[2024-01-24 12:39:39,991] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:39:39,994] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:39:39,994] [INFO] DQC Reference Directory: /var/lib/cwl/stg4866de9f-d13d-4dc7-ad78-7f47450b69d1/dqc_reference
[2024-01-24 12:39:41,294] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:39:41,295] [INFO] Task started: Prodigal
[2024-01-24 12:39:41,295] [INFO] Running command: gunzip -c /var/lib/cwl/stg603fdb60-8515-419f-b844-53041a046f47/GCF_005771405.1_ASM577140v1_genomic.fna.gz | prodigal -d GCF_005771405.1_ASM577140v1_genomic.fna/cds.fna -a GCF_005771405.1_ASM577140v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:39:57,252] [INFO] Task succeeded: Prodigal
[2024-01-24 12:39:57,252] [INFO] Task started: HMMsearch
[2024-01-24 12:39:57,253] [INFO] Running command: hmmsearch --tblout GCF_005771405.1_ASM577140v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4866de9f-d13d-4dc7-ad78-7f47450b69d1/dqc_reference/reference_markers.hmm GCF_005771405.1_ASM577140v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:39:57,588] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:39:57,589] [INFO] Found 6/6 markers.
[2024-01-24 12:39:57,633] [INFO] Query marker FASTA was written to GCF_005771405.1_ASM577140v1_genomic.fna/markers.fasta
[2024-01-24 12:39:57,634] [INFO] Task started: Blastn
[2024-01-24 12:39:57,634] [INFO] Running command: blastn -query GCF_005771405.1_ASM577140v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4866de9f-d13d-4dc7-ad78-7f47450b69d1/dqc_reference/reference_markers.fasta -out GCF_005771405.1_ASM577140v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:39:58,385] [INFO] Task succeeded: Blastn
[2024-01-24 12:39:58,390] [INFO] Selected 15 target genomes.
[2024-01-24 12:39:58,391] [INFO] Target genome list was writen to GCF_005771405.1_ASM577140v1_genomic.fna/target_genomes.txt
[2024-01-24 12:39:58,396] [INFO] Task started: fastANI
[2024-01-24 12:39:58,397] [INFO] Running command: fastANI --query /var/lib/cwl/stg603fdb60-8515-419f-b844-53041a046f47/GCF_005771405.1_ASM577140v1_genomic.fna.gz --refList GCF_005771405.1_ASM577140v1_genomic.fna/target_genomes.txt --output GCF_005771405.1_ASM577140v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:40:12,610] [INFO] Task succeeded: fastANI
[2024-01-24 12:40:12,610] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4866de9f-d13d-4dc7-ad78-7f47450b69d1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:40:12,611] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4866de9f-d13d-4dc7-ad78-7f47450b69d1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:40:12,623] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:40:12,623] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:40:12,623] [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	100.0	1605	1605	95	conclusive
Zongyanglinia huanghaiensis	strain=CY05	GCA_009753675.1	2682100	2682100	type	True	94.5268	1427	1605	95	below_threshold
Pseudophaeobacter arcticus	strain=DSM 23566	GCA_000473205.1	385492	385492	type	True	78.0267	410	1605	95	below_threshold
Leisingera aquimarina	strain=DSM 24565	GCA_000473165.1	476529	476529	type	True	78.0259	356	1605	95	below_threshold
Phaeobacter piscinae	strain=P14	GCA_002407245.1	1580596	1580596	type	True	77.9938	365	1605	95	below_threshold
Pseudophaeobacter leonis	strain=306	GCA_002087335.1	1144477	1144477	type	True	77.9809	387	1605	95	below_threshold
Phaeobacter italicus	strain=CECT 7645	GCA_001258055.1	481446	481446	type	True	77.921	326	1605	95	below_threshold
Phaeobacter italicus	strain=CECT 7645	GCA_001404195.1	481446	481446	type	True	77.921	326	1605	95	below_threshold
Phaeobacter italicus	strain=DSM 26436	GCA_900113345.1	481446	481446	type	True	77.8393	325	1605	95	below_threshold
Phaeobacter porticola	strain=P97	GCA_001888185.1	1844006	1844006	type	True	77.7779	321	1605	95	below_threshold
Pseudophaeobacter flagellatus	strain=MA21411-1	GCA_021228235.1	2899119	2899119	type	True	77.7285	384	1605	95	below_threshold
Falsiruegeria litorea	strain=CECT 7639	GCA_900172225.1	1280831	1280831	type	True	77.6896	300	1605	95	below_threshold
Leisingera methylohalidivorans	strain=DSM 14336; MB2	GCA_000511355.1	133924	133924	type	True	77.6313	356	1605	95	below_threshold
Gemmobacter fulva	strain=con5	GCA_018798885.1	2840474	2840474	type	True	76.6836	114	1605	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	76.6181	94	1605	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:40:12,625] [INFO] DFAST Taxonomy check result was written to GCF_005771405.1_ASM577140v1_genomic.fna/tc_result.tsv
[2024-01-24 12:40:12,627] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:40:12,628] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:40:12,628] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4866de9f-d13d-4dc7-ad78-7f47450b69d1/dqc_reference/checkm_data
[2024-01-24 12:40:12,630] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:40:12,680] [INFO] Task started: CheckM
[2024-01-24 12:40:12,680] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005771405.1_ASM577140v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005771405.1_ASM577140v1_genomic.fna/checkm_input GCF_005771405.1_ASM577140v1_genomic.fna/checkm_result
[2024-01-24 12:40:59,441] [INFO] Task succeeded: CheckM
[2024-01-24 12:40:59,443] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:40:59,464] [INFO] ===== Completeness check finished =====
[2024-01-24 12:40:59,465] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:40:59,465] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005771405.1_ASM577140v1_genomic.fna/markers.fasta)
[2024-01-24 12:40:59,465] [INFO] Task started: Blastn
[2024-01-24 12:40:59,466] [INFO] Running command: blastn -query GCF_005771405.1_ASM577140v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4866de9f-d13d-4dc7-ad78-7f47450b69d1/dqc_reference/reference_markers_gtdb.fasta -out GCF_005771405.1_ASM577140v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:41:00,383] [INFO] Task succeeded: Blastn
[2024-01-24 12:41:00,387] [INFO] Selected 11 target genomes.
[2024-01-24 12:41:00,388] [INFO] Target genome list was writen to GCF_005771405.1_ASM577140v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:41:00,422] [INFO] Task started: fastANI
[2024-01-24 12:41:00,422] [INFO] Running command: fastANI --query /var/lib/cwl/stg603fdb60-8515-419f-b844-53041a046f47/GCF_005771405.1_ASM577140v1_genomic.fna.gz --refList GCF_005771405.1_ASM577140v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005771405.1_ASM577140v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:41:10,500] [INFO] Task succeeded: fastANI
[2024-01-24 12:41:10,514] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:41:10,514] [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_005771405.1	s__Parasedimentitalea marina_A	100.0	1605	1605	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Parasedimentitalea	95.0	97.09	97.09	0.92	0.92	2	conclusive
GCF_009753675.1	s__Parasedimentitalea huanghaiensis	94.5268	1427	1605	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	81.9197	737	1605	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	80.6139	749	1605	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	80.2306	771	1605	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	80.1192	755	1605	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	79.8522	710	1605	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Parasedimentitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001258055.1	s__Phaeobacter italicus	77.921	326	1605	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Phaeobacter	95.0	99.00	98.06	0.96	0.92	7	-
GCF_000511355.1	s__Leisingera methylohalidivorans	77.6278	354	1605	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000622385.1	s__Sulfitobacter noctilucicola	76.9265	136	1605	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_016428585.1	s__Sedimentitalea sp016428585	76.5236	164	1605	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sedimentitalea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:41:10,516] [INFO] GTDB search result was written to GCF_005771405.1_ASM577140v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:41:10,516] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:41:10,520] [INFO] DFAST_QC result json was written to GCF_005771405.1_ASM577140v1_genomic.fna/dqc_result.json
[2024-01-24 12:41:10,520] [INFO] DFAST_QC completed!
[2024-01-24 12:41:10,520] [INFO] Total running time: 0h1m31s