[2024-01-24 13:55:19,947] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:55:19,949] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:55:19,949] [INFO] DQC Reference Directory: /var/lib/cwl/stgc520d5ef-bb4c-497c-9fa2-1bb08410ff12/dqc_reference
[2024-01-24 13:55:21,352] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:55:21,354] [INFO] Task started: Prodigal
[2024-01-24 13:55:21,354] [INFO] Running command: gunzip -c /var/lib/cwl/stg369177a2-d1fb-43fb-8e0e-317be6cd4cd7/GCF_014193675.1_ASM1419367v1_genomic.fna.gz | prodigal -d GCF_014193675.1_ASM1419367v1_genomic.fna/cds.fna -a GCF_014193675.1_ASM1419367v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:55:36,742] [INFO] Task succeeded: Prodigal
[2024-01-24 13:55:36,743] [INFO] Task started: HMMsearch
[2024-01-24 13:55:36,743] [INFO] Running command: hmmsearch --tblout GCF_014193675.1_ASM1419367v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc520d5ef-bb4c-497c-9fa2-1bb08410ff12/dqc_reference/reference_markers.hmm GCF_014193675.1_ASM1419367v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:55:37,093] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:55:37,095] [INFO] Found 6/6 markers.
[2024-01-24 13:55:37,162] [INFO] Query marker FASTA was written to GCF_014193675.1_ASM1419367v1_genomic.fna/markers.fasta
[2024-01-24 13:55:37,163] [INFO] Task started: Blastn
[2024-01-24 13:55:37,163] [INFO] Running command: blastn -query GCF_014193675.1_ASM1419367v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc520d5ef-bb4c-497c-9fa2-1bb08410ff12/dqc_reference/reference_markers.fasta -out GCF_014193675.1_ASM1419367v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:55:37,962] [INFO] Task succeeded: Blastn
[2024-01-24 13:55:37,971] [INFO] Selected 11 target genomes.
[2024-01-24 13:55:37,971] [INFO] Target genome list was writen to GCF_014193675.1_ASM1419367v1_genomic.fna/target_genomes.txt
[2024-01-24 13:55:37,980] [INFO] Task started: fastANI
[2024-01-24 13:55:37,980] [INFO] Running command: fastANI --query /var/lib/cwl/stg369177a2-d1fb-43fb-8e0e-317be6cd4cd7/GCF_014193675.1_ASM1419367v1_genomic.fna.gz --refList GCF_014193675.1_ASM1419367v1_genomic.fna/target_genomes.txt --output GCF_014193675.1_ASM1419367v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:55:50,627] [INFO] Task succeeded: fastANI
[2024-01-24 13:55:50,627] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc520d5ef-bb4c-497c-9fa2-1bb08410ff12/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:55:50,628] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc520d5ef-bb4c-497c-9fa2-1bb08410ff12/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:55:50,638] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:55:50,638] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:55:50,639] [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 limicola	strain=Red745	GCA_014193675.1	2740186	2740186	type	True	100.0	1733	1735	95	conclusive
Geomonas silvestris	strain=Red330	GCA_014193515.1	2740184	2740184	type	True	88.7867	1397	1735	95	below_threshold
Geomonas azotofigens	strain=Red51	GCA_018919395.1	2843196	2843196	type	True	81.2241	798	1735	95	below_threshold
Geomonas paludis	strain=Red736	GCA_014193585.1	2740185	2740185	type	True	81.2235	806	1735	95	below_threshold
Geomonas anaerohicana	strain=Red421	GCA_016458305.1	2798583	2798583	type	True	81.1709	787	1735	95	below_threshold
Geomonas oryzae	strain=S43	GCA_004117875.1	2364273	2364273	type	True	81.0204	746	1735	95	below_threshold
Geomonas propionica	strain=Red259	GCA_016458235.1	2798582	2798582	type	True	80.9675	771	1735	95	below_threshold
Geomonas ferrireducens	strain=S62	GCA_004917065.1	2570227	2570227	type	True	80.8006	727	1735	95	below_threshold
Geomonas agri	strain=RG53	GCA_020179605.1	2873702	2873702	type	True	80.7405	759	1735	95	below_threshold
Geomonas edaphica	strain=Red53	GCA_004917075.1	2570226	2570226	type	True	80.6134	723	1735	95	below_threshold
Geomonas terrae	strain=Red111	GCA_004791675.1	2562681	2562681	type	True	80.612	721	1735	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:55:50,640] [INFO] DFAST Taxonomy check result was written to GCF_014193675.1_ASM1419367v1_genomic.fna/tc_result.tsv
[2024-01-24 13:55:50,641] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:55:50,641] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:55:50,641] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc520d5ef-bb4c-497c-9fa2-1bb08410ff12/dqc_reference/checkm_data
[2024-01-24 13:55:50,643] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:55:50,697] [INFO] Task started: CheckM
[2024-01-24 13:55:50,697] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014193675.1_ASM1419367v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014193675.1_ASM1419367v1_genomic.fna/checkm_input GCF_014193675.1_ASM1419367v1_genomic.fna/checkm_result
[2024-01-24 13:56:34,952] [INFO] Task succeeded: CheckM
[2024-01-24 13:56:34,954] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:56:34,980] [INFO] ===== Completeness check finished =====
[2024-01-24 13:56:34,980] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:56:34,981] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014193675.1_ASM1419367v1_genomic.fna/markers.fasta)
[2024-01-24 13:56:34,981] [INFO] Task started: Blastn
[2024-01-24 13:56:34,982] [INFO] Running command: blastn -query GCF_014193675.1_ASM1419367v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc520d5ef-bb4c-497c-9fa2-1bb08410ff12/dqc_reference/reference_markers_gtdb.fasta -out GCF_014193675.1_ASM1419367v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:56:36,245] [INFO] Task succeeded: Blastn
[2024-01-24 13:56:36,250] [INFO] Selected 16 target genomes.
[2024-01-24 13:56:36,250] [INFO] Target genome list was writen to GCF_014193675.1_ASM1419367v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:56:36,262] [INFO] Task started: fastANI
[2024-01-24 13:56:36,262] [INFO] Running command: fastANI --query /var/lib/cwl/stg369177a2-d1fb-43fb-8e0e-317be6cd4cd7/GCF_014193675.1_ASM1419367v1_genomic.fna.gz --refList GCF_014193675.1_ASM1419367v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014193675.1_ASM1419367v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:56:53,980] [INFO] Task succeeded: fastANI
[2024-01-24 13:56:54,005] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:56:54,005] [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_014193675.1	s__Geomonas limicola	100.0	1733	1735	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_014193515.1	s__Geomonas silvestris	88.7867	1397	1735	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	81.2635	793	1735	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Geobacteraceae;g__Geomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014193585.1	s__Geomonas paludis	81.2261	806	1735	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Geobacteraceae;g__Geomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000175115.2	s__Geomonas sp000175115	81.1753	768	1735	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Geobacteraceae;g__Geomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016458305.1	s__Geomonas anaerohicana	81.1673	787	1735	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	81.1272	769	1735	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Geobacteraceae;g__Geomonas	95.0	99.24	99.10	0.94	0.94	3	-
GCF_004117875.1	s__Geomonas oryzae	81.0478	741	1735	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	80.9588	783	1735	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Geobacteraceae;g__Geomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004917065.1	s__Geomonas ferrireducens	80.7667	730	1735	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Geobacteraceae;g__Geomonas	95.0	96.45	96.45	0.86	0.86	2	-
GCF_002117975.1	s__Geomonas pelophila	80.696	717	1735	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Geobacteraceae;g__Geomonas	95.0	97.46	97.46	0.92	0.92	2	-
GCF_004917075.1	s__Geomonas edaphica	80.6159	722	1735	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Geobacteraceae;g__Geomonas	95.0	96.10	96.10	0.87	0.87	2	-
GCA_003490025.1	s__Geomonas sp003490025	80.5582	639	1735	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Geobacteraceae;g__Geomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000023645.1	s__Geomonas sp000023645	80.534	730	1735	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Geobacteraceae;g__Geomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000020725.1	s__Geomonas bemidjiensis	80.3559	736	1735	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Geobacteraceae;g__Geomonas	95.6689	N/A	N/A	N/A	N/A	1	-
GCA_903925075.1	s__Geomonas sp903925075	80.1677	642	1735	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Geobacteraceae;g__Geomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:56:54,007] [INFO] GTDB search result was written to GCF_014193675.1_ASM1419367v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:56:54,008] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:56:54,011] [INFO] DFAST_QC result json was written to GCF_014193675.1_ASM1419367v1_genomic.fna/dqc_result.json
[2024-01-24 13:56:54,011] [INFO] DFAST_QC completed!
[2024-01-24 13:56:54,011] [INFO] Total running time: 0h1m34s