[2024-01-24 13:27:58,684] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:27:58,686] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:27:58,687] [INFO] DQC Reference Directory: /var/lib/cwl/stgfe06c09e-c96e-4bb5-8096-4e26114f35f3/dqc_reference
[2024-01-24 13:27:59,946] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:27:59,947] [INFO] Task started: Prodigal
[2024-01-24 13:27:59,947] [INFO] Running command: gunzip -c /var/lib/cwl/stgc4478532-eee0-495a-b4a3-f6cdb7d2e70c/GCF_008011855.1_ASM801185v1_genomic.fna.gz | prodigal -d GCF_008011855.1_ASM801185v1_genomic.fna/cds.fna -a GCF_008011855.1_ASM801185v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:15,601] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:15,601] [INFO] Task started: HMMsearch
[2024-01-24 13:28:15,602] [INFO] Running command: hmmsearch --tblout GCF_008011855.1_ASM801185v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfe06c09e-c96e-4bb5-8096-4e26114f35f3/dqc_reference/reference_markers.hmm GCF_008011855.1_ASM801185v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:15,920] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:15,922] [INFO] Found 6/6 markers.
[2024-01-24 13:28:15,968] [INFO] Query marker FASTA was written to GCF_008011855.1_ASM801185v1_genomic.fna/markers.fasta
[2024-01-24 13:28:15,968] [INFO] Task started: Blastn
[2024-01-24 13:28:15,968] [INFO] Running command: blastn -query GCF_008011855.1_ASM801185v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfe06c09e-c96e-4bb5-8096-4e26114f35f3/dqc_reference/reference_markers.fasta -out GCF_008011855.1_ASM801185v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:16,911] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:16,914] [INFO] Selected 12 target genomes.
[2024-01-24 13:28:16,915] [INFO] Target genome list was writen to GCF_008011855.1_ASM801185v1_genomic.fna/target_genomes.txt
[2024-01-24 13:28:16,926] [INFO] Task started: fastANI
[2024-01-24 13:28:16,926] [INFO] Running command: fastANI --query /var/lib/cwl/stgc4478532-eee0-495a-b4a3-f6cdb7d2e70c/GCF_008011855.1_ASM801185v1_genomic.fna.gz --refList GCF_008011855.1_ASM801185v1_genomic.fna/target_genomes.txt --output GCF_008011855.1_ASM801185v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:28:31,289] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:31,290] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfe06c09e-c96e-4bb5-8096-4e26114f35f3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:28:31,290] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfe06c09e-c96e-4bb5-8096-4e26114f35f3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:28:31,300] [INFO] Found 12 fastANI hits (8 hits with ANI > threshold)
[2024-01-24 13:28:31,300] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:28:31,301] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Serratia bockelmannii	strain=S3	GCA_008011855.1	2703793	2703793	type	True	100.0	1750	1750	95	inconclusive
Serratia marcescens	strain=ATCC 13880	GCA_017654245.1	615	615	suspected-type	True	95.8431	1511	1750	95	inconclusive
Serratia marcescens	strain=ATCC 13880 substr. Sm_S65_jyu2015	GCA_017298975.1	615	615	suspected-type	True	95.8418	1505	1750	95	inconclusive
Serratia marcescens	strain=ATCC 13880 substr. Sm_S81_jyu2015	GCA_017298875.1	615	615	suspected-type	True	95.8418	1505	1750	95	inconclusive
Serratia nematodiphila	strain=CGMCC 1.6853	GCA_900101535.1	458197	458197	suspected-type	True	95.2613	1487	1750	95	inconclusive
Serratia ureilytica	strain=CCUG:50595	GCA_013375155.1	300181	300181	type	True	95.237	1485	1750	95	inconclusive
Serratia nematodiphila	strain=DSM 21420	GCA_000738675.1	458197	458197	suspected-type	True	95.2217	1502	1750	95	inconclusive
Serratia nevei	strain=S15	GCA_008364245.1	2703794	2703794	type	True	95.132	1497	1750	95	inconclusive
Serratia surfactantfaciens	strain=YD25	GCA_001642805.2	2741499	2741499	type	True	93.9315	1492	1750	95	below_threshold
Serratia entomophila	strain=A1	GCA_021462285.1	42906	42906	type	True	88.0921	1328	1750	95	below_threshold
Erwinia aphidicola	strain=X001	GCA_024169515.1	68334	68334	type	True	79.2041	634	1750	95	below_threshold
Rahnella rivi	strain=FC061912-K	GCA_019049655.1	2816249	2816249	type	True	79.0388	619	1750	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:28:31,302] [INFO] DFAST Taxonomy check result was written to GCF_008011855.1_ASM801185v1_genomic.fna/tc_result.tsv
[2024-01-24 13:28:31,303] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:28:31,303] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:28:31,303] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfe06c09e-c96e-4bb5-8096-4e26114f35f3/dqc_reference/checkm_data
[2024-01-24 13:28:31,304] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:28:31,354] [INFO] Task started: CheckM
[2024-01-24 13:28:31,354] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008011855.1_ASM801185v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008011855.1_ASM801185v1_genomic.fna/checkm_input GCF_008011855.1_ASM801185v1_genomic.fna/checkm_result
[2024-01-24 13:29:20,019] [INFO] Task succeeded: CheckM
[2024-01-24 13:29:20,021] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.44%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:29:20,039] [INFO] ===== Completeness check finished =====
[2024-01-24 13:29:20,039] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:29:20,040] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008011855.1_ASM801185v1_genomic.fna/markers.fasta)
[2024-01-24 13:29:20,040] [INFO] Task started: Blastn
[2024-01-24 13:29:20,040] [INFO] Running command: blastn -query GCF_008011855.1_ASM801185v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfe06c09e-c96e-4bb5-8096-4e26114f35f3/dqc_reference/reference_markers_gtdb.fasta -out GCF_008011855.1_ASM801185v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:29:21,300] [INFO] Task succeeded: Blastn
[2024-01-24 13:29:21,304] [INFO] Selected 13 target genomes.
[2024-01-24 13:29:21,305] [INFO] Target genome list was writen to GCF_008011855.1_ASM801185v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:29:21,322] [INFO] Task started: fastANI
[2024-01-24 13:29:21,323] [INFO] Running command: fastANI --query /var/lib/cwl/stgc4478532-eee0-495a-b4a3-f6cdb7d2e70c/GCF_008011855.1_ASM801185v1_genomic.fna.gz --refList GCF_008011855.1_ASM801185v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008011855.1_ASM801185v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:29:36,837] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:36,854] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:29:36,854] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_000513215.1	s__Serratia bockelmannii	98.7102	1580	1750	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	96.0065	98.98	98.60	0.94	0.92	42	conclusive
GCF_006715005.1	s__Serratia marcescens_J	95.9963	1524	1750	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	96.1913	98.92	98.92	0.95	0.95	2	-
GCF_017299535.1	s__Serratia marcescens	95.8407	1509	1750	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	96.8494	99.42	98.47	0.97	0.85	72	-
GCF_013375155.1	s__Serratia ureilytica	95.237	1485	1750	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	95.3985	98.73	97.62	0.94	0.88	142	-
GCF_000738675.1	s__Serratia nematodiphila	95.2217	1502	1750	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	96.8494	98.32	97.66	0.93	0.88	85	-
GCF_002220655.1	s__Serratia marcescens_K	95.1828	1484	1750	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	96.0833	98.79	98.10	0.94	0.88	411	-
GCF_016742975.1	s__Serratia nevei	95.076	1295	1750	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	96.1913	97.82	96.26	0.83	0.75	139	-
GCF_001642805.2	s__Serratia surfactantfaciens	93.9315	1492	1750	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	95.0	98.81	97.95	0.93	0.91	10	-
GCF_000633355.1	s__Serratia_A sp000633355	82.1368	961	1750	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia_A	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000743355.1	s__Chania sp000743355	81.5243	783	1750	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Chania	95.0	99.97	99.97	0.98	0.98	2	-
GCF_016909495.1	s__Erwinia coffeiphila	79.7433	598	1750	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia	95.0	96.75	96.67	0.88	0.87	4	-
GCF_006171285.1	s__Leclercia adecarboxylata_A	79.3169	611	1750	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Leclercia	95.0	97.80	96.55	0.92	0.89	4	-
GCF_001187905.1	s__Pantoea sp001187905	78.5099	509	1750	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	98.42	98.35	0.91	0.90	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:29:36,856] [INFO] GTDB search result was written to GCF_008011855.1_ASM801185v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:29:36,856] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:29:36,860] [INFO] DFAST_QC result json was written to GCF_008011855.1_ASM801185v1_genomic.fna/dqc_result.json
[2024-01-24 13:29:36,860] [INFO] DFAST_QC completed!
[2024-01-24 13:29:36,860] [INFO] Total running time: 0h1m38s