[2024-01-24 10:57:25,410] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:57:25,417] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:57:25,417] [INFO] DQC Reference Directory: /var/lib/cwl/stg77f72426-29ef-47f2-834b-37f8d2bf4bfc/dqc_reference
[2024-01-24 10:57:26,769] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:57:26,770] [INFO] Task started: Prodigal
[2024-01-24 10:57:26,770] [INFO] Running command: gunzip -c /var/lib/cwl/stge00e2c08-ac80-4190-a6f5-81b92f7a5e06/GCF_002120265.1_ASM212026v1_genomic.fna.gz | prodigal -d GCF_002120265.1_ASM212026v1_genomic.fna/cds.fna -a GCF_002120265.1_ASM212026v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:57:43,607] [INFO] Task succeeded: Prodigal
[2024-01-24 10:57:43,607] [INFO] Task started: HMMsearch
[2024-01-24 10:57:43,607] [INFO] Running command: hmmsearch --tblout GCF_002120265.1_ASM212026v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg77f72426-29ef-47f2-834b-37f8d2bf4bfc/dqc_reference/reference_markers.hmm GCF_002120265.1_ASM212026v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:57:43,915] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:57:43,916] [INFO] Found 6/6 markers.
[2024-01-24 10:57:43,952] [INFO] Query marker FASTA was written to GCF_002120265.1_ASM212026v1_genomic.fna/markers.fasta
[2024-01-24 10:57:43,953] [INFO] Task started: Blastn
[2024-01-24 10:57:43,953] [INFO] Running command: blastn -query GCF_002120265.1_ASM212026v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg77f72426-29ef-47f2-834b-37f8d2bf4bfc/dqc_reference/reference_markers.fasta -out GCF_002120265.1_ASM212026v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:57:44,604] [INFO] Task succeeded: Blastn
[2024-01-24 10:57:44,607] [INFO] Selected 15 target genomes.
[2024-01-24 10:57:44,608] [INFO] Target genome list was writen to GCF_002120265.1_ASM212026v1_genomic.fna/target_genomes.txt
[2024-01-24 10:57:44,613] [INFO] Task started: fastANI
[2024-01-24 10:57:44,614] [INFO] Running command: fastANI --query /var/lib/cwl/stge00e2c08-ac80-4190-a6f5-81b92f7a5e06/GCF_002120265.1_ASM212026v1_genomic.fna.gz --refList GCF_002120265.1_ASM212026v1_genomic.fna/target_genomes.txt --output GCF_002120265.1_ASM212026v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:57:54,935] [INFO] Task succeeded: fastANI
[2024-01-24 10:57:54,936] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg77f72426-29ef-47f2-834b-37f8d2bf4bfc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:57:54,936] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg77f72426-29ef-47f2-834b-37f8d2bf4bfc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:57:54,951] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 10:57:54,951] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:57:54,952] [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
Gramella flava	strain=JLT2011	GCA_002120265.1	1486245	1486245	type	True	100.0	1305	1307	95	conclusive
Gramella flava	strain=JLT2011	GCA_001951155.1	1486245	1486245	type	True	99.9986	1307	1307	95	conclusive
Gramella fulva	strain=SH35	GCA_003024155.1	2126553	2126553	type	True	78.6443	373	1307	95	below_threshold
Gramella echinicola	strain=DSM 19838	GCA_000423065.1	279359	279359	type	True	78.6376	299	1307	95	below_threshold
Gramella gaetbulicola	strain=DSM 23082	GCA_003054225.1	703340	703340	type	True	78.5214	325	1307	95	below_threshold
Gramella forsetii	strain=KT0803	GCA_000060345.1	411153	411153	type	True	78.5006	305	1307	95	below_threshold
Gramella forsetii	strain=CGMCC 1.15422	GCA_014642775.1	411153	411153	type	True	78.4452	305	1307	95	below_threshold
Gramella crocea	strain=YB25	GCA_022410465.1	2904124	2904124	type	True	78.4195	311	1307	95	below_threshold
Gramella lutea	strain=YJ019	GCA_022489035.1	1607951	1607951	type	True	78.334	306	1307	95	below_threshold
Gramella aestuarii	strain=BS12	GCA_009735585.1	1028746	1028746	type	True	78.2981	319	1307	95	below_threshold
Salinimicrobium catena	strain=DSM 23553	GCA_900107495.1	390640	390640	type	True	76.7611	141	1307	95	below_threshold
Salinimicrobium catena	strain=CGMCC 1.6101	GCA_900102915.1	390640	390640	type	True	76.7522	138	1307	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:57:54,955] [INFO] DFAST Taxonomy check result was written to GCF_002120265.1_ASM212026v1_genomic.fna/tc_result.tsv
[2024-01-24 10:57:54,956] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:57:54,956] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:57:54,957] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg77f72426-29ef-47f2-834b-37f8d2bf4bfc/dqc_reference/checkm_data
[2024-01-24 10:57:54,958] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:57:54,997] [INFO] Task started: CheckM
[2024-01-24 10:57:54,998] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002120265.1_ASM212026v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002120265.1_ASM212026v1_genomic.fna/checkm_input GCF_002120265.1_ASM212026v1_genomic.fna/checkm_result
[2024-01-24 10:58:45,589] [INFO] Task succeeded: CheckM
[2024-01-24 10:58:45,590] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 10:58:45,608] [INFO] ===== Completeness check finished =====
[2024-01-24 10:58:45,608] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:58:45,608] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002120265.1_ASM212026v1_genomic.fna/markers.fasta)
[2024-01-24 10:58:45,609] [INFO] Task started: Blastn
[2024-01-24 10:58:45,609] [INFO] Running command: blastn -query GCF_002120265.1_ASM212026v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg77f72426-29ef-47f2-834b-37f8d2bf4bfc/dqc_reference/reference_markers_gtdb.fasta -out GCF_002120265.1_ASM212026v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:46,466] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:46,470] [INFO] Selected 12 target genomes.
[2024-01-24 10:58:46,470] [INFO] Target genome list was writen to GCF_002120265.1_ASM212026v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:58:46,501] [INFO] Task started: fastANI
[2024-01-24 10:58:46,501] [INFO] Running command: fastANI --query /var/lib/cwl/stge00e2c08-ac80-4190-a6f5-81b92f7a5e06/GCF_002120265.1_ASM212026v1_genomic.fna.gz --refList GCF_002120265.1_ASM212026v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002120265.1_ASM212026v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:58:54,765] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:54,776] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:58:54,776] [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_001951155.1	s__Gramella flava	99.9986	1307	1307	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gramella	95.0	99.04	98.07	0.94	0.88	3	conclusive
GCF_009735695.1	s__Gramella sp009735695	78.9443	368	1307	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gramella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003024155.1	s__Gramella fulva	78.6443	373	1307	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gramella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000423065.1	s__Gramella echinicola	78.6376	299	1307	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gramella	95.0	97.44	97.44	0.87	0.87	2	-
GCF_003054225.1	s__Gramella gaetbulicola	78.5258	324	1307	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gramella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000060345.1	s__Gramella forsetii	78.4891	306	1307	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gramella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001889005.1	s__Gramella salexigens	78.4654	242	1307	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gramella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004332155.1	s__Gramella sp004332155	78.3899	291	1307	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gramella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009735585.1	s__Gramella aestuarii	78.3011	317	1307	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gramella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004362395.1	s__Salegentibacter sp004362395	78.121	165	1307	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102915.1	s__Salinimicrobium catena	76.7683	138	1307	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salinimicrobium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000423585.1	s__Salinimicrobium xinjiangense	76.7325	98	1307	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salinimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:58:54,778] [INFO] GTDB search result was written to GCF_002120265.1_ASM212026v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:58:54,778] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:58:54,782] [INFO] DFAST_QC result json was written to GCF_002120265.1_ASM212026v1_genomic.fna/dqc_result.json
[2024-01-24 10:58:54,783] [INFO] DFAST_QC completed!
[2024-01-24 10:58:54,783] [INFO] Total running time: 0h1m29s