[2024-01-24 10:57:38,869] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:57:38,871] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:57:38,871] [INFO] DQC Reference Directory: /var/lib/cwl/stg6c71cb1b-0737-4a79-bf08-1f3f5c6a23a6/dqc_reference
[2024-01-24 10:57:40,256] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:57:40,257] [INFO] Task started: Prodigal
[2024-01-24 10:57:40,258] [INFO] Running command: gunzip -c /var/lib/cwl/stgd98c1286-ca50-4273-a92e-785fa39d7759/GCF_016458305.1_ASM1645830v1_genomic.fna.gz | prodigal -d GCF_016458305.1_ASM1645830v1_genomic.fna/cds.fna -a GCF_016458305.1_ASM1645830v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:57:54,935] [INFO] Task succeeded: Prodigal
[2024-01-24 10:57:54,935] [INFO] Task started: HMMsearch
[2024-01-24 10:57:54,936] [INFO] Running command: hmmsearch --tblout GCF_016458305.1_ASM1645830v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6c71cb1b-0737-4a79-bf08-1f3f5c6a23a6/dqc_reference/reference_markers.hmm GCF_016458305.1_ASM1645830v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:57:55,237] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:57:55,239] [INFO] Found 6/6 markers.
[2024-01-24 10:57:55,283] [INFO] Query marker FASTA was written to GCF_016458305.1_ASM1645830v1_genomic.fna/markers.fasta
[2024-01-24 10:57:55,283] [INFO] Task started: Blastn
[2024-01-24 10:57:55,283] [INFO] Running command: blastn -query GCF_016458305.1_ASM1645830v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6c71cb1b-0737-4a79-bf08-1f3f5c6a23a6/dqc_reference/reference_markers.fasta -out GCF_016458305.1_ASM1645830v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:57:56,002] [INFO] Task succeeded: Blastn
[2024-01-24 10:57:56,006] [INFO] Selected 5 target genomes.
[2024-01-24 10:57:56,007] [INFO] Target genome list was writen to GCF_016458305.1_ASM1645830v1_genomic.fna/target_genomes.txt
[2024-01-24 10:57:56,010] [INFO] Task started: fastANI
[2024-01-24 10:57:56,010] [INFO] Running command: fastANI --query /var/lib/cwl/stgd98c1286-ca50-4273-a92e-785fa39d7759/GCF_016458305.1_ASM1645830v1_genomic.fna.gz --refList GCF_016458305.1_ASM1645830v1_genomic.fna/target_genomes.txt --output GCF_016458305.1_ASM1645830v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:58:04,599] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:04,600] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6c71cb1b-0737-4a79-bf08-1f3f5c6a23a6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:58:04,600] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6c71cb1b-0737-4a79-bf08-1f3f5c6a23a6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:58:04,609] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:58:04,609] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:58:04,609] [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
Geomonas anaerohicana	strain=Red421	GCA_016458305.1	2798583	2798583	type	True	100.0	1670	1671	95	conclusive
Geomonas paludis	strain=Red736	GCA_014193585.1	2740185	2740185	type	True	92.239	1418	1671	95	below_threshold
Geomonas azotofigens	strain=Red51	GCA_018919395.1	2843196	2843196	type	True	89.1857	1370	1671	95	below_threshold
Geomonas agri	strain=RG53	GCA_020179605.1	2873702	2873702	type	True	89.1456	1271	1671	95	below_threshold
Geomonas propionica	strain=Red259	GCA_016458235.1	2798582	2798582	type	True	88.6227	1326	1671	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:58:04,611] [INFO] DFAST Taxonomy check result was written to GCF_016458305.1_ASM1645830v1_genomic.fna/tc_result.tsv
[2024-01-24 10:58:04,612] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:58:04,612] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:58:04,612] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6c71cb1b-0737-4a79-bf08-1f3f5c6a23a6/dqc_reference/checkm_data
[2024-01-24 10:58:04,613] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:58:04,663] [INFO] Task started: CheckM
[2024-01-24 10:58:04,663] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016458305.1_ASM1645830v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016458305.1_ASM1645830v1_genomic.fna/checkm_input GCF_016458305.1_ASM1645830v1_genomic.fna/checkm_result
[2024-01-24 10:58:47,814] [INFO] Task succeeded: CheckM
[2024-01-24 10:58:47,815] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:58:47,830] [INFO] ===== Completeness check finished =====
[2024-01-24 10:58:47,830] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:58:47,830] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016458305.1_ASM1645830v1_genomic.fna/markers.fasta)
[2024-01-24 10:58:47,831] [INFO] Task started: Blastn
[2024-01-24 10:58:47,831] [INFO] Running command: blastn -query GCF_016458305.1_ASM1645830v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6c71cb1b-0737-4a79-bf08-1f3f5c6a23a6/dqc_reference/reference_markers_gtdb.fasta -out GCF_016458305.1_ASM1645830v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:48,887] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:48,891] [INFO] Selected 7 target genomes.
[2024-01-24 10:58:48,891] [INFO] Target genome list was writen to GCF_016458305.1_ASM1645830v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:58:48,897] [INFO] Task started: fastANI
[2024-01-24 10:58:48,897] [INFO] Running command: fastANI --query /var/lib/cwl/stgd98c1286-ca50-4273-a92e-785fa39d7759/GCF_016458305.1_ASM1645830v1_genomic.fna.gz --refList GCF_016458305.1_ASM1645830v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016458305.1_ASM1645830v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:58:59,958] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:59,970] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:58:59,970] [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_016458305.1	s__Geomonas anaerohicana	100.0	1670	1671	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Geobacteraceae;g__Geomonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014193585.1	s__Geomonas paludis	92.239	1418	1671	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Geobacteraceae;g__Geomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018919395.1	s__Geomonas sp018919395	89.1946	1369	1671	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Geobacteraceae;g__Geomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018986915.1	s__Geomonas sp018986915	89.0855	1344	1671	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Geobacteraceae;g__Geomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016458235.1	s__Geomonas propionica	88.6046	1328	1671	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Geobacteraceae;g__Geomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018986935.1	s__Geomonas sp018986935	88.1704	1289	1671	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Geobacteraceae;g__Geomonas	95.0	99.24	99.10	0.94	0.94	3	-
GCF_019203205.1	s__Geomonas sp019203205	88.1396	1334	1671	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Geobacteraceae;g__Geomonas	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 10:58:59,972] [INFO] GTDB search result was written to GCF_016458305.1_ASM1645830v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:58:59,972] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:58:59,977] [INFO] DFAST_QC result json was written to GCF_016458305.1_ASM1645830v1_genomic.fna/dqc_result.json
[2024-01-24 10:58:59,977] [INFO] DFAST_QC completed!
[2024-01-24 10:58:59,977] [INFO] Total running time: 0h1m21s