[2024-01-25 20:20:05,956] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:20:05,958] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:20:05,958] [INFO] DQC Reference Directory: /var/lib/cwl/stgf361927a-665b-46a6-83a7-0e297d59194b/dqc_reference
[2024-01-25 20:20:07,137] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:20:07,138] [INFO] Task started: Prodigal
[2024-01-25 20:20:07,138] [INFO] Running command: gunzip -c /var/lib/cwl/stgefdb6798-0167-4b68-8fc3-078291c6c691/GCF_001029455.1_ASM102945v1_genomic.fna.gz | prodigal -d GCF_001029455.1_ASM102945v1_genomic.fna/cds.fna -a GCF_001029455.1_ASM102945v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:20:20,312] [INFO] Task succeeded: Prodigal
[2024-01-25 20:20:20,312] [INFO] Task started: HMMsearch
[2024-01-25 20:20:20,312] [INFO] Running command: hmmsearch --tblout GCF_001029455.1_ASM102945v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf361927a-665b-46a6-83a7-0e297d59194b/dqc_reference/reference_markers.hmm GCF_001029455.1_ASM102945v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:20:20,700] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:20:20,701] [INFO] Found 6/6 markers.
[2024-01-25 20:20:20,746] [INFO] Query marker FASTA was written to GCF_001029455.1_ASM102945v1_genomic.fna/markers.fasta
[2024-01-25 20:20:20,747] [INFO] Task started: Blastn
[2024-01-25 20:20:20,747] [INFO] Running command: blastn -query GCF_001029455.1_ASM102945v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf361927a-665b-46a6-83a7-0e297d59194b/dqc_reference/reference_markers.fasta -out GCF_001029455.1_ASM102945v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:20:21,539] [INFO] Task succeeded: Blastn
[2024-01-25 20:20:21,542] [INFO] Selected 16 target genomes.
[2024-01-25 20:20:21,542] [INFO] Target genome list was writen to GCF_001029455.1_ASM102945v1_genomic.fna/target_genomes.txt
[2024-01-25 20:20:21,557] [INFO] Task started: fastANI
[2024-01-25 20:20:21,558] [INFO] Running command: fastANI --query /var/lib/cwl/stgefdb6798-0167-4b68-8fc3-078291c6c691/GCF_001029455.1_ASM102945v1_genomic.fna.gz --refList GCF_001029455.1_ASM102945v1_genomic.fna/target_genomes.txt --output GCF_001029455.1_ASM102945v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:20:37,513] [INFO] Task succeeded: fastANI
[2024-01-25 20:20:37,514] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf361927a-665b-46a6-83a7-0e297d59194b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:20:37,514] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf361927a-665b-46a6-83a7-0e297d59194b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:20:37,529] [INFO] Found 16 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 20:20:37,529] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:20:37,529] [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
Photobacterium ganghwense	strain=DSM 22954	GCA_001029455.1	320778	320778	type	True	100.0	1815	1817	95	conclusive
Photobacterium ganghwense	strain=JCM 12487	GCA_003025595.1	320778	320778	type	True	99.9993	1812	1817	95	conclusive
Photobacterium aphoticum	strain=DSM 25995	GCA_003025575.1	754436	754436	type	True	80.1976	549	1817	95	below_threshold
Photobacterium rosenbergii	strain=DSM 19138	GCA_003026455.1	294936	294936	type	True	80.1747	568	1817	95	below_threshold
Photobacterium sanctipauli	strain=A-394	GCA_000730475.1	1342794	1342794	type	True	80.1527	392	1817	95	below_threshold
Photobacterium aphoticum	strain=KCTC 23057	GCA_014652075.1	754436	754436	type	True	80.1258	591	1817	95	below_threshold
Photobacterium aphoticum	strain=DSM 25995	GCA_001029435.1	754436	754436	type	True	80.0901	585	1817	95	below_threshold
Photobacterium marinum	strain=AK15	GCA_000331515.1	1056511	1056511	type	True	79.8594	523	1817	95	below_threshold
Photobacterium aquae	strain=CGMCC 1.12159	GCA_001029445.1	1195763	1195763	type	True	79.8393	515	1817	95	below_threshold
Photobacterium alginatilyticum	strain=P03D4	GCA_009910675.1	1775171	1775171	type	True	79.5884	527	1817	95	below_threshold
Photobacterium proteolyticum	strain=13-12	GCA_001939735.1	1903952	1903952	type	True	79.4836	543	1817	95	below_threshold
Photobacterium galatheae	strain=DSM 100496	GCA_023653475.1	1654360	1654360	type	True	78.8916	414	1817	95	below_threshold
Vibrio furnissii	strain=PartQ-Vfurnissii-RM8376	GCA_022869905.1	29494	29494	type	True	78.0444	251	1817	95	below_threshold
Vibrio tarriae	strain=2521-89	GCA_002216685.1	2014742	2014742	type	True	78.0422	209	1817	95	below_threshold
Vibrio albus	strain=E4404	GCA_003144035.1	2200953	2200953	type	True	77.9246	185	1817	95	below_threshold
Vibrio vulnificus	strain=ATCC 27562	GCA_000299635.1	672	672	suspected-type	True	77.8295	161	1817	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:20:37,535] [INFO] DFAST Taxonomy check result was written to GCF_001029455.1_ASM102945v1_genomic.fna/tc_result.tsv
[2024-01-25 20:20:37,537] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:20:37,537] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:20:37,537] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf361927a-665b-46a6-83a7-0e297d59194b/dqc_reference/checkm_data
[2024-01-25 20:20:37,538] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:20:37,593] [INFO] Task started: CheckM
[2024-01-25 20:20:37,593] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001029455.1_ASM102945v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001029455.1_ASM102945v1_genomic.fna/checkm_input GCF_001029455.1_ASM102945v1_genomic.fna/checkm_result
[2024-01-25 20:21:18,409] [INFO] Task succeeded: CheckM
[2024-01-25 20:21:18,410] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:21:18,435] [INFO] ===== Completeness check finished =====
[2024-01-25 20:21:18,435] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:21:18,435] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001029455.1_ASM102945v1_genomic.fna/markers.fasta)
[2024-01-25 20:21:18,435] [INFO] Task started: Blastn
[2024-01-25 20:21:18,435] [INFO] Running command: blastn -query GCF_001029455.1_ASM102945v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf361927a-665b-46a6-83a7-0e297d59194b/dqc_reference/reference_markers_gtdb.fasta -out GCF_001029455.1_ASM102945v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:21:19,441] [INFO] Task succeeded: Blastn
[2024-01-25 20:21:19,444] [INFO] Selected 12 target genomes.
[2024-01-25 20:21:19,444] [INFO] Target genome list was writen to GCF_001029455.1_ASM102945v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:21:19,456] [INFO] Task started: fastANI
[2024-01-25 20:21:19,456] [INFO] Running command: fastANI --query /var/lib/cwl/stgefdb6798-0167-4b68-8fc3-078291c6c691/GCF_001029455.1_ASM102945v1_genomic.fna.gz --refList GCF_001029455.1_ASM102945v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001029455.1_ASM102945v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:21:32,694] [INFO] Task succeeded: fastANI
[2024-01-25 20:21:32,702] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:21:32,703] [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_003025595.1	s__Photobacterium ganghwense	99.9993	1812	1817	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	99.50	98.82	0.97	0.96	4	conclusive
GCF_003026455.1	s__Photobacterium rosenbergii	80.1845	567	1817	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	95.32	95.32	0.83	0.83	2	-
GCF_001029435.1	s__Photobacterium aphoticum	80.0796	586	1817	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	99.09	97.29	0.97	0.93	4	-
GCF_000940995.1	s__Photobacterium gaetbulicola	79.9159	620	1817	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	97.90	95.81	0.93	0.87	3	-
GCF_000331515.1	s__Photobacterium marinum	79.8493	524	1817	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	96.66	96.66	0.88	0.88	2	-
GCF_001029445.1	s__Photobacterium aquae	79.8471	515	1817	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003026495.1	s__Photobacterium sanctipauli	79.7958	539	1817	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009910675.1	s__Photobacterium alginatilyticum	79.5861	529	1817	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003025555.1	s__Photobacterium lutimaris	79.5447	575	1817	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001939735.1	s__Photobacterium proteolyticum	79.4794	543	1817	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018199995.1	s__Photobacterium sp018199995	78.9966	393	1817	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000425165.1	s__Photobacterium halotolerans	78.7225	428	1817	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	97.98	97.78	0.94	0.93	4	-
--------------------------------------------------------------------------------
[2024-01-25 20:21:32,704] [INFO] GTDB search result was written to GCF_001029455.1_ASM102945v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:21:32,704] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:21:32,707] [INFO] DFAST_QC result json was written to GCF_001029455.1_ASM102945v1_genomic.fna/dqc_result.json
[2024-01-25 20:21:32,708] [INFO] DFAST_QC completed!
[2024-01-25 20:21:32,708] [INFO] Total running time: 0h1m27s