[2024-01-25 17:41:50,722] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:41:50,724] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:41:50,724] [INFO] DQC Reference Directory: /var/lib/cwl/stg67b155f8-ced9-4066-ad82-99782e4f3c0a/dqc_reference
[2024-01-25 17:41:51,825] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:41:51,826] [INFO] Task started: Prodigal
[2024-01-25 17:41:51,826] [INFO] Running command: gunzip -c /var/lib/cwl/stg2612d655-9ed9-42e8-944c-5a19330e0741/GCF_028435365.1_ASM2843536v1_genomic.fna.gz | prodigal -d GCF_028435365.1_ASM2843536v1_genomic.fna/cds.fna -a GCF_028435365.1_ASM2843536v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:42:30,548] [INFO] Task succeeded: Prodigal
[2024-01-25 17:42:30,548] [INFO] Task started: HMMsearch
[2024-01-25 17:42:30,548] [INFO] Running command: hmmsearch --tblout GCF_028435365.1_ASM2843536v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg67b155f8-ced9-4066-ad82-99782e4f3c0a/dqc_reference/reference_markers.hmm GCF_028435365.1_ASM2843536v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:42:30,984] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:42:30,985] [INFO] Found 6/6 markers.
[2024-01-25 17:42:31,090] [INFO] Query marker FASTA was written to GCF_028435365.1_ASM2843536v1_genomic.fna/markers.fasta
[2024-01-25 17:42:31,090] [INFO] Task started: Blastn
[2024-01-25 17:42:31,090] [INFO] Running command: blastn -query GCF_028435365.1_ASM2843536v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg67b155f8-ced9-4066-ad82-99782e4f3c0a/dqc_reference/reference_markers.fasta -out GCF_028435365.1_ASM2843536v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:42:31,772] [INFO] Task succeeded: Blastn
[2024-01-25 17:42:31,775] [INFO] Selected 15 target genomes.
[2024-01-25 17:42:31,775] [INFO] Target genome list was writen to GCF_028435365.1_ASM2843536v1_genomic.fna/target_genomes.txt
[2024-01-25 17:42:31,787] [INFO] Task started: fastANI
[2024-01-25 17:42:31,787] [INFO] Running command: fastANI --query /var/lib/cwl/stg2612d655-9ed9-42e8-944c-5a19330e0741/GCF_028435365.1_ASM2843536v1_genomic.fna.gz --refList GCF_028435365.1_ASM2843536v1_genomic.fna/target_genomes.txt --output GCF_028435365.1_ASM2843536v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:43:05,246] [INFO] Task succeeded: fastANI
[2024-01-25 17:43:05,247] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg67b155f8-ced9-4066-ad82-99782e4f3c0a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:43:05,247] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg67b155f8-ced9-4066-ad82-99782e4f3c0a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:43:05,257] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 17:43:05,257] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 17:43:05,257] [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
Polyangium fumosum	strain=DSM 14668	GCA_005144585.1	889272	889272	neotype	True	90.2575	3439	4541	95	below_threshold
Polyangium spumosum	strain=DSM 14734	GCA_009649845.1	889282	889282	type	True	87.9706	2971	4541	95	below_threshold
Polyangium aurulentum	strain=SDU3-1	GCA_005144635.2	2567896	2567896	type	True	80.749	2155	4541	95	below_threshold
Chondromyces crocatus	strain=Cm c5	GCA_001189295.1	52	52	type	True	76.731	899	4541	95	below_threshold
Labilithrix luteola	strain=DSM 27648	GCA_001263205.1	1391654	1391654	type	True	75.8784	693	4541	95	below_threshold
Sandaracinus amylolyticus	strain=DSM 53668	GCA_000737325.2	927083	927083	type	True	75.3709	1196	4541	95	below_threshold
Halochromatium glycolicum	strain=DSM 11080	GCA_016584085.1	85075	85075	type	True	74.9436	172	4541	95	below_threshold
Thiobacillus denitrificans	strain=DSM 12475	GCA_000376425.1	36861	36861	type	True	74.8581	68	4541	95	below_threshold
Gemmatirosa kalamazoonensis	strain=KBS708	GCA_000522985.1	861299	861299	type	True	74.8489	701	4541	95	below_threshold
Aeromicrobium terrae	strain=CC-CFT486	GCA_008039565.1	2498846	2498846	type	True	74.8266	215	4541	95	below_threshold
Derxia lacustris	strain=HL-12	GCA_002105195.1	764842	764842	type	True	74.8059	318	4541	95	below_threshold
Cellulomonas fulva	strain=DKR-3	GCA_018531375.1	2835530	2835530	type	True	74.7702	349	4541	95	below_threshold
Aquisphaera giovannonii	strain=OJF2	GCA_008087625.1	406548	406548	type	True	74.7537	418	4541	95	below_threshold
Nocardioides thalensis	strain=DSM 103833	GCA_013410655.1	1914755	1914755	type	True	74.7516	321	4541	95	below_threshold
Promicromonospora soli	strain=CGMCC 4.7398	GCA_014653785.1	2035533	2035533	type	True	74.7074	296	4541	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:43:05,260] [INFO] DFAST Taxonomy check result was written to GCF_028435365.1_ASM2843536v1_genomic.fna/tc_result.tsv
[2024-01-25 17:43:05,261] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:43:05,261] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:43:05,261] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg67b155f8-ced9-4066-ad82-99782e4f3c0a/dqc_reference/checkm_data
[2024-01-25 17:43:05,262] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:43:05,388] [INFO] Task started: CheckM
[2024-01-25 17:43:05,389] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_028435365.1_ASM2843536v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_028435365.1_ASM2843536v1_genomic.fna/checkm_input GCF_028435365.1_ASM2843536v1_genomic.fna/checkm_result
[2024-01-25 17:45:53,298] [INFO] Task succeeded: CheckM
[2024-01-25 17:45:53,299] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 18.56%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-25 17:45:53,331] [INFO] ===== Completeness check finished =====
[2024-01-25 17:45:53,332] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:45:53,332] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_028435365.1_ASM2843536v1_genomic.fna/markers.fasta)
[2024-01-25 17:45:53,333] [INFO] Task started: Blastn
[2024-01-25 17:45:53,333] [INFO] Running command: blastn -query GCF_028435365.1_ASM2843536v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg67b155f8-ced9-4066-ad82-99782e4f3c0a/dqc_reference/reference_markers_gtdb.fasta -out GCF_028435365.1_ASM2843536v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:45:54,554] [INFO] Task succeeded: Blastn
[2024-01-25 17:45:54,557] [INFO] Selected 11 target genomes.
[2024-01-25 17:45:54,557] [INFO] Target genome list was writen to GCF_028435365.1_ASM2843536v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:45:54,568] [INFO] Task started: fastANI
[2024-01-25 17:45:54,568] [INFO] Running command: fastANI --query /var/lib/cwl/stg2612d655-9ed9-42e8-944c-5a19330e0741/GCF_028435365.1_ASM2843536v1_genomic.fna.gz --refList GCF_028435365.1_ASM2843536v1_genomic.fna/target_genomes_gtdb.txt --output GCF_028435365.1_ASM2843536v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:46:34,531] [INFO] Task succeeded: fastANI
[2024-01-25 17:46:34,539] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 17:46:34,539] [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_005144585.1	s__Polyangium fumosum	90.2725	3434	4541	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__Polyangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009649845.1	s__Polyangium spumosum	87.9748	2970	4541	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__Polyangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005144635.1	s__Polyangium sp005144635	80.7455	2139	4541	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__Polyangium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016715885.1	s__Polyangium sp016715885	77.4426	844	4541	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__Polyangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002950945.1	s__Sorangium cellulosum_E	77.34	1526	4541	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__Sorangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000067165.1	s__Sorangium cellulosum_B	77.2296	1408	4541	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__Sorangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004135735.1	s__Sorangium cellulosum_F	77.2241	1398	4541	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__Sorangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000418325.1	s__Sorangium cellulosum_D	77.1945	1588	4541	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__Sorangium	95.0	95.45	95.45	0.82	0.82	2	-
GCA_903906315.1	s__CAIVJW01 sp903906315	77.1031	1169	4541	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__CAIVJW01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001931535.1	s__Minicystis rosea	77.0355	1488	4541	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__Minicystis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903893335.1	s__CAITLX01 sp903893335	76.2129	630	4541	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__CAITLX01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:46:34,540] [INFO] GTDB search result was written to GCF_028435365.1_ASM2843536v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:46:34,541] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:46:34,551] [INFO] DFAST_QC result json was written to GCF_028435365.1_ASM2843536v1_genomic.fna/dqc_result.json
[2024-01-25 17:46:34,551] [INFO] DFAST_QC completed!
[2024-01-25 17:46:34,551] [INFO] Total running time: 0h4m44s