[2024-01-24 15:18:39,016] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:18:39,020] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:18:39,020] [INFO] DQC Reference Directory: /var/lib/cwl/stg0d2aab97-5959-431e-884f-96dc2aa481a7/dqc_reference
[2024-01-24 15:18:40,408] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:18:40,409] [INFO] Task started: Prodigal
[2024-01-24 15:18:40,410] [INFO] Running command: gunzip -c /var/lib/cwl/stg2a275d26-97d4-4fc6-9f05-5cda2346b8fa/GCF_027913215.1_ASM2791321v1_genomic.fna.gz | prodigal -d GCF_027913215.1_ASM2791321v1_genomic.fna/cds.fna -a GCF_027913215.1_ASM2791321v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:18:51,569] [INFO] Task succeeded: Prodigal
[2024-01-24 15:18:51,569] [INFO] Task started: HMMsearch
[2024-01-24 15:18:51,569] [INFO] Running command: hmmsearch --tblout GCF_027913215.1_ASM2791321v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0d2aab97-5959-431e-884f-96dc2aa481a7/dqc_reference/reference_markers.hmm GCF_027913215.1_ASM2791321v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:18:51,884] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:18:51,885] [INFO] Found 6/6 markers.
[2024-01-24 15:18:51,944] [INFO] Query marker FASTA was written to GCF_027913215.1_ASM2791321v1_genomic.fna/markers.fasta
[2024-01-24 15:18:51,944] [INFO] Task started: Blastn
[2024-01-24 15:18:51,944] [INFO] Running command: blastn -query GCF_027913215.1_ASM2791321v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0d2aab97-5959-431e-884f-96dc2aa481a7/dqc_reference/reference_markers.fasta -out GCF_027913215.1_ASM2791321v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:18:52,923] [INFO] Task succeeded: Blastn
[2024-01-24 15:18:52,927] [INFO] Selected 27 target genomes.
[2024-01-24 15:18:52,927] [INFO] Target genome list was writen to GCF_027913215.1_ASM2791321v1_genomic.fna/target_genomes.txt
[2024-01-24 15:18:52,937] [INFO] Task started: fastANI
[2024-01-24 15:18:52,937] [INFO] Running command: fastANI --query /var/lib/cwl/stg2a275d26-97d4-4fc6-9f05-5cda2346b8fa/GCF_027913215.1_ASM2791321v1_genomic.fna.gz --refList GCF_027913215.1_ASM2791321v1_genomic.fna/target_genomes.txt --output GCF_027913215.1_ASM2791321v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:19:12,650] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:12,650] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0d2aab97-5959-431e-884f-96dc2aa481a7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:19:12,651] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0d2aab97-5959-431e-884f-96dc2aa481a7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:19:12,671] [INFO] Found 27 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 15:19:12,671] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 15:19:12,672] [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
Paracoccus isoporae	strain=DSM 22220	GCA_900101865.1	591205	591205	type	True	81.5359	628	1185	95	below_threshold
Paracoccus halophilus	strain=CGMCC 1.6117	GCA_900111785.1	376733	376733	type	True	80.2455	435	1185	95	below_threshold
Paracoccus xiamenensis	strain=12-3	GCA_011308835.1	2714901	2714901	type	True	80.1777	552	1185	95	below_threshold
Paracoccus halophilus	strain=JCM 14014	GCA_000763905.1	376733	376733	type	True	80.0829	437	1185	95	below_threshold
Paracoccus aurantiacus	strain=TK008	GCA_007993065.1	2599412	2599412	type	True	80.0101	542	1185	95	below_threshold
Paracoccus jeotgali	strain=CBA4604	GCA_002865605.1	2065379	2065379	type	True	79.8324	513	1185	95	below_threshold
Paracoccus binzhouensis	strain=wg1	GCA_016446475.1	2796149	2796149	type	True	79.1484	416	1185	95	below_threshold
Paracoccus lutimaris	strain=CECT 8525	GCA_003337565.1	1490030	1490030	type	True	79.097	401	1185	95	below_threshold
Paracoccus alcaliphilus	strain=DSM 8512	GCA_900110285.1	34002	34002	type	True	78.9729	411	1185	95	below_threshold
Paracoccus siganidrum	strain=M26	GCA_003709565.1	1276757	1276757	type	True	78.8632	417	1185	95	below_threshold
Paracoccus siganidrum	strain=DSM 26381	GCA_003594835.1	1276757	1276757	type	True	78.8223	409	1185	95	below_threshold
Paracoccus denitrificans	strain=DSM 413	GCA_900100045.1	266	266	type	True	78.685	401	1185	95	below_threshold
Paracoccus thiocyanatus	strain=ATCC 700171	GCA_900156255.1	34006	34006	type	True	78.6619	350	1185	95	below_threshold
Paracoccus homiensis	strain=DSM 17862	GCA_900111675.1	364199	364199	type	True	78.6534	379	1185	95	below_threshold
Paracoccus denitrificans	strain=NBRC 102528	GCA_007989485.1	266	266	type	True	78.6488	396	1185	95	below_threshold
Paracoccus tegillarcae	strain=BM15	GCA_002847305.1	1529068	1529068	type	True	78.6346	351	1185	95	below_threshold
Paracoccus mutanolyticus	strain=RSP-02	GCA_003285265.1	1499308	1499308	type	True	78.6007	306	1185	95	below_threshold
Paracoccus versutus	strain=DSM 582	GCA_003387045.1	34007	34007	type	True	78.5923	409	1185	95	below_threshold
Paracoccus yeei	strain=ATCC BAA-599	GCA_000622145.1	147645	147645	type	True	78.5222	331	1185	95	below_threshold
Paracoccus versutus	strain=DSM 582	GCA_000763885.1	34007	34007	type	True	78.517	394	1185	95	below_threshold
Paracoccus nototheniae	strain=I-41R45	GCA_004335005.1	2489002	2489002	type	True	78.3331	380	1185	95	below_threshold
Paracoccus aestuarii	strain=DSM 19484	GCA_003594815.1	453842	453842	type	True	78.3312	348	1185	95	below_threshold
Paracoccus salsus	strain=EGI L200073	GCA_021556615.1	2911061	2911061	type	True	78.2192	334	1185	95	below_threshold
Paracoccus aerius	strain=KCTC 42845	GCA_016757275.1	1915382	1915382	type	True	78.1801	320	1185	95	below_threshold
Paracoccus aerius	strain=KCTC 42845	GCA_014656455.1	1915382	1915382	type	True	78.1716	318	1185	95	below_threshold
Paracoccus shandongensis	strain=wg2	GCA_017315735.1	2816048	2816048	type	True	78.1148	328	1185	95	below_threshold
Rhodobacter ruber	strain=CCP-1	GCA_009908315.1	1985673	1985673	type	True	77.6722	209	1185	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:19:12,674] [INFO] DFAST Taxonomy check result was written to GCF_027913215.1_ASM2791321v1_genomic.fna/tc_result.tsv
[2024-01-24 15:19:12,674] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:19:12,675] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:19:12,675] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0d2aab97-5959-431e-884f-96dc2aa481a7/dqc_reference/checkm_data
[2024-01-24 15:19:12,676] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:19:12,718] [INFO] Task started: CheckM
[2024-01-24 15:19:12,718] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_027913215.1_ASM2791321v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_027913215.1_ASM2791321v1_genomic.fna/checkm_input GCF_027913215.1_ASM2791321v1_genomic.fna/checkm_result
[2024-01-24 15:19:48,994] [INFO] Task succeeded: CheckM
[2024-01-24 15:19:48,996] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:19:49,019] [INFO] ===== Completeness check finished =====
[2024-01-24 15:19:49,020] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:19:49,020] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_027913215.1_ASM2791321v1_genomic.fna/markers.fasta)
[2024-01-24 15:19:49,021] [INFO] Task started: Blastn
[2024-01-24 15:19:49,021] [INFO] Running command: blastn -query GCF_027913215.1_ASM2791321v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0d2aab97-5959-431e-884f-96dc2aa481a7/dqc_reference/reference_markers_gtdb.fasta -out GCF_027913215.1_ASM2791321v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:19:50,593] [INFO] Task succeeded: Blastn
[2024-01-24 15:19:50,599] [INFO] Selected 18 target genomes.
[2024-01-24 15:19:50,599] [INFO] Target genome list was writen to GCF_027913215.1_ASM2791321v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:19:50,613] [INFO] Task started: fastANI
[2024-01-24 15:19:50,613] [INFO] Running command: fastANI --query /var/lib/cwl/stg2a275d26-97d4-4fc6-9f05-5cda2346b8fa/GCF_027913215.1_ASM2791321v1_genomic.fna.gz --refList GCF_027913215.1_ASM2791321v1_genomic.fna/target_genomes_gtdb.txt --output GCF_027913215.1_ASM2791321v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:20:04,659] [INFO] Task succeeded: fastANI
[2024-01-24 15:20:04,681] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 15:20:04,681] [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_900101865.1	s__Paracoccus isoporae	81.5359	628	1185	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005768755.1	s__Paracoccus denitrificans_B	80.5652	522	1185	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013868135.1	s__Paracoccus sp013868135	80.3329	555	1185	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011308835.1	s__Paracoccus xiamenensis	80.1678	553	1185	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000763905.1	s__Paracoccus halophilus	80.0827	437	1185	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	100.00	100.00	0.99	0.99	2	-
GCF_007993065.1	s__Paracoccus aurantiacus	79.9969	544	1185	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002865605.1	s__Paracoccus jeotgali	79.8008	513	1185	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	96.34	96.34	0.97	0.97	2	-
GCF_016446475.1	s__Paracoccus binzhouensis	79.0928	421	1185	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110285.1	s__Paracoccus alcaliphilus	78.969	412	1185	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003709565.1	s__Paracoccus siganidrum	78.8851	417	1185	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.99	99.99	0.98	0.98	2	-
GCF_001447385.1	s__Paracoccus sp001447385	78.8586	419	1185	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017744015.1	s__Paracoccus sp002732665	78.7404	390	1185	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.29	98.58	0.98	0.95	3	-
GCF_900100045.1	s__Paracoccus denitrificans	78.7047	401	1185	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.78	98.70	0.97	0.88	7	-
GCF_900111675.1	s__Paracoccus homiensis	78.6599	379	1185	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000622145.1	s__Paracoccus yeei	78.498	333	1185	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	96.0533	98.39	97.89	0.87	0.83	7	-
GCF_003594815.1	s__Paracoccus aestuarii	78.3602	347	1185	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014656455.1	s__Paracoccus aerius	78.1596	319	1185	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.01	98.03	0.91	0.84	3	-
GCF_002563775.1	s__Thioclava sp002563775	77.746	268	1185	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thioclava	95.0406	95.45	95.45	0.86	0.86	2	-
--------------------------------------------------------------------------------
[2024-01-24 15:20:04,683] [INFO] GTDB search result was written to GCF_027913215.1_ASM2791321v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:20:04,684] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:20:04,689] [INFO] DFAST_QC result json was written to GCF_027913215.1_ASM2791321v1_genomic.fna/dqc_result.json
[2024-01-24 15:20:04,689] [INFO] DFAST_QC completed!
[2024-01-24 15:20:04,689] [INFO] Total running time: 0h1m26s