[2024-01-25 17:48:05,675] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:48:05,676] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:48:05,676] [INFO] DQC Reference Directory: /var/lib/cwl/stg836a0dad-bbe5-473c-b2bc-150b34f17374/dqc_reference
[2024-01-25 17:48:06,826] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:48:06,827] [INFO] Task started: Prodigal
[2024-01-25 17:48:06,827] [INFO] Running command: gunzip -c /var/lib/cwl/stge11a7bf1-2ddd-4e1b-a71e-38abe7759fe2/GCF_027853795.1_ASM2785379v1_genomic.fna.gz | prodigal -d GCF_027853795.1_ASM2785379v1_genomic.fna/cds.fna -a GCF_027853795.1_ASM2785379v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:48:19,950] [INFO] Task succeeded: Prodigal
[2024-01-25 17:48:19,951] [INFO] Task started: HMMsearch
[2024-01-25 17:48:19,951] [INFO] Running command: hmmsearch --tblout GCF_027853795.1_ASM2785379v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg836a0dad-bbe5-473c-b2bc-150b34f17374/dqc_reference/reference_markers.hmm GCF_027853795.1_ASM2785379v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:48:20,237] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:48:20,238] [INFO] Found 6/6 markers.
[2024-01-25 17:48:20,279] [INFO] Query marker FASTA was written to GCF_027853795.1_ASM2785379v1_genomic.fna/markers.fasta
[2024-01-25 17:48:20,280] [INFO] Task started: Blastn
[2024-01-25 17:48:20,280] [INFO] Running command: blastn -query GCF_027853795.1_ASM2785379v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg836a0dad-bbe5-473c-b2bc-150b34f17374/dqc_reference/reference_markers.fasta -out GCF_027853795.1_ASM2785379v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:48:20,968] [INFO] Task succeeded: Blastn
[2024-01-25 17:48:20,972] [INFO] Selected 18 target genomes.
[2024-01-25 17:48:20,972] [INFO] Target genome list was writen to GCF_027853795.1_ASM2785379v1_genomic.fna/target_genomes.txt
[2024-01-25 17:48:20,978] [INFO] Task started: fastANI
[2024-01-25 17:48:20,978] [INFO] Running command: fastANI --query /var/lib/cwl/stge11a7bf1-2ddd-4e1b-a71e-38abe7759fe2/GCF_027853795.1_ASM2785379v1_genomic.fna.gz --refList GCF_027853795.1_ASM2785379v1_genomic.fna/target_genomes.txt --output GCF_027853795.1_ASM2785379v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:48:37,640] [INFO] Task succeeded: fastANI
[2024-01-25 17:48:37,640] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg836a0dad-bbe5-473c-b2bc-150b34f17374/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:48:37,641] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg836a0dad-bbe5-473c-b2bc-150b34f17374/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:48:37,652] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 17:48:37,652] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 17:48:37,653] [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	80.4797	742	1537	95	below_threshold
Zongyanglinia huanghaiensis	strain=CY05	GCA_009753675.1	2682100	2682100	type	True	80.2741	746	1537	95	below_threshold
Pseudophaeobacter arcticus	strain=DSM 23566	GCA_000473205.1	385492	385492	type	True	78.9091	607	1537	95	below_threshold
Leisingera methylohalidivorans	strain=DSM 14336; MB2	GCA_000511355.1	133924	133924	type	True	78.8137	586	1537	95	below_threshold
Leisingera aquaemixtae	strain=CECT 8399	GCA_001458395.1	1396826	1396826	type	True	78.7443	619	1537	95	below_threshold
Pseudophaeobacter flagellatus	strain=MA21411-1	GCA_021228235.1	2899119	2899119	type	True	78.66	589	1537	95	below_threshold
Phaeobacter gallaeciensis	strain=DSM 26640	GCA_000819625.1	60890	60890	type	True	78.6575	474	1537	95	below_threshold
Phaeobacter gallaeciensis	strain=DSM 26640	GCA_000511385.1	60890	60890	type	True	78.5785	485	1537	95	below_threshold
Leisingera aquimarina	strain=DSM 24565	GCA_000473165.1	476529	476529	type	True	78.5535	591	1537	95	below_threshold
Phaeobacter porticola	strain=P97	GCA_001888185.1	1844006	1844006	type	True	78.1366	474	1537	95	below_threshold
Falsiruegeria mediterranea	strain=CECT 7615	GCA_900302455.1	1280832	1280832	type	True	77.9575	420	1537	95	below_threshold
Tritonibacter multivorans	strain=CECT 7557	GCA_001458415.1	928856	928856	type	True	77.8745	434	1537	95	below_threshold
Tritonibacter multivorans	strain=DSM 26470	GCA_900112515.1	928856	928856	type	True	77.8506	435	1537	95	below_threshold
Falsiruegeria litorea	strain=CECT 7639	GCA_900172225.1	1280831	1280831	type	True	77.7758	424	1537	95	below_threshold
Tritonibacter mobilis	strain=NBRC101030	GCA_001681715.1	379347	379347	type	True	77.6797	401	1537	95	below_threshold
Cribrihabitans marinus	strain=CGMCC 1.13219	GCA_014640375.1	1227549	1227549	type	True	77.59	406	1537	95	below_threshold
Sulfitobacter indolifex	strain=DSM 14862	GCA_022788655.1	225422	225422	type	True	77.0213	242	1537	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	76.3672	184	1537	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:48:37,654] [INFO] DFAST Taxonomy check result was written to GCF_027853795.1_ASM2785379v1_genomic.fna/tc_result.tsv
[2024-01-25 17:48:37,654] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:48:37,655] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:48:37,655] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg836a0dad-bbe5-473c-b2bc-150b34f17374/dqc_reference/checkm_data
[2024-01-25 17:48:37,656] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:48:37,703] [INFO] Task started: CheckM
[2024-01-25 17:48:37,703] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_027853795.1_ASM2785379v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_027853795.1_ASM2785379v1_genomic.fna/checkm_input GCF_027853795.1_ASM2785379v1_genomic.fna/checkm_result
[2024-01-25 17:49:17,593] [INFO] Task succeeded: CheckM
[2024-01-25 17:49:17,594] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:49:17,616] [INFO] ===== Completeness check finished =====
[2024-01-25 17:49:17,616] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:49:17,616] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_027853795.1_ASM2785379v1_genomic.fna/markers.fasta)
[2024-01-25 17:49:17,617] [INFO] Task started: Blastn
[2024-01-25 17:49:17,617] [INFO] Running command: blastn -query GCF_027853795.1_ASM2785379v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg836a0dad-bbe5-473c-b2bc-150b34f17374/dqc_reference/reference_markers_gtdb.fasta -out GCF_027853795.1_ASM2785379v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:49:18,757] [INFO] Task succeeded: Blastn
[2024-01-25 17:49:18,760] [INFO] Selected 9 target genomes.
[2024-01-25 17:49:18,760] [INFO] Target genome list was writen to GCF_027853795.1_ASM2785379v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:49:18,778] [INFO] Task started: fastANI
[2024-01-25 17:49:18,778] [INFO] Running command: fastANI --query /var/lib/cwl/stge11a7bf1-2ddd-4e1b-a71e-38abe7759fe2/GCF_027853795.1_ASM2785379v1_genomic.fna.gz --refList GCF_027853795.1_ASM2785379v1_genomic.fna/target_genomes_gtdb.txt --output GCF_027853795.1_ASM2785379v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:49:28,754] [INFO] Task succeeded: fastANI
[2024-01-25 17:49:28,761] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 17:49:28,761] [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	93.6447	1326	1537	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	83.7052	1050	1537	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	82.9982	877	1537	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	82.6472	928	1537	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	81.8137	929	1537	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	80.4748	743	1537	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	80.2833	744	1537	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Parasedimentitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900143635.1	s__FREY01 sp900143635	78.8378	588	1537	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__FREY01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000511355.1	s__Leisingera methylohalidivorans	78.8187	586	1537	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:49:28,763] [INFO] GTDB search result was written to GCF_027853795.1_ASM2785379v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:49:28,764] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:49:28,770] [INFO] DFAST_QC result json was written to GCF_027853795.1_ASM2785379v1_genomic.fna/dqc_result.json
[2024-01-25 17:49:28,770] [INFO] DFAST_QC completed!
[2024-01-25 17:49:28,770] [INFO] Total running time: 0h1m23s