[2024-01-24 13:09:51,301] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:09:51,303] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:09:51,303] [INFO] DQC Reference Directory: /var/lib/cwl/stg073e34c7-f0b6-4bd6-8a9f-076aa761f308/dqc_reference
[2024-01-24 13:09:52,720] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:09:52,721] [INFO] Task started: Prodigal
[2024-01-24 13:09:52,722] [INFO] Running command: gunzip -c /var/lib/cwl/stg80c5757f-4b5d-4f32-a2c3-f6d8d3722532/GCF_024347435.1_ASM2434743v1_genomic.fna.gz | prodigal -d GCF_024347435.1_ASM2434743v1_genomic.fna/cds.fna -a GCF_024347435.1_ASM2434743v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:10:06,610] [INFO] Task succeeded: Prodigal
[2024-01-24 13:10:06,610] [INFO] Task started: HMMsearch
[2024-01-24 13:10:06,610] [INFO] Running command: hmmsearch --tblout GCF_024347435.1_ASM2434743v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg073e34c7-f0b6-4bd6-8a9f-076aa761f308/dqc_reference/reference_markers.hmm GCF_024347435.1_ASM2434743v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:10:06,958] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:10:06,959] [INFO] Found 6/6 markers.
[2024-01-24 13:10:06,999] [INFO] Query marker FASTA was written to GCF_024347435.1_ASM2434743v1_genomic.fna/markers.fasta
[2024-01-24 13:10:06,999] [INFO] Task started: Blastn
[2024-01-24 13:10:07,000] [INFO] Running command: blastn -query GCF_024347435.1_ASM2434743v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg073e34c7-f0b6-4bd6-8a9f-076aa761f308/dqc_reference/reference_markers.fasta -out GCF_024347435.1_ASM2434743v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:10:07,802] [INFO] Task succeeded: Blastn
[2024-01-24 13:10:07,805] [INFO] Selected 16 target genomes.
[2024-01-24 13:10:07,806] [INFO] Target genome list was writen to GCF_024347435.1_ASM2434743v1_genomic.fna/target_genomes.txt
[2024-01-24 13:10:07,822] [INFO] Task started: fastANI
[2024-01-24 13:10:07,822] [INFO] Running command: fastANI --query /var/lib/cwl/stg80c5757f-4b5d-4f32-a2c3-f6d8d3722532/GCF_024347435.1_ASM2434743v1_genomic.fna.gz --refList GCF_024347435.1_ASM2434743v1_genomic.fna/target_genomes.txt --output GCF_024347435.1_ASM2434743v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:10:28,260] [INFO] Task succeeded: fastANI
[2024-01-24 13:10:28,261] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg073e34c7-f0b6-4bd6-8a9f-076aa761f308/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:10:28,261] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg073e34c7-f0b6-4bd6-8a9f-076aa761f308/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:10:28,274] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:10:28,274] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:10:28,275] [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
Vibrio cyclitrophicus	strain=LMG 21359	GCA_024347435.1	47951	47951	type	True	100.0	1749	1757	95	conclusive
Vibrio celticus	strain=CECT 7224	GCA_900089965.1	446372	446372	type	True	89.2944	1336	1757	95	below_threshold
Vibrio celticus	strain=CECT 7224	GCA_024347335.1	446372	446372	type	True	89.2136	1414	1757	95	below_threshold
Vibrio celticus	strain=Rd 8.15	GCA_002156525.1	446372	446372	type	True	89.199	1336	1757	95	below_threshold
Vibrio coralliirubri	strain=DSM 27495	GCA_024347375.1	1516159	1516159	type	True	89.0699	1388	1757	95	below_threshold
Vibrio tasmaniensis	strain=LMG 20012	GCA_024347635.1	212663	212663	suspected-type	True	88.7349	1275	1757	95	below_threshold
Vibrio lentus	strain=40M4T	GCA_014878155.1	136468	136468	type	True	88.7079	1324	1757	95	below_threshold
Vibrio atlanticus	strain=CECT 7223	GCA_024347315.1	693153	693153	type	True	88.6974	1290	1757	95	below_threshold
Vibrio crassostreae	strain=LGP7	GCA_001048535.1	246167	246167	type	True	88.5959	1341	1757	95	below_threshold
Vibrio atlanticus	strain=CECT 7223	GCA_900089855.1	693153	693153	type	True	88.5902	1248	1757	95	below_threshold
Vibrio tasmaniensis	strain=LMG 20012	GCA_006333845.1	212663	212663	suspected-type	True	88.53	1218	1757	95	below_threshold
Vibrio pomeroyi	strain=LMG 20537	GCA_024347595.1	198832	198832	type	True	88.1493	1403	1757	95	below_threshold
Vibrio kanaloae	strain=LMG 20539	GCA_024347535.1	170673	170673	type	True	88.0766	1270	1757	95	below_threshold
Vibrio kanaloae	strain=CCUG 56968	GCA_008801285.1	170673	170673	type	True	87.9552	1242	1757	95	below_threshold
Vibrio gigantis	strain=LMG 22741	GCA_024347515.1	296199	296199	type	True	87.8901	1346	1757	95	below_threshold
Vibrio gigantis	strain=LGP 13	GCA_002156475.1	296199	296199	type	True	87.8276	1310	1757	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:10:28,277] [INFO] DFAST Taxonomy check result was written to GCF_024347435.1_ASM2434743v1_genomic.fna/tc_result.tsv
[2024-01-24 13:10:28,277] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:10:28,277] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:10:28,277] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg073e34c7-f0b6-4bd6-8a9f-076aa761f308/dqc_reference/checkm_data
[2024-01-24 13:10:28,279] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:10:28,333] [INFO] Task started: CheckM
[2024-01-24 13:10:28,334] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024347435.1_ASM2434743v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024347435.1_ASM2434743v1_genomic.fna/checkm_input GCF_024347435.1_ASM2434743v1_genomic.fna/checkm_result
[2024-01-24 13:11:13,747] [INFO] Task succeeded: CheckM
[2024-01-24 13:11:13,749] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:11:13,772] [INFO] ===== Completeness check finished =====
[2024-01-24 13:11:13,772] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:11:13,772] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024347435.1_ASM2434743v1_genomic.fna/markers.fasta)
[2024-01-24 13:11:13,773] [INFO] Task started: Blastn
[2024-01-24 13:11:13,773] [INFO] Running command: blastn -query GCF_024347435.1_ASM2434743v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg073e34c7-f0b6-4bd6-8a9f-076aa761f308/dqc_reference/reference_markers_gtdb.fasta -out GCF_024347435.1_ASM2434743v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:11:14,998] [INFO] Task succeeded: Blastn
[2024-01-24 13:11:15,002] [INFO] Selected 17 target genomes.
[2024-01-24 13:11:15,002] [INFO] Target genome list was writen to GCF_024347435.1_ASM2434743v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:11:15,013] [INFO] Task started: fastANI
[2024-01-24 13:11:15,013] [INFO] Running command: fastANI --query /var/lib/cwl/stg80c5757f-4b5d-4f32-a2c3-f6d8d3722532/GCF_024347435.1_ASM2434743v1_genomic.fna.gz --refList GCF_024347435.1_ASM2434743v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024347435.1_ASM2434743v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:11:35,084] [INFO] Task succeeded: fastANI
[2024-01-24 13:11:35,101] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:11:35,102] [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_005144905.1	s__Vibrio cyclitrophicus	98.9697	1567	1757	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	99.18	99.01	0.95	0.91	87	conclusive
GCF_000272045.2	s__Vibrio crassostreae_C	89.4201	1372	1757	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.007	97.54	97.16	0.89	0.87	25	-
GCF_002156525.1	s__Vibrio celticus	89.1938	1337	1757	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.2787	99.99	99.99	1.00	1.00	2	-
GCF_000272105.2	s__Vibrio splendidus_I	89.1038	1290	1757	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002873455.1	s__Vibrio splendidus_J	89.0867	1380	1757	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.45	97.37	0.93	0.92	7	-
GCF_002156455.1	s__Vibrio coralliirubri	89.0354	1318	1757	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.2787	96.55	95.77	0.88	0.83	22	-
GCF_002875945.1	s__Vibrio lentus_A	88.8242	1330	1757	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014878155.1	s__Vibrio lentus	88.7044	1325	1757	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.60	95.56	0.86	0.83	91	-
GCF_900089855.1	s__Vibrio atlanticus	88.6129	1246	1757	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	96.5791	N/A	N/A	N/A	N/A	1	-
GCF_001557875.1	s__Vibrio splendidus_F	88.5672	1316	1757	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.50	97.50	0.93	0.93	2	-
GCF_006333845.1	s__Vibrio tasmaniensis	88.5416	1217	1757	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	95.02	95.02	0.87	0.87	2	-
GCF_007858795.1	s__Vibrio sp007858795	88.5398	1298	1757	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000272405.2	s__Vibrio tasmaniensis_A	88.502	1195	1757	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	96.5791	97.23	97.01	0.87	0.85	20	-
GCF_013394185.1	s__Vibrio sp013394185	88.341	1375	1757	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	100.00	100.00	0.99	0.99	2	-
GCF_000316985.1	s__Vibrio sp000316985	88.338	1277	1757	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002875705.1	s__Vibrio sp002875705	88.3143	1289	1757	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	99.93	99.66	0.96	0.93	9	-
GCF_008801285.1	s__Vibrio kanaloae	87.9477	1243	1757	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.372	98.50	98.26	0.91	0.88	16	-
--------------------------------------------------------------------------------
[2024-01-24 13:11:35,103] [INFO] GTDB search result was written to GCF_024347435.1_ASM2434743v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:11:35,104] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:11:35,110] [INFO] DFAST_QC result json was written to GCF_024347435.1_ASM2434743v1_genomic.fna/dqc_result.json
[2024-01-24 13:11:35,111] [INFO] DFAST_QC completed!
[2024-01-24 13:11:35,111] [INFO] Total running time: 0h1m44s