[2024-01-24 13:22:01,486] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:22:01,489] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:22:01,489] [INFO] DQC Reference Directory: /var/lib/cwl/stg5a5aed35-0dc3-47a4-b50e-4c037353b66f/dqc_reference
[2024-01-24 13:22:02,834] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:22:02,835] [INFO] Task started: Prodigal
[2024-01-24 13:22:02,836] [INFO] Running command: gunzip -c /var/lib/cwl/stg8fc0fbf5-3cf6-4186-a0c2-891d3d415f1c/GCF_030285785.1_ASM3028578v1_genomic.fna.gz | prodigal -d GCF_030285785.1_ASM3028578v1_genomic.fna/cds.fna -a GCF_030285785.1_ASM3028578v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:22:18,953] [INFO] Task succeeded: Prodigal
[2024-01-24 13:22:18,953] [INFO] Task started: HMMsearch
[2024-01-24 13:22:18,954] [INFO] Running command: hmmsearch --tblout GCF_030285785.1_ASM3028578v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5a5aed35-0dc3-47a4-b50e-4c037353b66f/dqc_reference/reference_markers.hmm GCF_030285785.1_ASM3028578v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:22:19,330] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:22:19,332] [INFO] Found 6/6 markers.
[2024-01-24 13:22:19,373] [INFO] Query marker FASTA was written to GCF_030285785.1_ASM3028578v1_genomic.fna/markers.fasta
[2024-01-24 13:22:19,373] [INFO] Task started: Blastn
[2024-01-24 13:22:19,374] [INFO] Running command: blastn -query GCF_030285785.1_ASM3028578v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5a5aed35-0dc3-47a4-b50e-4c037353b66f/dqc_reference/reference_markers.fasta -out GCF_030285785.1_ASM3028578v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:20,108] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:20,112] [INFO] Selected 18 target genomes.
[2024-01-24 13:22:20,113] [INFO] Target genome list was writen to GCF_030285785.1_ASM3028578v1_genomic.fna/target_genomes.txt
[2024-01-24 13:22:20,124] [INFO] Task started: fastANI
[2024-01-24 13:22:20,125] [INFO] Running command: fastANI --query /var/lib/cwl/stg8fc0fbf5-3cf6-4186-a0c2-891d3d415f1c/GCF_030285785.1_ASM3028578v1_genomic.fna.gz --refList GCF_030285785.1_ASM3028578v1_genomic.fna/target_genomes.txt --output GCF_030285785.1_ASM3028578v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:22:36,644] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:36,645] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5a5aed35-0dc3-47a4-b50e-4c037353b66f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:22:36,645] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5a5aed35-0dc3-47a4-b50e-4c037353b66f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:22:36,660] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:22:36,660] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:22:36,660] [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 marina	strain=DSW4-44	GCA_005771405.1	2578117	2578117	type	True	80.4241	752	1667	95	below_threshold
Zongyanglinia huanghaiensis	strain=CY05	GCA_009753675.1	2682100	2682100	type	True	80.2376	761	1667	95	below_threshold
Pseudophaeobacter arcticus	strain=DSM 23566	GCA_000473205.1	385492	385492	type	True	79.1841	602	1667	95	below_threshold
Leisingera methylohalidivorans	strain=DSM 14336; MB2	GCA_000511355.1	133924	133924	type	True	79.0725	595	1667	95	below_threshold
Phaeobacter gallaeciensis	strain=DSM 26640	GCA_000511385.1	60890	60890	type	True	78.8669	480	1667	95	below_threshold
Leisingera aquimarina	strain=DSM 24565	GCA_000473165.1	476529	476529	type	True	78.834	595	1667	95	below_threshold
Leisingera aquaemixtae	strain=CECT 8399	GCA_001458395.1	1396826	1396826	type	True	78.8056	619	1667	95	below_threshold
Pseudophaeobacter flagellatus	strain=MA21411-1	GCA_021228235.1	2899119	2899119	type	True	78.6763	593	1667	95	below_threshold
Phaeobacter gallaeciensis	strain=DSM 26640	GCA_000819625.1	60890	60890	type	True	78.6477	472	1667	95	below_threshold
Phaeobacter porticola	strain=P97	GCA_001888185.1	1844006	1844006	type	True	78.5365	479	1667	95	below_threshold
Falsiruegeria litorea	strain=CECT 7639	GCA_900172225.1	1280831	1280831	type	True	77.9969	421	1667	95	below_threshold
Falsiruegeria mediterranea	strain=CECT 7615	GCA_900302455.1	1280832	1280832	type	True	77.9793	439	1667	95	below_threshold
Tritonibacter multivorans	strain=CECT 7557	GCA_001458415.1	928856	928856	type	True	77.9527	431	1667	95	below_threshold
Tritonibacter multivorans	strain=DSM 26470	GCA_900112515.1	928856	928856	type	True	77.9011	432	1667	95	below_threshold
Tritonibacter mobilis	strain=NBRC101030	GCA_001681715.1	379347	379347	type	True	77.86	400	1667	95	below_threshold
Cribrihabitans marinus	strain=CGMCC 1.13219	GCA_014640375.1	1227549	1227549	type	True	77.6337	424	1667	95	below_threshold
Sulfitobacter indolifex	strain=DSM 14862	GCA_022788655.1	225422	225422	type	True	77.4514	258	1667	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	76.6925	178	1667	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:22:36,662] [INFO] DFAST Taxonomy check result was written to GCF_030285785.1_ASM3028578v1_genomic.fna/tc_result.tsv
[2024-01-24 13:22:36,663] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:22:36,663] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:22:36,663] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5a5aed35-0dc3-47a4-b50e-4c037353b66f/dqc_reference/checkm_data
[2024-01-24 13:22:36,664] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:22:36,717] [INFO] Task started: CheckM
[2024-01-24 13:22:36,717] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030285785.1_ASM3028578v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030285785.1_ASM3028578v1_genomic.fna/checkm_input GCF_030285785.1_ASM3028578v1_genomic.fna/checkm_result
[2024-01-24 13:23:27,244] [INFO] Task succeeded: CheckM
[2024-01-24 13:23:27,245] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:23:27,267] [INFO] ===== Completeness check finished =====
[2024-01-24 13:23:27,268] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:23:27,268] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030285785.1_ASM3028578v1_genomic.fna/markers.fasta)
[2024-01-24 13:23:27,269] [INFO] Task started: Blastn
[2024-01-24 13:23:27,269] [INFO] Running command: blastn -query GCF_030285785.1_ASM3028578v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5a5aed35-0dc3-47a4-b50e-4c037353b66f/dqc_reference/reference_markers_gtdb.fasta -out GCF_030285785.1_ASM3028578v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:23:28,351] [INFO] Task succeeded: Blastn
[2024-01-24 13:23:28,356] [INFO] Selected 9 target genomes.
[2024-01-24 13:23:28,356] [INFO] Target genome list was writen to GCF_030285785.1_ASM3028578v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:23:28,384] [INFO] Task started: fastANI
[2024-01-24 13:23:28,385] [INFO] Running command: fastANI --query /var/lib/cwl/stg8fc0fbf5-3cf6-4186-a0c2-891d3d415f1c/GCF_030285785.1_ASM3028578v1_genomic.fna.gz --refList GCF_030285785.1_ASM3028578v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030285785.1_ASM3028578v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:23:37,892] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:37,905] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:23:37,905] [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_013214575.1	s__Parasedimentitalea sp013214575	93.6471	1360	1667	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	83.6281	1086	1667	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	82.8223	901	1667	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	82.6471	943	1667	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Parasedimentitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011813015.1	s__Parasedimentitalea sp011813015	81.776	953	1667	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Parasedimentitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005771405.1	s__Parasedimentitalea marina_A	80.4313	750	1667	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Parasedimentitalea	95.0	97.09	97.09	0.92	0.92	2	-
GCF_009753675.1	s__Parasedimentitalea huanghaiensis	80.2376	761	1667	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	79.0663	598	1667	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900143635.1	s__FREY01 sp900143635	78.8913	590	1667	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__FREY01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:23:37,906] [INFO] GTDB search result was written to GCF_030285785.1_ASM3028578v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:23:37,907] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:23:37,910] [INFO] DFAST_QC result json was written to GCF_030285785.1_ASM3028578v1_genomic.fna/dqc_result.json
[2024-01-24 13:23:37,910] [INFO] DFAST_QC completed!
[2024-01-24 13:23:37,910] [INFO] Total running time: 0h1m36s