[2024-01-24 12:29:28,996] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:29:28,999] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:29:28,999] [INFO] DQC Reference Directory: /var/lib/cwl/stge89b0576-0ee5-4061-ab21-45181479c54c/dqc_reference
[2024-01-24 12:29:30,302] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:29:30,303] [INFO] Task started: Prodigal
[2024-01-24 12:29:30,303] [INFO] Running command: gunzip -c /var/lib/cwl/stg052d2954-ab78-4ed9-967d-214d79edf9a1/GCF_004917065.1_ASM491706v1_genomic.fna.gz | prodigal -d GCF_004917065.1_ASM491706v1_genomic.fna/cds.fna -a GCF_004917065.1_ASM491706v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:29:44,422] [INFO] Task succeeded: Prodigal
[2024-01-24 12:29:44,423] [INFO] Task started: HMMsearch
[2024-01-24 12:29:44,423] [INFO] Running command: hmmsearch --tblout GCF_004917065.1_ASM491706v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge89b0576-0ee5-4061-ab21-45181479c54c/dqc_reference/reference_markers.hmm GCF_004917065.1_ASM491706v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:29:44,805] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:29:44,807] [INFO] Found 6/6 markers.
[2024-01-24 12:29:44,849] [INFO] Query marker FASTA was written to GCF_004917065.1_ASM491706v1_genomic.fna/markers.fasta
[2024-01-24 12:29:44,849] [INFO] Task started: Blastn
[2024-01-24 12:29:44,850] [INFO] Running command: blastn -query GCF_004917065.1_ASM491706v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge89b0576-0ee5-4061-ab21-45181479c54c/dqc_reference/reference_markers.fasta -out GCF_004917065.1_ASM491706v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:29:45,618] [INFO] Task succeeded: Blastn
[2024-01-24 12:29:45,621] [INFO] Selected 8 target genomes.
[2024-01-24 12:29:45,622] [INFO] Target genome list was writen to GCF_004917065.1_ASM491706v1_genomic.fna/target_genomes.txt
[2024-01-24 12:29:45,668] [INFO] Task started: fastANI
[2024-01-24 12:29:45,668] [INFO] Running command: fastANI --query /var/lib/cwl/stg052d2954-ab78-4ed9-967d-214d79edf9a1/GCF_004917065.1_ASM491706v1_genomic.fna.gz --refList GCF_004917065.1_ASM491706v1_genomic.fna/target_genomes.txt --output GCF_004917065.1_ASM491706v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:29:56,610] [INFO] Task succeeded: fastANI
[2024-01-24 12:29:56,610] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge89b0576-0ee5-4061-ab21-45181479c54c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:29:56,611] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge89b0576-0ee5-4061-ab21-45181479c54c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:29:56,619] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:29:56,619] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:29:56,619] [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 ferrireducens	strain=S62	GCA_004917065.1	2570227	2570227	type	True	100.0	1598	1598	95	conclusive
Geomonas terrae	strain=Red111	GCA_004791675.1	2562681	2562681	type	True	94.5127	1355	1598	95	below_threshold
Geomonas edaphica	strain=Red53	GCA_004917075.1	2570226	2570226	type	True	94.1375	1382	1598	95	below_threshold
Geomonas oryzae	strain=S43	GCA_004117875.1	2364273	2364273	type	True	92.6376	1369	1598	95	below_threshold
Geomonas azotofigens	strain=Red51	GCA_018919395.1	2843196	2843196	type	True	84.0054	1117	1598	95	below_threshold
Geomonas paludis	strain=Red736	GCA_014193585.1	2740185	2740185	type	True	83.944	1065	1598	95	below_threshold
Geomonas propionica	strain=Red259	GCA_016458235.1	2798582	2798582	type	True	83.649	1102	1598	95	below_threshold
Geomonas agri	strain=RG53	GCA_020179605.1	2873702	2873702	type	True	83.0503	1041	1598	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:29:56,621] [INFO] DFAST Taxonomy check result was written to GCF_004917065.1_ASM491706v1_genomic.fna/tc_result.tsv
[2024-01-24 12:29:56,621] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:29:56,621] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:29:56,622] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge89b0576-0ee5-4061-ab21-45181479c54c/dqc_reference/checkm_data
[2024-01-24 12:29:56,623] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:29:56,672] [INFO] Task started: CheckM
[2024-01-24 12:29:56,672] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004917065.1_ASM491706v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004917065.1_ASM491706v1_genomic.fna/checkm_input GCF_004917065.1_ASM491706v1_genomic.fna/checkm_result
[2024-01-24 12:30:40,181] [INFO] Task succeeded: CheckM
[2024-01-24 12:30:40,183] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:30:40,203] [INFO] ===== Completeness check finished =====
[2024-01-24 12:30:40,204] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:30:40,204] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004917065.1_ASM491706v1_genomic.fna/markers.fasta)
[2024-01-24 12:30:40,205] [INFO] Task started: Blastn
[2024-01-24 12:30:40,205] [INFO] Running command: blastn -query GCF_004917065.1_ASM491706v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge89b0576-0ee5-4061-ab21-45181479c54c/dqc_reference/reference_markers_gtdb.fasta -out GCF_004917065.1_ASM491706v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:30:41,294] [INFO] Task succeeded: Blastn
[2024-01-24 12:30:41,297] [INFO] Selected 9 target genomes.
[2024-01-24 12:30:41,297] [INFO] Target genome list was writen to GCF_004917065.1_ASM491706v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:30:41,305] [INFO] Task started: fastANI
[2024-01-24 12:30:41,306] [INFO] Running command: fastANI --query /var/lib/cwl/stg052d2954-ab78-4ed9-967d-214d79edf9a1/GCF_004917065.1_ASM491706v1_genomic.fna.gz --refList GCF_004917065.1_ASM491706v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004917065.1_ASM491706v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:30:53,141] [INFO] Task succeeded: fastANI
[2024-01-24 12:30:53,154] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:30:53,154] [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_004917065.1	s__Geomonas ferrireducens	100.0	1598	1598	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Geobacteraceae;g__Geomonas	95.0	96.45	96.45	0.86	0.86	2	conclusive
GCF_004917075.1	s__Geomonas edaphica	94.1234	1383	1598	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Geobacteraceae;g__Geomonas	95.0	96.10	96.10	0.87	0.87	2	-
GCF_004117875.1	s__Geomonas oryzae	92.6292	1370	1598	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	84.0043	1117	1598	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	83.9782	1107	1598	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Geobacteraceae;g__Geomonas	95.0	99.24	99.10	0.94	0.94	3	-
GCF_014193585.1	s__Geomonas paludis	83.9409	1065	1598	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	83.864	1082	1598	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Geobacteraceae;g__Geomonas	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000175115.2	s__Geomonas sp000175115	83.7834	1030	1598	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	83.4859	1107	1598	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 12:30:53,156] [INFO] GTDB search result was written to GCF_004917065.1_ASM491706v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:30:53,157] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:30:53,160] [INFO] DFAST_QC result json was written to GCF_004917065.1_ASM491706v1_genomic.fna/dqc_result.json
[2024-01-24 12:30:53,160] [INFO] DFAST_QC completed!
[2024-01-24 12:30:53,160] [INFO] Total running time: 0h1m24s