[2023-06-29 15:10:02,778] [INFO] DFAST_QC pipeline started.
[2023-06-29 15:10:02,781] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 15:10:02,781] [INFO] DQC Reference Directory: /var/lib/cwl/stgf370badf-1b64-4ce5-8409-03b955b29e6b/dqc_reference
[2023-06-29 15:10:04,121] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 15:10:04,122] [INFO] Task started: Prodigal
[2023-06-29 15:10:04,123] [INFO] Running command: gunzip -c /var/lib/cwl/stg9c62b319-31ca-47a6-a70d-b5128ed5c036/GCA_021647745.1_ASM2164774v1_genomic.fna.gz | prodigal -d GCA_021647745.1_ASM2164774v1_genomic.fna/cds.fna -a GCA_021647745.1_ASM2164774v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 15:10:12,243] [INFO] Task succeeded: Prodigal
[2023-06-29 15:10:12,243] [INFO] Task started: HMMsearch
[2023-06-29 15:10:12,243] [INFO] Running command: hmmsearch --tblout GCA_021647745.1_ASM2164774v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf370badf-1b64-4ce5-8409-03b955b29e6b/dqc_reference/reference_markers.hmm GCA_021647745.1_ASM2164774v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 15:10:12,525] [INFO] Task succeeded: HMMsearch
[2023-06-29 15:10:12,526] [INFO] Found 6/6 markers.
[2023-06-29 15:10:12,560] [INFO] Query marker FASTA was written to GCA_021647745.1_ASM2164774v1_genomic.fna/markers.fasta
[2023-06-29 15:10:12,560] [INFO] Task started: Blastn
[2023-06-29 15:10:12,561] [INFO] Running command: blastn -query GCA_021647745.1_ASM2164774v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf370badf-1b64-4ce5-8409-03b955b29e6b/dqc_reference/reference_markers.fasta -out GCA_021647745.1_ASM2164774v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 15:10:13,279] [INFO] Task succeeded: Blastn
[2023-06-29 15:10:13,283] [INFO] Selected 33 target genomes.
[2023-06-29 15:10:13,283] [INFO] Target genome list was writen to GCA_021647745.1_ASM2164774v1_genomic.fna/target_genomes.txt
[2023-06-29 15:10:13,286] [INFO] Task started: fastANI
[2023-06-29 15:10:13,286] [INFO] Running command: fastANI --query /var/lib/cwl/stg9c62b319-31ca-47a6-a70d-b5128ed5c036/GCA_021647745.1_ASM2164774v1_genomic.fna.gz --refList GCA_021647745.1_ASM2164774v1_genomic.fna/target_genomes.txt --output GCA_021647745.1_ASM2164774v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 15:10:34,333] [INFO] Task succeeded: fastANI
[2023-06-29 15:10:34,334] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf370badf-1b64-4ce5-8409-03b955b29e6b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 15:10:34,334] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf370badf-1b64-4ce5-8409-03b955b29e6b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 15:10:34,355] [INFO] Found 28 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 15:10:34,356] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 15:10:34,356] [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
Sulfitobacter brevis	strain=DSM 11443	GCA_900112755.1	74348	74348	type	True	76.3829	70	843	95	below_threshold
Halovulum dunhuangense	strain=YYQ-30	GCA_013093415.1	1505036	1505036	type	True	76.3262	79	843	95	below_threshold
Pararhodobacter oceanensis	strain=AM505	GCA_003076755.1	2172121	2172121	type	True	76.3036	95	843	95	below_threshold
Brevirhabdus pacifica	strain=DSM 27767	GCA_002797755.1	1267768	1267768	type	True	76.2946	62	843	95	below_threshold
Primorskyibacter marinus	strain=PX7	GCA_003313245.1	1977320	1977320	type	True	76.287	66	843	95	below_threshold
Actibacterium mucosum	strain=KCTC 23349	GCA_000647975.1	1087332	1087332	type	True	76.254	78	843	95	below_threshold
Rhodovulum sulfidophilum	strain=DSM 1374	GCA_001633165.1	35806	35806	type	True	76.1947	77	843	95	below_threshold
Rhodovulum sulfidophilum	strain=DSM 1374	GCA_000520135.2	35806	35806	type	True	76.1712	78	843	95	below_threshold
Gemmobacter fulva	strain=con5	GCA_018798885.1	2840474	2840474	type	True	76.1636	101	843	95	below_threshold
Rubricella aquisinus	strain=DSM 103377	GCA_014199445.1	2028108	2028108	type	True	76.1606	68	843	95	below_threshold
Primorskyibacter sedentarius	strain=DSM 104836	GCA_004342065.1	745311	745311	type	True	76.1274	77	843	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=DSM 26824	GCA_900129395.1	1402135	1402135	type	True	76.0844	68	843	95	below_threshold
Alkalilacustris brevis	strain=34079	GCA_003350345.1	2026338	2026338	type	True	76.0819	72	843	95	below_threshold
Gemmobacter aquarius	strain=HYN0069	GCA_003060865.1	2169400	2169400	type	True	76.0802	73	843	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=H3	GCA_000712315.1	1402135	1402135	type	True	76.0731	67	843	95	below_threshold
Rhodovulum visakhapatnamense	strain=JA181	GCA_004365965.1	364297	364297	type	True	76.0675	77	843	95	below_threshold
Roseovarius halotolerans	strain=DSM 29507	GCA_003634925.1	505353	505353	type	True	76.0533	87	843	95	below_threshold
Roseovarius halotolerans	strain=CECT 8110	GCA_900172255.1	505353	505353	type	True	76.0344	88	843	95	below_threshold
Paracoccus tegillarcae	strain=BM15	GCA_002847305.1	1529068	1529068	type	True	75.9637	61	843	95	below_threshold
Roseovarius faecimaris	strain=MME-070	GCA_009762325.1	2494550	2494550	type	True	75.9485	93	843	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	75.8742	77	843	95	below_threshold
Leisingera caerulea	strain=DSM 24564	GCA_000473325.1	506591	506591	type	True	75.8619	91	843	95	below_threshold
Rhodovulum steppense	strain=DSM 21153	GCA_004339675.1	540251	540251	type	True	75.8426	75	843	95	below_threshold
Celeribacter neptunius	strain=DSM 26471	GCA_900113955.1	588602	588602	type	True	75.834	65	843	95	below_threshold
Flavimaricola marinus	strain=CECT 8899	GCA_900184895.1	1819565	1819565	type	True	75.8256	51	843	95	below_threshold
Falsiruegeria litorea	strain=CECT 7639	GCA_900172225.1	1280831	1280831	type	True	75.8214	57	843	95	below_threshold
Yoonia vestfoldensis	strain=DSM 16212	GCA_000382265.1	245188	245188	type	True	75.7434	91	843	95	below_threshold
Halovulum marinum	strain=2CG4	GCA_009697225.1	2662447	2662447	type	True	75.7427	88	843	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 15:10:34,358] [INFO] DFAST Taxonomy check result was written to GCA_021647745.1_ASM2164774v1_genomic.fna/tc_result.tsv
[2023-06-29 15:10:34,359] [INFO] ===== Taxonomy check completed =====
[2023-06-29 15:10:34,359] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 15:10:34,359] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf370badf-1b64-4ce5-8409-03b955b29e6b/dqc_reference/checkm_data
[2023-06-29 15:10:34,361] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 15:10:34,393] [INFO] Task started: CheckM
[2023-06-29 15:10:34,393] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_021647745.1_ASM2164774v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_021647745.1_ASM2164774v1_genomic.fna/checkm_input GCA_021647745.1_ASM2164774v1_genomic.fna/checkm_result
[2023-06-29 15:11:03,172] [INFO] Task succeeded: CheckM
[2023-06-29 15:11:03,174] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.38%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-29 15:11:03,198] [INFO] ===== Completeness check finished =====
[2023-06-29 15:11:03,198] [INFO] ===== Start GTDB Search =====
[2023-06-29 15:11:03,199] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_021647745.1_ASM2164774v1_genomic.fna/markers.fasta)
[2023-06-29 15:11:03,199] [INFO] Task started: Blastn
[2023-06-29 15:11:03,200] [INFO] Running command: blastn -query GCA_021647745.1_ASM2164774v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf370badf-1b64-4ce5-8409-03b955b29e6b/dqc_reference/reference_markers_gtdb.fasta -out GCA_021647745.1_ASM2164774v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 15:11:04,403] [INFO] Task succeeded: Blastn
[2023-06-29 15:11:04,408] [INFO] Selected 17 target genomes.
[2023-06-29 15:11:04,408] [INFO] Target genome list was writen to GCA_021647745.1_ASM2164774v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 15:11:04,479] [INFO] Task started: fastANI
[2023-06-29 15:11:04,479] [INFO] Running command: fastANI --query /var/lib/cwl/stg9c62b319-31ca-47a6-a70d-b5128ed5c036/GCA_021647745.1_ASM2164774v1_genomic.fna.gz --refList GCA_021647745.1_ASM2164774v1_genomic.fna/target_genomes_gtdb.txt --output GCA_021647745.1_ASM2164774v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 15:11:14,339] [INFO] Task succeeded: fastANI
[2023-06-29 15:11:14,356] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 15:11:14,357] [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
GCA_015487255.1	s__UBA3077 sp015487255	80.8827	488	843	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA3077	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015485015.1	s__UBA3077 sp015485015	80.585	320	843	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA3077	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013139635.1	s__UBA3077 sp013139635	79.3927	385	843	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA3077	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002402045.2	s__UBA3077 sp002402045	78.9986	443	843	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA3077	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016744015.1	s__UBA3077 sp016744015	78.7904	421	843	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA3077	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002366685.1	s__UBA3077 sp002366685	78.382	266	843	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA3077	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015485375.1	s__UBA3077 sp015485375	76.8039	136	843	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA3077	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003228875.1	s__UBA3077 sp003228875	76.7865	184	843	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA3077	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002748285.1	s__Profundibacter sp002748285	76.5782	112	843	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Profundibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900172255.1	s__Roseovarius halotolerans	76.0344	88	843	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000473325.1	s__Leisingera caerulea	75.8619	91	843	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006226775.1	s__Marinovum sp006226775	75.8558	93	843	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marinovum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001730095.1	s__Leisingera sp001730095	75.8545	77	843	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113955.1	s__Celeribacter neptunius	75.834	65	843	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Celeribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000382265.1	s__Yoonia vestfoldensis	75.7434	91	843	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105075.1	s__Pseudogemmobacter sp900105075	75.4396	69	843	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudogemmobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 15:11:14,359] [INFO] GTDB search result was written to GCA_021647745.1_ASM2164774v1_genomic.fna/result_gtdb.tsv
[2023-06-29 15:11:14,359] [INFO] ===== GTDB Search completed =====
[2023-06-29 15:11:14,364] [INFO] DFAST_QC result json was written to GCA_021647745.1_ASM2164774v1_genomic.fna/dqc_result.json
[2023-06-29 15:11:14,365] [INFO] DFAST_QC completed!
[2023-06-29 15:11:14,365] [INFO] Total running time: 0h1m12s