[2024-01-25 17:37:35,556] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:37:35,559] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:37:35,559] [INFO] DQC Reference Directory: /var/lib/cwl/stg45d2627c-f46c-4bc7-a665-5d7fa5c6da39/dqc_reference
[2024-01-25 17:37:36,713] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:37:36,714] [INFO] Task started: Prodigal
[2024-01-25 17:37:36,714] [INFO] Running command: gunzip -c /var/lib/cwl/stgcebe8e19-efa1-4493-89d7-ecffb07347a2/GCF_020103725.1_ASM2010372v1_genomic.fna.gz | prodigal -d GCF_020103725.1_ASM2010372v1_genomic.fna/cds.fna -a GCF_020103725.1_ASM2010372v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:38:28,279] [INFO] Task succeeded: Prodigal
[2024-01-25 17:38:28,279] [INFO] Task started: HMMsearch
[2024-01-25 17:38:28,279] [INFO] Running command: hmmsearch --tblout GCF_020103725.1_ASM2010372v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg45d2627c-f46c-4bc7-a665-5d7fa5c6da39/dqc_reference/reference_markers.hmm GCF_020103725.1_ASM2010372v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:38:28,730] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:38:28,732] [INFO] Found 6/6 markers.
[2024-01-25 17:38:28,814] [INFO] Query marker FASTA was written to GCF_020103725.1_ASM2010372v1_genomic.fna/markers.fasta
[2024-01-25 17:38:28,814] [INFO] Task started: Blastn
[2024-01-25 17:38:28,814] [INFO] Running command: blastn -query GCF_020103725.1_ASM2010372v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg45d2627c-f46c-4bc7-a665-5d7fa5c6da39/dqc_reference/reference_markers.fasta -out GCF_020103725.1_ASM2010372v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:38:29,630] [INFO] Task succeeded: Blastn
[2024-01-25 17:38:29,634] [INFO] Selected 22 target genomes.
[2024-01-25 17:38:29,634] [INFO] Target genome list was writen to GCF_020103725.1_ASM2010372v1_genomic.fna/target_genomes.txt
[2024-01-25 17:38:29,663] [INFO] Task started: fastANI
[2024-01-25 17:38:29,663] [INFO] Running command: fastANI --query /var/lib/cwl/stgcebe8e19-efa1-4493-89d7-ecffb07347a2/GCF_020103725.1_ASM2010372v1_genomic.fna.gz --refList GCF_020103725.1_ASM2010372v1_genomic.fna/target_genomes.txt --output GCF_020103725.1_ASM2010372v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:39:11,851] [INFO] Task succeeded: fastANI
[2024-01-25 17:39:11,852] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg45d2627c-f46c-4bc7-a665-5d7fa5c6da39/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:39:11,852] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg45d2627c-f46c-4bc7-a665-5d7fa5c6da39/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:39:11,863] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 17:39:11,864] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 17:39:11,864] [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
Stigmatella hybrida	strain=DSM 14722	GCA_020103775.1	394097	394097	type	True	82.9838	1853	3865	95	below_threshold
Stigmatella aurantiaca	strain=DSM 17044	GCA_900109545.1	41	41	type	True	82.9793	1895	3865	95	below_threshold
Stigmatella erecta	strain=DSM 16858	GCA_900111745.1	83460	83460	type	True	82.9044	1894	3865	95	below_threshold
Pyxidicoccus trucidator	strain=CA060A	GCA_010894435.1	2709662	2709662	type	True	81.1423	1894	3865	95	below_threshold
Pyxidicoccus caerfyrddinensis	strain=CA032A	GCA_010894405.1	2709663	2709663	type	True	81.0459	1893	3865	95	below_threshold
Pyxidicoccus fallax	strain=DSM 14698	GCA_012933655.1	394095	394095	type	True	81.0036	1821	3865	95	below_threshold
Archangium gephyra	strain=DSM 2261	GCA_001027285.1	48	48	type	True	80.9776	1862	3865	95	below_threshold
Archangium gephyra	strain=DSM 2261	GCA_003387095.1	48	48	type	True	80.9377	1865	3865	95	below_threshold
Archangium violaceum	strain=Cb vi76	GCA_000733295.1	83451	83451	type	True	80.8922	1778	3865	95	below_threshold
Myxococcus vastator	strain=AM301	GCA_010894475.1	2709664	2709664	type	True	80.8179	1358	3865	95	below_threshold
Corallococcus silvisoli	strain=c25j21	GCA_009909145.1	2697031	2697031	type	True	80.6898	1527	3865	95	below_threshold
Corallococcus soli	strain=ZKHCc1 1396	GCA_014930455.1	2710757	2710757	type	True	80.6871	1610	3865	95	below_threshold
Myxococcus fulvus	strain=NBRC 100333	GCA_007991095.1	33	33	type	True	80.5988	1659	3865	95	below_threshold
Myxococcus fulvus	strain=DSM 16525	GCA_900111765.1	33	33	type	True	80.5916	1661	3865	95	below_threshold
Methylobacterium iners	strain=DSM 19015	GCA_022179305.1	418707	418707	type	True	75.2367	163	3865	95	below_threshold
Longimicrobium terrae	strain=CB-286315	GCA_013000925.1	1639882	1639882	type	True	75.1423	338	3865	95	below_threshold
Longimicrobium terrae	strain=CECT 8660	GCA_014198875.1	1639882	1639882	type	True	75.1135	340	3865	95	below_threshold
Longimicrobium terrae	strain=DSM 29007	GCA_014202995.1	1639882	1639882	type	True	75.0987	339	3865	95	below_threshold
Ancylobacter rudongensis	strain=CGMCC 1.1761	GCA_900100155.1	177413	177413	type	True	74.9618	199	3865	95	below_threshold
Roseomonas cervicalis	strain=ATCC 49957	GCA_000164635.1	204525	204525	type	True	74.9261	294	3865	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:39:11,866] [INFO] DFAST Taxonomy check result was written to GCF_020103725.1_ASM2010372v1_genomic.fna/tc_result.tsv
[2024-01-25 17:39:11,867] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:39:11,867] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:39:11,867] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg45d2627c-f46c-4bc7-a665-5d7fa5c6da39/dqc_reference/checkm_data
[2024-01-25 17:39:11,868] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:39:11,969] [INFO] Task started: CheckM
[2024-01-25 17:39:11,969] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020103725.1_ASM2010372v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020103725.1_ASM2010372v1_genomic.fna/checkm_input GCF_020103725.1_ASM2010372v1_genomic.fna/checkm_result
[2024-01-25 17:43:52,357] [INFO] Task succeeded: CheckM
[2024-01-25 17:43:52,358] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:43:52,381] [INFO] ===== Completeness check finished =====
[2024-01-25 17:43:52,381] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:43:52,382] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020103725.1_ASM2010372v1_genomic.fna/markers.fasta)
[2024-01-25 17:43:52,382] [INFO] Task started: Blastn
[2024-01-25 17:43:52,382] [INFO] Running command: blastn -query GCF_020103725.1_ASM2010372v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg45d2627c-f46c-4bc7-a665-5d7fa5c6da39/dqc_reference/reference_markers_gtdb.fasta -out GCF_020103725.1_ASM2010372v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:43:53,900] [INFO] Task succeeded: Blastn
[2024-01-25 17:43:53,903] [INFO] Selected 10 target genomes.
[2024-01-25 17:43:53,903] [INFO] Target genome list was writen to GCF_020103725.1_ASM2010372v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:43:53,909] [INFO] Task started: fastANI
[2024-01-25 17:43:53,909] [INFO] Running command: fastANI --query /var/lib/cwl/stgcebe8e19-efa1-4493-89d7-ecffb07347a2/GCF_020103725.1_ASM2010372v1_genomic.fna.gz --refList GCF_020103725.1_ASM2010372v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020103725.1_ASM2010372v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:44:23,362] [INFO] Task succeeded: fastANI
[2024-01-25 17:44:23,369] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 17:44:23,369] [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_016926755.1	s__Hyalangium sp016926755	86.0789	2094	3865	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Hyalangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000737315.1	s__Hyalangium minutum	85.1325	2446	3865	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Hyalangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109545.1	s__Stigmatella aurantiaca	82.9563	1900	3865	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Stigmatella	95.281	N/A	N/A	N/A	N/A	1	-
GCF_900111745.1	s__Stigmatella erecta	82.8997	1892	3865	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Stigmatella	95.281	N/A	N/A	N/A	N/A	1	-
GCF_000165485.1	s__Stigmatella aurantiaca_A	82.4352	1836	3865	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Stigmatella	95.0	99.99	99.99	1.00	1.00	2	-
GCF_010894435.1	s__Myxococcus trucidator	81.1107	1904	3865	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	81.0043	1821	3865	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Myxococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001027285.1	s__Archangium gephyra	80.9936	1860	3865	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Archangium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_016859125.1	s__Archangium violaceum_A	80.9541	1779	3865	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Archangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016887565.1	s__Archangium violaceum_B	80.952	1894	3865	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Archangium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:44:23,371] [INFO] GTDB search result was written to GCF_020103725.1_ASM2010372v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:44:23,371] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:44:23,375] [INFO] DFAST_QC result json was written to GCF_020103725.1_ASM2010372v1_genomic.fna/dqc_result.json
[2024-01-25 17:44:23,375] [INFO] DFAST_QC completed!
[2024-01-25 17:44:23,375] [INFO] Total running time: 0h6m48s