[2024-01-24 11:26:13,384] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:13,387] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:13,387] [INFO] DQC Reference Directory: /var/lib/cwl/stg867db95a-69d5-455b-a520-9131167059a8/dqc_reference
[2024-01-24 11:26:14,625] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:14,626] [INFO] Task started: Prodigal
[2024-01-24 11:26:14,626] [INFO] Running command: gunzip -c /var/lib/cwl/stg2667eca8-d572-4f38-a92c-980d083b0f49/GCF_018531165.1_ASM1853116v1_genomic.fna.gz | prodigal -d GCF_018531165.1_ASM1853116v1_genomic.fna/cds.fna -a GCF_018531165.1_ASM1853116v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:26:27,113] [INFO] Task succeeded: Prodigal
[2024-01-24 11:26:27,113] [INFO] Task started: HMMsearch
[2024-01-24 11:26:27,113] [INFO] Running command: hmmsearch --tblout GCF_018531165.1_ASM1853116v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg867db95a-69d5-455b-a520-9131167059a8/dqc_reference/reference_markers.hmm GCF_018531165.1_ASM1853116v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:26:27,457] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:26:27,458] [INFO] Found 6/6 markers.
[2024-01-24 11:26:27,506] [INFO] Query marker FASTA was written to GCF_018531165.1_ASM1853116v1_genomic.fna/markers.fasta
[2024-01-24 11:26:27,506] [INFO] Task started: Blastn
[2024-01-24 11:26:27,506] [INFO] Running command: blastn -query GCF_018531165.1_ASM1853116v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg867db95a-69d5-455b-a520-9131167059a8/dqc_reference/reference_markers.fasta -out GCF_018531165.1_ASM1853116v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:26:28,174] [INFO] Task succeeded: Blastn
[2024-01-24 11:26:28,178] [INFO] Selected 13 target genomes.
[2024-01-24 11:26:28,178] [INFO] Target genome list was writen to GCF_018531165.1_ASM1853116v1_genomic.fna/target_genomes.txt
[2024-01-24 11:26:28,181] [INFO] Task started: fastANI
[2024-01-24 11:26:28,181] [INFO] Running command: fastANI --query /var/lib/cwl/stg2667eca8-d572-4f38-a92c-980d083b0f49/GCF_018531165.1_ASM1853116v1_genomic.fna.gz --refList GCF_018531165.1_ASM1853116v1_genomic.fna/target_genomes.txt --output GCF_018531165.1_ASM1853116v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:26:38,278] [INFO] Task succeeded: fastANI
[2024-01-24 11:26:38,278] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg867db95a-69d5-455b-a520-9131167059a8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:26:38,279] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg867db95a-69d5-455b-a520-9131167059a8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:26:38,287] [INFO] Found 8 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:26:38,287] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 11:26:38,288] [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 grbiciae	strain=DSM 13689	GCA_018531165.1	155042	155042	type	True	100.0	1357	1359	95	inconclusive
Geobacter metallireducens	strain=GS-15	GCA_000012925.1	28232	28232	type	True	96.4786	1159	1359	95	inconclusive
Geobacter hydrogenophilus	strain=DSM 13691	GCA_018501225.1	40983	40983	type	True	92.216	1022	1359	95	below_threshold
Geobacter benzoatilyticus	strain=Jerry-YX	GCA_017338855.1	2815309	2815309	type	True	83.2489	756	1359	95	below_threshold
Geobacter pickeringii	strain=G13	GCA_000817955.1	345632	345632	type	True	82.0767	656	1359	95	below_threshold
Geobacter sulfurreducens	strain=PCA	GCA_000007985.2	35554	35554	type	True	80.3921	559	1359	95	below_threshold
Geobacter argillaceus	strain=ATCC BAA-1139	GCA_007830735.1	345631	345631	type	True	78.7903	373	1359	95	below_threshold
Geoalkalibacter halelectricus	strain=SAP-1	GCA_025263685.1	2847045	2847045	type	True	76.9098	98	1359	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:26:38,292] [INFO] DFAST Taxonomy check result was written to GCF_018531165.1_ASM1853116v1_genomic.fna/tc_result.tsv
[2024-01-24 11:26:38,293] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:26:38,293] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:26:38,293] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg867db95a-69d5-455b-a520-9131167059a8/dqc_reference/checkm_data
[2024-01-24 11:26:38,295] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:26:38,355] [INFO] Task started: CheckM
[2024-01-24 11:26:38,356] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018531165.1_ASM1853116v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018531165.1_ASM1853116v1_genomic.fna/checkm_input GCF_018531165.1_ASM1853116v1_genomic.fna/checkm_result
[2024-01-24 11:27:16,978] [INFO] Task succeeded: CheckM
[2024-01-24 11:27:16,979] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 97.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:27:17,002] [INFO] ===== Completeness check finished =====
[2024-01-24 11:27:17,002] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:27:17,003] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018531165.1_ASM1853116v1_genomic.fna/markers.fasta)
[2024-01-24 11:27:17,003] [INFO] Task started: Blastn
[2024-01-24 11:27:17,003] [INFO] Running command: blastn -query GCF_018531165.1_ASM1853116v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg867db95a-69d5-455b-a520-9131167059a8/dqc_reference/reference_markers_gtdb.fasta -out GCF_018531165.1_ASM1853116v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:17,894] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:17,898] [INFO] Selected 9 target genomes.
[2024-01-24 11:27:17,898] [INFO] Target genome list was writen to GCF_018531165.1_ASM1853116v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:27:17,905] [INFO] Task started: fastANI
[2024-01-24 11:27:17,906] [INFO] Running command: fastANI --query /var/lib/cwl/stg2667eca8-d572-4f38-a92c-980d083b0f49/GCF_018531165.1_ASM1853116v1_genomic.fna.gz --refList GCF_018531165.1_ASM1853116v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018531165.1_ASM1853116v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:27:25,508] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:25,519] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:27:25,520] [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_000012925.1	s__Geobacter metallireducens	96.4549	1160	1359	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Geobacteraceae;g__Geobacter	95.0	98.29	96.59	0.93	0.85	3	conclusive
GCF_018501225.1	s__Geobacter hydrogenophilus	92.216	1022	1359	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Geobacteraceae;g__Geobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011046855.1	s__Geobacter metallireducens_A	85.8311	797	1359	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	85.163	540	1359	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Geobacteraceae;g__Geobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017338855.1	s__Geobacter sp017338855	83.2603	755	1359	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Geobacteraceae;g__Geobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001628815.1	s__Geobacter anodireducens	80.5752	575	1359	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Geobacteraceae;g__Geobacter	95.0	99.35	99.24	0.91	0.90	4	-
GCF_000007985.2	s__Geobacter sulfurreducens	80.4064	558	1359	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Geobacteraceae;g__Geobacter	95.0	98.43	95.82	0.96	0.94	8	-
GCF_007830735.1	s__Geomobilibacter argillaceus	78.7965	373	1359	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Geobacteraceae;g__Geomobilibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:27:25,522] [INFO] GTDB search result was written to GCF_018531165.1_ASM1853116v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:27:25,522] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:27:25,526] [INFO] DFAST_QC result json was written to GCF_018531165.1_ASM1853116v1_genomic.fna/dqc_result.json
[2024-01-24 11:27:25,526] [INFO] DFAST_QC completed!
[2024-01-24 11:27:25,526] [INFO] Total running time: 0h1m12s