[2024-01-24 13:21:41,244] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:21:41,246] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:21:41,246] [INFO] DQC Reference Directory: /var/lib/cwl/stg38a75899-4988-4e9e-b3bf-1b43b3b6ff54/dqc_reference
[2024-01-24 13:21:42,530] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:21:42,531] [INFO] Task started: Prodigal
[2024-01-24 13:21:42,532] [INFO] Running command: gunzip -c /var/lib/cwl/stg76d03794-38cc-44f5-91df-7dad3c8d51db/GCF_015220045.1_ASM1522004v1_genomic.fna.gz | prodigal -d GCF_015220045.1_ASM1522004v1_genomic.fna/cds.fna -a GCF_015220045.1_ASM1522004v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:21:55,228] [INFO] Task succeeded: Prodigal
[2024-01-24 13:21:55,229] [INFO] Task started: HMMsearch
[2024-01-24 13:21:55,229] [INFO] Running command: hmmsearch --tblout GCF_015220045.1_ASM1522004v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg38a75899-4988-4e9e-b3bf-1b43b3b6ff54/dqc_reference/reference_markers.hmm GCF_015220045.1_ASM1522004v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:21:55,532] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:21:55,533] [INFO] Found 6/6 markers.
[2024-01-24 13:21:55,578] [INFO] Query marker FASTA was written to GCF_015220045.1_ASM1522004v1_genomic.fna/markers.fasta
[2024-01-24 13:21:55,578] [INFO] Task started: Blastn
[2024-01-24 13:21:55,578] [INFO] Running command: blastn -query GCF_015220045.1_ASM1522004v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg38a75899-4988-4e9e-b3bf-1b43b3b6ff54/dqc_reference/reference_markers.fasta -out GCF_015220045.1_ASM1522004v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:21:56,515] [INFO] Task succeeded: Blastn
[2024-01-24 13:21:56,518] [INFO] Selected 24 target genomes.
[2024-01-24 13:21:56,519] [INFO] Target genome list was writen to GCF_015220045.1_ASM1522004v1_genomic.fna/target_genomes.txt
[2024-01-24 13:21:56,528] [INFO] Task started: fastANI
[2024-01-24 13:21:56,528] [INFO] Running command: fastANI --query /var/lib/cwl/stg76d03794-38cc-44f5-91df-7dad3c8d51db/GCF_015220045.1_ASM1522004v1_genomic.fna.gz --refList GCF_015220045.1_ASM1522004v1_genomic.fna/target_genomes.txt --output GCF_015220045.1_ASM1522004v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:22:15,438] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:15,439] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg38a75899-4988-4e9e-b3bf-1b43b3b6ff54/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:22:15,439] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg38a75899-4988-4e9e-b3bf-1b43b3b6ff54/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:22:15,457] [INFO] Found 24 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:22:15,458] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:22:15,458] [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 aquimaris	strain=GSB7	GCA_015220045.1	2774876	2774876	type	True	100.0	1343	1346	95	conclusive
Salipiger profundus	strain=JLT2016	GCA_001969385.1	1229727	1229727	type	True	79.5923	374	1346	95	below_threshold
Salipiger profundus	strain=CGMCC 1.12377	GCA_014637265.1	1229727	1229727	type	True	79.2076	359	1346	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	78.9735	251	1346	95	below_threshold
Salipiger thiooxidans	strain=DSM 10146	GCA_900102075.1	282683	282683	type	True	78.4906	384	1346	95	below_threshold
Donghicola mangrovi	strain=B5-SW-15	GCA_013377535.1	2729614	2729614	type	True	78.4845	351	1346	95	below_threshold
Leisingera daeponensis	strain=DSM 23529	GCA_000473145.1	405746	405746	type	True	78.2749	317	1346	95	below_threshold
Marivivens niveibacter	strain=MCCC 1A06712	GCA_002150005.2	1930667	1930667	type	True	78.2699	316	1346	95	below_threshold
Actibacterium pelagium	strain=JN33	GCA_002285415.1	2029103	2029103	type	True	78.2091	229	1346	95	below_threshold
Roseivivax isoporae	strain=LMG 25204	GCA_000521865.1	591206	591206	type	True	78.1848	297	1346	95	below_threshold
Aliiroseovarius marinus	strain=A6024	GCA_004360145.1	2500159	2500159	type	True	77.9959	212	1346	95	below_threshold
Leisingera caerulea	strain=DSM 24564	GCA_000473325.1	506591	506591	type	True	77.909	251	1346	95	below_threshold
Yangia pacifica	strain=CGMCC 1.3455	GCA_900100725.1	311180	311180	suspected-type	True	77.8512	338	1346	95	below_threshold
Yangia pacifica	strain=DSM 26894	GCA_900116195.1	311180	311180	suspected-type	True	77.8154	340	1346	95	below_threshold
Limimaricola variabilis	strain=CECT 8572	GCA_014195545.1	1492771	1492771	type	True	77.7136	290	1346	95	below_threshold
Thalassobius mangrovi	strain=GS-10	GCA_009857745.1	2692236	2692236	type	True	77.7011	301	1346	95	below_threshold
Leisingera aquaemixtae	strain=CECT 8399	GCA_001458395.1	1396826	1396826	type	True	77.5752	281	1346	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_009908265.2	2852097	2852097	type	True	77.5649	240	1346	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_019130055.1	2852097	2852097	type	True	77.5404	242	1346	95	below_threshold
Aliiroseovarius pelagivivens	strain=CECT 8811	GCA_900302485.1	1639690	1639690	type	True	77.3776	208	1346	95	below_threshold
Mameliella alba	strain=CGMCC 1.7290	GCA_900101505.1	561184	561184	suspected-type	True	77.2767	286	1346	95	below_threshold
Mameliella alba	strain=DSM 26384	GCA_003051025.1	561184	561184	suspected-type	True	77.2719	286	1346	95	below_threshold
Cereibacter sphaeroides	strain=2.4.1	GCA_000273405.1	1063	1063	type	True	77.2042	242	1346	95	below_threshold
Cereibacter azotoformans	strain=KA25	GCA_003050905.1	43057	43057	type	True	77.1658	241	1346	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:22:15,460] [INFO] DFAST Taxonomy check result was written to GCF_015220045.1_ASM1522004v1_genomic.fna/tc_result.tsv
[2024-01-24 13:22:15,460] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:22:15,460] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:22:15,460] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg38a75899-4988-4e9e-b3bf-1b43b3b6ff54/dqc_reference/checkm_data
[2024-01-24 13:22:15,461] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:22:15,502] [INFO] Task started: CheckM
[2024-01-24 13:22:15,503] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_015220045.1_ASM1522004v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_015220045.1_ASM1522004v1_genomic.fna/checkm_input GCF_015220045.1_ASM1522004v1_genomic.fna/checkm_result
[2024-01-24 13:22:55,525] [INFO] Task succeeded: CheckM
[2024-01-24 13:22:55,526] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:22:55,543] [INFO] ===== Completeness check finished =====
[2024-01-24 13:22:55,544] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:22:55,544] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_015220045.1_ASM1522004v1_genomic.fna/markers.fasta)
[2024-01-24 13:22:55,544] [INFO] Task started: Blastn
[2024-01-24 13:22:55,544] [INFO] Running command: blastn -query GCF_015220045.1_ASM1522004v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg38a75899-4988-4e9e-b3bf-1b43b3b6ff54/dqc_reference/reference_markers_gtdb.fasta -out GCF_015220045.1_ASM1522004v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:57,278] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:57,286] [INFO] Selected 14 target genomes.
[2024-01-24 13:22:57,286] [INFO] Target genome list was writen to GCF_015220045.1_ASM1522004v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:22:57,299] [INFO] Task started: fastANI
[2024-01-24 13:22:57,299] [INFO] Running command: fastANI --query /var/lib/cwl/stg76d03794-38cc-44f5-91df-7dad3c8d51db/GCF_015220045.1_ASM1522004v1_genomic.fna.gz --refList GCF_015220045.1_ASM1522004v1_genomic.fna/target_genomes_gtdb.txt --output GCF_015220045.1_ASM1522004v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:23:07,618] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:07,630] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:23:07,631] [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_015220045.1	s__Marivivens aquimaris	100.0	1343	1346	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_011806565.1	s__Marivivens donghaensis	93.0056	1042	1346	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marivivens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002850435.1	s__Marivivens zhoushanense	80.1332	461	1346	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marivivens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001969385.1	s__Salipiger profundus	79.4904	370	1346	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	99.85	99.64	0.97	0.94	5	-
GCF_001908835.1	s__Marivivens sp001908835	79.3147	397	1346	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marivivens	95.0	98.73	98.07	0.98	0.97	4	-
GCF_900172235.1	s__Pseudoruegeria aquimaris	78.4231	296	1346	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudoruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002150005.2	s__Marivivens niveibacter	78.281	315	1346	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marivivens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000473145.1	s__Leisingera daeponensis	78.2661	318	1346	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	98.26	98.26	0.94	0.94	2	-
GCF_000169415.1	s__Sagittula stellata	78.1141	306	1346	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sagittula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009920775.1	s__Marivivens sp009920775	77.9878	236	1346	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marivivens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000473325.1	s__Leisingera caerulea	77.9629	253	1346	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101505.1	s__Mameliella alba	77.2767	286	1346	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Mameliella	95.0	98.60	98.14	0.96	0.94	14	-
GCF_017813235.1	s__Sagittula sp017813235	77.2332	254	1346	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sagittula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002366795.1	s__UBA3069 sp002366795	76.9748	231	1346	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA3069	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:23:07,632] [INFO] GTDB search result was written to GCF_015220045.1_ASM1522004v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:23:07,633] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:23:07,637] [INFO] DFAST_QC result json was written to GCF_015220045.1_ASM1522004v1_genomic.fna/dqc_result.json
[2024-01-24 13:23:07,638] [INFO] DFAST_QC completed!
[2024-01-24 13:23:07,638] [INFO] Total running time: 0h1m26s