[2024-01-25 19:44:50,421] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:44:50,423] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:44:50,423] [INFO] DQC Reference Directory: /var/lib/cwl/stgc6685f17-6176-4f95-b77d-fd5d1c9ada0e/dqc_reference
[2024-01-25 19:44:51,617] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:44:51,618] [INFO] Task started: Prodigal
[2024-01-25 19:44:51,618] [INFO] Running command: gunzip -c /var/lib/cwl/stg7b1f496e-8086-409d-a071-8e832d491c4b/GCF_002150005.2_ASM215000v2_genomic.fna.gz | prodigal -d GCF_002150005.2_ASM215000v2_genomic.fna/cds.fna -a GCF_002150005.2_ASM215000v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:45:00,320] [INFO] Task succeeded: Prodigal
[2024-01-25 19:45:00,320] [INFO] Task started: HMMsearch
[2024-01-25 19:45:00,320] [INFO] Running command: hmmsearch --tblout GCF_002150005.2_ASM215000v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc6685f17-6176-4f95-b77d-fd5d1c9ada0e/dqc_reference/reference_markers.hmm GCF_002150005.2_ASM215000v2_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:45:00,540] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:45:00,541] [INFO] Found 6/6 markers.
[2024-01-25 19:45:00,568] [INFO] Query marker FASTA was written to GCF_002150005.2_ASM215000v2_genomic.fna/markers.fasta
[2024-01-25 19:45:00,568] [INFO] Task started: Blastn
[2024-01-25 19:45:00,568] [INFO] Running command: blastn -query GCF_002150005.2_ASM215000v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgc6685f17-6176-4f95-b77d-fd5d1c9ada0e/dqc_reference/reference_markers.fasta -out GCF_002150005.2_ASM215000v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:45:01,202] [INFO] Task succeeded: Blastn
[2024-01-25 19:45:01,204] [INFO] Selected 23 target genomes.
[2024-01-25 19:45:01,205] [INFO] Target genome list was writen to GCF_002150005.2_ASM215000v2_genomic.fna/target_genomes.txt
[2024-01-25 19:45:01,237] [INFO] Task started: fastANI
[2024-01-25 19:45:01,238] [INFO] Running command: fastANI --query /var/lib/cwl/stg7b1f496e-8086-409d-a071-8e832d491c4b/GCF_002150005.2_ASM215000v2_genomic.fna.gz --refList GCF_002150005.2_ASM215000v2_genomic.fna/target_genomes.txt --output GCF_002150005.2_ASM215000v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:45:16,751] [INFO] Task succeeded: fastANI
[2024-01-25 19:45:16,751] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc6685f17-6176-4f95-b77d-fd5d1c9ada0e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:45:16,752] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc6685f17-6176-4f95-b77d-fd5d1c9ada0e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:45:16,765] [INFO] Found 23 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:45:16,765] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:45:16,766] [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
Marivivens niveibacter	strain=MCCC 1A06712	GCA_002150005.2	1930667	1930667	type	True	100.0	1018	1018	95	conclusive
Marivivens aquimaris	strain=GSB7	GCA_015220045.1	2774876	2774876	type	True	78.1403	325	1018	95	below_threshold
Donghicola mangrovi	strain=B5-SW-15	GCA_013377535.1	2729614	2729614	type	True	77.7202	246	1018	95	below_threshold
Thalassococcus halodurans	strain=DSM 26915	GCA_900108225.1	373675	373675	type	True	77.6951	225	1018	95	below_threshold
Donghicola tyrosinivorans	strain=DSM 100212	GCA_003003355.1	1652492	1652492	type	True	77.5639	229	1018	95	below_threshold
Falsiruegeria litorea	strain=CECT 7639	GCA_900172225.1	1280831	1280831	type	True	77.5526	154	1018	95	below_threshold
Pseudoprimorskyibacter insulae	strain=CECT 8871	GCA_900302505.1	1695997	1695997	type	True	77.4359	222	1018	95	below_threshold
Shimia thalassica	strain=CECT 7735	GCA_001458215.1	1715693	1715693	type	True	77.2428	153	1018	95	below_threshold
Aliiroseovarius marinus	strain=A6024	GCA_004360145.1	2500159	2500159	type	True	77.1965	160	1018	95	below_threshold
Sulfitobacter marinus	strain=DSM 23422	GCA_900116285.1	394264	394264	type	True	77.1354	137	1018	95	below_threshold
Loktanella salsilacus	strain=DSM 16199	GCA_900114485.1	195913	195913	type	True	76.936	184	1018	95	below_threshold
Lutimaribacter saemankumensis	strain=DSM 28010	GCA_900100005.1	490829	490829	type	True	76.8379	145	1018	95	below_threshold
Thalassobius mangrovi	strain=GS-10	GCA_009857745.1	2692236	2692236	type	True	76.8015	186	1018	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=H3	GCA_000712315.1	1402135	1402135	type	True	76.8	177	1018	95	below_threshold
Aestuariivita boseongensis	strain=BS-B2	GCA_001262635.1	1470562	1470562	type	True	76.7461	138	1018	95	below_threshold
Profundibacter amoris	strain=BAR1	GCA_003544895.1	2171755	2171755	type	True	76.6653	142	1018	95	below_threshold
Gemmobacter fulva	strain=con5	GCA_018798885.1	2840474	2840474	type	True	76.5454	105	1018	95	below_threshold
Antarcticimicrobium sediminis	strain=S4J41	GCA_004348975.1	2546227	2546227	type	True	76.504	133	1018	95	below_threshold
Octadecabacter arcticus	strain=238	GCA_000155735.2	53946	53946	type	True	76.4938	126	1018	95	below_threshold
Flavimaricola marinus	strain=CECT 8899	GCA_900184895.1	1819565	1819565	type	True	76.4143	125	1018	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	76.2612	139	1018	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_009908265.2	2852097	2852097	type	True	76.1365	104	1018	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_019130055.1	2852097	2852097	type	True	76.1365	104	1018	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:45:16,768] [INFO] DFAST Taxonomy check result was written to GCF_002150005.2_ASM215000v2_genomic.fna/tc_result.tsv
[2024-01-25 19:45:16,768] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:45:16,768] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:45:16,769] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc6685f17-6176-4f95-b77d-fd5d1c9ada0e/dqc_reference/checkm_data
[2024-01-25 19:45:16,769] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:45:16,805] [INFO] Task started: CheckM
[2024-01-25 19:45:16,805] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002150005.2_ASM215000v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002150005.2_ASM215000v2_genomic.fna/checkm_input GCF_002150005.2_ASM215000v2_genomic.fna/checkm_result
[2024-01-25 19:45:44,558] [INFO] Task succeeded: CheckM
[2024-01-25 19:45:44,559] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:45:44,574] [INFO] ===== Completeness check finished =====
[2024-01-25 19:45:44,574] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:45:44,575] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002150005.2_ASM215000v2_genomic.fna/markers.fasta)
[2024-01-25 19:45:44,575] [INFO] Task started: Blastn
[2024-01-25 19:45:44,575] [INFO] Running command: blastn -query GCF_002150005.2_ASM215000v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgc6685f17-6176-4f95-b77d-fd5d1c9ada0e/dqc_reference/reference_markers_gtdb.fasta -out GCF_002150005.2_ASM215000v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:45:45,516] [INFO] Task succeeded: Blastn
[2024-01-25 19:45:45,519] [INFO] Selected 14 target genomes.
[2024-01-25 19:45:45,519] [INFO] Target genome list was writen to GCF_002150005.2_ASM215000v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:45:45,535] [INFO] Task started: fastANI
[2024-01-25 19:45:45,536] [INFO] Running command: fastANI --query /var/lib/cwl/stg7b1f496e-8086-409d-a071-8e832d491c4b/GCF_002150005.2_ASM215000v2_genomic.fna.gz --refList GCF_002150005.2_ASM215000v2_genomic.fna/target_genomes_gtdb.txt --output GCF_002150005.2_ASM215000v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:45:55,712] [INFO] Task succeeded: fastANI
[2024-01-25 19:45:55,721] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:45:55,721] [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_002150005.2	s__Marivivens niveibacter	100.0	1018	1018	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marivivens	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002850435.1	s__Marivivens zhoushanense	79.4372	387	1018	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marivivens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001908835.1	s__Marivivens sp001908835	79.0306	377	1018	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marivivens	95.0	98.73	98.07	0.98	0.97	4	-
GCF_011806565.1	s__Marivivens donghaensis	78.271	323	1018	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marivivens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015220045.1	s__Marivivens aquimaris	78.155	323	1018	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marivivens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900108225.1	s__Thalassococcus halodurans	77.6975	224	1018	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassococcus	95.0	96.13	96.13	0.95	0.95	2	-
GCF_002933395.1	s__Yoonia maritima_A	77.5558	163	1018	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900172225.1	s__Ruegeria_E litorea	77.5526	154	1018	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013033355.1	s__Ruegeria lacuscaerulensis_A	77.2609	140	1018	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	97.80	95.61	0.96	0.93	5	-
GCF_004799325.1	s__Thalassobius vesicularis	77.1328	200	1018	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002366795.1	s__UBA3069 sp002366795	76.9846	161	1018	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA3069	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001420005.1	s__Loktanella sp001420005	76.729	170	1018	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Loktanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003544895.1	s__Profundibacter amoris	76.6772	142	1018	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Profundibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009920775.1	s__Marivivens sp009920775	76.4454	95	1018	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marivivens	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:45:55,722] [INFO] GTDB search result was written to GCF_002150005.2_ASM215000v2_genomic.fna/result_gtdb.tsv
[2024-01-25 19:45:55,723] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:45:55,726] [INFO] DFAST_QC result json was written to GCF_002150005.2_ASM215000v2_genomic.fna/dqc_result.json
[2024-01-25 19:45:55,727] [INFO] DFAST_QC completed!
[2024-01-25 19:45:55,727] [INFO] Total running time: 0h1m5s