[2024-01-24 14:46:54,736] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:46:54,738] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:46:54,739] [INFO] DQC Reference Directory: /var/lib/cwl/stg95d33752-1ca1-4b88-a123-23d648aa1337/dqc_reference
[2024-01-24 14:46:55,999] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:46:56,000] [INFO] Task started: Prodigal
[2024-01-24 14:46:56,000] [INFO] Running command: gunzip -c /var/lib/cwl/stga0c7b080-3bec-4ccb-be0a-a419c201e00e/GCF_014652595.1_ASM1465259v1_genomic.fna.gz | prodigal -d GCF_014652595.1_ASM1465259v1_genomic.fna/cds.fna -a GCF_014652595.1_ASM1465259v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:47:10,111] [INFO] Task succeeded: Prodigal
[2024-01-24 14:47:10,111] [INFO] Task started: HMMsearch
[2024-01-24 14:47:10,111] [INFO] Running command: hmmsearch --tblout GCF_014652595.1_ASM1465259v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg95d33752-1ca1-4b88-a123-23d648aa1337/dqc_reference/reference_markers.hmm GCF_014652595.1_ASM1465259v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:47:10,509] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:47:10,510] [INFO] Found 6/6 markers.
[2024-01-24 14:47:10,577] [INFO] Query marker FASTA was written to GCF_014652595.1_ASM1465259v1_genomic.fna/markers.fasta
[2024-01-24 14:47:10,578] [INFO] Task started: Blastn
[2024-01-24 14:47:10,578] [INFO] Running command: blastn -query GCF_014652595.1_ASM1465259v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg95d33752-1ca1-4b88-a123-23d648aa1337/dqc_reference/reference_markers.fasta -out GCF_014652595.1_ASM1465259v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:47:11,397] [INFO] Task succeeded: Blastn
[2024-01-24 14:47:11,400] [INFO] Selected 22 target genomes.
[2024-01-24 14:47:11,401] [INFO] Target genome list was writen to GCF_014652595.1_ASM1465259v1_genomic.fna/target_genomes.txt
[2024-01-24 14:47:11,415] [INFO] Task started: fastANI
[2024-01-24 14:47:11,415] [INFO] Running command: fastANI --query /var/lib/cwl/stga0c7b080-3bec-4ccb-be0a-a419c201e00e/GCF_014652595.1_ASM1465259v1_genomic.fna.gz --refList GCF_014652595.1_ASM1465259v1_genomic.fna/target_genomes.txt --output GCF_014652595.1_ASM1465259v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:47:30,210] [INFO] Task succeeded: fastANI
[2024-01-24 14:47:30,210] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg95d33752-1ca1-4b88-a123-23d648aa1337/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:47:30,210] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg95d33752-1ca1-4b88-a123-23d648aa1337/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:47:30,221] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:47:30,221] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:47:30,222] [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
Paraglaciecola mesophila	strain=KMM 241	GCA_000315015.1	197222	197222	type	True	82.9517	1007	1854	95	below_threshold
Motilimonas pumila	strain=PLHSC7-2	GCA_003596335.1	2303987	2303987	type	True	81.4393	69	1854	95	below_threshold
Paraglaciecola polaris	strain=LMG 21857	GCA_000315055.1	222814	222814	type	True	80.6176	707	1854	95	below_threshold
Alteromonas lipotrueae	strain=MD_652	GCA_019249215.1	2803814	2803814	type	True	78.5381	123	1854	95	below_threshold
Paraglaciecola marina	strain=D3211	GCA_004360155.1	2500157	2500157	type	True	77.9569	137	1854	95	below_threshold
Paraglaciecola aquimarina	strain=GGW-M5	GCA_021532655.1	1235557	1235557	type	True	77.9048	169	1854	95	below_threshold
Alteromonas mediterranea	strain=DE	GCA_000020585.3	314275	314275	type	True	77.782	95	1854	95	below_threshold
Paraglaciecola hydrolytica	strain=S66	GCA_001565895.1	1799789	1799789	type	True	77.7752	172	1854	95	below_threshold
Paraglaciecola arctica	strain=BSs20135	GCA_000314995.1	1128911	1128911	type	True	77.6928	167	1854	95	below_threshold
Alteromonas naphthalenivorans	strain=SN2	GCA_000213655.1	715451	715451	type	True	77.655	139	1854	95	below_threshold
Neptunicella marina	strain=S27-2	GCA_014270035.1	2125989	2125989	type	True	77.126	93	1854	95	below_threshold
Pseudoalteromonas caenipelagi	strain=JBTF-M23	GCA_013140855.1	2726988	2726988	type	True	76.4848	51	1854	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:47:30,223] [INFO] DFAST Taxonomy check result was written to GCF_014652595.1_ASM1465259v1_genomic.fna/tc_result.tsv
[2024-01-24 14:47:30,224] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:47:30,224] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:47:30,224] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg95d33752-1ca1-4b88-a123-23d648aa1337/dqc_reference/checkm_data
[2024-01-24 14:47:30,225] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:47:30,282] [INFO] Task started: CheckM
[2024-01-24 14:47:30,282] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014652595.1_ASM1465259v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014652595.1_ASM1465259v1_genomic.fna/checkm_input GCF_014652595.1_ASM1465259v1_genomic.fna/checkm_result
[2024-01-24 14:48:15,326] [INFO] Task succeeded: CheckM
[2024-01-24 14:48:15,327] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:48:15,351] [INFO] ===== Completeness check finished =====
[2024-01-24 14:48:15,352] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:48:15,352] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014652595.1_ASM1465259v1_genomic.fna/markers.fasta)
[2024-01-24 14:48:15,353] [INFO] Task started: Blastn
[2024-01-24 14:48:15,353] [INFO] Running command: blastn -query GCF_014652595.1_ASM1465259v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg95d33752-1ca1-4b88-a123-23d648aa1337/dqc_reference/reference_markers_gtdb.fasta -out GCF_014652595.1_ASM1465259v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:48:16,464] [INFO] Task succeeded: Blastn
[2024-01-24 14:48:16,469] [INFO] Selected 8 target genomes.
[2024-01-24 14:48:16,469] [INFO] Target genome list was writen to GCF_014652595.1_ASM1465259v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:48:16,477] [INFO] Task started: fastANI
[2024-01-24 14:48:16,477] [INFO] Running command: fastANI --query /var/lib/cwl/stga0c7b080-3bec-4ccb-be0a-a419c201e00e/GCF_014652595.1_ASM1465259v1_genomic.fna.gz --refList GCF_014652595.1_ASM1465259v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014652595.1_ASM1465259v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:48:25,822] [INFO] Task succeeded: fastANI
[2024-01-24 14:48:25,841] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:48:25,841] [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
GCA_000314955.1	s__Paraglaciecola chathamensis	98.4195	1567	1854	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	98.24	97.58	0.90	0.88	8	conclusive
GCF_009906955.1	s__Paraglaciecola mesophila_A	89.8772	1444	1854	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000315015.1	s__Paraglaciecola mesophila	82.9063	1013	1854	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	98.29	98.05	0.87	0.80	4	-
GCF_000014225.1	s__Paraglaciecola atlantica_A	81.6801	997	1854	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000315055.1	s__Paraglaciecola polaris	80.6176	707	1854	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009796745.1	s__Paraglaciecola sp009796745	79.9023	654	1854	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011378905.1	s__Paraglaciecola sp011378905	79.791	683	1854	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004353515.1	s__M269 sp004353515	77.2616	77	1854	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__M269	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:48:25,877] [INFO] GTDB search result was written to GCF_014652595.1_ASM1465259v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:48:25,879] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:48:25,885] [INFO] DFAST_QC result json was written to GCF_014652595.1_ASM1465259v1_genomic.fna/dqc_result.json
[2024-01-24 14:48:25,885] [INFO] DFAST_QC completed!
[2024-01-24 14:48:25,886] [INFO] Total running time: 0h1m31s