[2024-01-24 14:13:18,605] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:13:18,607] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:13:18,607] [INFO] DQC Reference Directory: /var/lib/cwl/stg203a4111-fb67-4bfd-91d5-a7885a1e162f/dqc_reference
[2024-01-24 14:13:19,925] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:13:19,927] [INFO] Task started: Prodigal
[2024-01-24 14:13:19,927] [INFO] Running command: gunzip -c /var/lib/cwl/stgb893949c-e370-4dc9-9273-88c0c2dcf24c/GCF_005048205.1_ASM504820v1_genomic.fna.gz | prodigal -d GCF_005048205.1_ASM504820v1_genomic.fna/cds.fna -a GCF_005048205.1_ASM504820v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:13:34,467] [INFO] Task succeeded: Prodigal
[2024-01-24 14:13:34,467] [INFO] Task started: HMMsearch
[2024-01-24 14:13:34,467] [INFO] Running command: hmmsearch --tblout GCF_005048205.1_ASM504820v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg203a4111-fb67-4bfd-91d5-a7885a1e162f/dqc_reference/reference_markers.hmm GCF_005048205.1_ASM504820v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:13:34,787] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:13:34,788] [INFO] Found 6/6 markers.
[2024-01-24 14:13:34,827] [INFO] Query marker FASTA was written to GCF_005048205.1_ASM504820v1_genomic.fna/markers.fasta
[2024-01-24 14:13:34,828] [INFO] Task started: Blastn
[2024-01-24 14:13:34,828] [INFO] Running command: blastn -query GCF_005048205.1_ASM504820v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg203a4111-fb67-4bfd-91d5-a7885a1e162f/dqc_reference/reference_markers.fasta -out GCF_005048205.1_ASM504820v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:13:35,643] [INFO] Task succeeded: Blastn
[2024-01-24 14:13:35,646] [INFO] Selected 20 target genomes.
[2024-01-24 14:13:35,647] [INFO] Target genome list was writen to GCF_005048205.1_ASM504820v1_genomic.fna/target_genomes.txt
[2024-01-24 14:13:35,665] [INFO] Task started: fastANI
[2024-01-24 14:13:35,665] [INFO] Running command: fastANI --query /var/lib/cwl/stgb893949c-e370-4dc9-9273-88c0c2dcf24c/GCF_005048205.1_ASM504820v1_genomic.fna.gz --refList GCF_005048205.1_ASM504820v1_genomic.fna/target_genomes.txt --output GCF_005048205.1_ASM504820v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:13:53,638] [INFO] Task succeeded: fastANI
[2024-01-24 14:13:53,639] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg203a4111-fb67-4bfd-91d5-a7885a1e162f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:13:53,639] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg203a4111-fb67-4bfd-91d5-a7885a1e162f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:13:53,664] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:13:53,664] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:13:53,665] [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
Chitiniphilus eburneus	strain=HX-2-15	GCA_005048205.1	2571148	2571148	type	True	100.0	1395	1399	95	conclusive
Chitiniphilus shinanonensis	strain=DSM 23277	GCA_000374805.1	553088	553088	type	True	86.9887	1154	1399	95	below_threshold
Andreprevotia lacus	strain=DSM 23236	GCA_900176275.1	1121000	1121000	type	True	79.4226	535	1399	95	below_threshold
Jeongeupia chitinilytica	strain=KCTC 23701	GCA_014652315.1	1041641	1041641	type	True	79.3728	513	1399	95	below_threshold
Jeongeupia naejangsanensis	strain=DSM 24253	GCA_016865585.1	613195	613195	type	True	79.1979	512	1399	95	below_threshold
Andreprevotia chitinilytica	strain=DSM 18519	GCA_000711875.1	396808	396808	type	True	78.8326	483	1399	95	below_threshold
Chitinilyticum litopenaei	strain=DSM 21440	GCA_000428145.1	1121276	1121276	type	True	78.4494	454	1399	95	below_threshold
Crenobacter luteus	strain=DSM 27258	GCA_004345725.1	1452487	1452487	type	True	78.2742	287	1399	95	below_threshold
Chitinilyticum aquatile	strain=DSM 21506	GCA_000430805.1	362520	362520	type	True	78.2423	373	1399	95	below_threshold
Formivibrio citricus	strain=DSM 6150	GCA_900115065.1	83765	83765	type	True	78.0399	273	1399	95	below_threshold
Chromobacterium sinusclupearum	strain=MWU13-2610	GCA_002902845.1	2077146	2077146	type	True	77.9227	302	1399	95	below_threshold
Chromobacterium amazonense	strain=DSM 26508	GCA_001855565.1	1382803	1382803	type	True	77.7678	300	1399	95	below_threshold
Chromobacterium alticapitis	strain=MWU14-2602	GCA_002924365.1	2073169	2073169	type	True	77.5458	319	1399	95	below_threshold
Herbaspirillum camelliae	strain=WT00C	GCA_001929405.1	1892903	1892903	type	True	77.1033	216	1399	95	below_threshold
Diaphorobacter aerolatus	strain=KACC 16536	GCA_014489535.1	1288495	1288495	type	True	76.51	133	1399	95	below_threshold
Paraburkholderia podalyriae	strain=WC7.3b	GCA_014397785.1	1938811	1938811	type	True	76.1452	179	1399	95	below_threshold
Paraburkholderia azotifigens	strain=NF 2-5-3	GCA_007995085.1	2057004	2057004	type	True	76.1447	160	1399	95	below_threshold
Fundidesulfovibrio putealis	strain=DSM 16056	GCA_000429325.1	270496	270496	type	True	75.322	50	1399	95	below_threshold
Rhodothalassium salexigens	strain=DSM 2132	GCA_016583875.1	1086	1086	type	True	75.3087	75	1399	95	below_threshold
Fundidesulfovibrio magnetotacticus	strain=FSS-1	GCA_013019105.1	2730080	2730080	type	True	75.218	54	1399	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:13:53,667] [INFO] DFAST Taxonomy check result was written to GCF_005048205.1_ASM504820v1_genomic.fna/tc_result.tsv
[2024-01-24 14:13:53,667] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:13:53,668] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:13:53,668] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg203a4111-fb67-4bfd-91d5-a7885a1e162f/dqc_reference/checkm_data
[2024-01-24 14:13:53,669] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:13:53,721] [INFO] Task started: CheckM
[2024-01-24 14:13:53,721] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005048205.1_ASM504820v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005048205.1_ASM504820v1_genomic.fna/checkm_input GCF_005048205.1_ASM504820v1_genomic.fna/checkm_result
[2024-01-24 14:14:37,562] [INFO] Task succeeded: CheckM
[2024-01-24 14:14:37,563] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:14:37,585] [INFO] ===== Completeness check finished =====
[2024-01-24 14:14:37,585] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:14:37,585] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005048205.1_ASM504820v1_genomic.fna/markers.fasta)
[2024-01-24 14:14:37,586] [INFO] Task started: Blastn
[2024-01-24 14:14:37,586] [INFO] Running command: blastn -query GCF_005048205.1_ASM504820v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg203a4111-fb67-4bfd-91d5-a7885a1e162f/dqc_reference/reference_markers_gtdb.fasta -out GCF_005048205.1_ASM504820v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:14:38,821] [INFO] Task succeeded: Blastn
[2024-01-24 14:14:38,826] [INFO] Selected 17 target genomes.
[2024-01-24 14:14:38,826] [INFO] Target genome list was writen to GCF_005048205.1_ASM504820v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:14:38,843] [INFO] Task started: fastANI
[2024-01-24 14:14:38,844] [INFO] Running command: fastANI --query /var/lib/cwl/stgb893949c-e370-4dc9-9273-88c0c2dcf24c/GCF_005048205.1_ASM504820v1_genomic.fna.gz --refList GCF_005048205.1_ASM504820v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005048205.1_ASM504820v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:14:53,047] [INFO] Task succeeded: fastANI
[2024-01-24 14:14:53,072] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:14:53,073] [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_005048205.1	s__Chitiniphilus eburneus	100.0	1395	1399	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Chitiniphilus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000374805.1	s__Chitiniphilus shinanonensis	86.9887	1154	1399	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Chitiniphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008033135.1	s__Chitinolyticbacter meiyuanensis	80.7928	731	1399	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Chitinolyticbacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001808185.1	s__Jeongeupia sp001808185	79.465	537	1399	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Jeongeupia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900176275.1	s__Andreprevotia lacus	79.3811	540	1399	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Andreprevotia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014652315.1	s__Jeongeupia chitinilytica	79.3632	514	1399	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Jeongeupia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009848685.1	s__Andreprevotia sp009848685	79.27	537	1399	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Andreprevotia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000711875.1	s__Andreprevotia chitinilytica	78.8177	485	1399	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Andreprevotia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015140455.1	s__Jeongeupia sp015140455	78.7552	454	1399	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Jeongeupia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000428145.1	s__Chitinilyticum litopenaei	78.4674	452	1399	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Chitinilyticum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000430805.1	s__Chitinilyticum aquatile	78.2479	371	1399	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Chitinilyticum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016428945.1	s__Chromobacterium sp016428945	77.8152	299	1399	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	97.99	97.99	0.89	0.89	2	-
GCF_001855565.1	s__Chromobacterium amazonense	77.7606	302	1399	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	97.81	97.67	0.91	0.90	4	-
GCA_013426785.1	s__UBA2250 sp013426785	76.6312	124	1399	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__UBA2250	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000429325.1	s__Fundidesulfovibrio putealis	75.322	50	1399	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Fundidesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013019105.1	s__Fundidesulfovibrio sp013019105	75.1934	56	1399	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Fundidesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:14:53,074] [INFO] GTDB search result was written to GCF_005048205.1_ASM504820v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:14:53,075] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:14:53,083] [INFO] DFAST_QC result json was written to GCF_005048205.1_ASM504820v1_genomic.fna/dqc_result.json
[2024-01-24 14:14:53,083] [INFO] DFAST_QC completed!
[2024-01-24 14:14:53,083] [INFO] Total running time: 0h1m34s