[2024-01-25 18:14:05,659] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:14:05,661] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:14:05,661] [INFO] DQC Reference Directory: /var/lib/cwl/stg9fcaa85c-704d-4a8d-aa9d-c2e99247e881/dqc_reference
[2024-01-25 18:14:06,809] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:14:06,809] [INFO] Task started: Prodigal
[2024-01-25 18:14:06,810] [INFO] Running command: gunzip -c /var/lib/cwl/stg8734938c-a5d2-4708-8239-6cdbdd016f8e/GCF_028875625.1_ASM2887562v1_genomic.fna.gz | prodigal -d GCF_028875625.1_ASM2887562v1_genomic.fna/cds.fna -a GCF_028875625.1_ASM2887562v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:14:14,237] [INFO] Task succeeded: Prodigal
[2024-01-25 18:14:14,237] [INFO] Task started: HMMsearch
[2024-01-25 18:14:14,237] [INFO] Running command: hmmsearch --tblout GCF_028875625.1_ASM2887562v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9fcaa85c-704d-4a8d-aa9d-c2e99247e881/dqc_reference/reference_markers.hmm GCF_028875625.1_ASM2887562v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:14:14,453] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:14:14,454] [INFO] Found 6/6 markers.
[2024-01-25 18:14:14,486] [INFO] Query marker FASTA was written to GCF_028875625.1_ASM2887562v1_genomic.fna/markers.fasta
[2024-01-25 18:14:14,487] [INFO] Task started: Blastn
[2024-01-25 18:14:14,487] [INFO] Running command: blastn -query GCF_028875625.1_ASM2887562v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9fcaa85c-704d-4a8d-aa9d-c2e99247e881/dqc_reference/reference_markers.fasta -out GCF_028875625.1_ASM2887562v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:14:15,081] [INFO] Task succeeded: Blastn
[2024-01-25 18:14:15,084] [INFO] Selected 26 target genomes.
[2024-01-25 18:14:15,084] [INFO] Target genome list was writen to GCF_028875625.1_ASM2887562v1_genomic.fna/target_genomes.txt
[2024-01-25 18:14:15,100] [INFO] Task started: fastANI
[2024-01-25 18:14:15,100] [INFO] Running command: fastANI --query /var/lib/cwl/stg8734938c-a5d2-4708-8239-6cdbdd016f8e/GCF_028875625.1_ASM2887562v1_genomic.fna.gz --refList GCF_028875625.1_ASM2887562v1_genomic.fna/target_genomes.txt --output GCF_028875625.1_ASM2887562v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:14:35,186] [INFO] Task succeeded: fastANI
[2024-01-25 18:14:35,187] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9fcaa85c-704d-4a8d-aa9d-c2e99247e881/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:14:35,187] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9fcaa85c-704d-4a8d-aa9d-c2e99247e881/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:14:35,196] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:14:35,196] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:14:35,196] [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
Rhodocaloribacter litoris	strain=ISCAR-4553	GCA_011682235.2	2558931	2558931	type	True	75.4293	63	1041	95	below_threshold
Gemmatirosa kalamazoonensis	strain=KBS708	GCA_000522985.1	861299	861299	type	True	75.3714	171	1041	95	below_threshold
Vulgatibacter incomptus	strain=DSM 27710	GCA_001263175.1	1391653	1391653	type	True	75.1715	63	1041	95	below_threshold
Paraconexibacter algicola	strain=Seoho-28	GCA_003044185.1	2133960	2133960	type	True	74.9749	91	1041	95	below_threshold
Polyangium spumosum	strain=DSM 14734	GCA_009649845.1	889282	889282	type	True	74.8853	128	1041	95	below_threshold
Archangium violaceum	strain=Cb vi76	GCA_000733295.1	83451	83451	type	True	74.852	78	1041	95	below_threshold
Aeromicrobium tamlense	strain=DSM 19087	GCA_013408555.1	375541	375541	type	True	74.8066	59	1041	95	below_threshold
Cnuibacter physcomitrellae	strain=XA(T)	GCA_002096055.1	1619308	1619308	type	True	74.7559	72	1041	95	below_threshold
Cnuibacter physcomitrellae	strain=CGMCC 1.15041	GCA_014640535.1	1619308	1619308	type	True	74.6986	70	1041	95	below_threshold
Aeromicrobium tamlense	strain=SSW1-57	GCA_014672995.1	375541	375541	type	True	74.6401	56	1041	95	below_threshold
Halorubrum aquaticum	strain=CGMCC 1.6377	GCA_900113615.1	387340	387340	type	True	74.6096	52	1041	95	below_threshold
Haloferax prahovense	strain=DSM 18310	GCA_000336815.1	381852	381852	type	True	74.5725	50	1041	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:14:35,197] [INFO] DFAST Taxonomy check result was written to GCF_028875625.1_ASM2887562v1_genomic.fna/tc_result.tsv
[2024-01-25 18:14:35,198] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:14:35,198] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:14:35,198] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9fcaa85c-704d-4a8d-aa9d-c2e99247e881/dqc_reference/checkm_data
[2024-01-25 18:14:35,199] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:14:35,232] [INFO] Task started: CheckM
[2024-01-25 18:14:35,233] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_028875625.1_ASM2887562v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_028875625.1_ASM2887562v1_genomic.fna/checkm_input GCF_028875625.1_ASM2887562v1_genomic.fna/checkm_result
[2024-01-25 18:15:03,251] [INFO] Task succeeded: CheckM
[2024-01-25 18:15:03,252] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:15:03,290] [INFO] ===== Completeness check finished =====
[2024-01-25 18:15:03,290] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:15:03,291] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_028875625.1_ASM2887562v1_genomic.fna/markers.fasta)
[2024-01-25 18:15:03,291] [INFO] Task started: Blastn
[2024-01-25 18:15:03,291] [INFO] Running command: blastn -query GCF_028875625.1_ASM2887562v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9fcaa85c-704d-4a8d-aa9d-c2e99247e881/dqc_reference/reference_markers_gtdb.fasta -out GCF_028875625.1_ASM2887562v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:15:04,244] [INFO] Task succeeded: Blastn
[2024-01-25 18:15:04,247] [INFO] Selected 5 target genomes.
[2024-01-25 18:15:04,247] [INFO] Target genome list was writen to GCF_028875625.1_ASM2887562v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:15:04,251] [INFO] Task started: fastANI
[2024-01-25 18:15:04,252] [INFO] Running command: fastANI --query /var/lib/cwl/stg8734938c-a5d2-4708-8239-6cdbdd016f8e/GCF_028875625.1_ASM2887562v1_genomic.fna.gz --refList GCF_028875625.1_ASM2887562v1_genomic.fna/target_genomes_gtdb.txt --output GCF_028875625.1_ASM2887562v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:15:08,967] [INFO] Task succeeded: fastANI
[2024-01-25 18:15:08,972] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:15:08,972] [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
GCA_009841005.1	s__JAAXHJ01 sp009841005	98.9497	850	1041	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__KS3-K002;f__JABDQB01;g__JAAXHJ01	95.0	96.67	96.60	0.84	0.81	5	conclusive
GCA_009841015.1	s__JAAXHJ01 sp009841015	90.4669	824	1041	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__KS3-K002;f__JABDQB01;g__JAAXHJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009840115.1	s__JAAXHJ01 sp009840115	90.2696	876	1041	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__KS3-K002;f__JABDQB01;g__JAAXHJ01	95.0	99.91	99.91	0.95	0.95	2	-
GCA_009838765.1	s__JAAXHJ01 sp009838765	90.2596	873	1041	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__KS3-K002;f__JABDQB01;g__JAAXHJ01	95.0	99.96	99.96	0.97	0.96	3	-
GCA_012270965.1	s__JAAXHJ01 sp012270965	88.389	810	1041	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__KS3-K002;f__JABDQB01;g__JAAXHJ01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:15:08,973] [INFO] GTDB search result was written to GCF_028875625.1_ASM2887562v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:15:08,974] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:15:08,976] [INFO] DFAST_QC result json was written to GCF_028875625.1_ASM2887562v1_genomic.fna/dqc_result.json
[2024-01-25 18:15:08,976] [INFO] DFAST_QC completed!
[2024-01-25 18:15:08,976] [INFO] Total running time: 0h1m3s