[2024-01-24 15:02:59,781] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:02:59,785] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:02:59,785] [INFO] DQC Reference Directory: /var/lib/cwl/stg12f4de41-cd2c-440a-b696-90900895c3c2/dqc_reference
[2024-01-24 15:03:01,213] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:03:01,214] [INFO] Task started: Prodigal
[2024-01-24 15:03:01,214] [INFO] Running command: gunzip -c /var/lib/cwl/stg258b33b3-3dbf-48ee-9bbc-49f36e073057/GCF_014641415.1_ASM1464141v1_genomic.fna.gz | prodigal -d GCF_014641415.1_ASM1464141v1_genomic.fna/cds.fna -a GCF_014641415.1_ASM1464141v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:03:16,853] [INFO] Task succeeded: Prodigal
[2024-01-24 15:03:16,854] [INFO] Task started: HMMsearch
[2024-01-24 15:03:16,854] [INFO] Running command: hmmsearch --tblout GCF_014641415.1_ASM1464141v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg12f4de41-cd2c-440a-b696-90900895c3c2/dqc_reference/reference_markers.hmm GCF_014641415.1_ASM1464141v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:03:17,148] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:03:17,150] [INFO] Found 6/6 markers.
[2024-01-24 15:03:17,193] [INFO] Query marker FASTA was written to GCF_014641415.1_ASM1464141v1_genomic.fna/markers.fasta
[2024-01-24 15:03:17,193] [INFO] Task started: Blastn
[2024-01-24 15:03:17,194] [INFO] Running command: blastn -query GCF_014641415.1_ASM1464141v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg12f4de41-cd2c-440a-b696-90900895c3c2/dqc_reference/reference_markers.fasta -out GCF_014641415.1_ASM1464141v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:03:18,187] [INFO] Task succeeded: Blastn
[2024-01-24 15:03:18,194] [INFO] Selected 14 target genomes.
[2024-01-24 15:03:18,195] [INFO] Target genome list was writen to GCF_014641415.1_ASM1464141v1_genomic.fna/target_genomes.txt
[2024-01-24 15:03:18,202] [INFO] Task started: fastANI
[2024-01-24 15:03:18,202] [INFO] Running command: fastANI --query /var/lib/cwl/stg258b33b3-3dbf-48ee-9bbc-49f36e073057/GCF_014641415.1_ASM1464141v1_genomic.fna.gz --refList GCF_014641415.1_ASM1464141v1_genomic.fna/target_genomes.txt --output GCF_014641415.1_ASM1464141v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:03:37,594] [INFO] Task succeeded: fastANI
[2024-01-24 15:03:37,594] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg12f4de41-cd2c-440a-b696-90900895c3c2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:03:37,595] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg12f4de41-cd2c-440a-b696-90900895c3c2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:03:37,611] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 15:03:37,611] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:03:37,611] [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
Massilia psychrophila	strain=CGMCC 1.15196	GCA_014641415.1	1603353	1603353	type	True	100.0	1529	1533	95	conclusive
Massilia psychrophila	strain=JCM 30813	GCA_002760665.1	1603353	1603353	type	True	99.9873	1512	1533	95	conclusive
Massilia eurypsychrophila	strain=JCM 30074	GCA_002760655.1	1485217	1485217	type	True	84.9544	1097	1533	95	below_threshold
Massilia atriviolacea	strain=SOD	GCA_003953935.1	2495579	2495579	type	True	82.4162	955	1533	95	below_threshold
Massilia glaciei	strain=B448-2	GCA_003011895.2	1524097	1524097	type	True	82.0205	849	1533	95	below_threshold
Massilia mucilaginosa	strain=CCM 8733	GCA_011682145.1	2609282	2609282	type	True	81.9936	962	1533	95	below_threshold
Massilia soli	strain=R798	GCA_016809835.2	2792854	2792854	type	True	81.977	870	1533	95	below_threshold
Massilia violaceinigra	strain=B2	GCA_002752675.1	2045208	2045208	type	True	81.9242	921	1533	95	below_threshold
Massilia cavernae	strain=K1S02-61	GCA_003590855.1	2320864	2320864	type	True	81.8671	801	1533	95	below_threshold
Massilia rubra	strain=CCM 8692	GCA_011682065.1	2607910	2607910	type	True	81.8536	949	1533	95	below_threshold
Massilia frigida	strain=CCM 8695	GCA_011682175.1	2609281	2609281	type	True	81.8258	948	1533	95	below_threshold
Massilia terrae	strain=JCM 31606	GCA_024753145.1	1811224	1811224	type	True	81.1124	826	1533	95	below_threshold
Massilia norwichensis	strain=LMG 28164	GCA_024753245.1	1442366	1442366	type	True	80.8382	854	1533	95	below_threshold
Massilia oculi	strain=CCUG 43427	GCA_003143515.1	945844	945844	type	True	80.7913	804	1533	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:03:37,613] [INFO] DFAST Taxonomy check result was written to GCF_014641415.1_ASM1464141v1_genomic.fna/tc_result.tsv
[2024-01-24 15:03:37,614] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:03:37,614] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:03:37,614] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg12f4de41-cd2c-440a-b696-90900895c3c2/dqc_reference/checkm_data
[2024-01-24 15:03:37,616] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:03:37,667] [INFO] Task started: CheckM
[2024-01-24 15:03:37,667] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014641415.1_ASM1464141v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014641415.1_ASM1464141v1_genomic.fna/checkm_input GCF_014641415.1_ASM1464141v1_genomic.fna/checkm_result
[2024-01-24 15:04:22,005] [INFO] Task succeeded: CheckM
[2024-01-24 15:04:22,007] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 97.92%
Contamintation: 6.25%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:04:22,031] [INFO] ===== Completeness check finished =====
[2024-01-24 15:04:22,032] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:04:22,032] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014641415.1_ASM1464141v1_genomic.fna/markers.fasta)
[2024-01-24 15:04:22,033] [INFO] Task started: Blastn
[2024-01-24 15:04:22,033] [INFO] Running command: blastn -query GCF_014641415.1_ASM1464141v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg12f4de41-cd2c-440a-b696-90900895c3c2/dqc_reference/reference_markers_gtdb.fasta -out GCF_014641415.1_ASM1464141v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:04:23,956] [INFO] Task succeeded: Blastn
[2024-01-24 15:04:23,961] [INFO] Selected 12 target genomes.
[2024-01-24 15:04:23,961] [INFO] Target genome list was writen to GCF_014641415.1_ASM1464141v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:04:23,970] [INFO] Task started: fastANI
[2024-01-24 15:04:23,971] [INFO] Running command: fastANI --query /var/lib/cwl/stg258b33b3-3dbf-48ee-9bbc-49f36e073057/GCF_014641415.1_ASM1464141v1_genomic.fna.gz --refList GCF_014641415.1_ASM1464141v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014641415.1_ASM1464141v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:04:40,761] [INFO] Task succeeded: fastANI
[2024-01-24 15:04:40,773] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:04:40,773] [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_002760665.1	s__Massilia psychrophila	99.9873	1512	1533	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	99.99	99.99	0.99	0.99	2	conclusive
GCF_002760655.1	s__Massilia eurypsychrophila	84.9747	1096	1533	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003953935.1	s__Massilia atriviolacea	82.4422	952	1533	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002428015.1	s__Massilia sp002428015	82.0638	862	1533	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003011895.2	s__Massilia glaciei	82.0293	848	1533	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011682145.1	s__Massilia mucilaginosa	81.9862	962	1533	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011682045.1	s__Massilia aquatica	81.8976	943	1533	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002752675.1	s__Massilia violaceinigra	81.8966	925	1533	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003590855.1	s__Massilia sp003590855	81.8758	800	1533	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011682065.1	s__Massilia rubra	81.8461	950	1533	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	96.47	95.98	0.89	0.89	3	-
GCF_011682175.1	s__Massilia frigida	81.8161	950	1533	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014379395.1	s__Janthinobacterium sp014379395	81.5635	460	1533	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Janthinobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:04:40,775] [INFO] GTDB search result was written to GCF_014641415.1_ASM1464141v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:04:40,775] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:04:40,779] [INFO] DFAST_QC result json was written to GCF_014641415.1_ASM1464141v1_genomic.fna/dqc_result.json
[2024-01-24 15:04:40,779] [INFO] DFAST_QC completed!
[2024-01-24 15:04:40,779] [INFO] Total running time: 0h1m41s