[2024-01-24 11:20:03,708] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:20:03,710] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:20:03,710] [INFO] DQC Reference Directory: /var/lib/cwl/stg2706f3f9-56aa-459d-8410-897cb5e0352a/dqc_reference
[2024-01-24 11:20:04,876] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:20:04,876] [INFO] Task started: Prodigal
[2024-01-24 11:20:04,877] [INFO] Running command: gunzip -c /var/lib/cwl/stg039a00a3-dd79-4cb5-8c4d-2bf55a44a160/GCF_003072065.1_ASM307206v1_genomic.fna.gz | prodigal -d GCF_003072065.1_ASM307206v1_genomic.fna/cds.fna -a GCF_003072065.1_ASM307206v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:20:15,396] [INFO] Task succeeded: Prodigal
[2024-01-24 11:20:15,396] [INFO] Task started: HMMsearch
[2024-01-24 11:20:15,396] [INFO] Running command: hmmsearch --tblout GCF_003072065.1_ASM307206v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2706f3f9-56aa-459d-8410-897cb5e0352a/dqc_reference/reference_markers.hmm GCF_003072065.1_ASM307206v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:20:15,605] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:20:15,606] [INFO] Found 6/6 markers.
[2024-01-24 11:20:15,635] [INFO] Query marker FASTA was written to GCF_003072065.1_ASM307206v1_genomic.fna/markers.fasta
[2024-01-24 11:20:15,635] [INFO] Task started: Blastn
[2024-01-24 11:20:15,636] [INFO] Running command: blastn -query GCF_003072065.1_ASM307206v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2706f3f9-56aa-459d-8410-897cb5e0352a/dqc_reference/reference_markers.fasta -out GCF_003072065.1_ASM307206v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:20:16,437] [INFO] Task succeeded: Blastn
[2024-01-24 11:20:16,440] [INFO] Selected 21 target genomes.
[2024-01-24 11:20:16,441] [INFO] Target genome list was writen to GCF_003072065.1_ASM307206v1_genomic.fna/target_genomes.txt
[2024-01-24 11:20:16,455] [INFO] Task started: fastANI
[2024-01-24 11:20:16,455] [INFO] Running command: fastANI --query /var/lib/cwl/stg039a00a3-dd79-4cb5-8c4d-2bf55a44a160/GCF_003072065.1_ASM307206v1_genomic.fna.gz --refList GCF_003072065.1_ASM307206v1_genomic.fna/target_genomes.txt --output GCF_003072065.1_ASM307206v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:20:31,560] [INFO] Task succeeded: fastANI
[2024-01-24 11:20:31,561] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2706f3f9-56aa-459d-8410-897cb5e0352a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:20:31,561] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2706f3f9-56aa-459d-8410-897cb5e0352a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:20:31,577] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:20:31,578] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:20:31,578] [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
Thalassorhabdomicrobium marinisediminis	strain=BH-SD16	GCA_003072065.1	2170577	2170577	type	True	100.0	1129	1130	95	conclusive
Pelagivirga sediminicola	strain=BH-SD19	GCA_003072125.1	2170575	2170575	type	True	78.6366	375	1130	95	below_threshold
Pseudooctadecabacter jejudonensis	strain=CECT 8397	GCA_900172275.1	1391910	1391910	type	True	78.6001	439	1130	95	below_threshold
Salibaculum griseiflavum	strain=WDS4C29	GCA_003129565.1	1914409	1914409	type	True	78.5363	430	1130	95	below_threshold
Salibaculum halophilum	strain=WDS1C4	GCA_002094885.1	1914408	1914408	type	True	78.4927	402	1130	95	below_threshold
Flavimaricola marinus	strain=CECT 8899	GCA_900184895.1	1819565	1819565	type	True	78.2665	328	1130	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	78.1186	325	1130	95	below_threshold
Thalassobius mangrovi	strain=GS-10	GCA_009857745.1	2692236	2692236	type	True	78.117	355	1130	95	below_threshold
Roseivivax lentus	strain=DSM 29430	GCA_900156805.1	633194	633194	type	True	78.0974	360	1130	95	below_threshold
Pseudooceanicola marinus	strain=LMG 23705	GCA_002786295.1	396013	396013	type	True	77.9276	347	1130	95	below_threshold
Pseudooceanicola marinus	strain=CECT 7751	GCA_900172385.1	396013	396013	type	True	77.9112	346	1130	95	below_threshold
Salipiger aestuarii	strain=AD8	GCA_008930655.1	568098	568098	type	True	77.8324	312	1130	95	below_threshold
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	77.7552	300	1130	95	below_threshold
Yangia pacifica	strain=DSM 26894	GCA_900116195.1	311180	311180	suspected-type	True	77.6115	374	1130	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	77.5558	286	1130	95	below_threshold
Puniceibacterium confluentis	strain=JSSK-17	GCA_007923445.1	1958944	1958944	type	True	77.5439	315	1130	95	below_threshold
Puniceibacterium sediminis	strain=DSM 29052	GCA_900188035.1	1608407	1608407	type	True	77.5336	276	1130	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_009908265.2	2852097	2852097	type	True	77.4864	308	1130	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	77.4529	334	1130	95	below_threshold
Octadecabacter antarcticus	strain=307	GCA_000155675.2	1217908	1217908	type	True	77.1677	308	1130	95	below_threshold
Octadecabacter arcticus	strain=238	GCA_000155735.2	53946	53946	type	True	77.1358	328	1130	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:20:31,579] [INFO] DFAST Taxonomy check result was written to GCF_003072065.1_ASM307206v1_genomic.fna/tc_result.tsv
[2024-01-24 11:20:31,580] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:20:31,580] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:20:31,580] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2706f3f9-56aa-459d-8410-897cb5e0352a/dqc_reference/checkm_data
[2024-01-24 11:20:31,581] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:20:31,615] [INFO] Task started: CheckM
[2024-01-24 11:20:31,616] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003072065.1_ASM307206v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003072065.1_ASM307206v1_genomic.fna/checkm_input GCF_003072065.1_ASM307206v1_genomic.fna/checkm_result
[2024-01-24 11:21:05,592] [INFO] Task succeeded: CheckM
[2024-01-24 11:21:05,593] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:21:05,609] [INFO] ===== Completeness check finished =====
[2024-01-24 11:21:05,610] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:21:05,610] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003072065.1_ASM307206v1_genomic.fna/markers.fasta)
[2024-01-24 11:21:05,610] [INFO] Task started: Blastn
[2024-01-24 11:21:05,610] [INFO] Running command: blastn -query GCF_003072065.1_ASM307206v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2706f3f9-56aa-459d-8410-897cb5e0352a/dqc_reference/reference_markers_gtdb.fasta -out GCF_003072065.1_ASM307206v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:21:06,949] [INFO] Task succeeded: Blastn
[2024-01-24 11:21:06,952] [INFO] Selected 22 target genomes.
[2024-01-24 11:21:06,952] [INFO] Target genome list was writen to GCF_003072065.1_ASM307206v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:21:06,965] [INFO] Task started: fastANI
[2024-01-24 11:21:06,965] [INFO] Running command: fastANI --query /var/lib/cwl/stg039a00a3-dd79-4cb5-8c4d-2bf55a44a160/GCF_003072065.1_ASM307206v1_genomic.fna.gz --refList GCF_003072065.1_ASM307206v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003072065.1_ASM307206v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:21:21,862] [INFO] Task succeeded: fastANI
[2024-01-24 11:21:21,879] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:21:21,879] [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_003072065.1	s__Thalassorhabdomicrobium marinisediminis	100.0	1129	1130	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassorhabdomicrobium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900172275.1	s__Pseudooctadecabacter jejudonensis	78.6001	439	1130	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooctadecabacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003072125.1	s__Roseovarius sediminicola	78.5923	379	1130	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142185.1	s__Lutimaribacter pacificus	78.5731	439	1130	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Lutimaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001420005.1	s__Loktanella sp001420005	78.5454	311	1130	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Loktanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003344785.1	s__Puniceibacterium profundi	78.5295	387	1130	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Puniceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002094885.1	s__Salibaculum halophilum	78.4929	402	1130	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009908505.1	s__Salibaculum sp009908505	78.4124	404	1130	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004145405.1	s__Loktanella sp004145405	78.3089	371	1130	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Loktanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014656415.1	s__Seohaeicola zhoushanensis	78.0369	376	1130	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Seohaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003651245.1	s__Roseovarius spongiae	78.0339	385	1130	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002786295.1	s__Pseudooceanicola marinus	77.914	346	1130	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	99.99	99.99	0.99	0.99	2	-
GCF_000153305.1	s__Oceanicola granulosus	77.858	391	1130	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005938225.1	s__Arenibacterium halophilum	77.7298	369	1130	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Arenibacterium	95.0	96.35	96.35	0.87	0.87	2	-
GCF_900110705.1	s__Loktanella sp900110705	77.7199	288	1130	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Loktanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110775.1	s__Litorimicrobium taeanense	77.6936	300	1130	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Litorimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003428585.1	s__Nioella sp003428585	77.5507	287	1130	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Nioella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188035.1	s__Puniceibacterium sediminis	77.5336	276	1130	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Puniceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017886375.1	s__Octadecabacter sp017886375	77.4321	300	1130	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Octadecabacter	95.0	99.96	99.96	0.97	0.97	2	-
GCA_018608045.1	s__Octadecabacter sp018608045	77.3842	262	1130	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Octadecabacter	95.0	98.68	98.68	0.85	0.85	2	-
GCF_000155675.2	s__Octadecabacter antarcticus	77.1593	309	1130	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Octadecabacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000155735.2	s__Octadecabacter arcticus	77.1274	329	1130	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Octadecabacter	95.0	96.73	96.73	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:21:21,881] [INFO] GTDB search result was written to GCF_003072065.1_ASM307206v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:21:21,881] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:21:21,885] [INFO] DFAST_QC result json was written to GCF_003072065.1_ASM307206v1_genomic.fna/dqc_result.json
[2024-01-24 11:21:21,886] [INFO] DFAST_QC completed!
[2024-01-24 11:21:21,886] [INFO] Total running time: 0h1m18s