[2024-01-24 12:22:48,479] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:22:48,481] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:22:48,481] [INFO] DQC Reference Directory: /var/lib/cwl/stgf311613a-56f4-4ca1-bb4b-0f44838773a9/dqc_reference
[2024-01-24 12:22:49,813] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:22:49,814] [INFO] Task started: Prodigal
[2024-01-24 12:22:49,814] [INFO] Running command: gunzip -c /var/lib/cwl/stg97922c89-f7ed-4d96-962f-e6ec14c8f0a0/GCF_018476905.1_ASM1847690v1_genomic.fna.gz | prodigal -d GCF_018476905.1_ASM1847690v1_genomic.fna/cds.fna -a GCF_018476905.1_ASM1847690v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:23:01,130] [INFO] Task succeeded: Prodigal
[2024-01-24 12:23:01,130] [INFO] Task started: HMMsearch
[2024-01-24 12:23:01,130] [INFO] Running command: hmmsearch --tblout GCF_018476905.1_ASM1847690v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf311613a-56f4-4ca1-bb4b-0f44838773a9/dqc_reference/reference_markers.hmm GCF_018476905.1_ASM1847690v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:23:01,483] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:23:01,484] [INFO] Found 6/6 markers.
[2024-01-24 12:23:01,518] [INFO] Query marker FASTA was written to GCF_018476905.1_ASM1847690v1_genomic.fna/markers.fasta
[2024-01-24 12:23:01,518] [INFO] Task started: Blastn
[2024-01-24 12:23:01,518] [INFO] Running command: blastn -query GCF_018476905.1_ASM1847690v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf311613a-56f4-4ca1-bb4b-0f44838773a9/dqc_reference/reference_markers.fasta -out GCF_018476905.1_ASM1847690v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:02,193] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:02,197] [INFO] Selected 15 target genomes.
[2024-01-24 12:23:02,197] [INFO] Target genome list was writen to GCF_018476905.1_ASM1847690v1_genomic.fna/target_genomes.txt
[2024-01-24 12:23:02,233] [INFO] Task started: fastANI
[2024-01-24 12:23:02,233] [INFO] Running command: fastANI --query /var/lib/cwl/stg97922c89-f7ed-4d96-962f-e6ec14c8f0a0/GCF_018476905.1_ASM1847690v1_genomic.fna.gz --refList GCF_018476905.1_ASM1847690v1_genomic.fna/target_genomes.txt --output GCF_018476905.1_ASM1847690v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:23:15,532] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:15,533] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf311613a-56f4-4ca1-bb4b-0f44838773a9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:23:15,533] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf311613a-56f4-4ca1-bb4b-0f44838773a9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:23:15,557] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:23:15,557] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:23:15,557] [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 luticola	strain=JCM 17780	GCA_018476905.1	1114878	1114878	type	True	100.0	1203	1204	95	conclusive
Geobacter hydrogenophilus	strain=DSM 13691	GCA_018501225.1	40983	40983	type	True	79.2668	383	1204	95	below_threshold
Geobacter pickeringii	strain=G13	GCA_000817955.1	345632	345632	type	True	79.2149	393	1204	95	below_threshold
Geobacter grbiciae	strain=DSM 13689	GCA_018531165.1	155042	155042	type	True	78.9906	374	1204	95	below_threshold
Geobacter metallireducens	strain=GS-15	GCA_000012925.1	28232	28232	type	True	78.9053	372	1204	95	below_threshold
Geobacter argillaceus	strain=ATCC BAA-1139	GCA_007830735.1	345631	345631	type	True	78.8463	348	1204	95	below_threshold
Geobacter benzoatilyticus	strain=Jerry-YX	GCA_017338855.1	2815309	2815309	type	True	78.5308	300	1204	95	below_threshold
Geobacter soli	strain=GSS01	GCA_000816575.1	1510391	1510391	type	True	78.344	348	1204	95	below_threshold
Geobacter sulfurreducens	strain=PCA	GCA_000007985.2	35554	35554	type	True	78.1744	340	1204	95	below_threshold
Geotalea uraniireducens	strain=Rf4	GCA_000016745.1	351604	351604	type	True	78.1094	337	1204	95	below_threshold
Geomonas azotofigens	strain=Red51	GCA_018919395.1	2843196	2843196	type	True	78.0217	314	1204	95	below_threshold
Oryzomonas japonica	strain=Red96	GCA_008802365.1	2603858	2603858	type	True	77.8546	245	1204	95	below_threshold
Geomonas paludis	strain=Red736	GCA_014193585.1	2740185	2740185	type	True	77.8458	324	1204	95	below_threshold
Geomonas limicola	strain=Red745	GCA_014193675.1	2740186	2740186	type	True	77.7502	306	1204	95	below_threshold
Desulfuromonas acetexigens		GCA_900111775.1	38815	38815	type	True	76.8388	106	1204	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:23:15,559] [INFO] DFAST Taxonomy check result was written to GCF_018476905.1_ASM1847690v1_genomic.fna/tc_result.tsv
[2024-01-24 12:23:15,560] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:23:15,560] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:23:15,560] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf311613a-56f4-4ca1-bb4b-0f44838773a9/dqc_reference/checkm_data
[2024-01-24 12:23:15,562] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:23:15,604] [INFO] Task started: CheckM
[2024-01-24 12:23:15,604] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018476905.1_ASM1847690v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018476905.1_ASM1847690v1_genomic.fna/checkm_input GCF_018476905.1_ASM1847690v1_genomic.fna/checkm_result
[2024-01-24 12:23:50,661] [INFO] Task succeeded: CheckM
[2024-01-24 12:23:50,663] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:23:50,685] [INFO] ===== Completeness check finished =====
[2024-01-24 12:23:50,685] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:23:50,686] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018476905.1_ASM1847690v1_genomic.fna/markers.fasta)
[2024-01-24 12:23:50,686] [INFO] Task started: Blastn
[2024-01-24 12:23:50,686] [INFO] Running command: blastn -query GCF_018476905.1_ASM1847690v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf311613a-56f4-4ca1-bb4b-0f44838773a9/dqc_reference/reference_markers_gtdb.fasta -out GCF_018476905.1_ASM1847690v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:51,510] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:51,514] [INFO] Selected 19 target genomes.
[2024-01-24 12:23:51,515] [INFO] Target genome list was writen to GCF_018476905.1_ASM1847690v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:23:51,549] [INFO] Task started: fastANI
[2024-01-24 12:23:51,550] [INFO] Running command: fastANI --query /var/lib/cwl/stg97922c89-f7ed-4d96-962f-e6ec14c8f0a0/GCF_018476905.1_ASM1847690v1_genomic.fna.gz --refList GCF_018476905.1_ASM1847690v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018476905.1_ASM1847690v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:24:04,295] [INFO] Task succeeded: fastANI
[2024-01-24 12:24:04,311] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:24:04,311] [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_018476905.1	s__Geomobilimonas luticola	100.0	1203	1204	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Geobacteraceae;g__Geomobilimonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_003574885.1	s__Geomobilimonas sp003574885	83.9812	783	1204	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Geobacteraceae;g__Geomobilimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011046855.1	s__Geobacter metallireducens_A	79.3073	402	1204	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	79.2856	381	1204	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	79.2244	393	1204	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	79.0244	364	1204	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	78.9062	369	1204	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Geobacteraceae;g__Geoanaerobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000012925.1	s__Geobacter metallireducens	78.9053	372	1204	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Geobacteraceae;g__Geobacter	95.0	98.29	96.59	0.93	0.85	3	-
GCA_905339345.1	s__Geobacter sp905339345	78.5121	243	1204	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	78.4343	346	1204	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Geobacteraceae;g__Geobacter	95.0	99.35	99.24	0.91	0.90	4	-
GCA_016223015.1	s__Geoanaerobacter sp016223015	78.3709	272	1204	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Geobacteraceae;g__Geoanaerobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009773645.1	s__WSYB01 sp009773645	78.2488	374	1204	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Geobacteraceae;g__WSYB01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018919395.1	s__Geomonas sp018919395	78.0106	315	1204	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	77.8358	325	1204	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Geobacteraceae;g__Geomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903925075.1	s__Geomonas sp903925075	77.6821	281	1204	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Geobacteraceae;g__Geomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017861215.1	s__VEOV01 sp017861215	77.567	111	1204	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Geobacteraceae;g__VEOV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012797715.1	s__RPRC01 sp012797715	76.9782	112	1204	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Geobacteraceae;g__RPRC01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:24:04,313] [INFO] GTDB search result was written to GCF_018476905.1_ASM1847690v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:24:04,313] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:24:04,317] [INFO] DFAST_QC result json was written to GCF_018476905.1_ASM1847690v1_genomic.fna/dqc_result.json
[2024-01-24 12:24:04,317] [INFO] DFAST_QC completed!
[2024-01-24 12:24:04,317] [INFO] Total running time: 0h1m16s