[2024-01-24 13:57:42,730] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:42,732] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:42,732] [INFO] DQC Reference Directory: /var/lib/cwl/stg63d0152e-8532-4aa5-a442-5547bc252f81/dqc_reference
[2024-01-24 13:57:44,085] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:44,085] [INFO] Task started: Prodigal
[2024-01-24 13:57:44,086] [INFO] Running command: gunzip -c /var/lib/cwl/stgf86775d8-a063-4cce-a6d2-2bb1f90f5b10/GCF_009753675.1_ASM975367v1_genomic.fna.gz | prodigal -d GCF_009753675.1_ASM975367v1_genomic.fna/cds.fna -a GCF_009753675.1_ASM975367v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:57:59,360] [INFO] Task succeeded: Prodigal
[2024-01-24 13:57:59,361] [INFO] Task started: HMMsearch
[2024-01-24 13:57:59,361] [INFO] Running command: hmmsearch --tblout GCF_009753675.1_ASM975367v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg63d0152e-8532-4aa5-a442-5547bc252f81/dqc_reference/reference_markers.hmm GCF_009753675.1_ASM975367v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:57:59,686] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:57:59,688] [INFO] Found 6/6 markers.
[2024-01-24 13:57:59,733] [INFO] Query marker FASTA was written to GCF_009753675.1_ASM975367v1_genomic.fna/markers.fasta
[2024-01-24 13:57:59,733] [INFO] Task started: Blastn
[2024-01-24 13:57:59,733] [INFO] Running command: blastn -query GCF_009753675.1_ASM975367v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg63d0152e-8532-4aa5-a442-5547bc252f81/dqc_reference/reference_markers.fasta -out GCF_009753675.1_ASM975367v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:00,523] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:00,528] [INFO] Selected 17 target genomes.
[2024-01-24 13:58:00,528] [INFO] Target genome list was writen to GCF_009753675.1_ASM975367v1_genomic.fna/target_genomes.txt
[2024-01-24 13:58:00,537] [INFO] Task started: fastANI
[2024-01-24 13:58:00,537] [INFO] Running command: fastANI --query /var/lib/cwl/stgf86775d8-a063-4cce-a6d2-2bb1f90f5b10/GCF_009753675.1_ASM975367v1_genomic.fna.gz --refList GCF_009753675.1_ASM975367v1_genomic.fna/target_genomes.txt --output GCF_009753675.1_ASM975367v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:15,309] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:15,309] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg63d0152e-8532-4aa5-a442-5547bc252f81/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:15,310] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg63d0152e-8532-4aa5-a442-5547bc252f81/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:15,324] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:58:15,324] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:58:15,324] [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
Zongyanglinia huanghaiensis	strain=CY05	GCA_009753675.1	2682100	2682100	type	True	100.0	1597	1599	95	conclusive
Zongyanglinia marina	strain=DSW4-44	GCA_005771405.1	2578117	2578117	type	True	94.4802	1415	1599	95	below_threshold
Pseudophaeobacter arcticus	strain=DSM 23566	GCA_000473205.1	385492	385492	type	True	78.1317	416	1599	95	below_threshold
Pseudophaeobacter flagellatus	strain=MA21411-1	GCA_021228235.1	2899119	2899119	type	True	77.9607	375	1599	95	below_threshold
Pseudophaeobacter leonis	strain=306	GCA_002087335.1	1144477	1144477	type	True	77.8657	383	1599	95	below_threshold
Leisingera aquimarina	strain=DSM 24565	GCA_000473165.1	476529	476529	type	True	77.7706	362	1599	95	below_threshold
Phaeobacter italicus	strain=CECT 7645	GCA_001258055.1	481446	481446	type	True	77.7683	354	1599	95	below_threshold
Phaeobacter italicus	strain=CECT 7645	GCA_001404195.1	481446	481446	type	True	77.7595	355	1599	95	below_threshold
Phaeobacter piscinae	strain=P14	GCA_002407245.1	1580596	1580596	type	True	77.7517	357	1599	95	below_threshold
Leisingera methylohalidivorans	strain=DSM 14336; MB2	GCA_000511355.1	133924	133924	type	True	77.7473	379	1599	95	below_threshold
Leisingera daeponensis	strain=DSM 23529	GCA_000473145.1	405746	405746	type	True	77.7406	364	1599	95	below_threshold
Phaeobacter italicus	strain=DSM 26436	GCA_900113345.1	481446	481446	type	True	77.7208	352	1599	95	below_threshold
Phaeobacter porticola	strain=P97	GCA_001888185.1	1844006	1844006	type	True	77.7119	340	1599	95	below_threshold
Falsiruegeria litorea	strain=CECT 7639	GCA_900172225.1	1280831	1280831	type	True	77.6272	299	1599	95	below_threshold
Phaeobacter inhibens	strain=DSM 16374	GCA_000473105.1	221822	221822	type	True	77.5814	364	1599	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	76.481	149	1599	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	76.3717	100	1599	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:15,326] [INFO] DFAST Taxonomy check result was written to GCF_009753675.1_ASM975367v1_genomic.fna/tc_result.tsv
[2024-01-24 13:58:15,326] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:15,327] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:15,327] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg63d0152e-8532-4aa5-a442-5547bc252f81/dqc_reference/checkm_data
[2024-01-24 13:58:15,328] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:15,376] [INFO] Task started: CheckM
[2024-01-24 13:58:15,377] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009753675.1_ASM975367v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009753675.1_ASM975367v1_genomic.fna/checkm_input GCF_009753675.1_ASM975367v1_genomic.fna/checkm_result
[2024-01-24 13:59:02,952] [INFO] Task succeeded: CheckM
[2024-01-24 13:59:02,953] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:59:02,983] [INFO] ===== Completeness check finished =====
[2024-01-24 13:59:02,983] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:59:02,984] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009753675.1_ASM975367v1_genomic.fna/markers.fasta)
[2024-01-24 13:59:02,984] [INFO] Task started: Blastn
[2024-01-24 13:59:02,984] [INFO] Running command: blastn -query GCF_009753675.1_ASM975367v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg63d0152e-8532-4aa5-a442-5547bc252f81/dqc_reference/reference_markers_gtdb.fasta -out GCF_009753675.1_ASM975367v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:03,998] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:04,002] [INFO] Selected 11 target genomes.
[2024-01-24 13:59:04,002] [INFO] Target genome list was writen to GCF_009753675.1_ASM975367v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:59:04,020] [INFO] Task started: fastANI
[2024-01-24 13:59:04,020] [INFO] Running command: fastANI --query /var/lib/cwl/stgf86775d8-a063-4cce-a6d2-2bb1f90f5b10/GCF_009753675.1_ASM975367v1_genomic.fna.gz --refList GCF_009753675.1_ASM975367v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009753675.1_ASM975367v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:59:14,007] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:14,023] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:59:14,024] [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_009753675.1	s__Parasedimentitalea huanghaiensis	100.0	1597	1599	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Parasedimentitalea	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_005771405.1	s__Parasedimentitalea marina_A	94.4675	1416	1599	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Parasedimentitalea	95.0	97.09	97.09	0.92	0.92	2	-
GCF_011813015.1	s__Parasedimentitalea sp011813015	81.9724	749	1599	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Parasedimentitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004006175.1	s__Parasedimentitalea marina	80.6947	748	1599	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Parasedimentitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002162795.1	s__Parasedimentitalea sp002162795	80.195	732	1599	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Parasedimentitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013214575.1	s__Parasedimentitalea sp013214575	80.1337	743	1599	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Parasedimentitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002401945.1	s__Parasedimentitalea sp002401945	79.8508	685	1599	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Parasedimentitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000511355.1	s__Leisingera methylohalidivorans	77.7537	380	1599	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009363615.1	s__Ruegeria sp009363615	77.1971	241	1599	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	97.20	96.03	0.88	0.85	16	-
GCF_013032025.1	s__Ruegeria atlantica_C	77.1739	245	1599	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	100.00	100.00	0.99	0.99	2	-
GCF_003443535.1	s__Ruegeria sp003443535	77.0343	259	1599	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:59:14,025] [INFO] GTDB search result was written to GCF_009753675.1_ASM975367v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:59:14,026] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:59:14,032] [INFO] DFAST_QC result json was written to GCF_009753675.1_ASM975367v1_genomic.fna/dqc_result.json
[2024-01-24 13:59:14,033] [INFO] DFAST_QC completed!
[2024-01-24 13:59:14,033] [INFO] Total running time: 0h1m31s