[2024-01-24 13:10:03,995] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:10:03,997] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:10:03,997] [INFO] DQC Reference Directory: /var/lib/cwl/stg25e81d66-4600-4d56-8d30-5e2be4dea0b3/dqc_reference
[2024-01-24 13:10:05,279] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:10:05,280] [INFO] Task started: Prodigal
[2024-01-24 13:10:05,280] [INFO] Running command: gunzip -c /var/lib/cwl/stg9c53cc96-a150-47db-8018-22b882c6d4a8/GCF_010894435.1_ASM1089443v1_genomic.fna.gz | prodigal -d GCF_010894435.1_ASM1089443v1_genomic.fna/cds.fna -a GCF_010894435.1_ASM1089443v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:11:30,353] [INFO] Task succeeded: Prodigal
[2024-01-24 13:11:30,354] [INFO] Task started: HMMsearch
[2024-01-24 13:11:30,354] [INFO] Running command: hmmsearch --tblout GCF_010894435.1_ASM1089443v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg25e81d66-4600-4d56-8d30-5e2be4dea0b3/dqc_reference/reference_markers.hmm GCF_010894435.1_ASM1089443v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:11:30,946] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:11:30,948] [INFO] Found 6/6 markers.
[2024-01-24 13:11:31,043] [INFO] Query marker FASTA was written to GCF_010894435.1_ASM1089443v1_genomic.fna/markers.fasta
[2024-01-24 13:11:31,043] [INFO] Task started: Blastn
[2024-01-24 13:11:31,043] [INFO] Running command: blastn -query GCF_010894435.1_ASM1089443v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg25e81d66-4600-4d56-8d30-5e2be4dea0b3/dqc_reference/reference_markers.fasta -out GCF_010894435.1_ASM1089443v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:11:31,730] [INFO] Task succeeded: Blastn
[2024-01-24 13:11:31,734] [INFO] Selected 17 target genomes.
[2024-01-24 13:11:31,735] [INFO] Target genome list was writen to GCF_010894435.1_ASM1089443v1_genomic.fna/target_genomes.txt
[2024-01-24 13:11:31,746] [INFO] Task started: fastANI
[2024-01-24 13:11:31,747] [INFO] Running command: fastANI --query /var/lib/cwl/stg9c53cc96-a150-47db-8018-22b882c6d4a8/GCF_010894435.1_ASM1089443v1_genomic.fna.gz --refList GCF_010894435.1_ASM1089443v1_genomic.fna/target_genomes.txt --output GCF_010894435.1_ASM1089443v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:12:16,302] [INFO] Task succeeded: fastANI
[2024-01-24 13:12:16,303] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg25e81d66-4600-4d56-8d30-5e2be4dea0b3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:12:16,303] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg25e81d66-4600-4d56-8d30-5e2be4dea0b3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:12:16,320] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:12:16,320] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:12:16,320] [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
Pyxidicoccus trucidator	strain=CA060A	GCA_010894435.1	2709662	2709662	type	True	100.0	4180	4181	95	conclusive
Pyxidicoccus caerfyrddinensis	strain=CA032A	GCA_010894405.1	2709663	2709663	type	True	89.2485	3258	4181	95	below_threshold
Pyxidicoccus fallax	strain=DSM 14698	GCA_012933655.1	394095	394095	type	True	87.5527	2829	4181	95	below_threshold
Myxococcus vastator	strain=AM301	GCA_010894475.1	2709664	2709664	type	True	84.912	1885	4181	95	below_threshold
Myxococcus virescens	strain=DSM 2260	GCA_900101905.1	83456	83456	type	True	84.6048	2172	4181	95	below_threshold
Myxococcus virescens	strain=NBRC 100334	GCA_007989405.1	83456	83456	type	True	84.5493	2153	4181	95	below_threshold
Myxococcus xanthus	strain=DSM 16526	GCA_900106535.1	34	34	type	True	84.4614	2166	4181	95	below_threshold
Myxococcus eversor	strain=AB053B	GCA_010894455.1	2709661	2709661	type	True	83.9209	2481	4181	95	below_threshold
Myxococcus stipitatus	strain=DSM 14675	GCA_000331735.1	83455	83455	neotype	True	83.2713	2205	4181	95	below_threshold
Corallococcus soli	strain=ZKHCc1 1396	GCA_014930455.1	2710757	2710757	type	True	82.4802	2089	4181	95	below_threshold
Corallococcus silvisoli	strain=c25j21	GCA_009909145.1	2697031	2697031	type	True	82.3659	1913	4181	95	below_threshold
Longimicrobium terrae	strain=CB-286315	GCA_013000925.1	1639882	1639882	type	True	75.2561	396	4181	95	below_threshold
Desulfohalovibrio reitneri	strain=L21-Syr-AB	GCA_000711295.1	1307759	1307759	type	True	75.1718	139	4181	95	below_threshold
Paucidesulfovibrio longus	strain=DSM 6739	GCA_000420485.1	889	889	type	True	75.0996	110	4181	95	below_threshold
Ancylobacter dichloromethanicus	strain=VKM B-2484	GCA_018390645.1	518825	518825	type	True	75.0471	222	4181	95	below_threshold
Roseomonas cervicalis	strain=ATCC 49957	GCA_000164635.1	204525	204525	type	True	74.9572	295	4181	95	below_threshold
Ancylobacter rudongensis	strain=CGMCC 1.1761	GCA_900100155.1	177413	177413	type	True	74.9488	221	4181	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:12:16,322] [INFO] DFAST Taxonomy check result was written to GCF_010894435.1_ASM1089443v1_genomic.fna/tc_result.tsv
[2024-01-24 13:12:16,322] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:12:16,322] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:12:16,322] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg25e81d66-4600-4d56-8d30-5e2be4dea0b3/dqc_reference/checkm_data
[2024-01-24 13:12:16,323] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:12:16,435] [INFO] Task started: CheckM
[2024-01-24 13:12:16,435] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_010894435.1_ASM1089443v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_010894435.1_ASM1089443v1_genomic.fna/checkm_input GCF_010894435.1_ASM1089443v1_genomic.fna/checkm_result
[2024-01-24 13:17:09,600] [INFO] Task succeeded: CheckM
[2024-01-24 13:17:09,602] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:17:09,633] [INFO] ===== Completeness check finished =====
[2024-01-24 13:17:09,634] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:17:09,634] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_010894435.1_ASM1089443v1_genomic.fna/markers.fasta)
[2024-01-24 13:17:09,635] [INFO] Task started: Blastn
[2024-01-24 13:17:09,635] [INFO] Running command: blastn -query GCF_010894435.1_ASM1089443v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg25e81d66-4600-4d56-8d30-5e2be4dea0b3/dqc_reference/reference_markers_gtdb.fasta -out GCF_010894435.1_ASM1089443v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:10,780] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:10,784] [INFO] Selected 11 target genomes.
[2024-01-24 13:17:10,784] [INFO] Target genome list was writen to GCF_010894435.1_ASM1089443v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:17:10,826] [INFO] Task started: fastANI
[2024-01-24 13:17:10,826] [INFO] Running command: fastANI --query /var/lib/cwl/stg9c53cc96-a150-47db-8018-22b882c6d4a8/GCF_010894435.1_ASM1089443v1_genomic.fna.gz --refList GCF_010894435.1_ASM1089443v1_genomic.fna/target_genomes_gtdb.txt --output GCF_010894435.1_ASM1089443v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:17:52,059] [INFO] Task succeeded: fastANI
[2024-01-24 13:17:52,069] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:17:52,069] [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_010894435.1	s__Myxococcus trucidator	100.0	4180	4181	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Myxococcus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_010894405.1	s__Myxococcus caerfyrddinensis	89.2469	3258	4181	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Myxococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012933655.1	s__Myxococcus fallax	87.5626	2828	4181	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Myxococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017301735.1	s__Myxococcus sp017301735	87.5583	3112	4181	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Myxococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002305895.1	s__Myxococcus macrosporus	85.0424	2224	4181	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Myxococcus	95.0	98.54	98.54	0.93	0.93	2	-
GCF_013372585.1	s__Myxococcus sp013372585	84.7769	2153	4181	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Myxococcus	95.0	99.53	99.53	0.97	0.97	2	-
GCF_900101905.1	s__Myxococcus virescens	84.5725	2180	4181	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Myxococcus	96.8216	98.11	97.12	0.95	0.93	4	-
GCF_006402735.1	s__Myxococcus xanthus_A	84.4951	2236	4181	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Myxococcus	96.2302	99.44	99.22	0.98	0.96	5	-
GCF_900106535.1	s__Myxococcus xanthus	84.4808	2162	4181	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Myxococcus	96.8216	99.36	96.84	0.98	0.91	10	-
GCF_014656495.1	s__Myxococcus sp014656495	84.4392	2203	4181	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Myxococcus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_010894455.1	s__Myxococcus eversor	83.9298	2480	4181	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Myxococcus	95.0	99.18	99.18	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:17:52,071] [INFO] GTDB search result was written to GCF_010894435.1_ASM1089443v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:17:52,072] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:17:52,076] [INFO] DFAST_QC result json was written to GCF_010894435.1_ASM1089443v1_genomic.fna/dqc_result.json
[2024-01-24 13:17:52,076] [INFO] DFAST_QC completed!
[2024-01-24 13:17:52,076] [INFO] Total running time: 0h7m48s