[2024-01-25 18:10:50,406] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:10:50,408] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:10:50,408] [INFO] DQC Reference Directory: /var/lib/cwl/stg7cc2c0d2-ec20-4216-8333-e28c3fadb314/dqc_reference
[2024-01-25 18:10:51,534] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:10:51,538] [INFO] Task started: Prodigal
[2024-01-25 18:10:51,538] [INFO] Running command: gunzip -c /var/lib/cwl/stg70c5f1b1-b741-450a-8678-2c6cb5ea6555/GCF_030297095.1_ASM3029709v1_genomic.fna.gz | prodigal -d GCF_030297095.1_ASM3029709v1_genomic.fna/cds.fna -a GCF_030297095.1_ASM3029709v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:11:02,424] [INFO] Task succeeded: Prodigal
[2024-01-25 18:11:02,424] [INFO] Task started: HMMsearch
[2024-01-25 18:11:02,424] [INFO] Running command: hmmsearch --tblout GCF_030297095.1_ASM3029709v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7cc2c0d2-ec20-4216-8333-e28c3fadb314/dqc_reference/reference_markers.hmm GCF_030297095.1_ASM3029709v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:11:02,639] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:11:02,640] [INFO] Found 6/6 markers.
[2024-01-25 18:11:02,673] [INFO] Query marker FASTA was written to GCF_030297095.1_ASM3029709v1_genomic.fna/markers.fasta
[2024-01-25 18:11:02,674] [INFO] Task started: Blastn
[2024-01-25 18:11:02,674] [INFO] Running command: blastn -query GCF_030297095.1_ASM3029709v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7cc2c0d2-ec20-4216-8333-e28c3fadb314/dqc_reference/reference_markers.fasta -out GCF_030297095.1_ASM3029709v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:11:03,261] [INFO] Task succeeded: Blastn
[2024-01-25 18:11:03,267] [INFO] Selected 7 target genomes.
[2024-01-25 18:11:03,267] [INFO] Target genome list was writen to GCF_030297095.1_ASM3029709v1_genomic.fna/target_genomes.txt
[2024-01-25 18:11:03,289] [INFO] Task started: fastANI
[2024-01-25 18:11:03,289] [INFO] Running command: fastANI --query /var/lib/cwl/stg70c5f1b1-b741-450a-8678-2c6cb5ea6555/GCF_030297095.1_ASM3029709v1_genomic.fna.gz --refList GCF_030297095.1_ASM3029709v1_genomic.fna/target_genomes.txt --output GCF_030297095.1_ASM3029709v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:11:09,655] [INFO] Task succeeded: fastANI
[2024-01-25 18:11:09,655] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7cc2c0d2-ec20-4216-8333-e28c3fadb314/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:11:09,656] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7cc2c0d2-ec20-4216-8333-e28c3fadb314/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:11:09,662] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:11:09,662] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:11:09,663] [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
Geobacter sulfurreducens	strain=PCA	GCA_000007985.2	35554	35554	type	True	95.6153	1144	1339	95	conclusive
Geobacter soli	strain=GSS01	GCA_000816575.1	1510391	1510391	type	True	93.2497	1054	1339	95	below_threshold
Geobacter hydrogenophilus	strain=DSM 13691	GCA_018501225.1	40983	40983	type	True	80.8857	572	1339	95	below_threshold
Geobacter grbiciae	strain=DSM 13689	GCA_018531165.1	155042	155042	type	True	80.7238	574	1339	95	below_threshold
Geobacter metallireducens	strain=GS-15	GCA_000012925.1	28232	28232	type	True	80.5999	565	1339	95	below_threshold
Geobacter pickeringii	strain=G13	GCA_000817955.1	345632	345632	type	True	80.5843	562	1339	95	below_threshold
Geobacter benzoatilyticus	strain=Jerry-YX	GCA_017338855.1	2815309	2815309	type	True	80.549	478	1339	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:11:09,664] [INFO] DFAST Taxonomy check result was written to GCF_030297095.1_ASM3029709v1_genomic.fna/tc_result.tsv
[2024-01-25 18:11:09,664] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:11:09,665] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:11:09,665] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7cc2c0d2-ec20-4216-8333-e28c3fadb314/dqc_reference/checkm_data
[2024-01-25 18:11:09,666] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:11:09,709] [INFO] Task started: CheckM
[2024-01-25 18:11:09,709] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030297095.1_ASM3029709v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030297095.1_ASM3029709v1_genomic.fna/checkm_input GCF_030297095.1_ASM3029709v1_genomic.fna/checkm_result
[2024-01-25 18:11:43,974] [INFO] Task succeeded: CheckM
[2024-01-25 18:11:43,975] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:11:43,997] [INFO] ===== Completeness check finished =====
[2024-01-25 18:11:43,997] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:11:43,997] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030297095.1_ASM3029709v1_genomic.fna/markers.fasta)
[2024-01-25 18:11:43,997] [INFO] Task started: Blastn
[2024-01-25 18:11:43,997] [INFO] Running command: blastn -query GCF_030297095.1_ASM3029709v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7cc2c0d2-ec20-4216-8333-e28c3fadb314/dqc_reference/reference_markers_gtdb.fasta -out GCF_030297095.1_ASM3029709v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:11:44,971] [INFO] Task succeeded: Blastn
[2024-01-25 18:11:44,975] [INFO] Selected 10 target genomes.
[2024-01-25 18:11:44,975] [INFO] Target genome list was writen to GCF_030297095.1_ASM3029709v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:11:44,995] [INFO] Task started: fastANI
[2024-01-25 18:11:44,995] [INFO] Running command: fastANI --query /var/lib/cwl/stg70c5f1b1-b741-450a-8678-2c6cb5ea6555/GCF_030297095.1_ASM3029709v1_genomic.fna.gz --refList GCF_030297095.1_ASM3029709v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030297095.1_ASM3029709v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:11:53,377] [INFO] Task succeeded: fastANI
[2024-01-25 18:11:53,385] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:11:53,385] [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_000007985.2	s__Geobacter sulfurreducens	95.6323	1144	1339	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Geobacteraceae;g__Geobacter	95.0	98.43	95.82	0.96	0.94	8	conclusive
GCA_001628815.1	s__Geobacter anodireducens	93.2657	1057	1339	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Geobacteraceae;g__Geobacter	95.0	99.35	99.24	0.91	0.90	4	-
GCA_011046855.1	s__Geobacter metallireducens_A	81.3961	597	1339	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Geobacteraceae;g__Geobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018501225.1	s__Geobacter hydrogenophilus	80.8859	572	1339	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Geobacteraceae;g__Geobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000817955.1	s__Geobacter pickeringii	80.6078	560	1339	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Geobacteraceae;g__Geobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000012925.1	s__Geobacter metallireducens	80.5844	564	1339	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Geobacteraceae;g__Geobacter	95.0	98.29	96.59	0.93	0.85	3	-
GCF_017338855.1	s__Geobacter sp017338855	80.5489	478	1339	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Geobacteraceae;g__Geobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003712145.1	s__Geobacter sp003712145	80.4585	549	1339	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Geobacteraceae;g__Geobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905339345.1	s__Geobacter sp905339345	80.2432	351	1339	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Geobacteraceae;g__Geobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:11:53,387] [INFO] GTDB search result was written to GCF_030297095.1_ASM3029709v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:11:53,387] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:11:53,390] [INFO] DFAST_QC result json was written to GCF_030297095.1_ASM3029709v1_genomic.fna/dqc_result.json
[2024-01-25 18:11:53,390] [INFO] DFAST_QC completed!
[2024-01-25 18:11:53,390] [INFO] Total running time: 0h1m3s