[2024-01-24 13:17:13,921] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:13,922] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:13,923] [INFO] DQC Reference Directory: /var/lib/cwl/stg135165d2-302d-45a5-9838-5edf14e39de4/dqc_reference
[2024-01-24 13:17:15,261] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:15,262] [INFO] Task started: Prodigal
[2024-01-24 13:17:15,262] [INFO] Running command: gunzip -c /var/lib/cwl/stg7ee1589c-c640-452e-81fa-2a80e7be9b83/GCF_007830735.1_ASM783073v1_genomic.fna.gz | prodigal -d GCF_007830735.1_ASM783073v1_genomic.fna/cds.fna -a GCF_007830735.1_ASM783073v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:17:27,944] [INFO] Task succeeded: Prodigal
[2024-01-24 13:17:27,945] [INFO] Task started: HMMsearch
[2024-01-24 13:17:27,945] [INFO] Running command: hmmsearch --tblout GCF_007830735.1_ASM783073v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg135165d2-302d-45a5-9838-5edf14e39de4/dqc_reference/reference_markers.hmm GCF_007830735.1_ASM783073v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:17:28,255] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:17:28,257] [INFO] Found 6/6 markers.
[2024-01-24 13:17:28,299] [INFO] Query marker FASTA was written to GCF_007830735.1_ASM783073v1_genomic.fna/markers.fasta
[2024-01-24 13:17:28,300] [INFO] Task started: Blastn
[2024-01-24 13:17:28,300] [INFO] Running command: blastn -query GCF_007830735.1_ASM783073v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg135165d2-302d-45a5-9838-5edf14e39de4/dqc_reference/reference_markers.fasta -out GCF_007830735.1_ASM783073v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:29,015] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:29,019] [INFO] Selected 14 target genomes.
[2024-01-24 13:17:29,020] [INFO] Target genome list was writen to GCF_007830735.1_ASM783073v1_genomic.fna/target_genomes.txt
[2024-01-24 13:17:29,028] [INFO] Task started: fastANI
[2024-01-24 13:17:29,028] [INFO] Running command: fastANI --query /var/lib/cwl/stg7ee1589c-c640-452e-81fa-2a80e7be9b83/GCF_007830735.1_ASM783073v1_genomic.fna.gz --refList GCF_007830735.1_ASM783073v1_genomic.fna/target_genomes.txt --output GCF_007830735.1_ASM783073v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:17:40,199] [INFO] Task succeeded: fastANI
[2024-01-24 13:17:40,200] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg135165d2-302d-45a5-9838-5edf14e39de4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:17:40,201] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg135165d2-302d-45a5-9838-5edf14e39de4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:17:40,219] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:17:40,219] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:17:40,220] [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 argillaceus	strain=ATCC BAA-1139	GCA_007830735.1	345631	345631	type	True	100.0	1419	1423	95	conclusive
Geobacter pickeringii	strain=G13	GCA_000817955.1	345632	345632	type	True	78.9863	367	1423	95	below_threshold
Geobacter luticola	strain=JCM 17780	GCA_018476905.1	1114878	1114878	type	True	78.7502	355	1423	95	below_threshold
Geobacter hydrogenophilus	strain=DSM 13691	GCA_018501225.1	40983	40983	type	True	78.6413	381	1423	95	below_threshold
Geobacter grbiciae	strain=DSM 13689	GCA_018531165.1	155042	155042	type	True	78.6254	395	1423	95	below_threshold
Geobacter metallireducens	strain=GS-15	GCA_000012925.1	28232	28232	type	True	78.5936	374	1423	95	below_threshold
Geobacter benzoatilyticus	strain=Jerry-YX	GCA_017338855.1	2815309	2815309	type	True	78.5682	268	1423	95	below_threshold
Oryzomonas sagensis	strain=Red100	GCA_008802355.1	2603857	2603857	type	True	78.4318	273	1423	95	below_threshold
Geobacter soli	strain=GSS01	GCA_000816575.1	1510391	1510391	type	True	78.2215	318	1423	95	below_threshold
Geobacter sulfurreducens	strain=PCA	GCA_000007985.2	35554	35554	type	True	77.888	305	1423	95	below_threshold
Geomonas anaerohicana	strain=Red421	GCA_016458305.1	2798583	2798583	type	True	77.8536	326	1423	95	below_threshold
Geomonas azotofigens	strain=Red51	GCA_018919395.1	2843196	2843196	type	True	77.7421	331	1423	95	below_threshold
Geomonas agri	strain=RG53	GCA_020179605.1	2873702	2873702	type	True	77.6576	297	1423	95	below_threshold
Geomonas edaphica	strain=Red53	GCA_004917075.1	2570226	2570226	type	True	77.4227	259	1423	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:17:40,221] [INFO] DFAST Taxonomy check result was written to GCF_007830735.1_ASM783073v1_genomic.fna/tc_result.tsv
[2024-01-24 13:17:40,222] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:17:40,222] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:17:40,222] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg135165d2-302d-45a5-9838-5edf14e39de4/dqc_reference/checkm_data
[2024-01-24 13:17:40,224] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:17:40,265] [INFO] Task started: CheckM
[2024-01-24 13:17:40,265] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007830735.1_ASM783073v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007830735.1_ASM783073v1_genomic.fna/checkm_input GCF_007830735.1_ASM783073v1_genomic.fna/checkm_result
[2024-01-24 13:18:20,913] [INFO] Task succeeded: CheckM
[2024-01-24 13:18:20,915] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:18:20,935] [INFO] ===== Completeness check finished =====
[2024-01-24 13:18:20,936] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:18:20,936] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007830735.1_ASM783073v1_genomic.fna/markers.fasta)
[2024-01-24 13:18:20,936] [INFO] Task started: Blastn
[2024-01-24 13:18:20,936] [INFO] Running command: blastn -query GCF_007830735.1_ASM783073v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg135165d2-302d-45a5-9838-5edf14e39de4/dqc_reference/reference_markers_gtdb.fasta -out GCF_007830735.1_ASM783073v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:21,928] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:21,933] [INFO] Selected 23 target genomes.
[2024-01-24 13:18:21,934] [INFO] Target genome list was writen to GCF_007830735.1_ASM783073v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:18:22,020] [INFO] Task started: fastANI
[2024-01-24 13:18:22,021] [INFO] Running command: fastANI --query /var/lib/cwl/stg7ee1589c-c640-452e-81fa-2a80e7be9b83/GCF_007830735.1_ASM783073v1_genomic.fna.gz --refList GCF_007830735.1_ASM783073v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007830735.1_ASM783073v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:18:37,987] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:38,008] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:18:38,008] [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_007830735.1	s__Geomobilibacter argillaceus	100.0	1419	1423	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Geobacteraceae;g__Geomobilibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000817955.1	s__Geobacter pickeringii	78.9815	368	1423	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	78.7845	367	1423	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Geobacteraceae;g__Geobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009684525.1	s__Geoanaerobacter sp009684525	78.7179	344	1423	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Geobacteraceae;g__Geoanaerobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011362645.1	s__DSSF01 sp011362645	78.6638	330	1423	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Geobacteraceae;g__DSSF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003712145.1	s__Geobacter sp003712145	78.6585	340	1423	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	78.6534	380	1423	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	78.559	268	1423	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Geobacteraceae;g__Geobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008802355.1	s__Oryzomonas sagensis	78.4531	271	1423	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Pseudopelobacteraceae;g__Oryzomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905339345.1	s__Geobacter sp905339345	78.4487	228	1423	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	78.2051	315	1423	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Geobacteraceae;g__Geobacter	95.0	99.35	99.24	0.91	0.90	4	-
GCA_003574885.1	s__Geomobilimonas sp003574885	78.0582	295	1423	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Geobacteraceae;g__Geomobilimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000007985.2	s__Geobacter sulfurreducens	77.8996	301	1423	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Geobacteraceae;g__Geobacter	95.0	98.43	95.82	0.96	0.94	8	-
GCF_016458305.1	s__Geomonas anaerohicana	77.8542	327	1423	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	77.7544	327	1423	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Geobacteraceae;g__Geomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019203205.1	s__Geomonas sp019203205	77.7544	330	1423	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Geobacteraceae;g__Geomonas	95.0	99.99	99.99	1.00	1.00	2	-
GCA_903857795.1	s__CAIOGM01 sp903857795	77.7004	267	1423	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__CAIOGM01;g__CAIOGM01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004917075.1	s__Geomonas edaphica	77.4163	258	1423	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Geobacteraceae;g__Geomonas	95.0	96.10	96.10	0.87	0.87	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:18:38,010] [INFO] GTDB search result was written to GCF_007830735.1_ASM783073v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:18:38,011] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:18:38,015] [INFO] DFAST_QC result json was written to GCF_007830735.1_ASM783073v1_genomic.fna/dqc_result.json
[2024-01-24 13:18:38,015] [INFO] DFAST_QC completed!
[2024-01-24 13:18:38,015] [INFO] Total running time: 0h1m24s