[2024-01-24 11:34:55,006] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:34:55,009] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:34:55,010] [INFO] DQC Reference Directory: /var/lib/cwl/stg0e335bd9-447d-4b8d-80c3-b450ef54cf76/dqc_reference
[2024-01-24 11:34:56,528] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:34:56,529] [INFO] Task started: Prodigal
[2024-01-24 11:34:56,530] [INFO] Running command: gunzip -c /var/lib/cwl/stg902d6592-f640-4260-833d-d226bda57b01/GCF_018919385.1_ASM1891938v1_genomic.fna.gz | prodigal -d GCF_018919385.1_ASM1891938v1_genomic.fna/cds.fna -a GCF_018919385.1_ASM1891938v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:35:09,912] [INFO] Task succeeded: Prodigal
[2024-01-24 11:35:09,912] [INFO] Task started: HMMsearch
[2024-01-24 11:35:09,913] [INFO] Running command: hmmsearch --tblout GCF_018919385.1_ASM1891938v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0e335bd9-447d-4b8d-80c3-b450ef54cf76/dqc_reference/reference_markers.hmm GCF_018919385.1_ASM1891938v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:35:10,224] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:35:10,225] [INFO] Found 6/6 markers.
[2024-01-24 11:35:10,276] [INFO] Query marker FASTA was written to GCF_018919385.1_ASM1891938v1_genomic.fna/markers.fasta
[2024-01-24 11:35:10,277] [INFO] Task started: Blastn
[2024-01-24 11:35:10,277] [INFO] Running command: blastn -query GCF_018919385.1_ASM1891938v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0e335bd9-447d-4b8d-80c3-b450ef54cf76/dqc_reference/reference_markers.fasta -out GCF_018919385.1_ASM1891938v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:10,975] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:10,978] [INFO] Selected 6 target genomes.
[2024-01-24 11:35:10,978] [INFO] Target genome list was writen to GCF_018919385.1_ASM1891938v1_genomic.fna/target_genomes.txt
[2024-01-24 11:35:10,981] [INFO] Task started: fastANI
[2024-01-24 11:35:10,982] [INFO] Running command: fastANI --query /var/lib/cwl/stg902d6592-f640-4260-833d-d226bda57b01/GCF_018919385.1_ASM1891938v1_genomic.fna.gz --refList GCF_018919385.1_ASM1891938v1_genomic.fna/target_genomes.txt --output GCF_018919385.1_ASM1891938v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:19,082] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:19,083] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0e335bd9-447d-4b8d-80c3-b450ef54cf76/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:19,083] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0e335bd9-447d-4b8d-80c3-b450ef54cf76/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:19,090] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:35:19,090] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:35:19,090] [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 azotofigens	strain=Red51	GCA_018919395.1	2843196	2843196	type	True	89.0285	1259	1531	95	below_threshold
Geomonas paludis	strain=Red736	GCA_014193585.1	2740185	2740185	type	True	88.7061	1230	1531	95	below_threshold
Geomonas anaerohicana	strain=Red421	GCA_016458305.1	2798583	2798583	type	True	88.2108	1268	1531	95	below_threshold
Geomonas propionica	strain=Red259	GCA_016458235.1	2798582	2798582	type	True	88.1551	1222	1531	95	below_threshold
Geomonas agri	strain=RG53	GCA_020179605.1	2873702	2873702	type	True	87.4375	1222	1531	95	below_threshold
Geomonas oryzae	strain=S43	GCA_004117875.1	2364273	2364273	type	True	84.2179	1110	1531	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:35:19,092] [INFO] DFAST Taxonomy check result was written to GCF_018919385.1_ASM1891938v1_genomic.fna/tc_result.tsv
[2024-01-24 11:35:19,092] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:19,092] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:19,092] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0e335bd9-447d-4b8d-80c3-b450ef54cf76/dqc_reference/checkm_data
[2024-01-24 11:35:19,093] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:35:19,138] [INFO] Task started: CheckM
[2024-01-24 11:35:19,138] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018919385.1_ASM1891938v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018919385.1_ASM1891938v1_genomic.fna/checkm_input GCF_018919385.1_ASM1891938v1_genomic.fna/checkm_result
[2024-01-24 11:35:59,208] [INFO] Task succeeded: CheckM
[2024-01-24 11:35:59,209] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:35:59,231] [INFO] ===== Completeness check finished =====
[2024-01-24 11:35:59,231] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:35:59,232] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018919385.1_ASM1891938v1_genomic.fna/markers.fasta)
[2024-01-24 11:35:59,232] [INFO] Task started: Blastn
[2024-01-24 11:35:59,232] [INFO] Running command: blastn -query GCF_018919385.1_ASM1891938v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0e335bd9-447d-4b8d-80c3-b450ef54cf76/dqc_reference/reference_markers_gtdb.fasta -out GCF_018919385.1_ASM1891938v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:36:00,390] [INFO] Task succeeded: Blastn
[2024-01-24 11:36:00,394] [INFO] Selected 7 target genomes.
[2024-01-24 11:36:00,394] [INFO] Target genome list was writen to GCF_018919385.1_ASM1891938v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:36:00,400] [INFO] Task started: fastANI
[2024-01-24 11:36:00,401] [INFO] Running command: fastANI --query /var/lib/cwl/stg902d6592-f640-4260-833d-d226bda57b01/GCF_018919385.1_ASM1891938v1_genomic.fna.gz --refList GCF_018919385.1_ASM1891938v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018919385.1_ASM1891938v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:36:09,434] [INFO] Task succeeded: fastANI
[2024-01-24 11:36:09,448] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:36:09,449] [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_018986935.1	s__Geomonas sp018986935	99.1024	1447	1531	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Geobacteraceae;g__Geomonas	95.0	99.24	99.10	0.94	0.94	3	conclusive
GCF_018986915.1	s__Geomonas sp018986915	89.2425	1300	1531	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	89.031	1258	1531	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	88.7456	1254	1531	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Geobacteraceae;g__Geomonas	95.0	99.99	99.99	1.00	1.00	2	-
GCF_014193585.1	s__Geomonas paludis	88.7129	1229	1531	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	88.2063	1268	1531	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Geobacteraceae;g__Geomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016458235.1	s__Geomonas propionica	88.1551	1222	1531	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 11:36:09,452] [INFO] GTDB search result was written to GCF_018919385.1_ASM1891938v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:36:09,453] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:36:09,457] [INFO] DFAST_QC result json was written to GCF_018919385.1_ASM1891938v1_genomic.fna/dqc_result.json
[2024-01-24 11:36:09,458] [INFO] DFAST_QC completed!
[2024-01-24 11:36:09,458] [INFO] Total running time: 0h1m14s