[2024-01-25 17:47:50,629] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:47:50,630] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:47:50,630] [INFO] DQC Reference Directory: /var/lib/cwl/stgaafcf1b7-da1b-4a59-9c23-425068de1bcf/dqc_reference
[2024-01-25 17:47:51,746] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:47:51,747] [INFO] Task started: Prodigal
[2024-01-25 17:47:51,747] [INFO] Running command: gunzip -c /var/lib/cwl/stg46307eb6-7d98-4ef7-a174-a9cd62287195/GCF_030161115.1_ASM3016111v1_genomic.fna.gz | prodigal -d GCF_030161115.1_ASM3016111v1_genomic.fna/cds.fna -a GCF_030161115.1_ASM3016111v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:47:59,488] [INFO] Task succeeded: Prodigal
[2024-01-25 17:47:59,489] [INFO] Task started: HMMsearch
[2024-01-25 17:47:59,489] [INFO] Running command: hmmsearch --tblout GCF_030161115.1_ASM3016111v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaafcf1b7-da1b-4a59-9c23-425068de1bcf/dqc_reference/reference_markers.hmm GCF_030161115.1_ASM3016111v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:47:59,716] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:47:59,717] [INFO] Found 6/6 markers.
[2024-01-25 17:47:59,752] [INFO] Query marker FASTA was written to GCF_030161115.1_ASM3016111v1_genomic.fna/markers.fasta
[2024-01-25 17:47:59,752] [INFO] Task started: Blastn
[2024-01-25 17:47:59,752] [INFO] Running command: blastn -query GCF_030161115.1_ASM3016111v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaafcf1b7-da1b-4a59-9c23-425068de1bcf/dqc_reference/reference_markers.fasta -out GCF_030161115.1_ASM3016111v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:48:00,447] [INFO] Task succeeded: Blastn
[2024-01-25 17:48:00,450] [INFO] Selected 23 target genomes.
[2024-01-25 17:48:00,450] [INFO] Target genome list was writen to GCF_030161115.1_ASM3016111v1_genomic.fna/target_genomes.txt
[2024-01-25 17:48:00,488] [INFO] Task started: fastANI
[2024-01-25 17:48:00,488] [INFO] Running command: fastANI --query /var/lib/cwl/stg46307eb6-7d98-4ef7-a174-a9cd62287195/GCF_030161115.1_ASM3016111v1_genomic.fna.gz --refList GCF_030161115.1_ASM3016111v1_genomic.fna/target_genomes.txt --output GCF_030161115.1_ASM3016111v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:48:19,069] [INFO] Task succeeded: fastANI
[2024-01-25 17:48:19,069] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaafcf1b7-da1b-4a59-9c23-425068de1bcf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:48:19,069] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaafcf1b7-da1b-4a59-9c23-425068de1bcf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:48:19,081] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 17:48:19,081] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 17:48:19,082] [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
Psychromonas hadalis	strain=ATCC BAA-638	GCA_000420245.1	211669	211669	type	True	79.7509	496	1453	95	below_threshold
Psychromonas arctica	strain=DSM 14288	GCA_000482725.1	168275	168275	type	True	78.8492	317	1453	95	below_threshold
Psychromonas ossibalaenae	strain=JAMM 0738	GCA_000381745.1	444922	444922	type	True	78.7636	318	1453	95	below_threshold
Psychromonas aquimarina	strain=ATCC BAA-1526	GCA_000428725.1	444919	444919	type	True	78.4274	305	1453	95	below_threshold
Psychromonas antarctica	strain=DSM 10704	GCA_022267535.1	67573	67573	type	True	78.1766	258	1453	95	below_threshold
Psychromonas ingrahamii	strain=37	GCA_000015285.1	357794	357794	type	True	77.9825	245	1453	95	below_threshold
Motilimonas pumila	strain=PLHSC7-2	GCA_003596335.1	2303987	2303987	type	True	77.7568	69	1453	95	below_threshold
Aliivibrio sifiae	strain=NBRC 105001	GCA_002954715.1	566293	566293	type	True	76.9631	97	1453	95	below_threshold
Pseudoalteromonas carrageenovora	strain=IAM 12662	GCA_014925295.1	227	227	type	True	76.9331	65	1453	95	below_threshold
Pseudoalteromonas carrageenovora	strain=ATCC 43555	GCA_900239935.1	227	227	type	True	76.8684	66	1453	95	below_threshold
Pseudoalteromonas carrageenovora	strain=NBRC 12985	GCA_006539245.1	227	227	type	True	76.7911	62	1453	95	below_threshold
Vibrio pomeroyi	strain=LMG 20537	GCA_024347595.1	198832	198832	type	True	76.7436	87	1453	95	below_threshold
Pseudoalteromonas lipolytica	strain=CGMCC 1.8499	GCA_900116435.1	570156	570156	suspected-type	True	76.6983	52	1453	95	below_threshold
Pseudoalteromonas phenolica	strain=O-BC30	GCA_014925335.1	161398	161398	suspected-type	True	76.5577	50	1453	95	below_threshold
Vibrio nitrifigilis	strain=NFV-1	GCA_015686695.1	2789781	2789781	type	True	76.5018	64	1453	95	below_threshold
Shewanella sairae	strain=JCM 11563	GCA_019655015.1	190310	190310	type	True	76.3244	73	1453	95	below_threshold
Shewanella inventionis	strain=KCTC 42807	GCA_023283595.1	1738770	1738770	type	True	76.1849	67	1453	95	below_threshold
Shewanella inventionis	strain=CGMCC 1.15339	GCA_014641855.1	1738770	1738770	type	True	76.1276	67	1453	95	below_threshold
Pseudoalteromonas rhizosphaerae	strain=RA15	GCA_902498845.1	2518973	2518973	type	True	76.0927	70	1453	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:48:19,086] [INFO] DFAST Taxonomy check result was written to GCF_030161115.1_ASM3016111v1_genomic.fna/tc_result.tsv
[2024-01-25 17:48:19,087] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:48:19,087] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:48:19,087] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaafcf1b7-da1b-4a59-9c23-425068de1bcf/dqc_reference/checkm_data
[2024-01-25 17:48:19,088] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:48:19,134] [INFO] Task started: CheckM
[2024-01-25 17:48:19,134] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030161115.1_ASM3016111v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030161115.1_ASM3016111v1_genomic.fna/checkm_input GCF_030161115.1_ASM3016111v1_genomic.fna/checkm_result
[2024-01-25 17:48:46,821] [INFO] Task succeeded: CheckM
[2024-01-25 17:48:46,822] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-25 17:48:46,843] [INFO] ===== Completeness check finished =====
[2024-01-25 17:48:46,843] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:48:46,844] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030161115.1_ASM3016111v1_genomic.fna/markers.fasta)
[2024-01-25 17:48:46,844] [INFO] Task started: Blastn
[2024-01-25 17:48:46,844] [INFO] Running command: blastn -query GCF_030161115.1_ASM3016111v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaafcf1b7-da1b-4a59-9c23-425068de1bcf/dqc_reference/reference_markers_gtdb.fasta -out GCF_030161115.1_ASM3016111v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:48:47,945] [INFO] Task succeeded: Blastn
[2024-01-25 17:48:47,948] [INFO] Selected 16 target genomes.
[2024-01-25 17:48:47,948] [INFO] Target genome list was writen to GCF_030161115.1_ASM3016111v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:48:47,969] [INFO] Task started: fastANI
[2024-01-25 17:48:47,969] [INFO] Running command: fastANI --query /var/lib/cwl/stg46307eb6-7d98-4ef7-a174-a9cd62287195/GCF_030161115.1_ASM3016111v1_genomic.fna.gz --refList GCF_030161115.1_ASM3016111v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030161115.1_ASM3016111v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:49:01,380] [INFO] Task succeeded: fastANI
[2024-01-25 17:49:01,390] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 17:49:01,391] [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_002835995.1	s__Psychromonas sp002835995	80.871	571	1453	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Psychromonadaceae;g__Psychromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002835465.1	s__Psychromonas sp002835465	80.5721	562	1453	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Psychromonadaceae;g__Psychromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000420245.1	s__Psychromonas hadalis	79.7309	499	1453	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Psychromonadaceae;g__Psychromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004378355.1	s__Psychromonas sp004378355	79.1773	293	1453	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Psychromonadaceae;g__Psychromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003318165.1	s__Psychromonas sp003318165	78.9872	299	1453	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Psychromonadaceae;g__Psychromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000470315.2	s__Psychromonas sp000470315	78.9025	327	1453	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Psychromonadaceae;g__Psychromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000482725.1	s__Psychromonas arctica	78.8619	316	1453	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Psychromonadaceae;g__Psychromonas	95.0	98.18	98.18	0.89	0.89	2	-
GCF_009828855.1	s__Psychromonas sp009828855	78.8345	352	1453	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Psychromonadaceae;g__Psychromonas	95.0	98.96	98.96	0.95	0.95	2	-
GCF_000381745.1	s__Psychromonas ossibalaenae	78.7969	315	1453	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Psychromonadaceae;g__Psychromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013619145.1	s__Psychromonas sp013619145	78.7076	333	1453	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Psychromonadaceae;g__Psychromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000153405.2	s__Psychromonas sp000153405	78.5332	219	1453	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Psychromonadaceae;g__Psychromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000428725.1	s__Psychromonas aquimarina	78.4155	307	1453	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Psychromonadaceae;g__Psychromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002954705.1	s__Aliivibrio sifiae_A	76.9473	106	1453	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Aliivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000953695.1	s__Aliivibrio wodanis	76.9334	100	1453	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Aliivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900312675.1	s__Aliivibrio sp900312675	76.915	98	1453	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Aliivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015686695.1	s__Vibrio nitrifigilis	76.4412	65	1453	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.79	98.79	0.95	0.95	2	-
--------------------------------------------------------------------------------
[2024-01-25 17:49:01,392] [INFO] GTDB search result was written to GCF_030161115.1_ASM3016111v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:49:01,392] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:49:01,396] [INFO] DFAST_QC result json was written to GCF_030161115.1_ASM3016111v1_genomic.fna/dqc_result.json
[2024-01-25 17:49:01,396] [INFO] DFAST_QC completed!
[2024-01-25 17:49:01,396] [INFO] Total running time: 0h1m11s