[2024-01-25 18:45:05,536] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:45:05,537] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:45:05,538] [INFO] DQC Reference Directory: /var/lib/cwl/stg42abcebc-8d82-4823-80f1-40cc9ba3f425/dqc_reference
[2024-01-25 18:45:06,724] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:45:06,725] [INFO] Task started: Prodigal
[2024-01-25 18:45:06,725] [INFO] Running command: gunzip -c /var/lib/cwl/stg1392fa9b-cc78-4675-afe4-ab0b77b1bd44/GCF_014199495.1_ASM1419949v1_genomic.fna.gz | prodigal -d GCF_014199495.1_ASM1419949v1_genomic.fna/cds.fna -a GCF_014199495.1_ASM1419949v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:45:13,709] [INFO] Task succeeded: Prodigal
[2024-01-25 18:45:13,709] [INFO] Task started: HMMsearch
[2024-01-25 18:45:13,709] [INFO] Running command: hmmsearch --tblout GCF_014199495.1_ASM1419949v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg42abcebc-8d82-4823-80f1-40cc9ba3f425/dqc_reference/reference_markers.hmm GCF_014199495.1_ASM1419949v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:45:13,907] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:45:13,908] [INFO] Found 6/6 markers.
[2024-01-25 18:45:13,936] [INFO] Query marker FASTA was written to GCF_014199495.1_ASM1419949v1_genomic.fna/markers.fasta
[2024-01-25 18:45:13,936] [INFO] Task started: Blastn
[2024-01-25 18:45:13,936] [INFO] Running command: blastn -query GCF_014199495.1_ASM1419949v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg42abcebc-8d82-4823-80f1-40cc9ba3f425/dqc_reference/reference_markers.fasta -out GCF_014199495.1_ASM1419949v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:45:14,813] [INFO] Task succeeded: Blastn
[2024-01-25 18:45:14,816] [INFO] Selected 20 target genomes.
[2024-01-25 18:45:14,816] [INFO] Target genome list was writen to GCF_014199495.1_ASM1419949v1_genomic.fna/target_genomes.txt
[2024-01-25 18:45:14,833] [INFO] Task started: fastANI
[2024-01-25 18:45:14,834] [INFO] Running command: fastANI --query /var/lib/cwl/stg1392fa9b-cc78-4675-afe4-ab0b77b1bd44/GCF_014199495.1_ASM1419949v1_genomic.fna.gz --refList GCF_014199495.1_ASM1419949v1_genomic.fna/target_genomes.txt --output GCF_014199495.1_ASM1419949v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:45:30,768] [INFO] Task succeeded: fastANI
[2024-01-25 18:45:30,769] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg42abcebc-8d82-4823-80f1-40cc9ba3f425/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:45:30,769] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg42abcebc-8d82-4823-80f1-40cc9ba3f425/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:45:30,781] [INFO] Found 20 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 18:45:30,781] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:45:30,781] [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
Amphiplicatus metriothermophilus	strain=DSM 105738	GCA_014199495.1	1519374	1519374	type	True	100.0	1050	1050	95	conclusive
Amphiplicatus metriothermophilus	strain=CGMCC 1.12710	GCA_900199215.1	1519374	1519374	type	True	99.9995	1046	1050	95	conclusive
Marinicaulis flavus	strain=SY-3-19	GCA_002943565.1	2058213	2058213	type	True	77.6715	414	1050	95	below_threshold
Aquisalinus flavus	strain=CGMCC 1.12921	GCA_014640095.1	1526572	1526572	type	True	77.1791	190	1050	95	below_threshold
Aquisalinus flavus	strain=D11M-2	GCA_022559625.1	1526572	1526572	type	True	77.1311	181	1050	95	below_threshold
Parvularcula oceani	strain=JLT2013	GCA_000733125.1	1247963	1247963	type	True	77.0862	242	1050	95	below_threshold
Marinicauda salina	strain=WD6-1	GCA_003122085.1	2135793	2135793	type	True	76.9441	240	1050	95	below_threshold
Blastochloris tepida	strain=GI	GCA_003966715.1	2233851	2233851	type	True	76.752	188	1050	95	below_threshold
Pelagibius marinus	strain=NBU2595	GCA_014925385.1	2762760	2762760	type	True	76.3129	154	1050	95	below_threshold
Starkeya koreensis	strain=Jip08	GCA_023016525.1	266121	266121	type	True	76.2964	205	1050	95	below_threshold
Paracoccus pantotrophus	strain=DSM 2944	GCA_003633525.1	82367	82367	type	True	76.2793	149	1050	95	below_threshold
Methylobrevis albus	strain=L22	GCA_015904235.1	2793297	2793297	type	True	76.2508	254	1050	95	below_threshold
Methylobacterium variabile	strain=DSM 16961	GCA_001043975.1	298794	298794	type	True	76.1102	201	1050	95	below_threshold
Bradyrhizobium agreste	strain=CNPSo 4010	GCA_016031625.1	2751811	2751811	type	True	76.0953	191	1050	95	below_threshold
Methylobacterium currus	strain=PR1016A	GCA_003058325.1	2051553	2051553	type	True	75.9703	220	1050	95	below_threshold
Parvibaculum lavamentivorans	strain=DS-1	GCA_000017565.1	256618	256618	type	True	75.9693	121	1050	95	below_threshold
Oceanicella actignis	strain=DSM 22673	GCA_008124525.1	1189325	1189325	type	True	75.9291	255	1050	95	below_threshold
Methylorubrum aminovorans	strain=NBRC 15686	GCA_022179725.1	269069	269069	type	True	75.9005	174	1050	95	below_threshold
Methylobacterium isbiliense	strain=DSM 17168	GCA_022179325.1	315478	315478	type	True	75.8984	224	1050	95	below_threshold
Roseivivax isoporae	strain=LMG 25204	GCA_000521865.1	591206	591206	type	True	75.8782	172	1050	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:45:30,784] [INFO] DFAST Taxonomy check result was written to GCF_014199495.1_ASM1419949v1_genomic.fna/tc_result.tsv
[2024-01-25 18:45:30,785] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:45:30,785] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:45:30,785] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg42abcebc-8d82-4823-80f1-40cc9ba3f425/dqc_reference/checkm_data
[2024-01-25 18:45:30,786] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:45:30,820] [INFO] Task started: CheckM
[2024-01-25 18:45:30,820] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014199495.1_ASM1419949v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014199495.1_ASM1419949v1_genomic.fna/checkm_input GCF_014199495.1_ASM1419949v1_genomic.fna/checkm_result
[2024-01-25 18:45:54,447] [INFO] Task succeeded: CheckM
[2024-01-25 18:45:54,448] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:45:54,464] [INFO] ===== Completeness check finished =====
[2024-01-25 18:45:54,465] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:45:54,465] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014199495.1_ASM1419949v1_genomic.fna/markers.fasta)
[2024-01-25 18:45:54,465] [INFO] Task started: Blastn
[2024-01-25 18:45:54,465] [INFO] Running command: blastn -query GCF_014199495.1_ASM1419949v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg42abcebc-8d82-4823-80f1-40cc9ba3f425/dqc_reference/reference_markers_gtdb.fasta -out GCF_014199495.1_ASM1419949v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:45:56,208] [INFO] Task succeeded: Blastn
[2024-01-25 18:45:56,210] [INFO] Selected 14 target genomes.
[2024-01-25 18:45:56,210] [INFO] Target genome list was writen to GCF_014199495.1_ASM1419949v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:45:56,224] [INFO] Task started: fastANI
[2024-01-25 18:45:56,224] [INFO] Running command: fastANI --query /var/lib/cwl/stg1392fa9b-cc78-4675-afe4-ab0b77b1bd44/GCF_014199495.1_ASM1419949v1_genomic.fna.gz --refList GCF_014199495.1_ASM1419949v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014199495.1_ASM1419949v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:46:05,745] [INFO] Task succeeded: fastANI
[2024-01-25 18:46:05,754] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:46:05,755] [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_900199215.1	s__Amphiplicatus metriothermophilus	99.9995	1046	1050	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Amphiplicatus	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCA_016125425.1	s__Amphiplicatus sp016125425	77.774	371	1050	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Amphiplicatus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001657385.1	s__Marinicaulis sp001657385	77.7343	413	1050	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Marinicaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002943565.1	s__Marinicaulis flavus	77.6876	412	1050	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Marinicaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013389105.1	s__JACADZ01 sp013389105	77.6181	309	1050	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__JACADZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001767925.1	s__CV81 sp001767925	77.4813	285	1050	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__CV81	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902826095.1	s__CV81 sp902826095	77.2258	358	1050	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__CV81	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003506635.1	s__CV81 sp003506635	77.1747	269	1050	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__CV81	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002704915.1	s__Marinicaulis sp002704915	77.1722	308	1050	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Marinicaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000733125.1	s__Parvularcula oceani	77.1081	240	1050	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Parvularcula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008824185.1	s__Paracoccus pantotrophus	76.2583	153	1050	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.22	98.98	0.90	0.84	8	-
GCA_008933605.1	s__Albidovulum sp008933605	76.0997	124	1050	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Albidovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008124525.1	s__Oceanicella actignis	75.9478	252	1050	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceanicella	95.0	98.87	98.87	0.96	0.96	3	-
GCF_000521865.1	s__Roseivivax isoporae	75.8543	175	1050	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseivivax	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:46:05,757] [INFO] GTDB search result was written to GCF_014199495.1_ASM1419949v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:46:05,757] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:46:05,760] [INFO] DFAST_QC result json was written to GCF_014199495.1_ASM1419949v1_genomic.fna/dqc_result.json
[2024-01-25 18:46:05,760] [INFO] DFAST_QC completed!
[2024-01-25 18:46:05,760] [INFO] Total running time: 0h1m0s