[2024-01-25 17:35:20,376] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:35:20,378] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:35:20,378] [INFO] DQC Reference Directory: /var/lib/cwl/stg987d6b7c-c861-4cd9-8cd5-6119d43dc564/dqc_reference
[2024-01-25 17:35:21,501] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:35:21,502] [INFO] Task started: Prodigal
[2024-01-25 17:35:21,502] [INFO] Running command: gunzip -c /var/lib/cwl/stgf893138e-d80b-4236-982c-ba748ef7465e/GCF_016132545.1_ASM1613254v1_genomic.fna.gz | prodigal -d GCF_016132545.1_ASM1613254v1_genomic.fna/cds.fna -a GCF_016132545.1_ASM1613254v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:35:32,899] [INFO] Task succeeded: Prodigal
[2024-01-25 17:35:32,899] [INFO] Task started: HMMsearch
[2024-01-25 17:35:32,899] [INFO] Running command: hmmsearch --tblout GCF_016132545.1_ASM1613254v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg987d6b7c-c861-4cd9-8cd5-6119d43dc564/dqc_reference/reference_markers.hmm GCF_016132545.1_ASM1613254v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:35:33,127] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:35:33,129] [INFO] Found 6/6 markers.
[2024-01-25 17:35:33,165] [INFO] Query marker FASTA was written to GCF_016132545.1_ASM1613254v1_genomic.fna/markers.fasta
[2024-01-25 17:35:33,165] [INFO] Task started: Blastn
[2024-01-25 17:35:33,165] [INFO] Running command: blastn -query GCF_016132545.1_ASM1613254v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg987d6b7c-c861-4cd9-8cd5-6119d43dc564/dqc_reference/reference_markers.fasta -out GCF_016132545.1_ASM1613254v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:35:33,931] [INFO] Task succeeded: Blastn
[2024-01-25 17:35:33,933] [INFO] Selected 20 target genomes.
[2024-01-25 17:35:33,934] [INFO] Target genome list was writen to GCF_016132545.1_ASM1613254v1_genomic.fna/target_genomes.txt
[2024-01-25 17:35:33,941] [INFO] Task started: fastANI
[2024-01-25 17:35:33,941] [INFO] Running command: fastANI --query /var/lib/cwl/stgf893138e-d80b-4236-982c-ba748ef7465e/GCF_016132545.1_ASM1613254v1_genomic.fna.gz --refList GCF_016132545.1_ASM1613254v1_genomic.fna/target_genomes.txt --output GCF_016132545.1_ASM1613254v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:35:50,909] [INFO] Task succeeded: fastANI
[2024-01-25 17:35:50,909] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg987d6b7c-c861-4cd9-8cd5-6119d43dc564/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:35:50,909] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg987d6b7c-c861-4cd9-8cd5-6119d43dc564/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:35:50,921] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:35:50,921] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:35:50,921] [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
Spongiibacter nanhainus	strain=csc3.9	GCA_016132545.1	2794344	2794344	type	True	100.0	1359	1359	95	conclusive
Spongiibacter tropicus	strain=DSM 19543	GCA_000420325.1	454602	454602	type	True	79.0382	264	1359	95	below_threshold
Spongiibacter taiwanensis	strain=SPT1	GCA_023702635.1	1748242	1748242	type	True	77.9407	285	1359	95	below_threshold
Spongiibacter thalassae	strain=KMU-166	GCA_012272835.1	2721624	2721624	type	True	77.8432	253	1359	95	below_threshold
Spongiibacter pelagi	strain=KMU-158	GCA_014705705.1	2760804	2760804	type	True	77.7309	191	1359	95	below_threshold
Litorivivens lipolytica	strain=CECT 8654	GCA_014191715.1	1524264	1524264	type	True	77.2004	142	1359	95	below_threshold
Halioglobus japonicus	strain=NBRC 107739	GCA_001983995.1	930805	930805	type	True	77.0757	87	1359	95	below_threshold
Parahaliea aestuarii	strain=S2-26	GCA_008064635.1	1852021	1852021	type	True	77.0188	130	1359	95	below_threshold
Alcanivorax profundimaris	strain=ST75FaO-1	GCA_015265435.1	2735259	2735259	type	True	76.9828	82	1359	95	below_threshold
Parahaliea mediterranea	strain=DSM 21924	GCA_003402235.1	651086	651086	type	True	76.9629	145	1359	95	below_threshold
Seongchinamella unica	strain=GH4-78	GCA_004354085.1	2547392	2547392	type	True	76.747	88	1359	95	below_threshold
Halioglobus japonicus	strain=S1-36	GCA_002869505.1	930805	930805	type	True	76.7007	82	1359	95	below_threshold
Pseudomaricurvus alkylphenolicus	strain=KCTC 32386	GCA_011683955.1	1306991	1306991	type	True	76.5558	60	1359	95	below_threshold
Alcanivorax limicola	strain=JB21	GCA_019931215.1	2874102	2874102	type	True	76.4885	61	1359	95	below_threshold
Marinobacterium stanieri	strain=DSM 7027	GCA_900155945.1	49186	49186	type	True	76.2375	52	1359	95	below_threshold
Pseudomonas cuatrocienegasensis	strain=CIP 109853	GCA_900110925.1	543360	543360	type	True	76.2024	61	1359	95	below_threshold
Pseudomonas aeruginosa	strain=DSM 50071	GCA_900167195.1	287	287	type	True	76.1465	75	1359	95	below_threshold
Pseudomonas aeruginosa	strain=DSM 50071	GCA_001042925.1	287	287	type	True	76.1465	75	1359	95	below_threshold
Pseudomonas aeruginosa	strain=DSM 50071	GCA_012987025.1	287	287	type	True	76.1465	75	1359	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:35:50,924] [INFO] DFAST Taxonomy check result was written to GCF_016132545.1_ASM1613254v1_genomic.fna/tc_result.tsv
[2024-01-25 17:35:50,924] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:35:50,925] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:35:50,925] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg987d6b7c-c861-4cd9-8cd5-6119d43dc564/dqc_reference/checkm_data
[2024-01-25 17:35:50,926] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:35:50,972] [INFO] Task started: CheckM
[2024-01-25 17:35:50,972] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016132545.1_ASM1613254v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016132545.1_ASM1613254v1_genomic.fna/checkm_input GCF_016132545.1_ASM1613254v1_genomic.fna/checkm_result
[2024-01-25 17:36:25,931] [INFO] Task succeeded: CheckM
[2024-01-25 17:36:25,932] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:36:25,952] [INFO] ===== Completeness check finished =====
[2024-01-25 17:36:25,952] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:36:25,953] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016132545.1_ASM1613254v1_genomic.fna/markers.fasta)
[2024-01-25 17:36:25,953] [INFO] Task started: Blastn
[2024-01-25 17:36:25,953] [INFO] Running command: blastn -query GCF_016132545.1_ASM1613254v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg987d6b7c-c861-4cd9-8cd5-6119d43dc564/dqc_reference/reference_markers_gtdb.fasta -out GCF_016132545.1_ASM1613254v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:36:27,301] [INFO] Task succeeded: Blastn
[2024-01-25 17:36:27,303] [INFO] Selected 18 target genomes.
[2024-01-25 17:36:27,303] [INFO] Target genome list was writen to GCF_016132545.1_ASM1613254v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:36:27,330] [INFO] Task started: fastANI
[2024-01-25 17:36:27,330] [INFO] Running command: fastANI --query /var/lib/cwl/stgf893138e-d80b-4236-982c-ba748ef7465e/GCF_016132545.1_ASM1613254v1_genomic.fna.gz --refList GCF_016132545.1_ASM1613254v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016132545.1_ASM1613254v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:36:41,102] [INFO] Task succeeded: fastANI
[2024-01-25 17:36:41,112] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:36:41,113] [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_016132545.1	s__CSC3-9 sp016132545	100.0	1359	1359	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__CSC3-9	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000420325.1	s__Spongiibacter tropicus	79.0382	264	1359	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Spongiibacter	95.0	98.00	97.89	0.92	0.88	9	-
GCF_016906995.1	s__Spongiibacter marinus	78.754	214	1359	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Spongiibacter	95.0	97.69	97.65	0.87	0.86	3	-
GCF_000422345.1	s__Spongiibacter marinus_A	77.9136	205	1359	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Spongiibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012272835.1	s__Spongiibacter sp012272835	77.8699	251	1359	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Spongiibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002915595.1	s__Marortus luteolus	77.3103	129	1359	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Marortus	95.0	97.55	97.55	0.86	0.86	2	-
GCF_014191715.1	s__Litorivivens lipolytica	77.1883	141	1359	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Litorivivens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017255185.1	s__Parahaliea mediterranea_A	77.1313	133	1359	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015265435.1	s__Alcanivorax profundimaris	76.9828	82	1359	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	97.49	97.23	0.85	0.77	11	-
GCA_002699145.1	s__Halioglobus sp002699145	76.7728	94	1359	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	99.96	99.96	0.98	0.98	2	-
GCF_001457615.1	s__Pseudomonas aeruginosa	76.666	76	1359	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	99.12	97.38	0.94	0.84	5623	-
GCF_004745945.1	s__Halioglobus sp004745945	76.649	115	1359	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000017205.1	s__Pseudomonas aeruginosa_A	76.5555	79	1359	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	99.07	98.78	0.93	0.80	42	-
GCF_003457605.1	s__Halioglobus sediminis	76.4511	121	1359	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900155945.1	s__Marinobacterium stanieri	76.205	53	1359	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	96.47	96.47	0.91	0.91	2	-
GCF_001650425.1	s__Pseudomonas_B oryzihabitans_B	76.0216	75	1359	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_B	95.0	97.78	97.39	0.90	0.88	6	-
GCF_017309075.1	s__Motiliproteus sp017309075	76.0207	79	1359	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Motiliproteus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:36:41,126] [INFO] GTDB search result was written to GCF_016132545.1_ASM1613254v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:36:41,126] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:36:41,130] [INFO] DFAST_QC result json was written to GCF_016132545.1_ASM1613254v1_genomic.fna/dqc_result.json
[2024-01-25 17:36:41,131] [INFO] DFAST_QC completed!
[2024-01-25 17:36:41,131] [INFO] Total running time: 0h1m21s