[2024-01-25 19:13:05,682] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:13:05,684] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:13:05,684] [INFO] DQC Reference Directory: /var/lib/cwl/stg0ad82669-ff68-4a24-80c5-5df4df6ce665/dqc_reference
[2024-01-25 19:13:06,889] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:13:06,890] [INFO] Task started: Prodigal
[2024-01-25 19:13:06,890] [INFO] Running command: gunzip -c /var/lib/cwl/stg7f0275f3-bb33-42e3-9731-1df598be1509/GCF_001889005.1_ASM188900v1_genomic.fna.gz | prodigal -d GCF_001889005.1_ASM188900v1_genomic.fna/cds.fna -a GCF_001889005.1_ASM188900v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:13:15,930] [INFO] Task succeeded: Prodigal
[2024-01-25 19:13:15,931] [INFO] Task started: HMMsearch
[2024-01-25 19:13:15,931] [INFO] Running command: hmmsearch --tblout GCF_001889005.1_ASM188900v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0ad82669-ff68-4a24-80c5-5df4df6ce665/dqc_reference/reference_markers.hmm GCF_001889005.1_ASM188900v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:13:16,156] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:13:16,160] [INFO] Found 6/6 markers.
[2024-01-25 19:13:16,186] [INFO] Query marker FASTA was written to GCF_001889005.1_ASM188900v1_genomic.fna/markers.fasta
[2024-01-25 19:13:16,187] [INFO] Task started: Blastn
[2024-01-25 19:13:16,187] [INFO] Running command: blastn -query GCF_001889005.1_ASM188900v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0ad82669-ff68-4a24-80c5-5df4df6ce665/dqc_reference/reference_markers.fasta -out GCF_001889005.1_ASM188900v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:13:16,850] [INFO] Task succeeded: Blastn
[2024-01-25 19:13:16,853] [INFO] Selected 15 target genomes.
[2024-01-25 19:13:16,853] [INFO] Target genome list was writen to GCF_001889005.1_ASM188900v1_genomic.fna/target_genomes.txt
[2024-01-25 19:13:16,866] [INFO] Task started: fastANI
[2024-01-25 19:13:16,866] [INFO] Running command: fastANI --query /var/lib/cwl/stg7f0275f3-bb33-42e3-9731-1df598be1509/GCF_001889005.1_ASM188900v1_genomic.fna.gz --refList GCF_001889005.1_ASM188900v1_genomic.fna/target_genomes.txt --output GCF_001889005.1_ASM188900v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:13:26,348] [INFO] Task succeeded: fastANI
[2024-01-25 19:13:26,349] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0ad82669-ff68-4a24-80c5-5df4df6ce665/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:13:26,349] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0ad82669-ff68-4a24-80c5-5df4df6ce665/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:13:26,358] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:13:26,358] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:13:26,358] [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 salexigens	strain=LPB0144	GCA_001889005.1	1913577	1913577	type	True	100.0	989	992	95	conclusive
Gramella gaetbulicola	strain=DSM 23082	GCA_003054225.1	703340	703340	type	True	79.3803	420	992	95	below_threshold
Gramella echinicola	strain=DSM 19838	GCA_000423065.1	279359	279359	type	True	79.3144	399	992	95	below_threshold
Gramella forsetii	strain=KT0803	GCA_000060345.1	411153	411153	type	True	79.2403	418	992	95	below_threshold
Gramella forsetii	strain=CGMCC 1.15422	GCA_014642775.1	411153	411153	type	True	79.0505	413	992	95	below_threshold
Gramella aestuarii	strain=BS12	GCA_009735585.1	1028746	1028746	type	True	79.0255	377	992	95	below_threshold
Gramella sabulilitoris	strain=HSMS-1	GCA_007050985.1	2583991	2583991	type	True	78.9945	379	992	95	below_threshold
Gramella lutea	strain=YJ019	GCA_022489035.1	1607951	1607951	type	True	78.9681	389	992	95	below_threshold
Gramella crocea	strain=YB25	GCA_022410465.1	2904124	2904124	type	True	78.8901	383	992	95	below_threshold
Gramella portivictoriae	strain=DSM 23547	GCA_000423045.1	326069	326069	type	True	78.8355	304	992	95	below_threshold
Zunongwangia mangrovi	strain=DSM 24499	GCA_900112105.1	1334022	1334022	type	True	77.4781	174	992	95	below_threshold
Salegentibacter lacus	strain=LM13S	GCA_020164555.1	2873599	2873599	type	True	77.2654	214	992	95	below_threshold
Polaribacter septentrionalilitoris	strain=ANORD1	GCA_009832745.1	2494657	2494657	type	True	76.6179	50	992	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:13:26,359] [INFO] DFAST Taxonomy check result was written to GCF_001889005.1_ASM188900v1_genomic.fna/tc_result.tsv
[2024-01-25 19:13:26,360] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:13:26,360] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:13:26,360] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0ad82669-ff68-4a24-80c5-5df4df6ce665/dqc_reference/checkm_data
[2024-01-25 19:13:26,361] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:13:26,392] [INFO] Task started: CheckM
[2024-01-25 19:13:26,393] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001889005.1_ASM188900v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001889005.1_ASM188900v1_genomic.fna/checkm_input GCF_001889005.1_ASM188900v1_genomic.fna/checkm_result
[2024-01-25 19:13:56,019] [INFO] Task succeeded: CheckM
[2024-01-25 19:13:56,020] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:13:56,037] [INFO] ===== Completeness check finished =====
[2024-01-25 19:13:56,038] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:13:56,038] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001889005.1_ASM188900v1_genomic.fna/markers.fasta)
[2024-01-25 19:13:56,038] [INFO] Task started: Blastn
[2024-01-25 19:13:56,038] [INFO] Running command: blastn -query GCF_001889005.1_ASM188900v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0ad82669-ff68-4a24-80c5-5df4df6ce665/dqc_reference/reference_markers_gtdb.fasta -out GCF_001889005.1_ASM188900v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:13:56,866] [INFO] Task succeeded: Blastn
[2024-01-25 19:13:56,869] [INFO] Selected 14 target genomes.
[2024-01-25 19:13:56,869] [INFO] Target genome list was writen to GCF_001889005.1_ASM188900v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:13:56,892] [INFO] Task started: fastANI
[2024-01-25 19:13:56,893] [INFO] Running command: fastANI --query /var/lib/cwl/stg7f0275f3-bb33-42e3-9731-1df598be1509/GCF_001889005.1_ASM188900v1_genomic.fna.gz --refList GCF_001889005.1_ASM188900v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001889005.1_ASM188900v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:14:06,127] [INFO] Task succeeded: fastANI
[2024-01-25 19:14:06,136] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:14:06,136] [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_001889005.1	s__Gramella salexigens	100.0	986	992	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gramella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003054225.1	s__Gramella gaetbulicola	79.3801	421	992	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gramella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105135.1	s__Gramella sp900105135	79.3328	413	992	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	79.3144	399	992	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gramella	95.0	97.44	97.44	0.87	0.87	2	-
GCF_000060345.1	s__Gramella forsetii	79.2403	418	992	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gramella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009735585.1	s__Gramella aestuarii	79.0255	377	992	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gramella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007050985.1	s__Gramella sabulilitoris	78.999	379	992	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	78.7991	369	992	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gramella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009735695.1	s__Gramella sp009735695	78.7334	340	992	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gramella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006714895.1	s__Gramella sp006714895	78.6737	335	992	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	78.2196	279	992	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gramella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900168265.1	s__Salegentibacter salarius	77.7836	199	992	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	100.00	99.99	1.00	0.99	3	-
GCF_900104765.1	s__Gillisia sp900104765	77.6223	177	992	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gillisia	95.0	98.23	98.23	0.92	0.92	2	-
GCF_900112105.1	s__Zunongwangia mangrovi	77.4781	174	992	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zunongwangia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:14:06,138] [INFO] GTDB search result was written to GCF_001889005.1_ASM188900v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:14:06,138] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:14:06,141] [INFO] DFAST_QC result json was written to GCF_001889005.1_ASM188900v1_genomic.fna/dqc_result.json
[2024-01-25 19:14:06,141] [INFO] DFAST_QC completed!
[2024-01-25 19:14:06,141] [INFO] Total running time: 0h1m0s