[2024-01-24 12:23:50,987] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:23:50,989] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:23:50,989] [INFO] DQC Reference Directory: /var/lib/cwl/stg8028b85e-623a-4229-9a7e-2e4e9e53d4e9/dqc_reference
[2024-01-24 12:23:52,261] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:23:52,262] [INFO] Task started: Prodigal
[2024-01-24 12:23:52,262] [INFO] Running command: gunzip -c /var/lib/cwl/stg0659ed70-d41f-4523-80a3-4de5a335ac6b/GCF_024733015.1_ASM2473301v1_genomic.fna.gz | prodigal -d GCF_024733015.1_ASM2473301v1_genomic.fna/cds.fna -a GCF_024733015.1_ASM2473301v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:24:03,511] [INFO] Task succeeded: Prodigal
[2024-01-24 12:24:03,512] [INFO] Task started: HMMsearch
[2024-01-24 12:24:03,512] [INFO] Running command: hmmsearch --tblout GCF_024733015.1_ASM2473301v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8028b85e-623a-4229-9a7e-2e4e9e53d4e9/dqc_reference/reference_markers.hmm GCF_024733015.1_ASM2473301v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:24:03,779] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:24:03,782] [INFO] Found 6/6 markers.
[2024-01-24 12:24:03,818] [INFO] Query marker FASTA was written to GCF_024733015.1_ASM2473301v1_genomic.fna/markers.fasta
[2024-01-24 12:24:03,819] [INFO] Task started: Blastn
[2024-01-24 12:24:03,819] [INFO] Running command: blastn -query GCF_024733015.1_ASM2473301v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8028b85e-623a-4229-9a7e-2e4e9e53d4e9/dqc_reference/reference_markers.fasta -out GCF_024733015.1_ASM2473301v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:24:04,790] [INFO] Task succeeded: Blastn
[2024-01-24 12:24:04,795] [INFO] Selected 22 target genomes.
[2024-01-24 12:24:04,795] [INFO] Target genome list was writen to GCF_024733015.1_ASM2473301v1_genomic.fna/target_genomes.txt
[2024-01-24 12:24:04,805] [INFO] Task started: fastANI
[2024-01-24 12:24:04,806] [INFO] Running command: fastANI --query /var/lib/cwl/stg0659ed70-d41f-4523-80a3-4de5a335ac6b/GCF_024733015.1_ASM2473301v1_genomic.fna.gz --refList GCF_024733015.1_ASM2473301v1_genomic.fna/target_genomes.txt --output GCF_024733015.1_ASM2473301v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:24:21,504] [INFO] Task succeeded: fastANI
[2024-01-24 12:24:21,504] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8028b85e-623a-4229-9a7e-2e4e9e53d4e9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:24:21,505] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8028b85e-623a-4229-9a7e-2e4e9e53d4e9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:24:21,540] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:24:21,541] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:24:21,541] [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
Pseudosulfitobacter pseudonitzschiae	strain=H3	GCA_000712315.1	1402135	1402135	type	True	85.236	891	1152	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=DSM 26824	GCA_900129395.1	1402135	1402135	type	True	85.1823	886	1152	95	below_threshold
Sulfitobacter sabulilitoris	strain=HSMS-29	GCA_005887615.1	2562655	2562655	type	True	79.4687	620	1152	95	below_threshold
Antarcticimicrobium luteum	strain=318-1	GCA_004358185.1	2547397	2547397	type	True	78.8806	549	1152	95	below_threshold
Cribrihabitans marinus	strain=DSM 29340	GCA_900109035.1	1227549	1227549	type	True	78.8284	521	1152	95	below_threshold
Cribrihabitans marinus	strain=CGMCC 1.13219	GCA_014640375.1	1227549	1227549	type	True	78.7489	526	1152	95	below_threshold
Ruegeria pomeroyi	strain=DSS-3	GCA_000011965.2	89184	89184	suspected-type	True	78.6775	543	1152	95	below_threshold
Lutimaribacter saemankumensis	strain=DSM 28010	GCA_900100005.1	490829	490829	type	True	78.6634	446	1152	95	below_threshold
Pelagivirga sediminicola	strain=BH-SD19	GCA_003072125.1	2170575	2170575	type	True	78.3821	423	1152	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	78.37	467	1152	95	below_threshold
Ruegeria marina	strain=CGMCC 1.9108	GCA_900101475.1	639004	639004	type	True	78.3116	481	1152	95	below_threshold
Sulfitobacter delicatus	strain=DSM 16477	GCA_900102535.1	218672	218672	type	True	78.2717	465	1152	95	below_threshold
Sulfitobacter indolifex	strain=HEL-45	GCA_000172095.1	225422	225422	type	True	78.2184	415	1152	95	below_threshold
Pseudooceanicola marinus	strain=LMG 23705	GCA_002786295.1	396013	396013	type	True	78.1196	396	1152	95	below_threshold
Pseudooceanicola marinus	strain=CECT 7751	GCA_900172385.1	396013	396013	type	True	78.1094	399	1152	95	below_threshold
Yoonia vestfoldensis	strain=DSM 16212	GCA_000382265.1	245188	245188	type	True	77.9711	388	1152	95	below_threshold
Chachezhania sediminis	strain=CAU 1508	GCA_009765275.1	2599291	2599291	type	True	77.8694	448	1152	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	77.7399	354	1152	95	below_threshold
Aliishimia ponticola	strain=MYP11	GCA_004803475.1	2499833	2499833	type	True	77.7258	434	1152	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	77.499	322	1152	95	below_threshold
Pseudophaeobacter flagellatus	strain=MA21411-1	GCA_021228235.1	2899119	2899119	type	True	77.2761	299	1152	95	below_threshold
Zongyanglinia marina	strain=DSW4-44	GCA_005771405.1	2578117	2578117	type	True	76.6788	170	1152	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:24:21,542] [INFO] DFAST Taxonomy check result was written to GCF_024733015.1_ASM2473301v1_genomic.fna/tc_result.tsv
[2024-01-24 12:24:21,543] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:24:21,543] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:24:21,543] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8028b85e-623a-4229-9a7e-2e4e9e53d4e9/dqc_reference/checkm_data
[2024-01-24 12:24:21,544] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:24:21,584] [INFO] Task started: CheckM
[2024-01-24 12:24:21,584] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024733015.1_ASM2473301v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024733015.1_ASM2473301v1_genomic.fna/checkm_input GCF_024733015.1_ASM2473301v1_genomic.fna/checkm_result
[2024-01-24 12:24:58,356] [INFO] Task succeeded: CheckM
[2024-01-24 12:24:58,357] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:24:58,380] [INFO] ===== Completeness check finished =====
[2024-01-24 12:24:58,380] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:24:58,381] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024733015.1_ASM2473301v1_genomic.fna/markers.fasta)
[2024-01-24 12:24:58,381] [INFO] Task started: Blastn
[2024-01-24 12:24:58,381] [INFO] Running command: blastn -query GCF_024733015.1_ASM2473301v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8028b85e-623a-4229-9a7e-2e4e9e53d4e9/dqc_reference/reference_markers_gtdb.fasta -out GCF_024733015.1_ASM2473301v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:25:00,191] [INFO] Task succeeded: Blastn
[2024-01-24 12:25:00,196] [INFO] Selected 9 target genomes.
[2024-01-24 12:25:00,196] [INFO] Target genome list was writen to GCF_024733015.1_ASM2473301v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:25:00,204] [INFO] Task started: fastANI
[2024-01-24 12:25:00,204] [INFO] Running command: fastANI --query /var/lib/cwl/stg0659ed70-d41f-4523-80a3-4de5a335ac6b/GCF_024733015.1_ASM2473301v1_genomic.fna.gz --refList GCF_024733015.1_ASM2473301v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024733015.1_ASM2473301v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:25:08,320] [INFO] Task succeeded: fastANI
[2024-01-24 12:25:08,334] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:25:08,334] [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_000620505.1	s__Ascidiaceihabitans sp000620505	85.3339	903	1152	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129395.1	s__Ascidiaceihabitans pseudonitzschiae	85.1821	886	1152	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	99.99	99.97	0.98	0.96	4	-
GCF_003335545.1	s__Ascidiaceihabitans sp003335545	84.8038	877	1152	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002222635.1	s__Ascidiaceihabitans pseudonitzschiae_A	84.5574	871	1152	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	99.92	99.92	0.96	0.96	2	-
GCF_005887615.1	s__Sulfitobacter_E sabulilitoris	79.4606	621	1152	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009363555.1	s__Sulfitobacter sp009363555	79.2205	562	1152	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004358185.1	s__Antarcticimicrobium luteum	78.8892	548	1152	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Antarcticimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002210165.1	s__CAU-1492 sp002210165	78.1322	444	1152	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CAU-1492	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016888515.1	s__Shimia_A biformata	78.0781	419	1152	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:25:08,335] [INFO] GTDB search result was written to GCF_024733015.1_ASM2473301v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:25:08,336] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:25:08,340] [INFO] DFAST_QC result json was written to GCF_024733015.1_ASM2473301v1_genomic.fna/dqc_result.json
[2024-01-24 12:25:08,340] [INFO] DFAST_QC completed!
[2024-01-24 12:25:08,340] [INFO] Total running time: 0h1m17s