[2024-01-24 13:18:55,570] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:18:55,573] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:18:55,573] [INFO] DQC Reference Directory: /var/lib/cwl/stgbd21c175-4050-4798-91c2-d555a830c752/dqc_reference
[2024-01-24 13:18:56,912] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:18:56,913] [INFO] Task started: Prodigal
[2024-01-24 13:18:56,913] [INFO] Running command: gunzip -c /var/lib/cwl/stg159b9249-34aa-45e6-bc1a-f61d64d9949a/GCF_016918935.1_ASM1691893v1_genomic.fna.gz | prodigal -d GCF_016918935.1_ASM1691893v1_genomic.fna/cds.fna -a GCF_016918935.1_ASM1691893v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:19:07,267] [INFO] Task succeeded: Prodigal
[2024-01-24 13:19:07,268] [INFO] Task started: HMMsearch
[2024-01-24 13:19:07,268] [INFO] Running command: hmmsearch --tblout GCF_016918935.1_ASM1691893v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbd21c175-4050-4798-91c2-d555a830c752/dqc_reference/reference_markers.hmm GCF_016918935.1_ASM1691893v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:19:07,547] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:19:07,548] [INFO] Found 6/6 markers.
[2024-01-24 13:19:07,589] [INFO] Query marker FASTA was written to GCF_016918935.1_ASM1691893v1_genomic.fna/markers.fasta
[2024-01-24 13:19:07,589] [INFO] Task started: Blastn
[2024-01-24 13:19:07,589] [INFO] Running command: blastn -query GCF_016918935.1_ASM1691893v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbd21c175-4050-4798-91c2-d555a830c752/dqc_reference/reference_markers.fasta -out GCF_016918935.1_ASM1691893v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:08,641] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:08,644] [INFO] Selected 22 target genomes.
[2024-01-24 13:19:08,644] [INFO] Target genome list was writen to GCF_016918935.1_ASM1691893v1_genomic.fna/target_genomes.txt
[2024-01-24 13:19:08,653] [INFO] Task started: fastANI
[2024-01-24 13:19:08,654] [INFO] Running command: fastANI --query /var/lib/cwl/stg159b9249-34aa-45e6-bc1a-f61d64d9949a/GCF_016918935.1_ASM1691893v1_genomic.fna.gz --refList GCF_016918935.1_ASM1691893v1_genomic.fna/target_genomes.txt --output GCF_016918935.1_ASM1691893v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:19:26,237] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:26,237] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbd21c175-4050-4798-91c2-d555a830c752/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:19:26,238] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbd21c175-4050-4798-91c2-d555a830c752/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:19:26,255] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:19:26,256] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:19:26,256] [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
Roseitranquillus sediminis	strain=MCCB 386	GCA_016918935.1	2809051	2809051	type	True	100.0	1225	1227	95	conclusive
Wenxinia marina	strain=DSM 24838	GCA_000379485.1	390641	390641	type	True	78.978	483	1227	95	below_threshold
Wenxinia marina	strain=DSM 24838	GCA_000836695.1	390641	390641	type	True	78.944	497	1227	95	below_threshold
Wenxinia marina	strain=CGMCC 1.6105	GCA_014645075.1	390641	390641	type	True	78.9425	490	1227	95	below_threshold
Roseivivax isoporae	strain=LMG 25204	GCA_000521865.1	591206	591206	type	True	78.6481	493	1227	95	below_threshold
Roseivivax halodurans	strain=JCM 10272	GCA_000521785.1	93683	93683	type	True	78.6129	405	1227	95	below_threshold
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	78.454	399	1227	95	below_threshold
Pseudooceanicola nanhaiensis	strain=DSM 18065	GCA_000688295.1	375761	375761	type	True	78.2884	431	1227	95	below_threshold
Pseudooceanicola nanhaiensis	strain=CGMCC 1.6293	GCA_014645095.1	375761	375761	type	True	78.2517	439	1227	95	below_threshold
Silicimonas algicola	strain=KC90	GCA_003970735.1	1826607	1826607	type	True	78.2071	362	1227	95	below_threshold
Silicimonas algicola	strain=DSM 103371	GCA_003148765.1	1826607	1826607	type	True	78.1503	368	1227	95	below_threshold
Roseivivax jejudonensis	strain=CECT 8625	GCA_900172265.1	1529041	1529041	type	True	78.1022	421	1227	95	below_threshold
Salipiger thiooxidans	strain=DSM 10146	GCA_900102075.1	282683	282683	type	True	78.0947	454	1227	95	below_threshold
Salipiger bermudensis	strain=HTCC2601	GCA_000153725.1	344736	344736	type	True	77.9371	438	1227	95	below_threshold
Cribrihabitans marinus	strain=DSM 29340	GCA_900109035.1	1227549	1227549	type	True	77.9009	358	1227	95	below_threshold
Cribrihabitans marinus	strain=CGMCC 1.13219	GCA_014640375.1	1227549	1227549	type	True	77.8657	353	1227	95	below_threshold
Rubellimicrobium roseum	strain=YIM 48858	GCA_006152145.1	687525	687525	type	True	77.7469	365	1227	95	below_threshold
Cereibacter ovatus	strain=JA234	GCA_900207575.1	439529	439529	type	True	77.6337	288	1227	95	below_threshold
Kangsaoukella pontilimi	strain=GH1-50	GCA_009830125.1	2691042	2691042	type	True	77.6237	292	1227	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	77.3515	267	1227	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	77.2477	255	1227	95	below_threshold
Marivivens aquimaris	strain=GSB7	GCA_015220045.1	2774876	2774876	type	True	76.6156	175	1227	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:19:26,258] [INFO] DFAST Taxonomy check result was written to GCF_016918935.1_ASM1691893v1_genomic.fna/tc_result.tsv
[2024-01-24 13:19:26,258] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:19:26,259] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:19:26,259] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbd21c175-4050-4798-91c2-d555a830c752/dqc_reference/checkm_data
[2024-01-24 13:19:26,262] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:19:26,310] [INFO] Task started: CheckM
[2024-01-24 13:19:26,310] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016918935.1_ASM1691893v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016918935.1_ASM1691893v1_genomic.fna/checkm_input GCF_016918935.1_ASM1691893v1_genomic.fna/checkm_result
[2024-01-24 13:20:01,113] [INFO] Task succeeded: CheckM
[2024-01-24 13:20:01,115] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:20:01,134] [INFO] ===== Completeness check finished =====
[2024-01-24 13:20:01,134] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:20:01,135] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016918935.1_ASM1691893v1_genomic.fna/markers.fasta)
[2024-01-24 13:20:01,135] [INFO] Task started: Blastn
[2024-01-24 13:20:01,135] [INFO] Running command: blastn -query GCF_016918935.1_ASM1691893v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbd21c175-4050-4798-91c2-d555a830c752/dqc_reference/reference_markers_gtdb.fasta -out GCF_016918935.1_ASM1691893v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:20:03,159] [INFO] Task succeeded: Blastn
[2024-01-24 13:20:03,162] [INFO] Selected 23 target genomes.
[2024-01-24 13:20:03,162] [INFO] Target genome list was writen to GCF_016918935.1_ASM1691893v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:20:03,250] [INFO] Task started: fastANI
[2024-01-24 13:20:03,250] [INFO] Running command: fastANI --query /var/lib/cwl/stg159b9249-34aa-45e6-bc1a-f61d64d9949a/GCF_016918935.1_ASM1691893v1_genomic.fna.gz --refList GCF_016918935.1_ASM1691893v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016918935.1_ASM1691893v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:20:20,265] [INFO] Task succeeded: fastANI
[2024-01-24 13:20:20,286] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:20:20,287] [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_016918935.1	s__MCCB-386 sp016918935	100.0	1225	1227	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__MCCB-386	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000379485.1	s__Wenxinia marina	78.9922	481	1227	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Wenxinia	95.0	99.99	99.99	0.99	0.99	3	-
GCF_000153305.1	s__Oceanicola granulosus	78.8414	484	1227	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115595.1	s__Tranquillimonas alkanivorans	78.8129	479	1227	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tranquillimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002869745.1	s__Oceaniglobus roseus	78.7216	472	1227	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceaniglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000521865.1	s__Roseivivax isoporae	78.6724	490	1227	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000521785.1	s__Roseivivax halodurans	78.613	405	1227	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003340565.1	s__HLUCCA09 sp003340565	78.5613	487	1227	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__HLUCCA09	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000688295.1	s__Pseudooceanicola nanhaiensis	78.3376	426	1227	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	100.00	100.00	1.00	1.00	2	-
GCA_015689705.1	s__HKCCE3408 sp015689705	78.2369	369	1227	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__HKCCE3408	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003148765.1	s__Silicimonas algicola	78.1706	366	1227	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Silicimonas	95.0	100.00	100.00	1.00	1.00	2	-
GCA_003605175.1	s__IMCC34051 sp003605175	78.0954	417	1227	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__IMCC34051	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001314685.1	s__HLUCCA09 sp001314685	78.0751	425	1227	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__HLUCCA09	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102075.1	s__Salipiger thiooxidans	78.0698	459	1227	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	97.34	95.88	0.90	0.85	6	-
GCF_002834145.1	s__Roseovarius salinarum	78.068	331	1227	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109035.1	s__Cribrihabitans marinus	77.891	359	1227	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cribrihabitans	95.0	100.00	100.00	0.99	0.99	2	-
GCF_003390865.1	s__HLUCCA09 sp003390865	77.8577	341	1227	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__HLUCCA09	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001314805.1	s__Roseicyclus sp001314805	77.8525	331	1227	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseicyclus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003651245.1	s__Roseovarius spongiae	77.7317	357	1227	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002720475.1	s__Roseovarius sp002720475	77.6964	254	1227	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	99.80	99.74	0.82	0.71	3	-
GCA_015487335.1	s__S012-89 sp015487335	77.5767	257	1227	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__S012-89	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003122205.1	s__QEYE01 sp003122205	77.4883	361	1227	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__QEYE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006227805.1	s__Aestuariivita sp006227805	77.4626	247	1227	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aestuariivita	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:20:20,289] [INFO] GTDB search result was written to GCF_016918935.1_ASM1691893v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:20:20,289] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:20:20,293] [INFO] DFAST_QC result json was written to GCF_016918935.1_ASM1691893v1_genomic.fna/dqc_result.json
[2024-01-24 13:20:20,294] [INFO] DFAST_QC completed!
[2024-01-24 13:20:20,294] [INFO] Total running time: 0h1m25s