[2024-01-24 13:32:42,022] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:32:42,024] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:32:42,024] [INFO] DQC Reference Directory: /var/lib/cwl/stg3afc3205-a795-471e-8b0a-daecd39e2f6c/dqc_reference
[2024-01-24 13:32:43,420] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:32:43,422] [INFO] Task started: Prodigal
[2024-01-24 13:32:43,423] [INFO] Running command: gunzip -c /var/lib/cwl/stg92c4bb44-eae1-41bc-ab7b-079fdef1ebb0/GCF_000018145.1_ASM1814v1_genomic.fna.gz | prodigal -d GCF_000018145.1_ASM1814v1_genomic.fna/cds.fna -a GCF_000018145.1_ASM1814v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:58,024] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:58,024] [INFO] Task started: HMMsearch
[2024-01-24 13:32:58,024] [INFO] Running command: hmmsearch --tblout GCF_000018145.1_ASM1814v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3afc3205-a795-471e-8b0a-daecd39e2f6c/dqc_reference/reference_markers.hmm GCF_000018145.1_ASM1814v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:58,278] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:58,279] [INFO] Found 6/6 markers.
[2024-01-24 13:32:58,319] [INFO] Query marker FASTA was written to GCF_000018145.1_ASM1814v1_genomic.fna/markers.fasta
[2024-01-24 13:32:58,319] [INFO] Task started: Blastn
[2024-01-24 13:32:58,319] [INFO] Running command: blastn -query GCF_000018145.1_ASM1814v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3afc3205-a795-471e-8b0a-daecd39e2f6c/dqc_reference/reference_markers.fasta -out GCF_000018145.1_ASM1814v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:59,275] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:59,279] [INFO] Selected 27 target genomes.
[2024-01-24 13:32:59,279] [INFO] Target genome list was writen to GCF_000018145.1_ASM1814v1_genomic.fna/target_genomes.txt
[2024-01-24 13:32:59,286] [INFO] Task started: fastANI
[2024-01-24 13:32:59,286] [INFO] Running command: fastANI --query /var/lib/cwl/stg92c4bb44-eae1-41bc-ab7b-079fdef1ebb0/GCF_000018145.1_ASM1814v1_genomic.fna.gz --refList GCF_000018145.1_ASM1814v1_genomic.fna/target_genomes.txt --output GCF_000018145.1_ASM1814v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:33:19,580] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:19,580] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3afc3205-a795-471e-8b0a-daecd39e2f6c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:33:19,581] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3afc3205-a795-471e-8b0a-daecd39e2f6c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:33:19,601] [INFO] Found 27 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:33:19,601] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:33:19,602] [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
Dinoroseobacter shibae	strain=DFL 12	GCA_000018145.1	215813	215813	type	True	100.0	1455	1470	95	conclusive
Rhodovulum adriaticum	strain=DSM 2781	GCA_016583705.1	35804	35804	type	True	79.5233	421	1470	95	below_threshold
Rhodovulum adriaticum	strain=DSM 2781	GCA_004345735.1	35804	35804	type	True	79.449	425	1470	95	below_threshold
Brevirhabdus pacifica	strain=22DY15	GCA_002094875.1	1267768	1267768	type	True	79.2963	359	1470	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	79.054	386	1470	95	below_threshold
Brevirhabdus pacifica	strain=DSM 27767	GCA_002797755.1	1267768	1267768	type	True	78.9556	416	1470	95	below_threshold
Cribrihabitans marinus	strain=CGMCC 1.13219	GCA_014640375.1	1227549	1227549	type	True	78.8255	497	1470	95	below_threshold
Cribrihabitans marinus	strain=DSM 29340	GCA_900109035.1	1227549	1227549	type	True	78.8169	504	1470	95	below_threshold
Antarcticimicrobium luteum	strain=318-1	GCA_004358185.1	2547397	2547397	type	True	78.6831	483	1470	95	below_threshold
Rhodovulum robiginosum	strain=DSM 12329	GCA_003944755.1	68292	68292	type	True	78.6825	478	1470	95	below_threshold
Paracoccus isoporae	strain=DSM 22220	GCA_900101865.1	591205	591205	type	True	78.5674	315	1470	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	78.5549	423	1470	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	78.5016	459	1470	95	below_threshold
Rhodovulum sulfidophilum	strain=DSM 1374	GCA_001633165.1	35806	35806	type	True	78.487	442	1470	95	below_threshold
Rhodovulum sulfidophilum	strain=DSM 1374	GCA_000520135.2	35806	35806	type	True	78.4075	451	1470	95	below_threshold
Rhodovulum strictum	strain=DSM 11289	GCA_009649175.1	58314	58314	type	True	78.3211	435	1470	95	below_threshold
Ruegeria sediminis	strain=CAU 1488	GCA_005938215.1	2583820	2583820	type	True	78.3101	396	1470	95	below_threshold
Rhodovulum visakhapatnamense	strain=JA181	GCA_004365965.1	364297	364297	type	True	78.2937	490	1470	95	below_threshold
Limimaricola variabilis	strain=CECT 8572	GCA_014195545.1	1492771	1492771	type	True	78.2673	396	1470	95	below_threshold
Jannaschia formosa	strain=12N15	GCA_003340555.1	2259592	2259592	type	True	78.2593	485	1470	95	below_threshold
Kangsaoukella pontilimi	strain=GH1-50	GCA_009830125.1	2691042	2691042	type	True	78.12	375	1470	95	below_threshold
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	77.9994	395	1470	95	below_threshold
Palleronia sediminis	strain=SS33	GCA_004358695.1	2547833	2547833	type	True	77.9061	375	1470	95	below_threshold
Mangrovicoccus ximenensis	strain=T1lg56	GCA_003056725.1	1911570	1911570	type	True	77.8764	421	1470	95	below_threshold
Thioclava electrotropha	strain=Elox9	GCA_002085925.2	1549850	1549850	type	True	77.7679	372	1470	95	below_threshold
Paracoccus aminovorans		GCA_900005615.1	34004	34004	type	True	77.5943	334	1470	95	below_threshold
Paracoccus aminovorans	strain=DSM 8537	GCA_900113565.1	34004	34004	type	True	77.5485	320	1470	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:33:19,606] [INFO] DFAST Taxonomy check result was written to GCF_000018145.1_ASM1814v1_genomic.fna/tc_result.tsv
[2024-01-24 13:33:19,607] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:33:19,607] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:33:19,607] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3afc3205-a795-471e-8b0a-daecd39e2f6c/dqc_reference/checkm_data
[2024-01-24 13:33:19,608] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:33:19,649] [INFO] Task started: CheckM
[2024-01-24 13:33:19,649] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000018145.1_ASM1814v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000018145.1_ASM1814v1_genomic.fna/checkm_input GCF_000018145.1_ASM1814v1_genomic.fna/checkm_result
[2024-01-24 13:34:05,022] [INFO] Task succeeded: CheckM
[2024-01-24 13:34:05,023] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:34:05,039] [INFO] ===== Completeness check finished =====
[2024-01-24 13:34:05,039] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:34:05,039] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000018145.1_ASM1814v1_genomic.fna/markers.fasta)
[2024-01-24 13:34:05,040] [INFO] Task started: Blastn
[2024-01-24 13:34:05,040] [INFO] Running command: blastn -query GCF_000018145.1_ASM1814v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3afc3205-a795-471e-8b0a-daecd39e2f6c/dqc_reference/reference_markers_gtdb.fasta -out GCF_000018145.1_ASM1814v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:34:06,708] [INFO] Task succeeded: Blastn
[2024-01-24 13:34:06,711] [INFO] Selected 27 target genomes.
[2024-01-24 13:34:06,711] [INFO] Target genome list was writen to GCF_000018145.1_ASM1814v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:34:06,756] [INFO] Task started: fastANI
[2024-01-24 13:34:06,757] [INFO] Running command: fastANI --query /var/lib/cwl/stg92c4bb44-eae1-41bc-ab7b-079fdef1ebb0/GCF_000018145.1_ASM1814v1_genomic.fna.gz --refList GCF_000018145.1_ASM1814v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000018145.1_ASM1814v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:34:26,284] [INFO] Task succeeded: fastANI
[2024-01-24 13:34:26,304] [INFO] Found 27 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:34:26,305] [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_000018145.1	s__Dinoroseobacter shibae	100.0	1459	1470	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Dinoroseobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002285435.1	s__Actibacterium ureilyticum	79.6924	512	1470	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Actibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003344785.1	s__Puniceibacterium profundi	79.5388	529	1470	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Puniceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004345735.1	s__Rhodovulum adriaticum	79.4371	426	1470	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	99.99	99.99	0.99	0.99	2	-
GCF_018139985.1	s__JAGSOU01 sp018139985	79.0494	509	1470	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAGSOU01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002797755.1	s__Brevirhabdus pacifica	79.0224	416	1470	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Brevirhabdus	95.0	99.99	99.97	0.99	0.98	4	-
GCF_900109035.1	s__Cribrihabitans marinus	78.813	505	1470	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cribrihabitans	95.0	100.00	100.00	0.99	0.99	2	-
GCF_004358185.1	s__Antarcticimicrobium luteum	78.6578	486	1470	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Antarcticimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101865.1	s__Paracoccus isoporae	78.5995	314	1470	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016428585.1	s__Sedimentitalea sp016428585	78.5548	423	1470	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sedimentitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002786325.1	s__Pseudooceanicola_C lipolyticus	78.5158	416	1470	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142935.1	s__Rhodovulum sp900142935	78.4908	464	1470	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011048875.1	s__Rhodovulum sp011048875	78.4594	334	1470	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	78.4048	393	1470	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116005.1	s__Poseidonocella sedimentorum	78.3563	385	1470	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Poseidonocella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004365965.1	s__Rhodovulum visakhapatnamense	78.3008	489	1470	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	98.55	98.44	0.90	0.89	5	-
GCF_009649175.1	s__Rhodovulum strictum	78.2958	438	1470	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004000255.1	s__Nioella ostreopsis	78.2722	410	1470	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Nioella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003340555.1	s__Jannaschia formosa	78.2672	484	1470	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jannaschia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009830125.1	s__GH1-50 sp009830125	78.1712	369	1470	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__GH1-50	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005870025.1	s__Mangrovicoccus sp005870025	78.0958	525	1470	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Mangrovicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003056725.1	s__Mangrovicoccus ximenensis	77.8883	420	1470	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Mangrovicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014763785.1	s__SZUA-611 sp014763785	77.8873	316	1470	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__SZUA-611	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001879715.1	s__Nioella nitratireducens	77.8337	385	1470	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Nioella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002085925.2	s__Thioclava electrotropha	77.7901	372	1470	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thioclava	96.2561	N/A	N/A	N/A	N/A	1	-
GCF_900005615.1	s__Paracoccus aminovorans	77.5429	336	1470	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.98	99.98	1.00	1.00	2	-
GCF_000740785.1	s__Paenirhodobacter enshiensis	77.2507	283	1470	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paenirhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:34:26,306] [INFO] GTDB search result was written to GCF_000018145.1_ASM1814v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:34:26,307] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:34:26,311] [INFO] DFAST_QC result json was written to GCF_000018145.1_ASM1814v1_genomic.fna/dqc_result.json
[2024-01-24 13:34:26,312] [INFO] DFAST_QC completed!
[2024-01-24 13:34:26,312] [INFO] Total running time: 0h1m44s