[2024-01-25 19:54:05,594] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:54:05,595] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:54:05,595] [INFO] DQC Reference Directory: /var/lib/cwl/stgca28a799-8e4d-4bdc-974b-6feb886c249c/dqc_reference
[2024-01-25 19:54:06,719] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:54:06,720] [INFO] Task started: Prodigal
[2024-01-25 19:54:06,720] [INFO] Running command: gunzip -c /var/lib/cwl/stg63c5ad9f-2fcc-4f8c-8e55-3da587cead96/GCF_003385555.1_ASM338555v1_genomic.fna.gz | prodigal -d GCF_003385555.1_ASM338555v1_genomic.fna/cds.fna -a GCF_003385555.1_ASM338555v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:54:13,655] [INFO] Task succeeded: Prodigal
[2024-01-25 19:54:13,656] [INFO] Task started: HMMsearch
[2024-01-25 19:54:13,656] [INFO] Running command: hmmsearch --tblout GCF_003385555.1_ASM338555v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgca28a799-8e4d-4bdc-974b-6feb886c249c/dqc_reference/reference_markers.hmm GCF_003385555.1_ASM338555v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:54:13,848] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:54:13,849] [INFO] Found 6/6 markers.
[2024-01-25 19:54:13,875] [INFO] Query marker FASTA was written to GCF_003385555.1_ASM338555v1_genomic.fna/markers.fasta
[2024-01-25 19:54:13,875] [INFO] Task started: Blastn
[2024-01-25 19:54:13,876] [INFO] Running command: blastn -query GCF_003385555.1_ASM338555v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgca28a799-8e4d-4bdc-974b-6feb886c249c/dqc_reference/reference_markers.fasta -out GCF_003385555.1_ASM338555v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:54:14,923] [INFO] Task succeeded: Blastn
[2024-01-25 19:54:14,925] [INFO] Selected 28 target genomes.
[2024-01-25 19:54:14,926] [INFO] Target genome list was writen to GCF_003385555.1_ASM338555v1_genomic.fna/target_genomes.txt
[2024-01-25 19:54:14,959] [INFO] Task started: fastANI
[2024-01-25 19:54:14,959] [INFO] Running command: fastANI --query /var/lib/cwl/stg63c5ad9f-2fcc-4f8c-8e55-3da587cead96/GCF_003385555.1_ASM338555v1_genomic.fna.gz --refList GCF_003385555.1_ASM338555v1_genomic.fna/target_genomes.txt --output GCF_003385555.1_ASM338555v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:54:37,390] [INFO] Task succeeded: fastANI
[2024-01-25 19:54:37,390] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgca28a799-8e4d-4bdc-974b-6feb886c249c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:54:37,390] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgca28a799-8e4d-4bdc-974b-6feb886c249c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:54:37,406] [INFO] Found 28 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:54:37,406] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:54:37,406] [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
Roseivivax isoporae	strain=LMG 25204	GCA_000521865.1	591206	591206	type	True	79.9203	601	1007	95	below_threshold
Roseivivax halodurans	strain=JCM 10272	GCA_000521785.1	93683	93683	type	True	79.6166	519	1007	95	below_threshold
Limimaricola pyoseonensis	strain=DSM 21424	GCA_900102015.1	521013	521013	type	True	79.5749	548	1007	95	below_threshold
Salipiger profundus	strain=CGMCC 1.12377	GCA_014637265.1	1229727	1229727	type	True	79.4749	523	1007	95	below_threshold
Roseivivax marinus	strain=DSM 27511	GCA_900109705.1	1379903	1379903	type	True	79.3555	504	1007	95	below_threshold
Roseivivax jejudonensis	strain=CECT 8625	GCA_900172265.1	1529041	1529041	type	True	79.3169	537	1007	95	below_threshold
Roseivivax lentus	strain=DSM 29430	GCA_900156805.1	633194	633194	type	True	79.2011	553	1007	95	below_threshold
Salipiger thiooxidans	strain=DSM 10146	GCA_900102075.1	282683	282683	type	True	79.1119	560	1007	95	below_threshold
Wenxinia saemankumensis	strain=DSM 100565	GCA_900141735.1	1447782	1447782	type	True	79.0065	495	1007	95	below_threshold
Allosediminivita pacifica	strain=CGMCC 1.12410	GCA_014637495.1	1267769	1267769	type	True	78.9779	494	1007	95	below_threshold
Pseudoroseicyclus aestuarii	strain=CECT 9025	GCA_003217255.1	1795041	1795041	type	True	78.7892	423	1007	95	below_threshold
Rubellimicrobium roseum	strain=YIM 48858	GCA_006152145.1	687525	687525	type	True	78.6409	421	1007	95	below_threshold
Jannaschia marina	strain=SHC163	GCA_013404595.1	2741674	2741674	type	True	78.6337	450	1007	95	below_threshold
Rhodovulum euryhalinum	strain=DSM 4868	GCA_004342445.1	35805	35805	type	True	78.5957	442	1007	95	below_threshold
Roseivivax halotolerans	strain=JCM 10271	GCA_900115815.1	93684	93684	type	True	78.4751	422	1007	95	below_threshold
Roseovarius indicus	strain=DSM 26383	GCA_900112725.1	540747	540747	type	True	78.4379	470	1007	95	below_threshold
Pseudoroseicyclus tamaricis	strain=CLL3-39	GCA_010435925.1	2705421	2705421	type	True	78.4127	481	1007	95	below_threshold
Halovulum dunhuangense	strain=YYQ-30	GCA_013093415.1	1505036	1505036	type	True	78.4008	390	1007	95	below_threshold
Sinirhodobacter hankyongi	strain=BO-81	GCA_003664585.1	2294033	2294033	type	True	78.3961	454	1007	95	below_threshold
Roseovarius indicus	strain=DSM 26383	GCA_008728195.1	540747	540747	type	True	78.3955	474	1007	95	below_threshold
Rubellimicrobium aerolatum	strain=DSM 19297	GCA_017872975.1	490979	490979	type	True	78.3739	427	1007	95	below_threshold
Halovulum marinum	strain=2CG4	GCA_009697225.1	2662447	2662447	type	True	78.3623	459	1007	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	78.3542	470	1007	95	below_threshold
Roseovarius indicus	strain=B108	GCA_001441635.1	540747	540747	type	True	78.3436	484	1007	95	below_threshold
Rhodovulum strictum	strain=DSM 11289	GCA_009649175.1	58314	58314	type	True	78.2171	435	1007	95	below_threshold
Palleronia rufa	strain=MOLA 401	GCA_000743715.1	1530186	1530186	type	True	78.0512	352	1007	95	below_threshold
Pelagivirga sediminicola	strain=BH-SD19	GCA_003072125.1	2170575	2170575	type	True	77.7551	379	1007	95	below_threshold
Paracoccus mutanolyticus	strain=RSP-02	GCA_003285265.1	1499308	1499308	type	True	77.5534	327	1007	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:54:37,408] [INFO] DFAST Taxonomy check result was written to GCF_003385555.1_ASM338555v1_genomic.fna/tc_result.tsv
[2024-01-25 19:54:37,408] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:54:37,408] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:54:37,409] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgca28a799-8e4d-4bdc-974b-6feb886c249c/dqc_reference/checkm_data
[2024-01-25 19:54:37,409] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:54:37,441] [INFO] Task started: CheckM
[2024-01-25 19:54:37,441] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003385555.1_ASM338555v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003385555.1_ASM338555v1_genomic.fna/checkm_input GCF_003385555.1_ASM338555v1_genomic.fna/checkm_result
[2024-01-25 19:55:04,379] [INFO] Task succeeded: CheckM
[2024-01-25 19:55:04,380] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:55:04,412] [INFO] ===== Completeness check finished =====
[2024-01-25 19:55:04,412] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:55:04,413] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003385555.1_ASM338555v1_genomic.fna/markers.fasta)
[2024-01-25 19:55:04,413] [INFO] Task started: Blastn
[2024-01-25 19:55:04,413] [INFO] Running command: blastn -query GCF_003385555.1_ASM338555v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgca28a799-8e4d-4bdc-974b-6feb886c249c/dqc_reference/reference_markers_gtdb.fasta -out GCF_003385555.1_ASM338555v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:55:06,578] [INFO] Task succeeded: Blastn
[2024-01-25 19:55:06,582] [INFO] Selected 17 target genomes.
[2024-01-25 19:55:06,582] [INFO] Target genome list was writen to GCF_003385555.1_ASM338555v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:55:06,603] [INFO] Task started: fastANI
[2024-01-25 19:55:06,603] [INFO] Running command: fastANI --query /var/lib/cwl/stg63c5ad9f-2fcc-4f8c-8e55-3da587cead96/GCF_003385555.1_ASM338555v1_genomic.fna.gz --refList GCF_003385555.1_ASM338555v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003385555.1_ASM338555v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:55:22,075] [INFO] Task succeeded: fastANI
[2024-01-25 19:55:22,086] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:55:22,087] [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_003385555.1	s__Rhodosalinus sediminis	100.0	1004	1007	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodosalinus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003298775.1	s__Rhodosalinus sp003298775	85.6078	792	1007	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodosalinus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000521865.1	s__Roseivivax isoporae	79.9339	599	1007	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002834145.1	s__Roseovarius salinarum	79.7164	522	1007	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102015.1	s__Limimaricola pyoseonensis	79.5289	553	1007	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Limimaricola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002166865.1	s__Roseovarius sp002166865	79.4974	536	1007	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000153305.1	s__Oceanicola granulosus	79.4407	538	1007	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018139985.1	s__JAGSOU01 sp018139985	79.4052	543	1007	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAGSOU01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900172265.1	s__Roseivivax jejudonensis	79.3226	537	1007	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008710275.1	s__Oceanicola sp008710275	79.2753	478	1007	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112685.1	s__Roseivivax sediminis	79.2608	535	1007	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156805.1	s__Roseivivax lentus	79.1915	554	1007	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003789055.1	s__Oceanicola lentulus	79.1097	531	1007	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900141735.1	s__Wenxinia saemankumensis	79.0113	494	1007	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Wenxinia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001975705.1	s__Salipiger abyssi	78.6577	497	1007	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002967695.1	s__Rhodobaculum sp002967695	78.4784	438	1007	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017916275.1	s__Rubellimicrobium sp017916275	78.1806	355	1007	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rubellimicrobium	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-25 19:55:22,088] [INFO] GTDB search result was written to GCF_003385555.1_ASM338555v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:55:22,089] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:55:22,092] [INFO] DFAST_QC result json was written to GCF_003385555.1_ASM338555v1_genomic.fna/dqc_result.json
[2024-01-25 19:55:22,093] [INFO] DFAST_QC completed!
[2024-01-25 19:55:22,093] [INFO] Total running time: 0h1m16s