[2024-01-24 14:19:01,309] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:19:01,312] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:19:01,312] [INFO] DQC Reference Directory: /var/lib/cwl/stga803719c-849a-4387-badd-c8cbf4d44710/dqc_reference
[2024-01-24 14:19:02,741] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:19:02,742] [INFO] Task started: Prodigal
[2024-01-24 14:19:02,742] [INFO] Running command: gunzip -c /var/lib/cwl/stg7cb4e3d0-91b6-4baa-9501-999f8fe87818/GCF_008802355.1_ASM880235v1_genomic.fna.gz | prodigal -d GCF_008802355.1_ASM880235v1_genomic.fna/cds.fna -a GCF_008802355.1_ASM880235v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:19:14,539] [INFO] Task succeeded: Prodigal
[2024-01-24 14:19:14,539] [INFO] Task started: HMMsearch
[2024-01-24 14:19:14,539] [INFO] Running command: hmmsearch --tblout GCF_008802355.1_ASM880235v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga803719c-849a-4387-badd-c8cbf4d44710/dqc_reference/reference_markers.hmm GCF_008802355.1_ASM880235v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:19:14,837] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:19:14,838] [INFO] Found 6/6 markers.
[2024-01-24 14:19:14,870] [INFO] Query marker FASTA was written to GCF_008802355.1_ASM880235v1_genomic.fna/markers.fasta
[2024-01-24 14:19:14,871] [INFO] Task started: Blastn
[2024-01-24 14:19:14,871] [INFO] Running command: blastn -query GCF_008802355.1_ASM880235v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga803719c-849a-4387-badd-c8cbf4d44710/dqc_reference/reference_markers.fasta -out GCF_008802355.1_ASM880235v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:19:15,703] [INFO] Task succeeded: Blastn
[2024-01-24 14:19:15,706] [INFO] Selected 11 target genomes.
[2024-01-24 14:19:15,707] [INFO] Target genome list was writen to GCF_008802355.1_ASM880235v1_genomic.fna/target_genomes.txt
[2024-01-24 14:19:15,711] [INFO] Task started: fastANI
[2024-01-24 14:19:15,712] [INFO] Running command: fastANI --query /var/lib/cwl/stg7cb4e3d0-91b6-4baa-9501-999f8fe87818/GCF_008802355.1_ASM880235v1_genomic.fna.gz --refList GCF_008802355.1_ASM880235v1_genomic.fna/target_genomes.txt --output GCF_008802355.1_ASM880235v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:19:25,306] [INFO] Task succeeded: fastANI
[2024-01-24 14:19:25,307] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga803719c-849a-4387-badd-c8cbf4d44710/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:19:25,307] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga803719c-849a-4387-badd-c8cbf4d44710/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:19:25,317] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:19:25,317] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 14:19:25,317] [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
Oryzomonas sagensis	strain=Red100	GCA_008802355.1	2603857	2603857	type	True	100.0	1198	1198	95	inconclusive
Oryzomonas rubra	strain=Red88	GCA_008369015.1	2509454	2509454	type	True	95.1331	1029	1198	95	inconclusive
Oryzomonas japonica	strain=Red96	GCA_008802365.1	2603858	2603858	type	True	94.6167	1047	1198	95	below_threshold
Pelobacter propionicus	strain=DSM 2379	GCA_000015045.1	29543	29543	type	True	79.0957	382	1198	95	below_threshold
Geobacter argillaceus	strain=ATCC BAA-1139	GCA_007830735.1	345631	345631	type	True	78.2575	288	1198	95	below_threshold
Geomonas silvestris	strain=Red330	GCA_014193515.1	2740184	2740184	type	True	77.5659	309	1198	95	below_threshold
Citrifermentans pelophilum	strain=DSM 12255	GCA_018476885.1	60036	60036	type	True	77.0641	159	1198	95	below_threshold
Geobacter chapellei	strain=DSM 13688	GCA_018531195.1	44671	44671	type	True	77.0539	199	1198	95	below_threshold
Rubrivivax gelatinosus	strain=DSM 1709	GCA_016583525.1	28068	28068	suspected-type	True	76.2668	53	1198	95	below_threshold
Rubrivivax gelatinosus	strain=DSM 1709	GCA_004340905.1	28068	28068	suspected-type	True	76.1994	52	1198	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:19:25,319] [INFO] DFAST Taxonomy check result was written to GCF_008802355.1_ASM880235v1_genomic.fna/tc_result.tsv
[2024-01-24 14:19:25,319] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:19:25,320] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:19:25,320] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga803719c-849a-4387-badd-c8cbf4d44710/dqc_reference/checkm_data
[2024-01-24 14:19:25,321] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:19:25,358] [INFO] Task started: CheckM
[2024-01-24 14:19:25,359] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008802355.1_ASM880235v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008802355.1_ASM880235v1_genomic.fna/checkm_input GCF_008802355.1_ASM880235v1_genomic.fna/checkm_result
[2024-01-24 14:20:02,413] [INFO] Task succeeded: CheckM
[2024-01-24 14:20:02,415] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:20:02,434] [INFO] ===== Completeness check finished =====
[2024-01-24 14:20:02,434] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:20:02,435] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008802355.1_ASM880235v1_genomic.fna/markers.fasta)
[2024-01-24 14:20:02,435] [INFO] Task started: Blastn
[2024-01-24 14:20:02,435] [INFO] Running command: blastn -query GCF_008802355.1_ASM880235v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga803719c-849a-4387-badd-c8cbf4d44710/dqc_reference/reference_markers_gtdb.fasta -out GCF_008802355.1_ASM880235v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:20:03,759] [INFO] Task succeeded: Blastn
[2024-01-24 14:20:03,766] [INFO] Selected 11 target genomes.
[2024-01-24 14:20:03,767] [INFO] Target genome list was writen to GCF_008802355.1_ASM880235v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:20:03,797] [INFO] Task started: fastANI
[2024-01-24 14:20:03,797] [INFO] Running command: fastANI --query /var/lib/cwl/stg7cb4e3d0-91b6-4baa-9501-999f8fe87818/GCF_008802355.1_ASM880235v1_genomic.fna.gz --refList GCF_008802355.1_ASM880235v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008802355.1_ASM880235v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:20:14,383] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:14,399] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:20:14,399] [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_008802355.1	s__Oryzomonas sagensis	100.0	1198	1198	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Pseudopelobacteraceae;g__Oryzomonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_008802365.1	s__Oryzomonas japonica	94.6167	1047	1198	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Pseudopelobacteraceae;g__Oryzomonas	95.0	96.07	96.07	0.87	0.87	2	-
GCF_008330225.1	s__Oryzomonas sp008330225	89.3446	986	1198	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Pseudopelobacteraceae;g__Oryzomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003151775.1	s__Oryzomonas sp003151775	85.199	567	1198	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Pseudopelobacteraceae;g__Oryzomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016182975.1	s__JACPFJ01 sp016182975	80.5879	368	1198	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Pseudopelobacteraceae;g__JACPFJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015688915.1	s__JACPFJ01 sp015688915	80.1147	438	1198	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Pseudopelobacteraceae;g__JACPFJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002298925.1	s__Pelotalea sp002298925	79.1287	388	1198	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Pseudopelobacteraceae;g__Pelotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000015045.1	s__Pseudopelobacter propionicus	79.1012	381	1198	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Pseudopelobacteraceae;g__Pseudopelobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016650295.1	s__CAIPTY01 sp016650295	78.8213	376	1198	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Pseudopelobacteraceae;g__CAIPTY01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016865365.1	s__Pelotalea sp012556225	78.7831	436	1198	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Pseudopelobacteraceae;g__Pelotalea	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:20:14,401] [INFO] GTDB search result was written to GCF_008802355.1_ASM880235v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:20:14,401] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:20:14,404] [INFO] DFAST_QC result json was written to GCF_008802355.1_ASM880235v1_genomic.fna/dqc_result.json
[2024-01-24 14:20:14,405] [INFO] DFAST_QC completed!
[2024-01-24 14:20:14,405] [INFO] Total running time: 0h1m13s