[2024-01-24 14:30:44,470] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:30:44,472] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:30:44,472] [INFO] DQC Reference Directory: /var/lib/cwl/stgb054d47e-bd2c-46dd-8ad2-eb0e1d19a66b/dqc_reference
[2024-01-24 14:30:45,862] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:30:45,863] [INFO] Task started: Prodigal
[2024-01-24 14:30:45,863] [INFO] Running command: gunzip -c /var/lib/cwl/stg6f29fea4-beb9-4169-bbde-1ed8762295cb/GCF_029210495.1_ASM2921049v1_genomic.fna.gz | prodigal -d GCF_029210495.1_ASM2921049v1_genomic.fna/cds.fna -a GCF_029210495.1_ASM2921049v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:30:55,577] [INFO] Task succeeded: Prodigal
[2024-01-24 14:30:55,578] [INFO] Task started: HMMsearch
[2024-01-24 14:30:55,578] [INFO] Running command: hmmsearch --tblout GCF_029210495.1_ASM2921049v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb054d47e-bd2c-46dd-8ad2-eb0e1d19a66b/dqc_reference/reference_markers.hmm GCF_029210495.1_ASM2921049v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:30:55,852] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:30:55,853] [INFO] Found 6/6 markers.
[2024-01-24 14:30:55,894] [INFO] Query marker FASTA was written to GCF_029210495.1_ASM2921049v1_genomic.fna/markers.fasta
[2024-01-24 14:30:55,895] [INFO] Task started: Blastn
[2024-01-24 14:30:55,895] [INFO] Running command: blastn -query GCF_029210495.1_ASM2921049v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb054d47e-bd2c-46dd-8ad2-eb0e1d19a66b/dqc_reference/reference_markers.fasta -out GCF_029210495.1_ASM2921049v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:30:56,952] [INFO] Task succeeded: Blastn
[2024-01-24 14:30:56,956] [INFO] Selected 19 target genomes.
[2024-01-24 14:30:56,956] [INFO] Target genome list was writen to GCF_029210495.1_ASM2921049v1_genomic.fna/target_genomes.txt
[2024-01-24 14:30:56,960] [INFO] Task started: fastANI
[2024-01-24 14:30:56,961] [INFO] Running command: fastANI --query /var/lib/cwl/stg6f29fea4-beb9-4169-bbde-1ed8762295cb/GCF_029210495.1_ASM2921049v1_genomic.fna.gz --refList GCF_029210495.1_ASM2921049v1_genomic.fna/target_genomes.txt --output GCF_029210495.1_ASM2921049v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:31:11,117] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:11,118] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb054d47e-bd2c-46dd-8ad2-eb0e1d19a66b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:31:11,118] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb054d47e-bd2c-46dd-8ad2-eb0e1d19a66b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:31:11,133] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:31:11,133] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:31:11,133] [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
Thioclava pacifica	strain=DSM 10166	GCA_000714535.1	285109	285109	type	True	80.7014	576	982	95	below_threshold
Thioclava marina	strain=11.10-0-13	GCA_002020135.1	1915077	1915077	type	True	80.693	580	982	95	below_threshold
Thioclava atlantica	strain=13D2W-2	GCA_000737065.1	1317124	1317124	type	True	80.6411	579	982	95	below_threshold
Thioclava electrotropha	strain=Elox9	GCA_002085925.2	1549850	1549850	type	True	80.5695	596	982	95	below_threshold
Sinirhodobacter hankyongi	strain=BO-81	GCA_003664585.1	2294033	2294033	type	True	80.5477	546	982	95	below_threshold
Thioclava sediminum	strain=TAW-CT134	GCA_002020355.1	1915319	1915319	type	True	80.5437	580	982	95	below_threshold
Sinirhodobacter huangdaonensis	strain=CGMCC 1.12963	GCA_004022465.1	2501515	2501515	type	True	80.4137	550	982	95	below_threshold
Sinirhodobacter ferrireducens	strain=CCTCC AB2012026	GCA_004022265.1	1215032	1215032	type	True	80.2477	556	982	95	below_threshold
Thioclava nitratireducens	strain=25B10_4	GCA_001940525.2	1915078	1915078	type	True	80.1925	571	982	95	below_threshold
Rhodobacter capsulatus	strain=DSM 1710	GCA_003254295.1	1061	1061	type	True	79.6011	504	982	95	below_threshold
Rhodobacter viridis	strain=JA737	GCA_003217355.1	1054202	1054202	type	True	79.5597	500	982	95	below_threshold
Phaeovulum vinaykumarii	strain=JA123	GCA_900217755.1	407234	407234	type	True	79.3001	466	982	95	below_threshold
Phaeovulum vinaykumarii	strain=DSM 18714	GCA_900156695.1	407234	407234	type	True	79.2753	462	982	95	below_threshold
Rhodobacter aestuarii	strain=DSM 19945	GCA_900156655.1	453582	453582	type	True	78.7293	393	982	95	below_threshold
Cereibacter ovatus	strain=JA234	GCA_900207575.1	439529	439529	type	True	78.3475	369	982	95	below_threshold
Paracoccus mutanolyticus	strain=RSP-02	GCA_003285265.1	1499308	1499308	type	True	78.1936	305	982	95	below_threshold
Halovulum dunhuangense	strain=YYQ-30	GCA_013093415.1	1505036	1505036	type	True	77.7442	288	982	95	below_threshold
Mangrovicoccus algicola	strain=HB182678	GCA_014903745.1	2771008	2771008	type	True	77.7069	316	982	95	below_threshold
Paracoccus nototheniae	strain=I-41R45	GCA_004335005.1	2489002	2489002	type	True	77.6486	310	982	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:31:11,135] [INFO] DFAST Taxonomy check result was written to GCF_029210495.1_ASM2921049v1_genomic.fna/tc_result.tsv
[2024-01-24 14:31:11,136] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:31:11,136] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:31:11,136] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb054d47e-bd2c-46dd-8ad2-eb0e1d19a66b/dqc_reference/checkm_data
[2024-01-24 14:31:11,137] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:31:11,169] [INFO] Task started: CheckM
[2024-01-24 14:31:11,170] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_029210495.1_ASM2921049v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_029210495.1_ASM2921049v1_genomic.fna/checkm_input GCF_029210495.1_ASM2921049v1_genomic.fna/checkm_result
[2024-01-24 14:31:44,306] [INFO] Task succeeded: CheckM
[2024-01-24 14:31:44,307] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:31:44,325] [INFO] ===== Completeness check finished =====
[2024-01-24 14:31:44,325] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:31:44,326] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_029210495.1_ASM2921049v1_genomic.fna/markers.fasta)
[2024-01-24 14:31:44,326] [INFO] Task started: Blastn
[2024-01-24 14:31:44,326] [INFO] Running command: blastn -query GCF_029210495.1_ASM2921049v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb054d47e-bd2c-46dd-8ad2-eb0e1d19a66b/dqc_reference/reference_markers_gtdb.fasta -out GCF_029210495.1_ASM2921049v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:46,203] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:46,208] [INFO] Selected 17 target genomes.
[2024-01-24 14:31:46,208] [INFO] Target genome list was writen to GCF_029210495.1_ASM2921049v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:31:46,216] [INFO] Task started: fastANI
[2024-01-24 14:31:46,216] [INFO] Running command: fastANI --query /var/lib/cwl/stg6f29fea4-beb9-4169-bbde-1ed8762295cb/GCF_029210495.1_ASM2921049v1_genomic.fna.gz --refList GCF_029210495.1_ASM2921049v1_genomic.fna/target_genomes_gtdb.txt --output GCF_029210495.1_ASM2921049v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:31:58,281] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:58,297] [INFO] Found 17 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 14:31:58,297] [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_002358085.1	s__Thioclava arenosa	82.458	637	982	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thioclava	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001856665.1	s__LPB0142 sp001856665	80.979	609	982	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__LPB0142	95.0	98.52	98.52	0.91	0.91	2	-
GCA_002452815.1	s__UBA6796 sp002452815	80.7243	642	982	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA6796	95.0	97.98	97.98	0.95	0.95	2	-
GCF_000714535.1	s__Thioclava pacifica	80.7014	576	982	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thioclava	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002020135.1	s__Thioclava marina	80.6891	580	982	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thioclava	95.0	98.70	98.47	0.89	0.86	6	-
GCF_009296265.1	s__Thioclava sp009296265	80.6528	570	982	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thioclava	96.2474	N/A	N/A	N/A	N/A	1	-
GCA_014763785.1	s__SZUA-611 sp014763785	80.6328	507	982	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__SZUA-611	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000737065.1	s__Thioclava atlantica	80.6305	580	982	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thioclava	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002563775.1	s__Thioclava sp002563775	80.6029	594	982	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thioclava	95.0406	95.45	95.45	0.86	0.86	2	-
GCF_003664585.1	s__Paenirhodobacter hankyongi	80.5826	542	982	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paenirhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002020355.1	s__Thioclava sediminum	80.5268	580	982	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thioclava	96.2561	96.53	96.29	0.92	0.90	8	-
GCA_003249215.1	s__SZUA-611 sp003249215	80.5125	507	982	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__SZUA-611	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004022265.1	s__Paenirhodobacter ferrireducens	80.2785	553	982	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paenirhodobacter	95.0	96.45	95.14	0.91	0.87	4	-
GCF_001940525.2	s__Thioclava nitratireducens	80.2118	570	982	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thioclava	95.0	98.60	98.50	0.92	0.89	7	-
GCF_003254295.1	s__Rhodobacter capsulatus	79.6269	501	982	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobacter	95.0	99.61	98.47	0.97	0.92	5	-
GCF_005144475.1	s__Rhodobacter capsulatus_C	79.6208	489	982	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004022215.1	s__Paenirhodobacter populi	79.3658	415	982	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paenirhodobacter	95.0	97.06	96.55	0.86	0.79	5	-
--------------------------------------------------------------------------------
[2024-01-24 14:31:58,299] [INFO] GTDB search result was written to GCF_029210495.1_ASM2921049v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:31:58,299] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:31:58,303] [INFO] DFAST_QC result json was written to GCF_029210495.1_ASM2921049v1_genomic.fna/dqc_result.json
[2024-01-24 14:31:58,303] [INFO] DFAST_QC completed!
[2024-01-24 14:31:58,303] [INFO] Total running time: 0h1m14s