[2024-01-24 13:22:40,345] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:22:40,357] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:22:40,357] [INFO] DQC Reference Directory: /var/lib/cwl/stged19bd0e-0c63-452d-a569-4ad03327a0ef/dqc_reference
[2024-01-24 13:22:41,756] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:22:41,757] [INFO] Task started: Prodigal
[2024-01-24 13:22:41,757] [INFO] Running command: gunzip -c /var/lib/cwl/stg0e81f42a-de8c-4765-8a5f-68458a6ec1fb/GCF_030505015.1_ASM3050501v1_genomic.fna.gz | prodigal -d GCF_030505015.1_ASM3050501v1_genomic.fna/cds.fna -a GCF_030505015.1_ASM3050501v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:23:03,084] [INFO] Task succeeded: Prodigal
[2024-01-24 13:23:03,084] [INFO] Task started: HMMsearch
[2024-01-24 13:23:03,084] [INFO] Running command: hmmsearch --tblout GCF_030505015.1_ASM3050501v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stged19bd0e-0c63-452d-a569-4ad03327a0ef/dqc_reference/reference_markers.hmm GCF_030505015.1_ASM3050501v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:23:03,335] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:23:03,337] [INFO] Found 6/6 markers.
[2024-01-24 13:23:03,376] [INFO] Query marker FASTA was written to GCF_030505015.1_ASM3050501v1_genomic.fna/markers.fasta
[2024-01-24 13:23:03,377] [INFO] Task started: Blastn
[2024-01-24 13:23:03,377] [INFO] Running command: blastn -query GCF_030505015.1_ASM3050501v1_genomic.fna/markers.fasta -db /var/lib/cwl/stged19bd0e-0c63-452d-a569-4ad03327a0ef/dqc_reference/reference_markers.fasta -out GCF_030505015.1_ASM3050501v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:23:04,044] [INFO] Task succeeded: Blastn
[2024-01-24 13:23:04,050] [INFO] Selected 20 target genomes.
[2024-01-24 13:23:04,050] [INFO] Target genome list was writen to GCF_030505015.1_ASM3050501v1_genomic.fna/target_genomes.txt
[2024-01-24 13:23:04,059] [INFO] Task started: fastANI
[2024-01-24 13:23:04,059] [INFO] Running command: fastANI --query /var/lib/cwl/stg0e81f42a-de8c-4765-8a5f-68458a6ec1fb/GCF_030505015.1_ASM3050501v1_genomic.fna.gz --refList GCF_030505015.1_ASM3050501v1_genomic.fna/target_genomes.txt --output GCF_030505015.1_ASM3050501v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:23:19,144] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:19,145] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stged19bd0e-0c63-452d-a569-4ad03327a0ef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:23:19,145] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stged19bd0e-0c63-452d-a569-4ad03327a0ef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:23:19,159] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:23:19,159] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:23:19,160] [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
Maribacter sedimenticola	strain=DSM 19840	GCA_900188415.1	228956	228956	type	True	97.2805	1240	1559	95	conclusive
Maribacter dokdonensis	strain=DSW-8	GCA_001447995.1	320912	320912	type	True	81.0143	598	1559	95	below_threshold
Maribacter stanieri	strain=DSM 19891	GCA_900112245.1	440514	440514	type	True	79.7414	597	1559	95	below_threshold
Maribacter litoralis	strain=SDRB-Phe2	GCA_003075045.1	2059726	2059726	type	True	79.489	569	1559	95	below_threshold
Maribacter forsetii	strain=DSM 18668	GCA_000744105.1	444515	444515	type	True	79.2837	548	1559	95	below_threshold
Maribacter spongiicola	strain=DSM 25233	GCA_004364165.1	1206753	1206753	type	True	79.1996	535	1559	95	below_threshold
Maribacter orientalis	strain=DSM 16471	GCA_900109345.1	228957	228957	type	True	79.1845	563	1559	95	below_threshold
Maribacter arcticus	strain=DSM 23546	GCA_900167935.1	561365	561365	type	True	79.162	547	1559	95	below_threshold
Maribacter hydrothermalis	strain=T28	GCA_001913155.1	1836467	1836467	type	True	79.0104	577	1559	95	below_threshold
Maribacter ulvicola	strain=DSM 15366	GCA_900155985.1	228959	228959	type	True	78.956	535	1559	95	below_threshold
Maribacter hydrothermalis	strain=T28	GCA_001673755.1	1836467	1836467	type	True	78.8909	578	1559	95	below_threshold
Maribacter thermophilus	strain=HT7-2	GCA_001020565.1	1197874	1197874	type	True	77.9033	285	1559	95	below_threshold
Aurantibacter crassamenti	strain=HG732	GCA_016811105.1	1837375	1837375	type	True	77.2139	171	1559	95	below_threshold
Arenibacter palladensis	strain=DSM 17539	GCA_900129275.1	237373	237373	type	True	76.9207	162	1559	95	below_threshold
Muricauda aurantiaca	strain=HME9304	GCA_003269425.1	1383885	1383885	type	True	76.8564	125	1559	95	below_threshold
Aestuariivivens marinum	strain=MT3-5-12	GCA_022662175.1	2913555	2913555	type	True	76.7887	59	1559	95	below_threshold
Arenibacter troitsensis	strain=DSM 19835	GCA_900177645.1	188872	188872	type	True	76.7444	162	1559	95	below_threshold
Aureibaculum flavum	strain=A20	GCA_016406085.1	2795986	2795986	type	True	76.3989	71	1559	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:23:19,162] [INFO] DFAST Taxonomy check result was written to GCF_030505015.1_ASM3050501v1_genomic.fna/tc_result.tsv
[2024-01-24 13:23:19,162] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:23:19,162] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:23:19,162] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stged19bd0e-0c63-452d-a569-4ad03327a0ef/dqc_reference/checkm_data
[2024-01-24 13:23:19,164] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:23:19,209] [INFO] Task started: CheckM
[2024-01-24 13:23:19,210] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030505015.1_ASM3050501v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030505015.1_ASM3050501v1_genomic.fna/checkm_input GCF_030505015.1_ASM3050501v1_genomic.fna/checkm_result
[2024-01-24 13:24:14,224] [INFO] Task succeeded: CheckM
[2024-01-24 13:24:14,225] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 17.71%
Strain heterogeneity: 95.45%
--------------------------------------------------------------------------------
[2024-01-24 13:24:14,252] [INFO] ===== Completeness check finished =====
[2024-01-24 13:24:14,252] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:24:14,253] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030505015.1_ASM3050501v1_genomic.fna/markers.fasta)
[2024-01-24 13:24:14,253] [INFO] Task started: Blastn
[2024-01-24 13:24:14,253] [INFO] Running command: blastn -query GCF_030505015.1_ASM3050501v1_genomic.fna/markers.fasta -db /var/lib/cwl/stged19bd0e-0c63-452d-a569-4ad03327a0ef/dqc_reference/reference_markers_gtdb.fasta -out GCF_030505015.1_ASM3050501v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:24:15,127] [INFO] Task succeeded: Blastn
[2024-01-24 13:24:15,130] [INFO] Selected 16 target genomes.
[2024-01-24 13:24:15,130] [INFO] Target genome list was writen to GCF_030505015.1_ASM3050501v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:24:15,164] [INFO] Task started: fastANI
[2024-01-24 13:24:15,165] [INFO] Running command: fastANI --query /var/lib/cwl/stg0e81f42a-de8c-4765-8a5f-68458a6ec1fb/GCF_030505015.1_ASM3050501v1_genomic.fna.gz --refList GCF_030505015.1_ASM3050501v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030505015.1_ASM3050501v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:24:28,195] [INFO] Task succeeded: fastANI
[2024-01-24 13:24:28,208] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:24:28,209] [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_900188415.1	s__Maribacter sedimenticola	97.2671	1241	1559	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	97.95	97.95	0.90	0.90	2	conclusive
GCF_001447995.1	s__Maribacter dokdonensis	81.0075	595	1559	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	97.64	97.51	0.89	0.86	13	-
GCF_900112245.1	s__Maribacter stanieri	79.725	599	1559	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	98.09	98.09	0.92	0.92	2	-
GCF_900142175.1	s__Maribacter aquivivus	79.5084	564	1559	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003075045.1	s__Maribacter litoralis	79.4843	570	1559	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	97.43	97.43	0.90	0.90	2	-
GCF_000744105.1	s__Maribacter forsetii	79.304	546	1559	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004364165.1	s__Maribacter spongiicola	79.2075	534	1559	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109345.1	s__Maribacter orientalis	79.1924	563	1559	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011050675.1	s__Maribacter sp011050675	79.165	536	1559	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	100.00	100.00	0.99	0.99	2	-
GCF_900167935.1	s__Maribacter arcticus	79.1623	547	1559	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001913155.1	s__Maribacter hydrothermalis	79.0167	579	1559	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900155985.1	s__Maribacter ulvicola	78.9921	531	1559	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005771495.1	s__Maribacter sp005771495	78.9287	511	1559	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003970695.1	s__Maribacter sp002742365	77.7572	256	1559	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	96.61	96.61	0.86	0.86	2	-
GCF_000153165.2	s__Maribacter_A sp000153165	77.3079	155	1559	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016811105.1	s__Aurantibacter_A crassamenti	77.2417	170	1559	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aurantibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:24:28,210] [INFO] GTDB search result was written to GCF_030505015.1_ASM3050501v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:24:28,211] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:24:28,215] [INFO] DFAST_QC result json was written to GCF_030505015.1_ASM3050501v1_genomic.fna/dqc_result.json
[2024-01-24 13:24:28,215] [INFO] DFAST_QC completed!
[2024-01-24 13:24:28,215] [INFO] Total running time: 0h1m48s