[2024-01-24 12:34:20,572] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:34:20,574] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:34:20,574] [INFO] DQC Reference Directory: /var/lib/cwl/stgc885c852-dbe8-48b4-8d04-8f637639f286/dqc_reference
[2024-01-24 12:34:21,762] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:34:21,763] [INFO] Task started: Prodigal
[2024-01-24 12:34:21,763] [INFO] Running command: gunzip -c /var/lib/cwl/stg17fbaea6-b140-4177-a745-03b74d2f75c0/GCF_024648885.1_ASM2464888v1_genomic.fna.gz | prodigal -d GCF_024648885.1_ASM2464888v1_genomic.fna/cds.fna -a GCF_024648885.1_ASM2464888v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:34:38,944] [INFO] Task succeeded: Prodigal
[2024-01-24 12:34:38,944] [INFO] Task started: HMMsearch
[2024-01-24 12:34:38,945] [INFO] Running command: hmmsearch --tblout GCF_024648885.1_ASM2464888v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc885c852-dbe8-48b4-8d04-8f637639f286/dqc_reference/reference_markers.hmm GCF_024648885.1_ASM2464888v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:34:39,252] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:34:39,253] [INFO] Found 6/6 markers.
[2024-01-24 12:34:39,298] [INFO] Query marker FASTA was written to GCF_024648885.1_ASM2464888v1_genomic.fna/markers.fasta
[2024-01-24 12:34:39,299] [INFO] Task started: Blastn
[2024-01-24 12:34:39,299] [INFO] Running command: blastn -query GCF_024648885.1_ASM2464888v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc885c852-dbe8-48b4-8d04-8f637639f286/dqc_reference/reference_markers.fasta -out GCF_024648885.1_ASM2464888v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:34:40,589] [INFO] Task succeeded: Blastn
[2024-01-24 12:34:40,593] [INFO] Selected 12 target genomes.
[2024-01-24 12:34:40,593] [INFO] Target genome list was writen to GCF_024648885.1_ASM2464888v1_genomic.fna/target_genomes.txt
[2024-01-24 12:34:40,599] [INFO] Task started: fastANI
[2024-01-24 12:34:40,599] [INFO] Running command: fastANI --query /var/lib/cwl/stg17fbaea6-b140-4177-a745-03b74d2f75c0/GCF_024648885.1_ASM2464888v1_genomic.fna.gz --refList GCF_024648885.1_ASM2464888v1_genomic.fna/target_genomes.txt --output GCF_024648885.1_ASM2464888v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:34:56,202] [INFO] Task succeeded: fastANI
[2024-01-24 12:34:56,203] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc885c852-dbe8-48b4-8d04-8f637639f286/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:34:56,203] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc885c852-dbe8-48b4-8d04-8f637639f286/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:34:56,218] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:34:56,219] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:34:56,219] [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
Prauserella isguenensis	strain=CECT 8577	GCA_014191605.1	1470180	1470180	type	True	88.8223	1421	1874	95	below_threshold
Prauserella aidingensis	strain=DSM 45266	GCA_024171865.1	387890	387890	type	True	88.6224	1442	1874	95	below_threshold
Prauserella rugosa	strain=DSM 43194	GCA_007829565.1	43354	43354	type	True	83.9685	1287	1874	95	below_threshold
Prauserella rugosa	strain=NRRL B-2295	GCA_000719975.1	43354	43354	type	True	83.9542	1272	1874	95	below_threshold
Prauserella cavernicola	strain=ASG 168	GCA_016595675.1	2800127	2800127	type	True	80.2626	956	1874	95	below_threshold
Prauserella muralis	strain=DSM 45305	GCA_003202285.1	588067	588067	type	True	80.2593	969	1874	95	below_threshold
Prauserella muralis	strain=DSM 45305	GCA_007993965.1	588067	588067	type	True	80.1693	974	1874	95	below_threshold
Amycolatopsis thermalba	strain=NRRL B-24845	GCA_003385215.1	944492	944492	type	True	79.3696	823	1874	95	below_threshold
Saccharomonospora piscinae	strain=KCTC 19743	GCA_005862235.1	687388	687388	type	True	79.3512	684	1874	95	below_threshold
Amycolatopsis viridis	strain=DSM 45668	GCA_011758765.1	185678	185678	type	True	79.25	766	1874	95	below_threshold
Amycolatopsis camponoti	strain=A23	GCA_902497555.1	2606593	2606593	type	True	78.7309	819	1874	95	below_threshold
Amycolatopsis pittospori	strain=PIP199	GCA_013870525.1	2749434	2749434	type	True	78.4715	725	1874	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:34:56,220] [INFO] DFAST Taxonomy check result was written to GCF_024648885.1_ASM2464888v1_genomic.fna/tc_result.tsv
[2024-01-24 12:34:56,221] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:34:56,221] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:34:56,221] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc885c852-dbe8-48b4-8d04-8f637639f286/dqc_reference/checkm_data
[2024-01-24 12:34:56,222] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:34:56,277] [INFO] Task started: CheckM
[2024-01-24 12:34:56,278] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024648885.1_ASM2464888v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024648885.1_ASM2464888v1_genomic.fna/checkm_input GCF_024648885.1_ASM2464888v1_genomic.fna/checkm_result
[2024-01-24 12:35:57,218] [INFO] Task succeeded: CheckM
[2024-01-24 12:35:57,219] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:35:57,240] [INFO] ===== Completeness check finished =====
[2024-01-24 12:35:57,241] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:35:57,241] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024648885.1_ASM2464888v1_genomic.fna/markers.fasta)
[2024-01-24 12:35:57,242] [INFO] Task started: Blastn
[2024-01-24 12:35:57,242] [INFO] Running command: blastn -query GCF_024648885.1_ASM2464888v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc885c852-dbe8-48b4-8d04-8f637639f286/dqc_reference/reference_markers_gtdb.fasta -out GCF_024648885.1_ASM2464888v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:35:59,191] [INFO] Task succeeded: Blastn
[2024-01-24 12:35:59,195] [INFO] Selected 11 target genomes.
[2024-01-24 12:35:59,195] [INFO] Target genome list was writen to GCF_024648885.1_ASM2464888v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:35:59,203] [INFO] Task started: fastANI
[2024-01-24 12:35:59,203] [INFO] Running command: fastANI --query /var/lib/cwl/stg17fbaea6-b140-4177-a745-03b74d2f75c0/GCF_024648885.1_ASM2464888v1_genomic.fna.gz --refList GCF_024648885.1_ASM2464888v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024648885.1_ASM2464888v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:36:13,743] [INFO] Task succeeded: fastANI
[2024-01-24 12:36:13,758] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:36:13,758] [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_014195435.1	s__Saccharomonospora sediminis	99.3539	1716	1874	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014191605.1	s__Saccharomonospora isguenensis	88.8223	1421	1874	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000719975.1	s__Saccharomonospora rugosa	83.9541	1272	1874	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	99.54	99.08	0.98	0.95	3	-
GCF_001942305.1	s__Saccharomonospora sp001942305	83.4454	1151	1874	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005146945.1	s__Saccharomonospora endophytica	80.3846	992	1874	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	99.14	99.02	0.90	0.90	3	-
GCF_003202235.1	s__Saccharomonospora sp003202235	80.3666	1030	1874	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003202285.1	s__Saccharomonospora muralis	80.2692	966	1874	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	100.00	100.00	1.00	1.00	2	-
GCF_016595675.1	s__Saccharomonospora sp016595675	80.2535	958	1874	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005862235.1	s__Saccharomonospora piscinae	79.3279	686	1874	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	98.79	98.27	0.95	0.94	3	-
GCF_011758765.1	s__Amycolatopsis viridis	79.2723	763	1874	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.9842	N/A	N/A	N/A	N/A	1	-
GCF_013870525.1	s__Amycolatopsis pittospori	78.4659	726	1874	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:36:13,760] [INFO] GTDB search result was written to GCF_024648885.1_ASM2464888v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:36:13,760] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:36:13,764] [INFO] DFAST_QC result json was written to GCF_024648885.1_ASM2464888v1_genomic.fna/dqc_result.json
[2024-01-24 12:36:13,764] [INFO] DFAST_QC completed!
[2024-01-24 12:36:13,764] [INFO] Total running time: 0h1m53s