[2024-01-24 13:55:58,111] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:55:58,112] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:55:58,113] [INFO] DQC Reference Directory: /var/lib/cwl/stg826b74a3-aee1-44a4-9080-b306c20e0173/dqc_reference
[2024-01-24 13:55:59,332] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:55:59,333] [INFO] Task started: Prodigal
[2024-01-24 13:55:59,334] [INFO] Running command: gunzip -c /var/lib/cwl/stg92ad387b-c8a4-48c8-8b22-73072502bfbb/GCF_021049285.1_ASM2104928v1_genomic.fna.gz | prodigal -d GCF_021049285.1_ASM2104928v1_genomic.fna/cds.fna -a GCF_021049285.1_ASM2104928v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:56:13,155] [INFO] Task succeeded: Prodigal
[2024-01-24 13:56:13,155] [INFO] Task started: HMMsearch
[2024-01-24 13:56:13,155] [INFO] Running command: hmmsearch --tblout GCF_021049285.1_ASM2104928v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg826b74a3-aee1-44a4-9080-b306c20e0173/dqc_reference/reference_markers.hmm GCF_021049285.1_ASM2104928v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:56:13,424] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:56:13,426] [INFO] Found 6/6 markers.
[2024-01-24 13:56:13,471] [INFO] Query marker FASTA was written to GCF_021049285.1_ASM2104928v1_genomic.fna/markers.fasta
[2024-01-24 13:56:13,472] [INFO] Task started: Blastn
[2024-01-24 13:56:13,472] [INFO] Running command: blastn -query GCF_021049285.1_ASM2104928v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg826b74a3-aee1-44a4-9080-b306c20e0173/dqc_reference/reference_markers.fasta -out GCF_021049285.1_ASM2104928v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:56:14,527] [INFO] Task succeeded: Blastn
[2024-01-24 13:56:14,531] [INFO] Selected 14 target genomes.
[2024-01-24 13:56:14,531] [INFO] Target genome list was writen to GCF_021049285.1_ASM2104928v1_genomic.fna/target_genomes.txt
[2024-01-24 13:56:14,547] [INFO] Task started: fastANI
[2024-01-24 13:56:14,548] [INFO] Running command: fastANI --query /var/lib/cwl/stg92ad387b-c8a4-48c8-8b22-73072502bfbb/GCF_021049285.1_ASM2104928v1_genomic.fna.gz --refList GCF_021049285.1_ASM2104928v1_genomic.fna/target_genomes.txt --output GCF_021049285.1_ASM2104928v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:56:27,964] [INFO] Task succeeded: fastANI
[2024-01-24 13:56:27,965] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg826b74a3-aee1-44a4-9080-b306c20e0173/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:56:27,966] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg826b74a3-aee1-44a4-9080-b306c20e0173/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:56:27,984] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:56:27,984] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:56:27,984] [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 halotolerans	strain=M4N3S171	GCA_021049285.1	2897773	2897773	type	True	100.0	1423	1423	95	conclusive
Ruania alba	strain=DSM 21368	GCA_900105765.1	648782	648782	type	True	82.9813	948	1423	95	below_threshold
Ruania alkalisoli	strain=RN3S43	GCA_014960965.1	2779775	2779775	type	True	81.7262	841	1423	95	below_threshold
Ruania rhizosphaerae	strain=LNNU 22110	GCA_009805705.1	1840413	1840413	type	True	81.5297	824	1423	95	below_threshold
Ruania suaedae	strain=LR1S40	GCA_021049265.1	2897774	2897774	type	True	80.7689	766	1423	95	below_threshold
Ruania zhangjianzhongii	strain=HY168	GCA_008000995.1	2603206	2603206	type	True	78.8639	532	1423	95	below_threshold
Ruania albidiflava	strain=DSM 18029	GCA_000421225.1	366586	366586	type	True	78.7379	526	1423	95	below_threshold
Occultella kanbiaonis	strain=HY164	GCA_009708215.1	2675754	2675754	type	True	78.5132	513	1423	95	below_threshold
Occultella aeris	strain=CIP 111667	GCA_902703175.1	2761496	2761496	type	True	78.4335	490	1423	95	below_threshold
Occultella gossypii	strain=N2-46	GCA_019947135.1	2800820	2800820	type	True	78.2927	511	1423	95	below_threshold
Pseudactinotalea suaedae	strain=KACC 17839	GCA_009733815.1	1524924	1524924	type	True	77.7339	366	1423	95	below_threshold
Streptomyces smyrnaeus	strain=DSM 42105	GCA_017676345.1	1387713	1387713	type	True	76.2295	162	1423	95	below_threshold
Streptomyces qinglanensis	strain=172205	GCA_003265665.1	943816	943816	type	True	75.9688	168	1423	95	below_threshold
Streptomyces qinglanensis	strain=CGMCC 4.6825	GCA_900111245.1	943816	943816	type	True	75.8817	169	1423	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:56:27,986] [INFO] DFAST Taxonomy check result was written to GCF_021049285.1_ASM2104928v1_genomic.fna/tc_result.tsv
[2024-01-24 13:56:27,986] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:56:27,987] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:56:27,987] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg826b74a3-aee1-44a4-9080-b306c20e0173/dqc_reference/checkm_data
[2024-01-24 13:56:27,988] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:56:28,028] [INFO] Task started: CheckM
[2024-01-24 13:56:28,029] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021049285.1_ASM2104928v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021049285.1_ASM2104928v1_genomic.fna/checkm_input GCF_021049285.1_ASM2104928v1_genomic.fna/checkm_result
[2024-01-24 13:57:27,475] [INFO] Task succeeded: CheckM
[2024-01-24 13:57:27,477] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:57:27,497] [INFO] ===== Completeness check finished =====
[2024-01-24 13:57:27,498] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:57:27,498] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021049285.1_ASM2104928v1_genomic.fna/markers.fasta)
[2024-01-24 13:57:27,499] [INFO] Task started: Blastn
[2024-01-24 13:57:27,499] [INFO] Running command: blastn -query GCF_021049285.1_ASM2104928v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg826b74a3-aee1-44a4-9080-b306c20e0173/dqc_reference/reference_markers_gtdb.fasta -out GCF_021049285.1_ASM2104928v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:29,157] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:29,160] [INFO] Selected 13 target genomes.
[2024-01-24 13:57:29,160] [INFO] Target genome list was writen to GCF_021049285.1_ASM2104928v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:57:29,175] [INFO] Task started: fastANI
[2024-01-24 13:57:29,175] [INFO] Running command: fastANI --query /var/lib/cwl/stg92ad387b-c8a4-48c8-8b22-73072502bfbb/GCF_021049285.1_ASM2104928v1_genomic.fna.gz --refList GCF_021049285.1_ASM2104928v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021049285.1_ASM2104928v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:57:41,472] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:41,483] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:57:41,484] [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_900105765.1	s__Haloactinobacterium album	82.9706	952	1423	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	81.7256	841	1423	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Beutenbergiaceae;g__Haloactinobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009805705.1	s__Haloactinobacterium sp009805705	81.5554	821	1423	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Beutenbergiaceae;g__Haloactinobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008000995.1	s__Ruania sp008000995	78.8716	534	1423	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Beutenbergiaceae;g__Ruania	95.0	99.97	99.97	0.98	0.98	2	-
GCF_000421225.1	s__Ruania albidiflava	78.7234	526	1423	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Beutenbergiaceae;g__Ruania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019116305.1	s__Ruania gallistercoris	78.7025	504	1423	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Beutenbergiaceae;g__Ruania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009708215.1	s__Occultella sp009708215	78.4924	515	1423	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Beutenbergiaceae;g__Occultella	95.0	97.28	97.28	0.86	0.86	2	-
GCF_004353825.1	s__Occultella glacieicola	78.2799	494	1423	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Beutenbergiaceae;g__Occultella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009733815.1	s__Pseudactinotalea suaedae	77.725	367	1423	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Beutenbergiaceae;g__Pseudactinotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000424965.1	s__Streptomyces sp000424965	76.3307	151	1423	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017676345.1	s__Streptomyces smyrnaeus	76.2187	163	1423	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.11	97.08	0.90	0.88	5	-
GCF_000424765.1	s__Streptomyces sp000424765	76.0178	166	1423	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.13	98.98	0.93	0.92	5	-
GCF_900111245.1	s__Streptomyces qinglanensis	75.8936	170	1423	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.98	99.98	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:57:41,486] [INFO] GTDB search result was written to GCF_021049285.1_ASM2104928v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:57:41,487] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:57:41,492] [INFO] DFAST_QC result json was written to GCF_021049285.1_ASM2104928v1_genomic.fna/dqc_result.json
[2024-01-24 13:57:41,493] [INFO] DFAST_QC completed!
[2024-01-24 13:57:41,493] [INFO] Total running time: 0h1m43s