 10000000 INFO @ Sun, 21 Jun 2020 19:32:07: 4000000 INFO @ Sun, 21 Jun 2020 19:32:08: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:32:08: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:32:08: #1 total tags in treatment: 10720712 INFO @ Sun, 21 Jun 2020 19:32:08: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:32:08: #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 19:32:08: #1 tags after filtering in treatment: 10720083 INFO @ Sun, 21 Jun 2020 19:32:08: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:32:08: #1 finished! INFO @ Sun, 21 Jun 2020 19:32:08: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:32:08: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:32:09: #2 number of paired peaks: 6721 INFO @ Sun, 21 Jun 2020 19:32:09: start model_add_line... INFO @ Sun, 21 Jun 2020 19:32:09: start X-correlation... INFO @ Sun, 21 Jun 2020 19:32:09: end of X-cor INFO @ Sun, 21 Jun 2020 19:32:09: #2 finished! INFO @ Sun, 21 Jun 2020 19:32:09: #2 predicted fragment length is 193 bps INFO @ Sun, 21 Jun 2020 19:32:09: #2 alternative fragment length(s) may be 193 bps INFO @ Sun, 21 Jun 2020 19:32:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3011232/SRX3011232.05_model.r INFO @ Sun, 21 Jun 2020 19:32:09: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:32:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:32:12: 5000000 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 19:32:16: 6000000 INFO @ Sun, 21 Jun 2020 19:32:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3011232/SRX3011232.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3011232/SRX3011232.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3011232/SRX3011232.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3011232/SRX3011232.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 19:32:17: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:32:17: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:32:21: 7000000 INFO @ Sun, 21 Jun 2020 19:32:22: 1000000 INFO @ Sun, 21 Jun 2020 19:32:26: 8000000 INFO @ Sun, 21 Jun 2020 19:32:27: 2000000 INFO @ Sun, 21 Jun 2020 19:32:31: 9000000 INFO @ Sun, 21 Jun 2020 19:32:32: 3000000 INFO @ Sun, 21 Jun 2020 19:32:36: 10000000 INFO @ Sun, 21 Jun 2020 19:32:37: 4000000 INFO @ Sun, 21 Jun 2020 19:32:40: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:32:40: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:32:40: #1 total tags in treatment: 10720712 INFO @ Sun, 21 Jun 2020 19:32:40: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:32:40: #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 19:32:40: #1 tags after filtering in treatment: 10720083 INFO @ Sun, 21 Jun 2020 19:32:40: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:32:40: #1 finished! INFO @ Sun, 21 Jun 2020 19:32:40: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:32:40: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:32:41: #2 number of paired peaks: 6721 INFO @ Sun, 21 Jun 2020 19:32:41: start model_add_line... INFO @ Sun, 21 Jun 2020 19:32:41: start X-correlation... INFO @ Sun, 21 Jun 2020 19:32:41: end of X-cor INFO @ Sun, 21 Jun 2020 19:32:41: #2 finished! INFO @ Sun, 21 Jun 2020 19:32:41: #2 predicted fragment length is 193 bps INFO @ Sun, 21 Jun 2020 19:32:41: #2 alternative fragment length(s) may be 193 bps INFO @ Sun, 21 Jun 2020 19:32:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3011232/SRX3011232.10_model.r INFO @ Sun, 21 Jun 2020 19:32:41: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:32:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:32:42: 5000000 INFO @ Sun, 21 Jun 2020 19:32:44: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:32:46: 6000000 INFO @ Sun, 21 Jun 2020 19:32:51: 7000000 INFO @ Sun, 21 Jun 2020 19:32:56: 8000000 INFO @ Sun, 21 Jun 2020 19:32:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3011232/SRX3011232.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:32:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3011232/SRX3011232.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:32:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3011232/SRX3011232.05_summits.bed INFO @ Sun, 21 Jun 2020 19:32:59: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (9812 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:33:01: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:33:06: 10000000 INFO @ Sun, 21 Jun 2020 19:33:09: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:33:09: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:33:09: #1 total tags in treatment: 10720712 INFO @ Sun, 21 Jun 2020 19:33:09: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:33:09: #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 19:33:09: #1 tags after filtering in treatment: 10720083 INFO @ Sun, 21 Jun 2020 19:33:09: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:33:09: #1 finished! INFO @ Sun, 21 Jun 2020 19:33:09: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:33:09: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:33:11: #2 number of paired peaks: 6721 INFO @ Sun, 21 Jun 2020 19:33:11: start model_add_line... INFO @ Sun, 21 Jun 2020 19:33:11: start X-correlation... INFO @ Sun, 21 Jun 2020 19:33:11: end of X-cor INFO @ Sun, 21 Jun 2020 19:33:11: #2 finished! INFO @ Sun, 21 Jun 2020 19:33:11: #2 predicted fragment length is 193 bps INFO @ Sun, 21 Jun 2020 19:33:11: #2 alternative fragment length(s) may be 193 bps INFO @ Sun, 21 Jun 2020 19:33:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3011232/SRX3011232.20_model.r INFO @ Sun, 21 Jun 2020 19:33:11: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:33:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:33:16: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:33:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3011232/SRX3011232.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:33:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3011232/SRX3011232.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:33:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3011232/SRX3011232.10_summits.bed INFO @ Sun, 21 Jun 2020 19:33:31: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (7697 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:33:45: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:34:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3011232/SRX3011232.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:34:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3011232/SRX3011232.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:34:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3011232/SRX3011232.20_summits.bed INFO @ Sun, 21 Jun 2020 19:34:00: Done! pass1 - making usageList (12 chroms): 2 millis pass2 - checking and writing primary data (5729 records, 4 fields): 6 millis CompletedMACS2peakCalling