[2024-01-25 17:51:50,369] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:51:50,371] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:51:50,371] [INFO] DQC Reference Directory: /var/lib/cwl/stg8d649b2c-5c2c-4440-ba06-97b0316e08bb/dqc_reference
[2024-01-25 17:51:51,514] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:51:51,515] [INFO] Task started: Prodigal
[2024-01-25 17:51:51,515] [INFO] Running command: gunzip -c /var/lib/cwl/stgd839b4ce-6299-42ce-8a0c-ca9b01dc8cad/GCF_003667345.1_ASM366734v1_genomic.fna.gz | prodigal -d GCF_003667345.1_ASM366734v1_genomic.fna/cds.fna -a GCF_003667345.1_ASM366734v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:51:55,309] [INFO] Task succeeded: Prodigal
[2024-01-25 17:51:55,310] [INFO] Task started: HMMsearch
[2024-01-25 17:51:55,310] [INFO] Running command: hmmsearch --tblout GCF_003667345.1_ASM366734v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8d649b2c-5c2c-4440-ba06-97b0316e08bb/dqc_reference/reference_markers.hmm GCF_003667345.1_ASM366734v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:51:55,528] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:51:55,530] [INFO] Found 6/6 markers.
[2024-01-25 17:51:55,556] [INFO] Query marker FASTA was written to GCF_003667345.1_ASM366734v1_genomic.fna/markers.fasta
[2024-01-25 17:51:55,556] [INFO] Task started: Blastn
[2024-01-25 17:51:55,556] [INFO] Running command: blastn -query GCF_003667345.1_ASM366734v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8d649b2c-5c2c-4440-ba06-97b0316e08bb/dqc_reference/reference_markers.fasta -out GCF_003667345.1_ASM366734v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:51:56,126] [INFO] Task succeeded: Blastn
[2024-01-25 17:51:56,128] [INFO] Selected 21 target genomes.
[2024-01-25 17:51:56,129] [INFO] Target genome list was writen to GCF_003667345.1_ASM366734v1_genomic.fna/target_genomes.txt
[2024-01-25 17:51:56,167] [INFO] Task started: fastANI
[2024-01-25 17:51:56,168] [INFO] Running command: fastANI --query /var/lib/cwl/stgd839b4ce-6299-42ce-8a0c-ca9b01dc8cad/GCF_003667345.1_ASM366734v1_genomic.fna.gz --refList GCF_003667345.1_ASM366734v1_genomic.fna/target_genomes.txt --output GCF_003667345.1_ASM366734v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:52:07,978] [INFO] Task succeeded: fastANI
[2024-01-25 17:52:07,979] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8d649b2c-5c2c-4440-ba06-97b0316e08bb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:52:07,979] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8d649b2c-5c2c-4440-ba06-97b0316e08bb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:52:07,994] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 17:52:07,994] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 17:52:07,995] [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
Poseidonibacter lekithochrous	strain=DSM 100870	GCA_013283835.1	1904463	1904463	type	True	80.8432	530	952	95	below_threshold
Poseidonibacter lekithochrous	strain=LFT 1.7	GCA_001878855.1	1904463	1904463	type	True	80.783	528	952	95	below_threshold
Arcobacter acticola	strain=KCTC 52212	GCA_013177675.1	1849015	1849015	type	True	80.635	526	952	95	below_threshold
Arcobacter suis	strain=CECT 7833	GCA_003544815.1	1278212	1278212	type	True	80.4953	450	952	95	below_threshold
Arcobacter suis	strain=CECT7833	GCA_004023465.1	1278212	1278212	type	True	80.4304	449	952	95	below_threshold
Arcobacter venerupis	strain=CECT7836	GCA_004023405.1	1054033	1054033	type	True	80.3104	499	952	95	below_threshold
Arcobacter venerupis	strain=LMG 26156	GCA_013201665.1	1054033	1054033	type	True	80.2883	501	952	95	below_threshold
Arcobacter defluvii	strain=LMG 25694	GCA_013201725.1	873191	873191	type	True	80.2334	500	952	95	below_threshold
Arcobacter defluvii	strain=CECT 7697	GCA_004115775.1	873191	873191	type	True	80.2302	487	952	95	below_threshold
Arcobacter ellisii	strain=LMG 26155	GCA_003544915.1	913109	913109	type	True	80.2178	480	952	95	below_threshold
Arcobacter ellisii	strain=CECT 7837	GCA_004115815.1	913109	913109	type	True	80.2048	481	952	95	below_threshold
Malaciobacter pacificus	strain=LMG 26638	GCA_004214795.1	1080223	1080223	type	True	80.0828	448	952	95	below_threshold
Arcobacter aquimarinus	strain=CECT 8442	GCA_004115795.1	1315211	1315211	type	True	80.0632	434	952	95	below_threshold
Arcobacter cloacae	strain=CECT 7834	GCA_004115805.1	1054034	1054034	type	True	79.9445	444	952	95	below_threshold
Arcobacter aquimarinus	strain=W63	GCA_013177635.1	1315211	1315211	type	True	79.9071	453	952	95	below_threshold
Malaciobacter marinus	strain=JCM 15502	GCA_003544855.1	505249	505249	type	True	78.763	369	952	95	below_threshold
Aliarcobacter vitoriensis	strain=CECT 9230	GCA_003316695.1	2011099	2011099	type	True	78.6254	309	952	95	below_threshold
Aliarcobacter vitoriensis	strain=LMG 30050	GCA_024583985.1	2011099	2011099	type	True	78.5554	311	952	95	below_threshold
Aliarcobacter faecis	strain=LMG 28519	GCA_024584135.1	1564138	1564138	type	True	78.5461	311	952	95	below_threshold
Arcobacter vandammei	strain=LMG 31429	GCA_024583975.1	2782243	2782243	type	True	78.1954	284	952	95	below_threshold
Arcobacter vandammei	strain=R-73987	GCA_016106035.1	2782243	2782243	type	True	78.1891	282	952	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:52:08,002] [INFO] DFAST Taxonomy check result was written to GCF_003667345.1_ASM366734v1_genomic.fna/tc_result.tsv
[2024-01-25 17:52:08,002] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:52:08,002] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:52:08,002] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8d649b2c-5c2c-4440-ba06-97b0316e08bb/dqc_reference/checkm_data
[2024-01-25 17:52:08,003] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:52:08,035] [INFO] Task started: CheckM
[2024-01-25 17:52:08,035] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003667345.1_ASM366734v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003667345.1_ASM366734v1_genomic.fna/checkm_input GCF_003667345.1_ASM366734v1_genomic.fna/checkm_result
[2024-01-25 17:52:25,531] [INFO] Task succeeded: CheckM
[2024-01-25 17:52:25,531] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:52:25,568] [INFO] ===== Completeness check finished =====
[2024-01-25 17:52:25,568] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:52:25,569] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003667345.1_ASM366734v1_genomic.fna/markers.fasta)
[2024-01-25 17:52:25,569] [INFO] Task started: Blastn
[2024-01-25 17:52:25,569] [INFO] Running command: blastn -query GCF_003667345.1_ASM366734v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8d649b2c-5c2c-4440-ba06-97b0316e08bb/dqc_reference/reference_markers_gtdb.fasta -out GCF_003667345.1_ASM366734v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:52:26,361] [INFO] Task succeeded: Blastn
[2024-01-25 17:52:26,364] [INFO] Selected 12 target genomes.
[2024-01-25 17:52:26,364] [INFO] Target genome list was writen to GCF_003667345.1_ASM366734v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:52:26,375] [INFO] Task started: fastANI
[2024-01-25 17:52:26,376] [INFO] Running command: fastANI --query /var/lib/cwl/stgd839b4ce-6299-42ce-8a0c-ca9b01dc8cad/GCF_003667345.1_ASM366734v1_genomic.fna.gz --refList GCF_003667345.1_ASM366734v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003667345.1_ASM366734v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:52:33,846] [INFO] Task succeeded: fastANI
[2024-01-25 17:52:33,855] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:52:33,856] [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_003667345.1	s__Poseidonibacter antarcticus	100.0	951	952	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Poseidonibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001956695.1	s__Poseidonibacter parvus	84.5343	639	952	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Poseidonibacter	95.0	98.33	98.33	0.91	0.91	2	-
GCF_009208075.1	s__Poseidonibacter sp009208075	84.0019	574	952	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Poseidonibacter	95.0	99.63	99.63	0.93	0.93	3	-
GCF_018861145.1	s__Poseidonibacter lekithochrous_A	83.9472	645	952	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Poseidonibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905479135.1	s__Poseidonibacter sp905479135	83.3462	364	952	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Poseidonibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002685075.1	s__Poseidonibacter sp002685075	83.0313	496	952	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Poseidonibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013283835.1	s__Poseidonibacter lekithochrous	80.8032	533	952	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Poseidonibacter	95.0	99.16	98.33	0.97	0.93	3	-
GCF_013201935.1	s__Aliarcobacter cloacae	79.9223	448	952	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	97.96	95.91	0.93	0.87	3	-
GCA_013215915.1	s__NORP36 sp013215915	78.7922	322	952	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__NORP36	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003544855.1	s__Malaciobacter marinus	78.774	368	952	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Malaciobacter	95.0	98.03	95.41	0.91	0.86	14	-
GCA_003316695.1	s__Aliarcobacter sp003316695	78.6187	310	952	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	97.67	97.67	0.88	0.88	2	-
GCF_003660105.1	s__Aliarcobacter cryaerophilus	78.5691	300	952	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	99.99	99.99	1.00	0.99	3	-
--------------------------------------------------------------------------------
[2024-01-25 17:52:33,857] [INFO] GTDB search result was written to GCF_003667345.1_ASM366734v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:52:33,858] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:52:33,861] [INFO] DFAST_QC result json was written to GCF_003667345.1_ASM366734v1_genomic.fna/dqc_result.json
[2024-01-25 17:52:33,861] [INFO] DFAST_QC completed!
[2024-01-25 17:52:33,861] [INFO] Total running time: 0h0m43s