[2024-01-24 13:17:03,671] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:03,674] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:03,674] [INFO] DQC Reference Directory: /var/lib/cwl/stg3bff0a47-69ba-4f24-aa71-8e9b3d78fb1b/dqc_reference
[2024-01-24 13:17:04,949] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:04,950] [INFO] Task started: Prodigal
[2024-01-24 13:17:04,950] [INFO] Running command: gunzip -c /var/lib/cwl/stgb3bc57ac-d0be-4a76-8ce3-067340ca9a1c/GCF_004295665.1_ASM429566v1_genomic.fna.gz | prodigal -d GCF_004295665.1_ASM429566v1_genomic.fna/cds.fna -a GCF_004295665.1_ASM429566v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:17:13,782] [INFO] Task succeeded: Prodigal
[2024-01-24 13:17:13,782] [INFO] Task started: HMMsearch
[2024-01-24 13:17:13,782] [INFO] Running command: hmmsearch --tblout GCF_004295665.1_ASM429566v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3bff0a47-69ba-4f24-aa71-8e9b3d78fb1b/dqc_reference/reference_markers.hmm GCF_004295665.1_ASM429566v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:17:14,103] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:17:14,104] [INFO] Found 6/6 markers.
[2024-01-24 13:17:14,161] [INFO] Query marker FASTA was written to GCF_004295665.1_ASM429566v1_genomic.fna/markers.fasta
[2024-01-24 13:17:14,162] [INFO] Task started: Blastn
[2024-01-24 13:17:14,162] [INFO] Running command: blastn -query GCF_004295665.1_ASM429566v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3bff0a47-69ba-4f24-aa71-8e9b3d78fb1b/dqc_reference/reference_markers.fasta -out GCF_004295665.1_ASM429566v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:14,889] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:14,892] [INFO] Selected 15 target genomes.
[2024-01-24 13:17:14,892] [INFO] Target genome list was writen to GCF_004295665.1_ASM429566v1_genomic.fna/target_genomes.txt
[2024-01-24 13:17:14,898] [INFO] Task started: fastANI
[2024-01-24 13:17:14,898] [INFO] Running command: fastANI --query /var/lib/cwl/stgb3bc57ac-d0be-4a76-8ce3-067340ca9a1c/GCF_004295665.1_ASM429566v1_genomic.fna.gz --refList GCF_004295665.1_ASM429566v1_genomic.fna/target_genomes.txt --output GCF_004295665.1_ASM429566v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:17:26,989] [INFO] Task succeeded: fastANI
[2024-01-24 13:17:26,989] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3bff0a47-69ba-4f24-aa71-8e9b3d78fb1b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:17:26,990] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3bff0a47-69ba-4f24-aa71-8e9b3d78fb1b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:17:27,002] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:17:27,002] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:17:27,002] [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
Litorilituus sediminis	strain=JCM 17549	GCA_004295665.1	718192	718192	type	True	100.0	1423	1425	95	conclusive
Litorilituus lipolyticus	strain=RZ04	GCA_006439335.1	2491017	2491017	type	True	79.6824	506	1425	95	below_threshold
Thalassotalea crassostreae	strain=LPB0090	GCA_001831495.1	1763536	1763536	type	True	78.9798	150	1425	95	below_threshold
Colwellia ponticola	strain=OISW-25	GCA_005885605.1	2304625	2304625	type	True	78.7266	315	1425	95	below_threshold
Vibrio algicola	strain=SM1977	GCA_009601765.2	2662262	2662262	type	True	78.6789	51	1425	95	below_threshold
Photobacterium sanguinicancri	strain=CECT 7579	GCA_024346675.1	875932	875932	type	True	78.5897	56	1425	95	below_threshold
Colwellia echini	strain=A3	GCA_002843355.2	1982103	1982103	type	True	78.5074	298	1425	95	below_threshold
Thalassotalea agarivorans	strain=DSM 19706	GCA_900111755.1	349064	349064	type	True	78.4601	151	1425	95	below_threshold
Colwellia demingiae	strain=ACAM 459	GCA_007954275.1	89401	89401	type	True	78.4286	360	1425	95	below_threshold
Colwellia piezophila	strain=ATCC BAA-637	GCA_000378625.1	211668	211668	type	True	78.3561	348	1425	95	below_threshold
Thalassotalea crassostreae	strain=LPB0090	GCA_001652445.1	1763536	1763536	type	True	78.3106	137	1425	95	below_threshold
Thalassotalea piscium	strain=DSM 26287	GCA_014207645.1	1230533	1230533	type	True	77.9212	196	1425	95	below_threshold
Paraneptunicella aestuarii	strain=NBU2194	GCA_019900845.1	2831148	2831148	type	True	77.2506	55	1425	95	below_threshold
Pseudoalteromonas distincta	strain=ATCC 700518	GCA_000814675.1	77608	77608	type	True	76.8764	92	1425	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:17:27,004] [INFO] DFAST Taxonomy check result was written to GCF_004295665.1_ASM429566v1_genomic.fna/tc_result.tsv
[2024-01-24 13:17:27,005] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:17:27,005] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:17:27,005] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3bff0a47-69ba-4f24-aa71-8e9b3d78fb1b/dqc_reference/checkm_data
[2024-01-24 13:17:27,006] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:17:27,051] [INFO] Task started: CheckM
[2024-01-24 13:17:27,052] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004295665.1_ASM429566v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004295665.1_ASM429566v1_genomic.fna/checkm_input GCF_004295665.1_ASM429566v1_genomic.fna/checkm_result
[2024-01-24 13:17:58,765] [INFO] Task succeeded: CheckM
[2024-01-24 13:17:58,766] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:17:58,788] [INFO] ===== Completeness check finished =====
[2024-01-24 13:17:58,788] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:17:58,789] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004295665.1_ASM429566v1_genomic.fna/markers.fasta)
[2024-01-24 13:17:58,789] [INFO] Task started: Blastn
[2024-01-24 13:17:58,789] [INFO] Running command: blastn -query GCF_004295665.1_ASM429566v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3bff0a47-69ba-4f24-aa71-8e9b3d78fb1b/dqc_reference/reference_markers_gtdb.fasta -out GCF_004295665.1_ASM429566v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:59,906] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:59,909] [INFO] Selected 17 target genomes.
[2024-01-24 13:17:59,909] [INFO] Target genome list was writen to GCF_004295665.1_ASM429566v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:17:59,925] [INFO] Task started: fastANI
[2024-01-24 13:17:59,926] [INFO] Running command: fastANI --query /var/lib/cwl/stgb3bc57ac-d0be-4a76-8ce3-067340ca9a1c/GCF_004295665.1_ASM429566v1_genomic.fna.gz --refList GCF_004295665.1_ASM429566v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004295665.1_ASM429566v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:18:13,486] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:13,514] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:18:13,514] [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_004295665.1	s__Litorilituus sediminis	100.0	1423	1425	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Litorilituus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_006439335.1	s__Litorilituus lipolyticus	79.6624	508	1425	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Litorilituus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003545765.1	s__Litorilituus sp003545765	79.4039	462	1425	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Litorilituus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009832865.1	s__Colwellia sp009832865	79.0049	294	1425	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860755.1	s__Colwellia sp018860755	78.9029	377	1425	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002836255.1	s__Colwellia sp002836255	78.788	361	1425	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000012325.1	s__Colwellia psychrerythraea_A	78.6959	372	1425	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	98.43	98.43	0.88	0.88	2	-
GCF_000764185.1	s__Colwellia psychrerythraea_B	78.6874	373	1425	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016745015.1	s__Colwellia sp016745015	78.6355	261	1425	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013215465.1	s__Colwellia sp013215465	78.5408	318	1425	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	96.15	96.15	0.84	0.84	2	-
GCF_002843355.2	s__Colwellia echini	78.5342	296	1425	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013214175.1	s__Colwellia sp013214175	78.5147	403	1425	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	95.17	95.17	0.89	0.89	2	-
GCA_002163005.1	s__Colwellia psychrerythraea_C	78.2576	333	1425	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002836775.1	s__Colwellia sp002836775	78.2465	374	1425	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002733765.1	s__Colwellia sp002733765	78.103	288	1425	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	99.46	99.46	0.95	0.95	2	-
GCA_003521815.1	s__Colwellia sp003521815	78.0115	209	1425	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016765685.1	s__Colwellia sp016765685	77.4704	221	1425	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:18:13,516] [INFO] GTDB search result was written to GCF_004295665.1_ASM429566v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:18:13,516] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:18:13,520] [INFO] DFAST_QC result json was written to GCF_004295665.1_ASM429566v1_genomic.fna/dqc_result.json
[2024-01-24 13:18:13,520] [INFO] DFAST_QC completed!
[2024-01-24 13:18:13,520] [INFO] Total running time: 0h1m10s