[2024-01-25 18:42:50,600] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:42:50,602] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:42:50,602] [INFO] DQC Reference Directory: /var/lib/cwl/stgd186afe8-ca0f-4121-b47b-15850c3e4486/dqc_reference
[2024-01-25 18:42:51,796] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:42:51,796] [INFO] Task started: Prodigal
[2024-01-25 18:42:51,797] [INFO] Running command: gunzip -c /var/lib/cwl/stgad6e12bb-8e78-4bd4-b59f-0616e4caa547/GCF_002285435.1_ASM228543v1_genomic.fna.gz | prodigal -d GCF_002285435.1_ASM228543v1_genomic.fna/cds.fna -a GCF_002285435.1_ASM228543v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:43:02,807] [INFO] Task succeeded: Prodigal
[2024-01-25 18:43:02,807] [INFO] Task started: HMMsearch
[2024-01-25 18:43:02,807] [INFO] Running command: hmmsearch --tblout GCF_002285435.1_ASM228543v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd186afe8-ca0f-4121-b47b-15850c3e4486/dqc_reference/reference_markers.hmm GCF_002285435.1_ASM228543v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:43:03,034] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:43:03,035] [INFO] Found 6/6 markers.
[2024-01-25 18:43:03,072] [INFO] Query marker FASTA was written to GCF_002285435.1_ASM228543v1_genomic.fna/markers.fasta
[2024-01-25 18:43:03,072] [INFO] Task started: Blastn
[2024-01-25 18:43:03,072] [INFO] Running command: blastn -query GCF_002285435.1_ASM228543v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd186afe8-ca0f-4121-b47b-15850c3e4486/dqc_reference/reference_markers.fasta -out GCF_002285435.1_ASM228543v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:43:04,003] [INFO] Task succeeded: Blastn
[2024-01-25 18:43:04,007] [INFO] Selected 25 target genomes.
[2024-01-25 18:43:04,007] [INFO] Target genome list was writen to GCF_002285435.1_ASM228543v1_genomic.fna/target_genomes.txt
[2024-01-25 18:43:04,027] [INFO] Task started: fastANI
[2024-01-25 18:43:04,028] [INFO] Running command: fastANI --query /var/lib/cwl/stgad6e12bb-8e78-4bd4-b59f-0616e4caa547/GCF_002285435.1_ASM228543v1_genomic.fna.gz --refList GCF_002285435.1_ASM228543v1_genomic.fna/target_genomes.txt --output GCF_002285435.1_ASM228543v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:43:24,859] [INFO] Task succeeded: fastANI
[2024-01-25 18:43:24,859] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd186afe8-ca0f-4121-b47b-15850c3e4486/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:43:24,859] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd186afe8-ca0f-4121-b47b-15850c3e4486/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:43:24,873] [INFO] Found 25 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:43:24,874] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:43:24,874] [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
Rhodovulum adriaticum	strain=DSM 2781	GCA_016583705.1	35804	35804	type	True	80.7065	570	1362	95	below_threshold
Rhodovulum adriaticum	strain=DSM 2781	GCA_004345735.1	35804	35804	type	True	80.5699	574	1362	95	below_threshold
Rhodovulum marinum	strain=DSM 18063	GCA_004343075.1	320662	320662	type	True	80.3359	633	1362	95	below_threshold
Rhodovulum steppense	strain=DSM 21153	GCA_004339675.1	540251	540251	type	True	79.8294	584	1362	95	below_threshold
Antarcticimicrobium luteum	strain=318-1	GCA_004358185.1	2547397	2547397	type	True	79.6919	618	1362	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	79.6761	584	1362	95	below_threshold
Rhodovulum strictum	strain=DSM 11289	GCA_009649175.1	58314	58314	type	True	79.6442	597	1362	95	below_threshold
Ruegeria pomeroyi	strain=DSS-3	GCA_000011965.2	89184	89184	suspected-type	True	79.6193	613	1362	95	below_threshold
Thalassobius mangrovi	strain=GS-10	GCA_009857745.1	2692236	2692236	type	True	79.5968	626	1362	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	79.5647	579	1362	95	below_threshold
Ruegeria intermedia	strain=DSM 29341	GCA_900129345.1	996115	996115	type	True	79.5139	547	1362	95	below_threshold
Dinoroseobacter shibae	strain=DFL 12	GCA_000018145.1	215813	215813	type	True	79.4143	523	1362	95	below_threshold
Actibacterium mucosum	strain=KCTC 23349	GCA_000647975.1	1087332	1087332	type	True	79.4073	524	1362	95	below_threshold
Pseudodonghicola xiamenensis	strain=CGMCC 1.7081	GCA_014653505.1	337702	337702	type	True	79.3685	522	1362	95	below_threshold
Pseudodonghicola xiamenensis	strain=DSM 18339	GCA_000429365.1	337702	337702	type	True	79.268	517	1362	95	below_threshold
Ruegeria marisrubri	strain=ZGT118	GCA_001507595.1	1685379	1685379	type	True	79.2329	493	1362	95	below_threshold
Ruegeria marina	strain=CGMCC 1.9108	GCA_900101475.1	639004	639004	type	True	78.9976	521	1362	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	78.8399	494	1362	95	below_threshold
Actibacterium atlanticum	strain=22II-S11-z10	GCA_000671395.1	1461693	1461693	type	True	78.7463	455	1362	95	below_threshold
Mameliella alba	strain=DSM 26384	GCA_003051025.1	561184	561184	suspected-type	True	78.7069	557	1362	95	below_threshold
Mameliella alba	strain=CGMCC 1.7290	GCA_900101505.1	561184	561184	suspected-type	True	78.6987	551	1362	95	below_threshold
Roseovarius faecimaris	strain=MME-070	GCA_009762325.1	2494550	2494550	type	True	78.6871	462	1362	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	78.6326	432	1362	95	below_threshold
Chachezhania sediminis	strain=CAU 1508	GCA_009765275.1	2599291	2599291	type	True	78.4622	512	1362	95	below_threshold
Pseudogemmobacter bohemicus	strain=Cd-10	GCA_003290025.1	2250708	2250708	type	True	77.3149	364	1362	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:43:24,877] [INFO] DFAST Taxonomy check result was written to GCF_002285435.1_ASM228543v1_genomic.fna/tc_result.tsv
[2024-01-25 18:43:24,877] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:43:24,877] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:43:24,878] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd186afe8-ca0f-4121-b47b-15850c3e4486/dqc_reference/checkm_data
[2024-01-25 18:43:24,878] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:43:24,920] [INFO] Task started: CheckM
[2024-01-25 18:43:24,920] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002285435.1_ASM228543v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002285435.1_ASM228543v1_genomic.fna/checkm_input GCF_002285435.1_ASM228543v1_genomic.fna/checkm_result
[2024-01-25 18:44:02,666] [INFO] Task succeeded: CheckM
[2024-01-25 18:44:02,667] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:44:02,683] [INFO] ===== Completeness check finished =====
[2024-01-25 18:44:02,683] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:44:02,684] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002285435.1_ASM228543v1_genomic.fna/markers.fasta)
[2024-01-25 18:44:02,684] [INFO] Task started: Blastn
[2024-01-25 18:44:02,684] [INFO] Running command: blastn -query GCF_002285435.1_ASM228543v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd186afe8-ca0f-4121-b47b-15850c3e4486/dqc_reference/reference_markers_gtdb.fasta -out GCF_002285435.1_ASM228543v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:44:04,470] [INFO] Task succeeded: Blastn
[2024-01-25 18:44:04,474] [INFO] Selected 17 target genomes.
[2024-01-25 18:44:04,474] [INFO] Target genome list was writen to GCF_002285435.1_ASM228543v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:44:04,485] [INFO] Task started: fastANI
[2024-01-25 18:44:04,485] [INFO] Running command: fastANI --query /var/lib/cwl/stgad6e12bb-8e78-4bd4-b59f-0616e4caa547/GCF_002285435.1_ASM228543v1_genomic.fna.gz --refList GCF_002285435.1_ASM228543v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002285435.1_ASM228543v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:44:17,705] [INFO] Task succeeded: fastANI
[2024-01-25 18:44:17,716] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:44:17,716] [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_002285435.1	s__Actibacterium ureilyticum	100.0	1358	1362	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Actibacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000744955.1	s__Actibacterium sp000744955	89.5838	1012	1362	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Actibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014196965.1	s__Actibacterium_A naphthalenivorans	81.3545	691	1362	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Actibacterium_A	95.0	98.28	97.38	0.93	0.89	4	-
GCF_900142185.1	s__Lutimaribacter pacificus	80.8586	669	1362	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Lutimaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_018139985.1	s__JAGSOU01 sp018139985	80.5899	645	1362	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAGSOU01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004345735.1	s__Rhodovulum adriaticum	80.5841	572	1362	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	99.99	99.99	0.99	0.99	2	-
GCF_004343075.1	s__Rhodovulum marinum	80.3051	636	1362	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016938875.1	s__Rhodovulum sp016938875	79.8686	570	1362	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004339675.1	s__Rhodovulum steppense	79.847	582	1362	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009649175.1	s__Rhodovulum strictum	79.627	599	1362	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000161775.1	s__Ruegeria lacuscaerulensis	79.5315	504	1362	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	99.98	99.98	1.00	1.00	2	-
GCF_900129345.1	s__Ruegeria intermedia	79.5119	548	1362	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011048875.1	s__Rhodovulum sp011048875	79.4977	423	1362	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000647975.1	s__Actibacterium mucosum	79.3933	526	1362	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Actibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016278325.1	s__JADQCB01 sp016278325	79.1703	521	1362	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JADQCB01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000671395.1	s__Actibacterium atlanticum	78.7549	454	1362	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Actibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003122205.1	s__QEYE01 sp003122205	78.4555	472	1362	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__QEYE01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:44:17,717] [INFO] GTDB search result was written to GCF_002285435.1_ASM228543v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:44:17,718] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:44:17,722] [INFO] DFAST_QC result json was written to GCF_002285435.1_ASM228543v1_genomic.fna/dqc_result.json
[2024-01-25 18:44:17,722] [INFO] DFAST_QC completed!
[2024-01-25 18:44:17,722] [INFO] Total running time: 0h1m27s