[2024-01-24 11:03:32,851] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:03:32,853] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:03:32,853] [INFO] DQC Reference Directory: /var/lib/cwl/stg43a95931-d0ba-4dde-8e84-2df5994314b7/dqc_reference
[2024-01-24 11:03:34,047] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:03:34,048] [INFO] Task started: Prodigal
[2024-01-24 11:03:34,048] [INFO] Running command: gunzip -c /var/lib/cwl/stgcdbb721c-db29-466a-9502-9c554830f6b0/GCF_021049265.1_ASM2104926v1_genomic.fna.gz | prodigal -d GCF_021049265.1_ASM2104926v1_genomic.fna/cds.fna -a GCF_021049265.1_ASM2104926v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:03:44,581] [INFO] Task succeeded: Prodigal
[2024-01-24 11:03:44,581] [INFO] Task started: HMMsearch
[2024-01-24 11:03:44,582] [INFO] Running command: hmmsearch --tblout GCF_021049265.1_ASM2104926v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg43a95931-d0ba-4dde-8e84-2df5994314b7/dqc_reference/reference_markers.hmm GCF_021049265.1_ASM2104926v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:03:44,850] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:03:44,852] [INFO] Found 6/6 markers.
[2024-01-24 11:03:44,887] [INFO] Query marker FASTA was written to GCF_021049265.1_ASM2104926v1_genomic.fna/markers.fasta
[2024-01-24 11:03:44,888] [INFO] Task started: Blastn
[2024-01-24 11:03:44,888] [INFO] Running command: blastn -query GCF_021049265.1_ASM2104926v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg43a95931-d0ba-4dde-8e84-2df5994314b7/dqc_reference/reference_markers.fasta -out GCF_021049265.1_ASM2104926v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:03:46,111] [INFO] Task succeeded: Blastn
[2024-01-24 11:03:46,115] [INFO] Selected 13 target genomes.
[2024-01-24 11:03:46,115] [INFO] Target genome list was writen to GCF_021049265.1_ASM2104926v1_genomic.fna/target_genomes.txt
[2024-01-24 11:03:46,124] [INFO] Task started: fastANI
[2024-01-24 11:03:46,124] [INFO] Running command: fastANI --query /var/lib/cwl/stgcdbb721c-db29-466a-9502-9c554830f6b0/GCF_021049265.1_ASM2104926v1_genomic.fna.gz --refList GCF_021049265.1_ASM2104926v1_genomic.fna/target_genomes.txt --output GCF_021049265.1_ASM2104926v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:03:58,322] [INFO] Task succeeded: fastANI
[2024-01-24 11:03:58,323] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg43a95931-d0ba-4dde-8e84-2df5994314b7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:03:58,324] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg43a95931-d0ba-4dde-8e84-2df5994314b7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:03:58,346] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:03:58,346] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:03:58,346] [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
Ruania suaedae	strain=LR1S40	GCA_021049265.1	2897774	2897774	type	True	100.0	1185	1185	95	conclusive
Ruania rhizosphaerae	strain=LNNU 22110	GCA_009805705.1	1840413	1840413	type	True	83.4624	856	1185	95	below_threshold
Ruania alkalisoli	strain=RN3S43	GCA_014960965.1	2779775	2779775	type	True	83.3479	865	1185	95	below_threshold
Ruania alba	strain=DSM 21368	GCA_900105765.1	648782	648782	type	True	81.7297	814	1185	95	below_threshold
Ruania halotolerans	strain=M4N3S171	GCA_021049285.1	2897773	2897773	type	True	80.8191	783	1185	95	below_threshold
Ruania zhangjianzhongii	strain=HY168	GCA_008000995.1	2603206	2603206	type	True	79.4335	573	1185	95	below_threshold
Occultella gossypii	strain=N2-46	GCA_019947135.1	2800820	2800820	type	True	79.2415	568	1185	95	below_threshold
Occultella kanbiaonis	strain=HY164	GCA_009708215.1	2675754	2675754	type	True	79.0954	589	1185	95	below_threshold
Occultella glacieicola	strain=T3246-1	GCA_004353825.1	2518684	2518684	type	True	79.0848	585	1185	95	below_threshold
Nocardioides solisilvae	strain=Ka25	GCA_003194625.1	1542435	1542435	type	True	76.7309	243	1185	95	below_threshold
Streptomyces platensis	strain=ATCC 23948	GCA_008704855.1	58346	58346	type	True	76.6197	244	1185	95	below_threshold
Streptomyces platensis	strain=DSM 40041	GCA_002119195.1	58346	58346	type	True	76.3337	242	1185	95	below_threshold
Streptomyces lonarensis	strain=NCL716	GCA_012033735.1	700599	700599	type	True	76.2805	255	1185	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:03:58,348] [INFO] DFAST Taxonomy check result was written to GCF_021049265.1_ASM2104926v1_genomic.fna/tc_result.tsv
[2024-01-24 11:03:58,349] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:03:58,349] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:03:58,349] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg43a95931-d0ba-4dde-8e84-2df5994314b7/dqc_reference/checkm_data
[2024-01-24 11:03:58,350] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:03:58,389] [INFO] Task started: CheckM
[2024-01-24 11:03:58,389] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021049265.1_ASM2104926v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021049265.1_ASM2104926v1_genomic.fna/checkm_input GCF_021049265.1_ASM2104926v1_genomic.fna/checkm_result
[2024-01-24 11:04:59,676] [INFO] Task succeeded: CheckM
[2024-01-24 11:04:59,678] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:04:59,699] [INFO] ===== Completeness check finished =====
[2024-01-24 11:04:59,700] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:04:59,700] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021049265.1_ASM2104926v1_genomic.fna/markers.fasta)
[2024-01-24 11:04:59,701] [INFO] Task started: Blastn
[2024-01-24 11:04:59,701] [INFO] Running command: blastn -query GCF_021049265.1_ASM2104926v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg43a95931-d0ba-4dde-8e84-2df5994314b7/dqc_reference/reference_markers_gtdb.fasta -out GCF_021049265.1_ASM2104926v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:05:01,598] [INFO] Task succeeded: Blastn
[2024-01-24 11:05:01,602] [INFO] Selected 14 target genomes.
[2024-01-24 11:05:01,603] [INFO] Target genome list was writen to GCF_021049265.1_ASM2104926v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:05:01,662] [INFO] Task started: fastANI
[2024-01-24 11:05:01,663] [INFO] Running command: fastANI --query /var/lib/cwl/stgcdbb721c-db29-466a-9502-9c554830f6b0/GCF_021049265.1_ASM2104926v1_genomic.fna.gz --refList GCF_021049265.1_ASM2104926v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021049265.1_ASM2104926v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:05:13,436] [INFO] Task succeeded: fastANI
[2024-01-24 11:05:13,453] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 11:05:13,453] [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_009805705.1	s__Haloactinobacterium sp009805705	83.4522	857	1185	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Beutenbergiaceae;g__Haloactinobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014960965.1	s__Haloactinobacterium sp014960965	83.3513	866	1185	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Beutenbergiaceae;g__Haloactinobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105765.1	s__Haloactinobacterium album	81.712	816	1185	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Beutenbergiaceae;g__Haloactinobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000421225.1	s__Ruania albidiflava	79.7375	554	1185	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Beutenbergiaceae;g__Ruania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008000995.1	s__Ruania sp008000995	79.421	570	1185	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Beutenbergiaceae;g__Ruania	95.0	99.97	99.97	0.98	0.98	2	-
GCA_019116305.1	s__Ruania gallistercoris	79.3853	511	1185	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Beutenbergiaceae;g__Ruania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004353825.1	s__Occultella glacieicola	79.1001	583	1185	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Beutenbergiaceae;g__Occultella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009708215.1	s__Occultella sp009708215	79.0686	584	1185	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Beutenbergiaceae;g__Occultella	95.0	97.28	97.28	0.86	0.86	2	-
GCF_009733795.1	s__Pseudactinotalea caeni	78.6721	475	1185	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Beutenbergiaceae;g__Pseudactinotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016649925.1	s__JAENWO01 sp016649925	78.3871	308	1185	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Beutenbergiaceae;g__JAENWO01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902805925.1	s__Nocardioides sp902805925	76.8517	216	1185	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003194625.1	s__Nocardioides solisilvae	76.7308	243	1185	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013408795.1	s__Spinactinospora alkalitolerans	76.4919	266	1185	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spinactinospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012033735.1	s__Streptomyces lonarensis	76.2815	256	1185	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:05:13,455] [INFO] GTDB search result was written to GCF_021049265.1_ASM2104926v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:05:13,456] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:05:13,459] [INFO] DFAST_QC result json was written to GCF_021049265.1_ASM2104926v1_genomic.fna/dqc_result.json
[2024-01-24 11:05:13,459] [INFO] DFAST_QC completed!
[2024-01-24 11:05:13,459] [INFO] Total running time: 0h1m41s