[2024-01-24 13:40:32,567] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:32,569] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:32,569] [INFO] DQC Reference Directory: /var/lib/cwl/stg28ce5d3f-2cbf-4e44-a9d1-c3bb198e2374/dqc_reference
[2024-01-24 13:40:33,809] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:33,810] [INFO] Task started: Prodigal
[2024-01-24 13:40:33,810] [INFO] Running command: gunzip -c /var/lib/cwl/stg828856f2-3075-4b9c-852b-d3ad51c84a2e/GCF_005871165.1_ASM587116v1_genomic.fna.gz | prodigal -d GCF_005871165.1_ASM587116v1_genomic.fna/cds.fna -a GCF_005871165.1_ASM587116v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:44,422] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:44,422] [INFO] Task started: HMMsearch
[2024-01-24 13:40:44,423] [INFO] Running command: hmmsearch --tblout GCF_005871165.1_ASM587116v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg28ce5d3f-2cbf-4e44-a9d1-c3bb198e2374/dqc_reference/reference_markers.hmm GCF_005871165.1_ASM587116v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:44,711] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:44,712] [INFO] Found 6/6 markers.
[2024-01-24 13:40:44,745] [INFO] Query marker FASTA was written to GCF_005871165.1_ASM587116v1_genomic.fna/markers.fasta
[2024-01-24 13:40:44,745] [INFO] Task started: Blastn
[2024-01-24 13:40:44,745] [INFO] Running command: blastn -query GCF_005871165.1_ASM587116v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg28ce5d3f-2cbf-4e44-a9d1-c3bb198e2374/dqc_reference/reference_markers.fasta -out GCF_005871165.1_ASM587116v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:45,655] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:45,659] [INFO] Selected 18 target genomes.
[2024-01-24 13:40:45,659] [INFO] Target genome list was writen to GCF_005871165.1_ASM587116v1_genomic.fna/target_genomes.txt
[2024-01-24 13:40:45,666] [INFO] Task started: fastANI
[2024-01-24 13:40:45,666] [INFO] Running command: fastANI --query /var/lib/cwl/stg828856f2-3075-4b9c-852b-d3ad51c84a2e/GCF_005871165.1_ASM587116v1_genomic.fna.gz --refList GCF_005871165.1_ASM587116v1_genomic.fna/target_genomes.txt --output GCF_005871165.1_ASM587116v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:00,399] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:00,400] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg28ce5d3f-2cbf-4e44-a9d1-c3bb198e2374/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:00,400] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg28ce5d3f-2cbf-4e44-a9d1-c3bb198e2374/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:00,415] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:41:00,415] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:00,416] [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
Maricaulis alexandrii	strain=LZ-16-1	GCA_005871165.1	2570354	2570354	type	True	100.0	1110	1110	95	conclusive
Maricaulis maris	strain=DSM 4734	GCA_003634045.1	74318	74318	type	True	80.6198	661	1110	95	below_threshold
Maricaulis salignorans	strain=DSM 16077	GCA_900103475.1	144026	144026	type	True	78.9587	499	1110	95	below_threshold
Marinicauda pacifica	strain=P-1 km-3	GCA_004793635.1	1133559	1133559	type	True	77.6972	244	1110	95	below_threshold
Marinicauda pacifica	strain=CGMCC 1.11031	GCA_014636415.1	1133559	1133559	type	True	77.6941	241	1110	95	below_threshold
Hyphobacterium indicum	strain=2ED5	GCA_003129605.1	2162714	2162714	type	True	77.5677	235	1110	95	below_threshold
Glycocaulis alkaliphilus	strain=CGMCC 1.12428	GCA_014637625.1	1434191	1434191	type	True	77.4956	212	1110	95	below_threshold
Glycocaulis alkaliphilus	strain=6B-8	GCA_004000605.1	1434191	1434191	type	True	77.4927	212	1110	95	below_threshold
Martelella endophytica	strain=YC6887	GCA_000960975.1	1486262	1486262	type	True	76.8129	81	1110	95	below_threshold
Brevundimonas albigilva	strain=KEME 9005-016	GCA_023503965.1	1312364	1312364	type	True	76.8091	128	1110	95	below_threshold
Mesorhizobium australicum	strain=WSM2073	GCA_000230995.3	536018	536018	type	True	76.4788	96	1110	95	below_threshold
Xanthobacter oligotrophicus	strain=29k	GCA_008364685.1	2607286	2607286	type	True	76.3905	104	1110	95	below_threshold
Bradyrhizobium viridifuturi	strain=SEMIA 690	GCA_001238275.1	1654716	1654716	type	True	76.2242	102	1110	95	below_threshold
Methylobacterium radiotolerans	strain=JCM 2831	GCA_000019725.1	31998	31998	type	True	76.1751	106	1110	95	below_threshold
Thalassobius mangrovi	strain=GS-10	GCA_009857745.1	2692236	2692236	type	True	76.1058	90	1110	95	below_threshold
Microvirga roseola	strain=SM2	GCA_020866965.1	2883126	2883126	type	True	76.0866	94	1110	95	below_threshold
Azospirillum palustre	strain=B2	GCA_002573965.1	2044885	2044885	type	True	75.9778	128	1110	95	below_threshold
Rhodoligotrophos defluvii	strain=lm1	GCA_005281615.1	2561934	2561934	type	True	75.9244	83	1110	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:00,417] [INFO] DFAST Taxonomy check result was written to GCF_005871165.1_ASM587116v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:00,418] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:00,418] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:00,418] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg28ce5d3f-2cbf-4e44-a9d1-c3bb198e2374/dqc_reference/checkm_data
[2024-01-24 13:41:00,420] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:00,456] [INFO] Task started: CheckM
[2024-01-24 13:41:00,456] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005871165.1_ASM587116v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005871165.1_ASM587116v1_genomic.fna/checkm_input GCF_005871165.1_ASM587116v1_genomic.fna/checkm_result
[2024-01-24 13:41:52,865] [INFO] Task succeeded: CheckM
[2024-01-24 13:41:52,866] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:41:52,887] [INFO] ===== Completeness check finished =====
[2024-01-24 13:41:52,888] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:41:52,888] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005871165.1_ASM587116v1_genomic.fna/markers.fasta)
[2024-01-24 13:41:52,889] [INFO] Task started: Blastn
[2024-01-24 13:41:52,889] [INFO] Running command: blastn -query GCF_005871165.1_ASM587116v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg28ce5d3f-2cbf-4e44-a9d1-c3bb198e2374/dqc_reference/reference_markers_gtdb.fasta -out GCF_005871165.1_ASM587116v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:54,558] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:54,562] [INFO] Selected 9 target genomes.
[2024-01-24 13:41:54,562] [INFO] Target genome list was writen to GCF_005871165.1_ASM587116v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:41:54,568] [INFO] Task started: fastANI
[2024-01-24 13:41:54,569] [INFO] Running command: fastANI --query /var/lib/cwl/stg828856f2-3075-4b9c-852b-d3ad51c84a2e/GCF_005871165.1_ASM587116v1_genomic.fna.gz --refList GCF_005871165.1_ASM587116v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005871165.1_ASM587116v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:01,223] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:01,235] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:42:01,236] [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_005871165.1	s__Maricaulis sp005871165	100.0	1110	1110	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002694345.1	s__Maricaulis sp002694345	87.3964	545	1110	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016817355.1	s__Maricaulis parjimensis	86.729	917	1110	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017642925.1	s__Maricaulis sp017642925	82.0155	729	1110	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002707795.1	s__Maricaulis sp002707795	81.5916	536	1110	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	99.42	99.36	0.71	0.69	3	-
GCA_015665295.1	s__Maricaulis sp015665295	80.6643	633	1110	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003634045.1	s__Maricaulis maris	80.6382	659	1110	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	98.04	98.04	0.96	0.96	2	-
GCF_000014745.1	s__Maricaulis maris_A	80.5151	618	1110	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	98.51	98.49	0.94	0.92	3	-
GCA_905480005.1	s__Maricaulis sp905480005	80.1859	567	1110	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:42:01,238] [INFO] GTDB search result was written to GCF_005871165.1_ASM587116v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:01,238] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:01,242] [INFO] DFAST_QC result json was written to GCF_005871165.1_ASM587116v1_genomic.fna/dqc_result.json
[2024-01-24 13:42:01,242] [INFO] DFAST_QC completed!
[2024-01-24 13:42:01,242] [INFO] Total running time: 0h1m29s