[2023-06-18 22:56:59,076] [INFO] DFAST_QC pipeline started.
[2023-06-18 22:56:59,079] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 22:56:59,079] [INFO] DQC Reference Directory: /var/lib/cwl/stgc3b39073-6764-461e-8da5-93ef0e3eb203/dqc_reference
[2023-06-18 22:57:00,316] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 22:57:00,317] [INFO] Task started: Prodigal
[2023-06-18 22:57:00,318] [INFO] Running command: gunzip -c /var/lib/cwl/stg17ee984f-2a47-4176-877d-73ea8e1e93cd/GCA_018224485.1_ASM1822448v1_genomic.fna.gz | prodigal -d GCA_018224485.1_ASM1822448v1_genomic.fna/cds.fna -a GCA_018224485.1_ASM1822448v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 22:57:05,535] [INFO] Task succeeded: Prodigal
[2023-06-18 22:57:05,535] [INFO] Task started: HMMsearch
[2023-06-18 22:57:05,535] [INFO] Running command: hmmsearch --tblout GCA_018224485.1_ASM1822448v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc3b39073-6764-461e-8da5-93ef0e3eb203/dqc_reference/reference_markers.hmm GCA_018224485.1_ASM1822448v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 22:57:05,708] [INFO] Task succeeded: HMMsearch
[2023-06-18 22:57:05,709] [INFO] Found 6/6 markers.
[2023-06-18 22:57:05,731] [INFO] Query marker FASTA was written to GCA_018224485.1_ASM1822448v1_genomic.fna/markers.fasta
[2023-06-18 22:57:05,731] [INFO] Task started: Blastn
[2023-06-18 22:57:05,732] [INFO] Running command: blastn -query GCA_018224485.1_ASM1822448v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc3b39073-6764-461e-8da5-93ef0e3eb203/dqc_reference/reference_markers.fasta -out GCA_018224485.1_ASM1822448v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 22:57:06,586] [INFO] Task succeeded: Blastn
[2023-06-18 22:57:06,590] [INFO] Selected 21 target genomes.
[2023-06-18 22:57:06,591] [INFO] Target genome list was writen to GCA_018224485.1_ASM1822448v1_genomic.fna/target_genomes.txt
[2023-06-18 22:57:06,592] [INFO] Task started: fastANI
[2023-06-18 22:57:06,592] [INFO] Running command: fastANI --query /var/lib/cwl/stg17ee984f-2a47-4176-877d-73ea8e1e93cd/GCA_018224485.1_ASM1822448v1_genomic.fna.gz --refList GCA_018224485.1_ASM1822448v1_genomic.fna/target_genomes.txt --output GCA_018224485.1_ASM1822448v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 22:57:19,471] [INFO] Task succeeded: fastANI
[2023-06-18 22:57:19,472] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc3b39073-6764-461e-8da5-93ef0e3eb203/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 22:57:19,472] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc3b39073-6764-461e-8da5-93ef0e3eb203/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 22:57:19,488] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 22:57:19,488] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-18 22:57:19,488] [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
Thioalkalivibrio nitratireducens	strain=DSM 14787	GCA_000321415.2	186931	186931	type	True	79.8002	344	586	95	below_threshold
Thioalkalivibrio paradoxus	strain=ARh 1	GCA_000227685.3	108010	108010	type	True	79.7029	345	586	95	below_threshold
Thioalkalivibrio thiocyanoxidans	strain=ARh2	GCA_000385215.1	152475	152475	type	True	78.5184	236	586	95	below_threshold
Thioalkalivibrio halophilus	strain=HL17	GCA_001995255.1	252474	252474	type	True	78.372	225	586	95	below_threshold
Thioalkalivibrio versutus	strain=AL 2	GCA_001999325.1	106634	106634	type	True	78.0758	230	586	95	below_threshold
Thioalkalivibrio sulfidiphilus	strain=HL-EbGR7	GCA_000021985.1	1033854	1033854	type	True	78.0311	184	586	95	below_threshold
Thioalkalivibrio denitrificans	strain=ALJD	GCA_002000365.1	108003	108003	type	True	77.617	148	586	95	below_threshold
Thiohalobacter thiocyanaticus	strain=Hrh1	GCA_003932505.1	585455	585455	type	True	77.3222	110	586	95	below_threshold
Guyparkeria hydrothermalis	strain=R3	GCA_023555375.1	923	923	type	True	76.9158	91	586	95	below_threshold
Marichromatium purpuratum	strain=984	GCA_000224005.3	37487	37487	type	True	76.7295	101	586	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	76.6832	93	586	95	below_threshold
Natronocella acetinitrilica	strain=ANL 6-2	GCA_024170285.1	414046	414046	type	True	76.5422	53	586	95	below_threshold
Pseudomonas aromaticivorans	strain=MAP12	GCA_019097855.1	2849492	2849492	type	True	76.5195	75	586	95	below_threshold
Pseudomonas oryzae	strain=KCTC 32247	GCA_900104805.1	1392877	1392877	type	True	76.3605	108	586	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	76.3175	77	586	95	below_threshold
[Pseudomonas] nosocomialis	strain=A31/70	GCA_005876855.1	1056496	1056496	type	True	76.2346	78	586	95	below_threshold
Thiorhodococcus mannitoliphagus	strain=DSM 18266	GCA_010915725.1	329406	329406	type	True	76.126	57	586	95	below_threshold
Stutzerimonas degradans	strain=DSM 50238	GCA_024448505.1	2968968	2968968	type	True	75.9911	64	586	95	below_threshold
Stutzerimonas degradans	strain=FDAARGOS_876	GCA_016028635.1	2968968	2968968	suspected-type	True	75.9441	66	586	95	below_threshold
Pseudomonas maumuensis	strain=COW77	GCA_019139675.1	2842354	2842354	type	True	75.4965	57	586	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-18 22:57:19,491] [INFO] DFAST Taxonomy check result was written to GCA_018224485.1_ASM1822448v1_genomic.fna/tc_result.tsv
[2023-06-18 22:57:19,492] [INFO] ===== Taxonomy check completed =====
[2023-06-18 22:57:19,492] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 22:57:19,492] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc3b39073-6764-461e-8da5-93ef0e3eb203/dqc_reference/checkm_data
[2023-06-18 22:57:19,494] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 22:57:19,519] [INFO] Task started: CheckM
[2023-06-18 22:57:19,520] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018224485.1_ASM1822448v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018224485.1_ASM1822448v1_genomic.fna/checkm_input GCA_018224485.1_ASM1822448v1_genomic.fna/checkm_result
[2023-06-18 22:57:40,497] [INFO] Task succeeded: CheckM
[2023-06-18 22:57:40,498] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 22:57:40,516] [INFO] ===== Completeness check finished =====
[2023-06-18 22:57:40,517] [INFO] ===== Start GTDB Search =====
[2023-06-18 22:57:40,517] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018224485.1_ASM1822448v1_genomic.fna/markers.fasta)
[2023-06-18 22:57:40,518] [INFO] Task started: Blastn
[2023-06-18 22:57:40,518] [INFO] Running command: blastn -query GCA_018224485.1_ASM1822448v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc3b39073-6764-461e-8da5-93ef0e3eb203/dqc_reference/reference_markers_gtdb.fasta -out GCA_018224485.1_ASM1822448v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 22:57:42,102] [INFO] Task succeeded: Blastn
[2023-06-18 22:57:42,106] [INFO] Selected 11 target genomes.
[2023-06-18 22:57:42,106] [INFO] Target genome list was writen to GCA_018224485.1_ASM1822448v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 22:57:42,111] [INFO] Task started: fastANI
[2023-06-18 22:57:42,111] [INFO] Running command: fastANI --query /var/lib/cwl/stg17ee984f-2a47-4176-877d-73ea8e1e93cd/GCA_018224485.1_ASM1822448v1_genomic.fna.gz --refList GCA_018224485.1_ASM1822448v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018224485.1_ASM1822448v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 22:57:47,875] [INFO] Task succeeded: fastANI
[2023-06-18 22:57:47,886] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 22:57:47,886] [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
GCA_018224485.1	s__Thioalkalivibrio_B sp018224485	100.0	579	586	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Thioalkalivibrionaceae;g__Thioalkalivibrio_B	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_011389655.1	s__Thioalkalivibrio_B sp011389655	91.3088	518	586	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Thioalkalivibrionaceae;g__Thioalkalivibrio_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007692435.1	s__Thioalkalivibrio_B sp007692435	88.5507	478	586	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Thioalkalivibrionaceae;g__Thioalkalivibrio_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003563455.1	s__Thioalkalivibrio_B sp003563455	85.6614	382	586	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Thioalkalivibrionaceae;g__Thioalkalivibrio_B	95.0	98.96	98.96	0.85	0.85	2	-
GCA_003550945.1	s__Thioalkalivibrio_B sp003550945	82.0006	278	586	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Thioalkalivibrionaceae;g__Thioalkalivibrio_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007692535.1	s__Thioalkalivibrio_B sp007692535	80.1333	381	586	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Thioalkalivibrionaceae;g__Thioalkalivibrio_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007116035.1	s__Thioalkalivibrio_B sp007116035	80.1011	373	586	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Thioalkalivibrionaceae;g__Thioalkalivibrio_B	95.0	99.33	99.33	0.75	0.75	2	-
GCF_000227685.2	s__Thioalkalivibrio_B paradoxus	79.7029	345	586	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Thioalkalivibrionaceae;g__Thioalkalivibrio_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003553165.1	s__Thioalkalivibrio_B sp003553165	79.6433	231	586	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Thioalkalivibrionaceae;g__Thioalkalivibrio_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003555285.1	s__Thioalkalivibrio_B sp003555285	79.3832	291	586	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Thioalkalivibrionaceae;g__Thioalkalivibrio_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007133115.1	s__Thioalkalivibrio_B sp007133115	78.5089	172	586	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Thioalkalivibrionaceae;g__Thioalkalivibrio_B	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-18 22:57:47,888] [INFO] GTDB search result was written to GCA_018224485.1_ASM1822448v1_genomic.fna/result_gtdb.tsv
[2023-06-18 22:57:47,888] [INFO] ===== GTDB Search completed =====
[2023-06-18 22:57:47,892] [INFO] DFAST_QC result json was written to GCA_018224485.1_ASM1822448v1_genomic.fna/dqc_result.json
[2023-06-18 22:57:47,892] [INFO] DFAST_QC completed!
[2023-06-18 22:57:47,892] [INFO] Total running time: 0h0m49s