[2024-01-24 11:26:54,309] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:54,312] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:54,312] [INFO] DQC Reference Directory: /var/lib/cwl/stg07a37606-d8d6-4dd7-a4c7-eb5686b839af/dqc_reference
[2024-01-24 11:26:58,221] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:58,224] [INFO] Task started: Prodigal
[2024-01-24 11:26:58,224] [INFO] Running command: gunzip -c /var/lib/cwl/stg1e4cffcc-948a-49df-8564-3be8e62f1152/GCF_002786325.1_157.Hcov.spades_scaffolds_517_genomic.fna.gz | prodigal -d GCF_002786325.1_157.Hcov.spades_scaffolds_517_genomic.fna/cds.fna -a GCF_002786325.1_157.Hcov.spades_scaffolds_517_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:27:12,616] [INFO] Task succeeded: Prodigal
[2024-01-24 11:27:12,616] [INFO] Task started: HMMsearch
[2024-01-24 11:27:12,616] [INFO] Running command: hmmsearch --tblout GCF_002786325.1_157.Hcov.spades_scaffolds_517_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg07a37606-d8d6-4dd7-a4c7-eb5686b839af/dqc_reference/reference_markers.hmm GCF_002786325.1_157.Hcov.spades_scaffolds_517_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:27:12,919] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:27:12,920] [INFO] Found 6/6 markers.
[2024-01-24 11:27:12,967] [INFO] Query marker FASTA was written to GCF_002786325.1_157.Hcov.spades_scaffolds_517_genomic.fna/markers.fasta
[2024-01-24 11:27:12,968] [INFO] Task started: Blastn
[2024-01-24 11:27:12,968] [INFO] Running command: blastn -query GCF_002786325.1_157.Hcov.spades_scaffolds_517_genomic.fna/markers.fasta -db /var/lib/cwl/stg07a37606-d8d6-4dd7-a4c7-eb5686b839af/dqc_reference/reference_markers.fasta -out GCF_002786325.1_157.Hcov.spades_scaffolds_517_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:13,908] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:13,911] [INFO] Selected 24 target genomes.
[2024-01-24 11:27:13,912] [INFO] Target genome list was writen to GCF_002786325.1_157.Hcov.spades_scaffolds_517_genomic.fna/target_genomes.txt
[2024-01-24 11:27:13,921] [INFO] Task started: fastANI
[2024-01-24 11:27:13,921] [INFO] Running command: fastANI --query /var/lib/cwl/stg1e4cffcc-948a-49df-8564-3be8e62f1152/GCF_002786325.1_157.Hcov.spades_scaffolds_517_genomic.fna.gz --refList GCF_002786325.1_157.Hcov.spades_scaffolds_517_genomic.fna/target_genomes.txt --output GCF_002786325.1_157.Hcov.spades_scaffolds_517_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:27:33,961] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:33,962] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg07a37606-d8d6-4dd7-a4c7-eb5686b839af/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:27:33,962] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg07a37606-d8d6-4dd7-a4c7-eb5686b839af/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:27:33,980] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:27:33,980] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:27:33,980] [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
Cribrihabitans marinus	strain=CGMCC 1.13219	GCA_014640375.1	1227549	1227549	type	True	80.8094	602	1530	95	below_threshold
Antarcticimicrobium luteum	strain=318-1	GCA_004358185.1	2547397	2547397	type	True	80.8068	682	1530	95	below_threshold
Cribrihabitans marinus	strain=DSM 29340	GCA_900109035.1	1227549	1227549	type	True	80.8051	605	1530	95	below_threshold
Ruegeria pomeroyi	strain=DSS-3	GCA_000011965.2	89184	89184	suspected-type	True	80.4887	622	1530	95	below_threshold
Roseovarius atlanticus	strain=R12B	GCA_001441615.1	1641875	1641875	type	True	80.3613	498	1530	95	below_threshold
Ruegeria intermedia	strain=DSM 29341	GCA_900129345.1	996115	996115	type	True	80.179	532	1530	95	below_threshold
Thalassobius mangrovi	strain=GS-10	GCA_009857745.1	2692236	2692236	type	True	79.9977	588	1530	95	below_threshold
Ruegeria marisrubri	strain=ZGT118	GCA_001507595.1	1685379	1685379	type	True	79.9404	512	1530	95	below_threshold
Leisingera daeponensis	strain=DSM 23529	GCA_000473145.1	405746	405746	type	True	79.7423	596	1530	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	79.7357	582	1530	95	below_threshold
Ruegeria sediminis	strain=CAU 1488	GCA_005938215.1	2583820	2583820	type	True	79.6882	525	1530	95	below_threshold
Antarcticimicrobium sediminis	strain=S4J41	GCA_004348975.1	2546227	2546227	type	True	79.6099	601	1530	95	below_threshold
Leisingera aquaemixtae	strain=CECT 8399	GCA_001458395.1	1396826	1396826	type	True	79.5403	559	1530	95	below_threshold
Thalassobius aquimarinus	strain=KMM 8518	GCA_018219815.1	2785917	2785917	type	True	79.5183	528	1530	95	below_threshold
Leisingera caerulea	strain=DSM 24564	GCA_000473325.1	506591	506591	type	True	79.316	549	1530	95	below_threshold
Leisingera methylohalidivorans	strain=DSM 14336; MB2	GCA_000511355.1	133924	133924	type	True	79.2001	528	1530	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	79.1648	445	1530	95	below_threshold
Roseovarius litoreus	strain=DSM 28249	GCA_900142765.1	1155722	1155722	type	True	78.9523	402	1530	95	below_threshold
Mangrovicoccus algicola	strain=HB182678	GCA_014903745.1	2771008	2771008	type	True	78.9094	437	1530	95	below_threshold
Chachezhania sediminis	strain=CAU 1508	GCA_009765275.1	2599291	2599291	type	True	78.6863	556	1530	95	below_threshold
Mameliella sediminis	strain=DP3N28-2	GCA_019218285.1	2836866	2836866	type	True	78.1392	433	1530	95	below_threshold
Palleronia sediminis	strain=SS33	GCA_004358695.1	2547833	2547833	type	True	78.0556	335	1530	95	below_threshold
Puniceibacterium sediminis	strain=DSM 29052	GCA_900188035.1	1608407	1608407	type	True	77.9173	359	1530	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	77.7655	375	1530	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:27:33,982] [INFO] DFAST Taxonomy check result was written to GCF_002786325.1_157.Hcov.spades_scaffolds_517_genomic.fna/tc_result.tsv
[2024-01-24 11:27:33,982] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:27:33,982] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:27:33,983] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg07a37606-d8d6-4dd7-a4c7-eb5686b839af/dqc_reference/checkm_data
[2024-01-24 11:27:33,983] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:27:34,041] [INFO] Task started: CheckM
[2024-01-24 11:27:34,041] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002786325.1_157.Hcov.spades_scaffolds_517_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002786325.1_157.Hcov.spades_scaffolds_517_genomic.fna/checkm_input GCF_002786325.1_157.Hcov.spades_scaffolds_517_genomic.fna/checkm_result
[2024-01-24 11:28:18,820] [INFO] Task succeeded: CheckM
[2024-01-24 11:28:18,821] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:28:18,846] [INFO] ===== Completeness check finished =====
[2024-01-24 11:28:18,847] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:28:18,847] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002786325.1_157.Hcov.spades_scaffolds_517_genomic.fna/markers.fasta)
[2024-01-24 11:28:18,848] [INFO] Task started: Blastn
[2024-01-24 11:28:18,848] [INFO] Running command: blastn -query GCF_002786325.1_157.Hcov.spades_scaffolds_517_genomic.fna/markers.fasta -db /var/lib/cwl/stg07a37606-d8d6-4dd7-a4c7-eb5686b839af/dqc_reference/reference_markers_gtdb.fasta -out GCF_002786325.1_157.Hcov.spades_scaffolds_517_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:28:20,570] [INFO] Task succeeded: Blastn
[2024-01-24 11:28:20,574] [INFO] Selected 22 target genomes.
[2024-01-24 11:28:20,575] [INFO] Target genome list was writen to GCF_002786325.1_157.Hcov.spades_scaffolds_517_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:28:20,590] [INFO] Task started: fastANI
[2024-01-24 11:28:20,591] [INFO] Running command: fastANI --query /var/lib/cwl/stg1e4cffcc-948a-49df-8564-3be8e62f1152/GCF_002786325.1_157.Hcov.spades_scaffolds_517_genomic.fna.gz --refList GCF_002786325.1_157.Hcov.spades_scaffolds_517_genomic.fna/target_genomes_gtdb.txt --output GCF_002786325.1_157.Hcov.spades_scaffolds_517_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:28:42,768] [INFO] Task succeeded: fastANI
[2024-01-24 11:28:42,794] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:28:42,794] [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_002786325.1	s__Pseudooceanicola_C lipolyticus	100.0	1520	1530	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola_C	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001886735.1	s__Sulfitobacter alexandrii	82.1585	573	1530	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002210165.1	s__CAU-1492 sp002210165	81.066	621	1530	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CAU-1492	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004358185.1	s__Antarcticimicrobium luteum	80.8004	683	1530	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Antarcticimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109035.1	s__Cribrihabitans marinus	80.7835	607	1530	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cribrihabitans	95.0	100.00	100.00	0.99	0.99	2	-
GCF_003008555.2	s__Pukyongiella litopenaei	80.7151	623	1530	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pukyongiella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016758075.1	s__CAU-1492 sp016758075	80.6947	606	1530	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CAU-1492	95.0	99.98	99.98	0.95	0.95	2	-
GCF_005938225.1	s__Arenibacterium halophilum	80.6307	664	1530	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Arenibacterium	95.0	96.35	96.35	0.87	0.87	2	-
GCF_014656415.1	s__Seohaeicola zhoushanensis	80.615	710	1530	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Seohaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000011965.2	s__Ruegeria_B pomeroyi	80.5088	619	1530	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria_B	95.0	99.97	99.92	0.99	0.98	5	-
GCF_002210095.1	s__Marinibacterium profundimaris	80.3782	725	1530	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marinibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129345.1	s__Ruegeria intermedia	80.173	534	1530	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003217735.2	s__Marinibacterium sp003217735	80.0495	719	1530	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marinibacterium	95.0	98.81	98.75	0.89	0.89	3	-
GCF_009857745.1	s__Thalassobius mangrovi	80.0226	585	1530	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001507595.1	s__Ruegeria marisrubri	79.9645	509	1530	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900108275.1	s__Jhaorihella thermophila	79.7211	530	1530	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jhaorihella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005938215.1	s__Ruegeria sediminis	79.6892	525	1530	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003344785.1	s__Puniceibacterium profundi	79.6504	556	1530	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Puniceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016428585.1	s__Sedimentitalea sp016428585	79.6262	507	1530	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sedimentitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004348975.1	s__Antarcticimicrobium sediminis	79.5964	603	1530	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Antarcticimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016938875.1	s__Rhodovulum sp016938875	79.0747	417	1530	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014762635.1	s__JABURR01 sp014762635	78.7968	397	1530	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JABURR01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:28:42,796] [INFO] GTDB search result was written to GCF_002786325.1_157.Hcov.spades_scaffolds_517_genomic.fna/result_gtdb.tsv
[2024-01-24 11:28:42,797] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:28:42,803] [INFO] DFAST_QC result json was written to GCF_002786325.1_157.Hcov.spades_scaffolds_517_genomic.fna/dqc_result.json
[2024-01-24 11:28:42,804] [INFO] DFAST_QC completed!
[2024-01-24 11:28:42,804] [INFO] Total running time: 0h1m48s