[2024-01-24 14:05:16,198] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:05:16,200] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:05:16,200] [INFO] DQC Reference Directory: /var/lib/cwl/stge2d9cdac-2fd0-46cc-a98a-4ef307cd1c19/dqc_reference
[2024-01-24 14:05:17,444] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:05:17,445] [INFO] Task started: Prodigal
[2024-01-24 14:05:17,445] [INFO] Running command: gunzip -c /var/lib/cwl/stg5250c60f-8bf2-4d25-8a71-b696a607150b/GCF_009763245.1_ASM976324v1_genomic.fna.gz | prodigal -d GCF_009763245.1_ASM976324v1_genomic.fna/cds.fna -a GCF_009763245.1_ASM976324v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:05:29,395] [INFO] Task succeeded: Prodigal
[2024-01-24 14:05:29,395] [INFO] Task started: HMMsearch
[2024-01-24 14:05:29,396] [INFO] Running command: hmmsearch --tblout GCF_009763245.1_ASM976324v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge2d9cdac-2fd0-46cc-a98a-4ef307cd1c19/dqc_reference/reference_markers.hmm GCF_009763245.1_ASM976324v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:05:29,701] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:05:29,703] [INFO] Found 6/6 markers.
[2024-01-24 14:05:29,744] [INFO] Query marker FASTA was written to GCF_009763245.1_ASM976324v1_genomic.fna/markers.fasta
[2024-01-24 14:05:29,745] [INFO] Task started: Blastn
[2024-01-24 14:05:29,745] [INFO] Running command: blastn -query GCF_009763245.1_ASM976324v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge2d9cdac-2fd0-46cc-a98a-4ef307cd1c19/dqc_reference/reference_markers.fasta -out GCF_009763245.1_ASM976324v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:05:30,804] [INFO] Task succeeded: Blastn
[2024-01-24 14:05:30,808] [INFO] Selected 23 target genomes.
[2024-01-24 14:05:30,808] [INFO] Target genome list was writen to GCF_009763245.1_ASM976324v1_genomic.fna/target_genomes.txt
[2024-01-24 14:05:30,820] [INFO] Task started: fastANI
[2024-01-24 14:05:30,820] [INFO] Running command: fastANI --query /var/lib/cwl/stg5250c60f-8bf2-4d25-8a71-b696a607150b/GCF_009763245.1_ASM976324v1_genomic.fna.gz --refList GCF_009763245.1_ASM976324v1_genomic.fna/target_genomes.txt --output GCF_009763245.1_ASM976324v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:05:54,832] [INFO] Task succeeded: fastANI
[2024-01-24 14:05:54,833] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge2d9cdac-2fd0-46cc-a98a-4ef307cd1c19/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:05:54,833] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge2d9cdac-2fd0-46cc-a98a-4ef307cd1c19/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:05:54,857] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:05:54,858] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:05:54,858] [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 lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	84.202	918	1316	95	below_threshold
Pseudomonas benzenivorans	strain=DSM 8628	GCA_900100495.1	556533	556533	type	True	83.9322	967	1316	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	83.7781	939	1316	95	below_threshold
Pseudomonas borbori	strain=DSM 17834	GCA_900115555.1	289003	289003	type	True	83.7622	898	1316	95	below_threshold
Pseudomonas guguanensis	strain=JCM 18416	GCA_900104265.1	1198456	1198456	type	True	83.5088	927	1316	95	below_threshold
Pseudomonas tumuqii	strain=LAMW06	GCA_013184545.1	2715755	2715755	type	True	83.4984	937	1316	95	below_threshold
Pseudomonas peli	strain=DSM 17833	GCA_012986145.1	592361	592361	type	True	83.4658	948	1316	95	below_threshold
Pseudomonas peli	strain=DSM 17833	GCA_900099645.1	592361	592361	type	True	83.3739	953	1316	95	below_threshold
Pseudomonas sihuiensis	strain=KCTC 32246	GCA_900106015.1	1274359	1274359	type	True	83.0827	915	1316	95	below_threshold
Pseudomonas alcaligenes	strain=NBRC 14159	GCA_000467105.1	43263	43263	type	True	83.0614	882	1316	95	below_threshold
Pseudomonas alcaligenes	strain=NCTC10367	GCA_900455475.1	43263	43263	type	True	83.0134	880	1316	95	below_threshold
Pseudomonas yangonensis	strain=MY50	GCA_009932725.1	2579922	2579922	type	True	82.8451	892	1316	95	below_threshold
Pseudomonas cuatrocienegasensis	strain=CIP 109853	GCA_900110925.1	543360	543360	type	True	82.788	857	1316	95	below_threshold
Pseudomonas argentinensis	strain=CCUG 50743	GCA_008801645.1	289370	289370	type	True	82.0858	747	1316	95	below_threshold
Pseudomonas argentinensis	strain=LMG 22563	GCA_900113905.1	289370	289370	type	True	81.9726	733	1316	95	below_threshold
Pseudomonas sagittaria	strain=JCM 18195	GCA_900115715.1	1135990	1135990	type	True	81.9027	681	1316	95	below_threshold
Pseudomonas insulae	strain=UL073	GCA_016901015.1	2809017	2809017	type	True	81.7963	783	1316	95	below_threshold
Pseudomonas linyingensis	strain=LMG 25967	GCA_900109175.1	915471	915471	type	True	81.7174	657	1316	95	below_threshold
Pseudomonas furukawaii	strain=KF707	GCA_002355475.1	1149133	1149133	type	True	81.6022	817	1316	95	below_threshold
Pseudomonas furukawaii	strain=KF707	GCA_000262065.3	1149133	1149133	type	True	81.5805	813	1316	95	below_threshold
Pseudomonas flavescens	strain=LMG 18387	GCA_900100535.1	29435	29435	type	True	81.1754	722	1316	95	below_threshold
Pseudomonas flavescens	strain=NBRC 103044	GCA_002091575.1	29435	29435	type	True	81.1388	721	1316	95	below_threshold
[Pseudomonas] nosocomialis	strain=A31/70	GCA_005876855.1	1056496	1056496	type	True	80.7922	662	1316	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:05:54,860] [INFO] DFAST Taxonomy check result was written to GCF_009763245.1_ASM976324v1_genomic.fna/tc_result.tsv
[2024-01-24 14:05:54,861] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:05:54,861] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:05:54,861] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge2d9cdac-2fd0-46cc-a98a-4ef307cd1c19/dqc_reference/checkm_data
[2024-01-24 14:05:54,863] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:05:54,907] [INFO] Task started: CheckM
[2024-01-24 14:05:54,907] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009763245.1_ASM976324v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009763245.1_ASM976324v1_genomic.fna/checkm_input GCF_009763245.1_ASM976324v1_genomic.fna/checkm_result
[2024-01-24 14:06:32,909] [INFO] Task succeeded: CheckM
[2024-01-24 14:06:32,911] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:06:32,934] [INFO] ===== Completeness check finished =====
[2024-01-24 14:06:32,935] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:06:32,936] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009763245.1_ASM976324v1_genomic.fna/markers.fasta)
[2024-01-24 14:06:32,936] [INFO] Task started: Blastn
[2024-01-24 14:06:32,936] [INFO] Running command: blastn -query GCF_009763245.1_ASM976324v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge2d9cdac-2fd0-46cc-a98a-4ef307cd1c19/dqc_reference/reference_markers_gtdb.fasta -out GCF_009763245.1_ASM976324v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:35,102] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:35,105] [INFO] Selected 20 target genomes.
[2024-01-24 14:06:35,105] [INFO] Target genome list was writen to GCF_009763245.1_ASM976324v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:06:35,126] [INFO] Task started: fastANI
[2024-01-24 14:06:35,126] [INFO] Running command: fastANI --query /var/lib/cwl/stg5250c60f-8bf2-4d25-8a71-b696a607150b/GCF_009763245.1_ASM976324v1_genomic.fna.gz --refList GCF_009763245.1_ASM976324v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009763245.1_ASM976324v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:06:56,098] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:56,114] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:06:56,115] [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_009763245.1	s__Pseudomonas_E sp009763245	100.0	1316	1316	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003696305.1	s__Pseudomonas_E sp003696305	84.72	983	1316	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_018398425.1	s__Pseudomonas_E lalucatii	84.2043	918	1316	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.68	99.28	0.97	0.92	4	-
GCF_900100495.1	s__Pseudomonas_E benzenivorans	83.9237	969	1316	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_000016565.1	s__Pseudomonas_E mendocina_A	83.8029	947	1316	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.76	97.37	0.90	0.88	7	-
GCF_900115555.1	s__Pseudomonas_E borbori	83.7544	898	1316	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_009799925.1	s__Pseudomonas_E sp009799925	83.6616	917	1316	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_003205495.1	s__Pseudomonas_E alcaligenes_B	83.4181	888	1316	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_002354655.1	s__Pseudomonas_E sp002354655	83.2476	919	1316	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.84	99.84	0.95	0.95	2	-
GCF_003060885.1	s__Pseudomonas_E sp003060885	83.2229	913	1316	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_014851565.1	s__Pseudomonas_E sp014851565	82.6849	844	1316	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_000761545.1	s__Pseudomonas_E sp000761545	82.6573	811	1316	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_004327355.1	s__Pseudomonas_E dryadis	82.5345	825	1316	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.58	99.16	0.96	0.92	3	-
GCF_001839655.1	s__Pseudomonas_E argentinensis_B	82.1379	777	1316	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_001465025.1	s__Pseudomonas_E sp001465025	82.0745	794	1316	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	95.96	95.96	0.61	0.61	2	-
GCF_000213805.1	s__Pseudomonas_E fulva_B	81.9354	753	1316	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.53	96.12	0.92	0.90	6	-
GCF_900115715.1	s__Pseudomonas_K sagittaria	81.9186	679	1316	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_K	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112645.1	s__Pseudomonas_E straminea	81.7461	758	1316	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.06	98.06	0.94	0.94	2	-
GCF_900109175.1	s__Pseudomonas_K linyingensis	81.6845	660	1316	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_K	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002304225.1	s__Pseudomonas_E sp002304225	81.627	758	1316	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	95.09	95.09	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:06:56,117] [INFO] GTDB search result was written to GCF_009763245.1_ASM976324v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:06:56,117] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:06:56,123] [INFO] DFAST_QC result json was written to GCF_009763245.1_ASM976324v1_genomic.fna/dqc_result.json
[2024-01-24 14:06:56,123] [INFO] DFAST_QC completed!
[2024-01-24 14:06:56,123] [INFO] Total running time: 0h1m40s