[2024-01-24 15:02:23,966] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:02:23,969] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:02:23,969] [INFO] DQC Reference Directory: /var/lib/cwl/stg1eeaf419-1aad-45b0-889c-d8f419813c62/dqc_reference
[2024-01-24 15:02:26,425] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:02:26,426] [INFO] Task started: Prodigal
[2024-01-24 15:02:26,426] [INFO] Running command: gunzip -c /var/lib/cwl/stg45752bc5-8128-43ca-bd90-31425d4055d1/GCF_007858235.1_ASM785823v1_genomic.fna.gz | prodigal -d GCF_007858235.1_ASM785823v1_genomic.fna/cds.fna -a GCF_007858235.1_ASM785823v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:02:54,700] [INFO] Task succeeded: Prodigal
[2024-01-24 15:02:54,701] [INFO] Task started: HMMsearch
[2024-01-24 15:02:54,701] [INFO] Running command: hmmsearch --tblout GCF_007858235.1_ASM785823v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1eeaf419-1aad-45b0-889c-d8f419813c62/dqc_reference/reference_markers.hmm GCF_007858235.1_ASM785823v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:02:55,044] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:02:55,045] [INFO] Found 6/6 markers.
[2024-01-24 15:02:55,104] [INFO] Query marker FASTA was written to GCF_007858235.1_ASM785823v1_genomic.fna/markers.fasta
[2024-01-24 15:02:55,105] [INFO] Task started: Blastn
[2024-01-24 15:02:55,105] [INFO] Running command: blastn -query GCF_007858235.1_ASM785823v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1eeaf419-1aad-45b0-889c-d8f419813c62/dqc_reference/reference_markers.fasta -out GCF_007858235.1_ASM785823v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:02:56,089] [INFO] Task succeeded: Blastn
[2024-01-24 15:02:56,094] [INFO] Selected 16 target genomes.
[2024-01-24 15:02:56,094] [INFO] Target genome list was writen to GCF_007858235.1_ASM785823v1_genomic.fna/target_genomes.txt
[2024-01-24 15:02:56,104] [INFO] Task started: fastANI
[2024-01-24 15:02:56,105] [INFO] Running command: fastANI --query /var/lib/cwl/stg45752bc5-8128-43ca-bd90-31425d4055d1/GCF_007858235.1_ASM785823v1_genomic.fna.gz --refList GCF_007858235.1_ASM785823v1_genomic.fna/target_genomes.txt --output GCF_007858235.1_ASM785823v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:03:20,799] [INFO] Task succeeded: fastANI
[2024-01-24 15:03:20,800] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1eeaf419-1aad-45b0-889c-d8f419813c62/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:03:20,800] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1eeaf419-1aad-45b0-889c-d8f419813c62/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:03:20,813] [INFO] Found 16 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 15:03:20,813] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:03:20,814] [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
Pseudomonas extremaustralis	strain=DSM 17835	GCA_007858235.1	359110	359110	type	True	100.0	2148	2150	95	conclusive
Pseudomonas extremaustralis	strain=DSM 17835	GCA_900102035.1	359110	359110	type	True	99.9948	2150	2150	95	conclusive
Pseudomonas extremaustralis		GCA_900625045.1	359110	359110	type	True	99.9939	2132	2150	95	conclusive
Pseudomonas extremaustralis	strain=14-3 substr. 14-3b	GCA_000242115.2	359110	359110	type	True	99.9868	2105	2150	95	conclusive
Pseudomonas marginalis	strain=DSM 13124	GCA_007858155.1	298	298	suspected-type	True	89.2216	1547	2150	95	below_threshold
Pseudomonas pergaminensis	strain=1008	GCA_024112395.1	2853159	2853159	type	True	88.4644	1509	2150	95	below_threshold
Pseudomonas lurida	strain=LMG 21995	GCA_002563895.1	244566	244566	type	True	88.2947	1471	2150	95	below_threshold
Pseudomonas salomonii	strain=ICMP 14252	GCA_900107155.1	191391	191391	type	True	87.8389	1450	2150	95	below_threshold
Pseudomonas salomonii	strain=LMG 22120	GCA_001730645.1	191391	191391	type	True	87.7984	1467	2150	95	below_threshold
Pseudomonas fluorescens	strain=NBRC 14160	GCA_002091595.1	294	294	suspected-type	True	87.7068	1431	2150	95	below_threshold
Pseudomonas fluorescens	strain=DSM 50090	GCA_007858165.1	294	294	suspected-type	True	87.6703	1457	2150	95	below_threshold
Pseudomonas fluorescens	strain=NCTC10038	GCA_900475215.1	294	294	suspected-type	True	87.6425	1468	2150	95	below_threshold
Pseudomonas edaphica	strain=RD25	GCA_005863185.1	2006980	2006980	type	True	87.3255	1127	2150	95	below_threshold
Pseudomonas spelaei	strain=CCM 7893	GCA_009724245.1	1055469	1055469	type	True	86.0135	1338	2150	95	below_threshold
Pseudomonas karstica	strain=CCM 7891	GCA_009707515.1	1055468	1055468	type	True	85.1567	1214	2150	95	below_threshold
Marinobacterium halophilum	strain=DSM 17586	GCA_003014615.1	267374	267374	type	True	76.2042	111	2150	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:03:20,815] [INFO] DFAST Taxonomy check result was written to GCF_007858235.1_ASM785823v1_genomic.fna/tc_result.tsv
[2024-01-24 15:03:20,816] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:03:20,816] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:03:20,816] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1eeaf419-1aad-45b0-889c-d8f419813c62/dqc_reference/checkm_data
[2024-01-24 15:03:20,818] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:03:20,879] [INFO] Task started: CheckM
[2024-01-24 15:03:20,880] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007858235.1_ASM785823v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007858235.1_ASM785823v1_genomic.fna/checkm_input GCF_007858235.1_ASM785823v1_genomic.fna/checkm_result
[2024-01-24 15:04:40,013] [INFO] Task succeeded: CheckM
[2024-01-24 15:04:40,015] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:04:40,036] [INFO] ===== Completeness check finished =====
[2024-01-24 15:04:40,036] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:04:40,036] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007858235.1_ASM785823v1_genomic.fna/markers.fasta)
[2024-01-24 15:04:40,037] [INFO] Task started: Blastn
[2024-01-24 15:04:40,037] [INFO] Running command: blastn -query GCF_007858235.1_ASM785823v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1eeaf419-1aad-45b0-889c-d8f419813c62/dqc_reference/reference_markers_gtdb.fasta -out GCF_007858235.1_ASM785823v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:04:41,488] [INFO] Task succeeded: Blastn
[2024-01-24 15:04:41,493] [INFO] Selected 26 target genomes.
[2024-01-24 15:04:41,494] [INFO] Target genome list was writen to GCF_007858235.1_ASM785823v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:04:41,516] [INFO] Task started: fastANI
[2024-01-24 15:04:41,517] [INFO] Running command: fastANI --query /var/lib/cwl/stg45752bc5-8128-43ca-bd90-31425d4055d1/GCF_007858235.1_ASM785823v1_genomic.fna.gz --refList GCF_007858235.1_ASM785823v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007858235.1_ASM785823v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:05:18,825] [INFO] Task succeeded: fastANI
[2024-01-24 15:05:18,845] [INFO] Found 25 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:05:18,845] [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_900102035.1	s__Pseudomonas_E extremaustralis	99.9948	2150	2150	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.74	98.99	0.98	0.92	5	conclusive
GCF_001439695.1	s__Pseudomonas_E veronii	89.6784	1640	2150	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.79	98.13	0.89	0.82	43	-
GCF_003097075.1	s__Pseudomonas_E sp003097075	89.2294	1464	2150	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.77	98.77	0.94	0.94	2	-
GCF_900105325.1	s__Pseudomonas_E marginalis	89.1771	1575	2150	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.53	96.47	0.90	0.85	19	-
GCF_003612935.1	s__Pseudomonas_E sp003013355	89.1224	1527	2150	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.87	98.56	0.95	0.92	7	-
GCF_900580675.1	s__Pseudomonas_E sp900580675	88.9718	1401	2150	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002843605.1	s__Pseudomonas_E sp002843605	88.9101	1544	2150	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.70	97.45	0.92	0.91	7	-
GCF_000612585.1	s__Pseudomonas_E sp000612585	88.7449	1431	2150	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001708445.1	s__Pseudomonas_E fluorescens_AN	88.7187	1548	2150	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.17	98.56	0.90	0.82	34	-
GCF_001050345.1	s__Pseudomonas_E fildesensis	88.7096	1497	2150	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001645105.1	s__Pseudomonas_E marginalis_B	88.4643	1497	2150	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.70	98.28	0.91	0.87	10	-
GCF_002563895.1	s__Pseudomonas_E lurida	88.2897	1472	2150	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.19	99.03	0.94	0.91	25	-
GCF_009834565.1	s__Pseudomonas_E sp009834565	88.1406	1447	2150	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.71	97.35	0.93	0.93	3	-
GCF_001647715.1	s__Pseudomonas_E antarctica_A	87.8722	1453	2150	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.45	97.45	0.91	0.91	2	-
GCF_900107155.1	s__Pseudomonas_E salomonii	87.8331	1450	2150	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.30	96.43	0.92	0.87	14	-
GCF_005938045.2	s__Pseudomonas_E sp005938045	87.7415	1446	2150	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	95.18	95.16	0.86	0.86	3	-
GCF_013385965.1	s__Pseudomonas_E edaphica	87.6627	1450	2150	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.04	98.93	0.94	0.92	9	-
GCF_900215245.1	s__Pseudomonas_E fluorescens	87.6299	1458	2150	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.68	99.25	0.98	0.92	14	-
GCF_003208475.1	s__Pseudomonas_E sp003208475	87.1045	1390	2150	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009296165.1	s__Pseudomonas_E kitaguniensis	86.877	1242	2150	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.01	96.76	0.90	0.88	5	-
GCF_003626995.1	s__Pseudomonas_E fluorescens_BA	86.2884	1359	2150	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.95	98.57	0.93	0.88	19	-
GCF_013403585.1	s__Pseudomonas_E yamanorum_B	85.8301	1364	2150	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.31	98.31	0.89	0.89	2	-
GCA_002840155.1	s__Pseudomonas_E sp002840155	80.3141	669	2150	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002345575.1	s__Pseudomonas_A stutzeri_S	78.4264	465	2150	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003014615.1	s__Marinobacterium halophilum	76.207	111	2150	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	98.87	98.87	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2024-01-24 15:05:18,847] [INFO] GTDB search result was written to GCF_007858235.1_ASM785823v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:05:18,848] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:05:18,852] [INFO] DFAST_QC result json was written to GCF_007858235.1_ASM785823v1_genomic.fna/dqc_result.json
[2024-01-24 15:05:18,852] [INFO] DFAST_QC completed!
[2024-01-24 15:05:18,852] [INFO] Total running time: 0h2m55s