[2024-01-24 11:58:56,606] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:58:56,609] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:58:56,610] [INFO] DQC Reference Directory: /var/lib/cwl/stg6e834f89-7334-4814-91fd-c736df507fa9/dqc_reference
[2024-01-24 11:58:58,064] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:58:58,065] [INFO] Task started: Prodigal
[2024-01-24 11:58:58,065] [INFO] Running command: gunzip -c /var/lib/cwl/stg6e59dbdb-9b19-4706-b0a3-6b4cb57f3d0d/GCF_900104265.1_IMG-taxon_2663762796_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900104265.1_IMG-taxon_2663762796_annotated_assembly_genomic.fna/cds.fna -a GCF_900104265.1_IMG-taxon_2663762796_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:59:13,984] [INFO] Task succeeded: Prodigal
[2024-01-24 11:59:13,984] [INFO] Task started: HMMsearch
[2024-01-24 11:59:13,984] [INFO] Running command: hmmsearch --tblout GCF_900104265.1_IMG-taxon_2663762796_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6e834f89-7334-4814-91fd-c736df507fa9/dqc_reference/reference_markers.hmm GCF_900104265.1_IMG-taxon_2663762796_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:59:14,362] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:59:14,365] [INFO] Found 6/6 markers.
[2024-01-24 11:59:14,458] [INFO] Query marker FASTA was written to GCF_900104265.1_IMG-taxon_2663762796_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 11:59:14,459] [INFO] Task started: Blastn
[2024-01-24 11:59:14,459] [INFO] Running command: blastn -query GCF_900104265.1_IMG-taxon_2663762796_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg6e834f89-7334-4814-91fd-c736df507fa9/dqc_reference/reference_markers.fasta -out GCF_900104265.1_IMG-taxon_2663762796_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:59:15,602] [INFO] Task succeeded: Blastn
[2024-01-24 11:59:15,606] [INFO] Selected 14 target genomes.
[2024-01-24 11:59:15,606] [INFO] Target genome list was writen to GCF_900104265.1_IMG-taxon_2663762796_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 11:59:15,610] [INFO] Task started: fastANI
[2024-01-24 11:59:15,610] [INFO] Running command: fastANI --query /var/lib/cwl/stg6e59dbdb-9b19-4706-b0a3-6b4cb57f3d0d/GCF_900104265.1_IMG-taxon_2663762796_annotated_assembly_genomic.fna.gz --refList GCF_900104265.1_IMG-taxon_2663762796_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900104265.1_IMG-taxon_2663762796_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:59:34,051] [INFO] Task succeeded: fastANI
[2024-01-24 11:59:34,052] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6e834f89-7334-4814-91fd-c736df507fa9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:59:34,052] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6e834f89-7334-4814-91fd-c736df507fa9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:59:34,064] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:59:34,065] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:59:34,065] [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 guguanensis	strain=JCM 18416	GCA_900104265.1	1198456	1198456	type	True	100.0	1676	1680	95	conclusive
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	91.8593	1412	1680	95	below_threshold
Pseudomonas yangonensis	strain=MY50	GCA_009932725.1	2579922	2579922	type	True	91.6829	1343	1680	95	below_threshold
Pseudomonas toyotomiensis	strain=DSM 26169	GCA_002741095.1	554344	554344	type	True	89.9077	1384	1680	95	below_threshold
Pseudomonas toyotomiensis	strain=JCM 15604	GCA_900115695.1	554344	554344	type	True	89.9023	1390	1680	95	below_threshold
Pseudomonas chengduensis	strain=MBR	GCA_017905455.1	489632	489632	type	True	89.8607	1344	1680	95	below_threshold
Pseudomonas mendocina	strain=NCTC10897	GCA_900636545.1	300	300	suspected-type	True	89.8248	1355	1680	95	below_threshold
Pseudomonas mendocina	strain=NBRC 14162	GCA_000813265.1	300	300	suspected-type	True	89.7591	1354	1680	95	below_threshold
Pseudomonas sihuiensis	strain=KCTC 32246	GCA_900106015.1	1274359	1274359	type	True	89.7517	1386	1680	95	below_threshold
Pseudomonas alcaliphila	strain=NBRC 102411	GCA_002091495.1	101564	101564	type	True	89.7022	1374	1680	95	below_threshold
Pseudomonas alcaliphila	strain=JCM 10630	GCA_900101755.1	101564	101564	type	True	89.6963	1371	1680	95	below_threshold
Pseudomonas composti	strain=CCUG 59231	GCA_900115475.1	658457	658457	type	True	88.7136	1385	1680	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	84.2733	996	1680	95	below_threshold
Pseudomonas insulae	strain=UL073	GCA_016901015.1	2809017	2809017	type	True	82.7356	951	1680	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:59:34,067] [INFO] DFAST Taxonomy check result was written to GCF_900104265.1_IMG-taxon_2663762796_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 11:59:34,068] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:59:34,068] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:59:34,068] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6e834f89-7334-4814-91fd-c736df507fa9/dqc_reference/checkm_data
[2024-01-24 11:59:34,070] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:59:34,120] [INFO] Task started: CheckM
[2024-01-24 11:59:34,121] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900104265.1_IMG-taxon_2663762796_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900104265.1_IMG-taxon_2663762796_annotated_assembly_genomic.fna/checkm_input GCF_900104265.1_IMG-taxon_2663762796_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 12:00:19,990] [INFO] Task succeeded: CheckM
[2024-01-24 12:00:19,991] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:00:20,009] [INFO] ===== Completeness check finished =====
[2024-01-24 12:00:20,009] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:00:20,009] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900104265.1_IMG-taxon_2663762796_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 12:00:20,009] [INFO] Task started: Blastn
[2024-01-24 12:00:20,010] [INFO] Running command: blastn -query GCF_900104265.1_IMG-taxon_2663762796_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg6e834f89-7334-4814-91fd-c736df507fa9/dqc_reference/reference_markers_gtdb.fasta -out GCF_900104265.1_IMG-taxon_2663762796_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:00:22,143] [INFO] Task succeeded: Blastn
[2024-01-24 12:00:22,146] [INFO] Selected 14 target genomes.
[2024-01-24 12:00:22,147] [INFO] Target genome list was writen to GCF_900104265.1_IMG-taxon_2663762796_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:00:22,155] [INFO] Task started: fastANI
[2024-01-24 12:00:22,155] [INFO] Running command: fastANI --query /var/lib/cwl/stg6e59dbdb-9b19-4706-b0a3-6b4cb57f3d0d/GCF_900104265.1_IMG-taxon_2663762796_annotated_assembly_genomic.fna.gz --refList GCF_900104265.1_IMG-taxon_2663762796_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900104265.1_IMG-taxon_2663762796_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:00:40,599] [INFO] Task succeeded: fastANI
[2024-01-24 12:00:40,610] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:00:40,611] [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_900104265.1	s__Pseudomonas_E guguanensis	100.0	1676	1680	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.13	97.13	0.85	0.85	2	conclusive
GCF_000418555.1	s__Pseudomonas_E sp000418555	92.9073	1391	1680	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	91.8402	1413	1680	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_009932725.1	s__Pseudomonas_E sp009932725	91.6955	1342	1680	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.40	98.35	0.94	0.88	4	-
GCF_016008875.1	s__Pseudomonas_E sp002439135	90.2029	1323	1680	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.91	96.75	0.87	0.85	5	-
GCF_002803095.1	s__Pseudomonas_E sp002803095	90.0816	1386	1680	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.6432	99.96	99.96	0.99	0.99	2	-
GCF_900636545.1	s__Pseudomonas_E mendocina	89.8248	1355	1680	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.91	97.19	0.93	0.89	14	-
GCF_900102635.1	s__Pseudomonas_E chengduensis	89.8082	1356	1680	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	96.7402	99.23	98.24	0.94	0.89	5	-
GCF_900106015.1	s__Pseudomonas_E sihuiensis	89.7468	1387	1680	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	96.7402	N/A	N/A	N/A	N/A	1	-
GCF_900101755.1	s__Pseudomonas_E alcaliphila	89.6851	1372	1680	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.74	97.49	0.95	0.92	3	-
GCF_008041835.1	s__Pseudomonas_E sp002282595	89.3794	1107	1680	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	95.53	95.53	0.75	0.75	2	-
GCF_902506495.1	s__Pseudomonas_E sp902506495	89.1347	1351	1680	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.72	95.94	0.90	0.87	3	-
GCF_003696305.1	s__Pseudomonas_E sp003696305	88.6523	1215	1680	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_004521985.1	s__Pseudomonas_E khazarica	88.1571	1309	1680	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.35	98.01	0.91	0.87	12	-
--------------------------------------------------------------------------------
[2024-01-24 12:00:40,612] [INFO] GTDB search result was written to GCF_900104265.1_IMG-taxon_2663762796_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 12:00:40,612] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:00:40,616] [INFO] DFAST_QC result json was written to GCF_900104265.1_IMG-taxon_2663762796_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 12:00:40,616] [INFO] DFAST_QC completed!
[2024-01-24 12:00:40,616] [INFO] Total running time: 0h1m44s