[2024-01-25 17:45:05,398] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:45:05,400] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:45:05,400] [INFO] DQC Reference Directory: /var/lib/cwl/stg5c3151c2-fbc1-4149-87f4-19b24dc49962/dqc_reference
[2024-01-25 17:45:06,557] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:45:06,557] [INFO] Task started: Prodigal
[2024-01-25 17:45:06,558] [INFO] Running command: gunzip -c /var/lib/cwl/stg16be19c0-5196-4fe7-9fa5-71a1abaa9c51/GCF_003148665.1_ASM314866v1_genomic.fna.gz | prodigal -d GCF_003148665.1_ASM314866v1_genomic.fna/cds.fna -a GCF_003148665.1_ASM314866v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:45:27,618] [INFO] Task succeeded: Prodigal
[2024-01-25 17:45:27,619] [INFO] Task started: HMMsearch
[2024-01-25 17:45:27,619] [INFO] Running command: hmmsearch --tblout GCF_003148665.1_ASM314866v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5c3151c2-fbc1-4149-87f4-19b24dc49962/dqc_reference/reference_markers.hmm GCF_003148665.1_ASM314866v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:45:27,882] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:45:27,883] [INFO] Found 6/6 markers.
[2024-01-25 17:45:27,923] [INFO] Query marker FASTA was written to GCF_003148665.1_ASM314866v1_genomic.fna/markers.fasta
[2024-01-25 17:45:27,923] [INFO] Task started: Blastn
[2024-01-25 17:45:27,923] [INFO] Running command: blastn -query GCF_003148665.1_ASM314866v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5c3151c2-fbc1-4149-87f4-19b24dc49962/dqc_reference/reference_markers.fasta -out GCF_003148665.1_ASM314866v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:45:28,542] [INFO] Task succeeded: Blastn
[2024-01-25 17:45:28,545] [INFO] Selected 18 target genomes.
[2024-01-25 17:45:28,545] [INFO] Target genome list was writen to GCF_003148665.1_ASM314866v1_genomic.fna/target_genomes.txt
[2024-01-25 17:45:28,582] [INFO] Task started: fastANI
[2024-01-25 17:45:28,582] [INFO] Running command: fastANI --query /var/lib/cwl/stg16be19c0-5196-4fe7-9fa5-71a1abaa9c51/GCF_003148665.1_ASM314866v1_genomic.fna.gz --refList GCF_003148665.1_ASM314866v1_genomic.fna/target_genomes.txt --output GCF_003148665.1_ASM314866v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:45:44,724] [INFO] Task succeeded: fastANI
[2024-01-25 17:45:44,725] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5c3151c2-fbc1-4149-87f4-19b24dc49962/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:45:44,725] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5c3151c2-fbc1-4149-87f4-19b24dc49962/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:45:44,735] [INFO] Found 16 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 17:45:44,735] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:45:44,735] [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
Maribacter polysiphoniae	strain=DSM 23514	GCA_003148665.1	429344	429344	type	True	100.0	1687	1694	95	conclusive
Maribacter polysiphoniae	strain=KCTC 22021	GCA_014673435.1	429344	429344	type	True	99.982	1682	1694	95	conclusive
Maribacter luteus	strain=RZ05	GCA_009674825.1	2594478	2594478	type	True	82.5681	942	1694	95	below_threshold
Maribacter arenosus	strain=CAU 1321	GCA_014610845.1	1854708	1854708	type	True	79.1702	583	1694	95	below_threshold
Maribacter caenipelagi	strain=CECT 8455	GCA_004364175.1	1447781	1447781	type	True	77.8208	146	1694	95	below_threshold
Muricauda aurea	strain=BC31-1-A7	GCA_017313785.1	2915619	2915619	type	True	77.5227	144	1694	95	below_threshold
Kriegella aquimaris	strain=DSM 19886	GCA_900103215.1	192904	192904	type	True	77.4171	194	1694	95	below_threshold
Maribacter ulvicola	strain=DSM 15366	GCA_900155985.1	228959	228959	type	True	77.3078	137	1694	95	below_threshold
Maribacter dokdonensis	strain=DSW-8	GCA_001447995.1	320912	320912	type	True	76.9869	150	1694	95	below_threshold
Arenibacter palladensis	strain=DSM 17539	GCA_900129275.1	237373	237373	type	True	76.9832	168	1694	95	below_threshold
Muricauda flava	strain=DSM 22638	GCA_900129665.1	570519	570519	type	True	76.9739	92	1694	95	below_threshold
Arenibacter troitsensis	strain=DSM 19835	GCA_900177645.1	188872	188872	type	True	76.9737	171	1694	95	below_threshold
Ulvibacterium marinum	strain=CCMM003	GCA_003626755.1	2419782	2419782	type	True	76.9716	184	1694	95	below_threshold
Zobellia barbeyronii	strain=KMM 6746	GCA_018603515.1	2748009	2748009	type	True	76.8733	150	1694	95	below_threshold
Muricauda brasiliensis	strain=K001	GCA_003057865.1	2162892	2162892	type	True	76.7231	118	1694	95	below_threshold
Maribacter arcticus	strain=DSM 23546	GCA_900167935.1	561365	561365	type	True	76.6524	146	1694	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:45:44,737] [INFO] DFAST Taxonomy check result was written to GCF_003148665.1_ASM314866v1_genomic.fna/tc_result.tsv
[2024-01-25 17:45:44,737] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:45:44,737] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:45:44,738] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5c3151c2-fbc1-4149-87f4-19b24dc49962/dqc_reference/checkm_data
[2024-01-25 17:45:44,738] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:45:44,786] [INFO] Task started: CheckM
[2024-01-25 17:45:44,787] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003148665.1_ASM314866v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003148665.1_ASM314866v1_genomic.fna/checkm_input GCF_003148665.1_ASM314866v1_genomic.fna/checkm_result
[2024-01-25 17:46:42,306] [INFO] Task succeeded: CheckM
[2024-01-25 17:46:42,307] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:46:42,328] [INFO] ===== Completeness check finished =====
[2024-01-25 17:46:42,329] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:46:42,330] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003148665.1_ASM314866v1_genomic.fna/markers.fasta)
[2024-01-25 17:46:42,330] [INFO] Task started: Blastn
[2024-01-25 17:46:42,330] [INFO] Running command: blastn -query GCF_003148665.1_ASM314866v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5c3151c2-fbc1-4149-87f4-19b24dc49962/dqc_reference/reference_markers_gtdb.fasta -out GCF_003148665.1_ASM314866v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:46:43,241] [INFO] Task succeeded: Blastn
[2024-01-25 17:46:43,244] [INFO] Selected 10 target genomes.
[2024-01-25 17:46:43,244] [INFO] Target genome list was writen to GCF_003148665.1_ASM314866v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:46:43,255] [INFO] Task started: fastANI
[2024-01-25 17:46:43,256] [INFO] Running command: fastANI --query /var/lib/cwl/stg16be19c0-5196-4fe7-9fa5-71a1abaa9c51/GCF_003148665.1_ASM314866v1_genomic.fna.gz --refList GCF_003148665.1_ASM314866v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003148665.1_ASM314866v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:46:52,392] [INFO] Task succeeded: fastANI
[2024-01-25 17:46:52,400] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:46:52,400] [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_003148665.1	s__Maribacter_A polysiphoniae	100.0	1687	1694	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter_A	95.0	99.27	98.55	0.95	0.91	3	conclusive
GCF_014596745.1	s__Maribacter_A sp014596745	92.895	1305	1694	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002749285.1	s__Maribacter_A sp002749285	83.3607	560	1694	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009674825.1	s__Maribacter_A luteus	82.5766	941	1694	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014610845.1	s__Maribacter_A arenosus	79.1619	584	1694	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000153165.2	s__Maribacter_A sp000153165	78.1518	337	1694	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004364175.1	s__Maribacter caenipelagi	77.8208	146	1694	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900155985.1	s__Maribacter ulvicola	77.287	138	1694	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003970695.1	s__Maribacter sp002742365	77.1512	143	1694	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	96.61	96.61	0.86	0.86	2	-
GCF_900167935.1	s__Maribacter arcticus	76.6647	145	1694	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:46:52,401] [INFO] GTDB search result was written to GCF_003148665.1_ASM314866v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:46:52,402] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:46:52,405] [INFO] DFAST_QC result json was written to GCF_003148665.1_ASM314866v1_genomic.fna/dqc_result.json
[2024-01-25 17:46:52,405] [INFO] DFAST_QC completed!
[2024-01-25 17:46:52,405] [INFO] Total running time: 0h1m47s