[2024-01-24 14:23:02,399] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:23:02,401] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:23:02,401] [INFO] DQC Reference Directory: /var/lib/cwl/stg68fb10b6-683c-4bd7-adfa-7e957d880227/dqc_reference
[2024-01-24 14:23:03,676] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:23:03,677] [INFO] Task started: Prodigal
[2024-01-24 14:23:03,677] [INFO] Running command: gunzip -c /var/lib/cwl/stgb0089357-819e-4f94-a7c7-f738e2784818/GCF_003965815.1_ASM396581v1_genomic.fna.gz | prodigal -d GCF_003965815.1_ASM396581v1_genomic.fna/cds.fna -a GCF_003965815.1_ASM396581v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:23:24,654] [INFO] Task succeeded: Prodigal
[2024-01-24 14:23:24,655] [INFO] Task started: HMMsearch
[2024-01-24 14:23:24,655] [INFO] Running command: hmmsearch --tblout GCF_003965815.1_ASM396581v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg68fb10b6-683c-4bd7-adfa-7e957d880227/dqc_reference/reference_markers.hmm GCF_003965815.1_ASM396581v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:23:25,011] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:23:25,012] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgb0089357-819e-4f94-a7c7-f738e2784818/GCF_003965815.1_ASM396581v1_genomic.fna.gz]
[2024-01-24 14:23:25,071] [INFO] Query marker FASTA was written to GCF_003965815.1_ASM396581v1_genomic.fna/markers.fasta
[2024-01-24 14:23:25,072] [INFO] Task started: Blastn
[2024-01-24 14:23:25,072] [INFO] Running command: blastn -query GCF_003965815.1_ASM396581v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg68fb10b6-683c-4bd7-adfa-7e957d880227/dqc_reference/reference_markers.fasta -out GCF_003965815.1_ASM396581v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:23:25,968] [INFO] Task succeeded: Blastn
[2024-01-24 14:23:25,984] [INFO] Selected 10 target genomes.
[2024-01-24 14:23:25,985] [INFO] Target genome list was writen to GCF_003965815.1_ASM396581v1_genomic.fna/target_genomes.txt
[2024-01-24 14:23:25,990] [INFO] Task started: fastANI
[2024-01-24 14:23:25,990] [INFO] Running command: fastANI --query /var/lib/cwl/stgb0089357-819e-4f94-a7c7-f738e2784818/GCF_003965815.1_ASM396581v1_genomic.fna.gz --refList GCF_003965815.1_ASM396581v1_genomic.fna/target_genomes.txt --output GCF_003965815.1_ASM396581v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:23:42,125] [INFO] Task succeeded: fastANI
[2024-01-24 14:23:42,126] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg68fb10b6-683c-4bd7-adfa-7e957d880227/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:23:42,126] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg68fb10b6-683c-4bd7-adfa-7e957d880227/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:23:42,136] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:23:42,136] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:23:42,136] [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
Variovorax gossypii	strain=DSM 100435	GCA_003965815.1	1679495	1679495	type	True	100.0	2092	2093	95	conclusive
Variovorax guangxiensis	strain=DSM 27352	GCA_003952165.1	1775474	1775474	type	True	92.2166	1548	2093	95	below_threshold
Variovorax boronicumulans	strain=NBRC 103145	GCA_001591345.1	436515	436515	type	True	88.3805	1274	2093	95	below_threshold
Variovorax paradoxus	strain=NBRC 15149	GCA_001591365.1	34073	34073	suspected-type	True	87.2972	1315	2093	95	below_threshold
Variovorax beijingensis	strain=502	GCA_003951285.1	2496117	2496117	type	True	87.1161	1270	2093	95	below_threshold
Xylophilus ampelinus	strain=CFBP 1192	GCA_024832295.1	54067	54067	type	True	80.9898	586	2093	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	80.7478	664	2093	95	below_threshold
Ramlibacter humi	strain=18x22-1	GCA_004681975.1	2530451	2530451	type	True	80.6593	679	2093	95	below_threshold
Ramlibacter pinisoli	strain=MAH-25	GCA_009758015.1	2682844	2682844	type	True	80.3821	738	2093	95	below_threshold
Ramlibacter agri	strain=G-1-2-2	GCA_012927085.1	2728837	2728837	type	True	80.2928	834	2093	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:23:42,138] [INFO] DFAST Taxonomy check result was written to GCF_003965815.1_ASM396581v1_genomic.fna/tc_result.tsv
[2024-01-24 14:23:42,138] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:23:42,139] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:23:42,139] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg68fb10b6-683c-4bd7-adfa-7e957d880227/dqc_reference/checkm_data
[2024-01-24 14:23:42,140] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:23:42,200] [INFO] Task started: CheckM
[2024-01-24 14:23:42,200] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003965815.1_ASM396581v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003965815.1_ASM396581v1_genomic.fna/checkm_input GCF_003965815.1_ASM396581v1_genomic.fna/checkm_result
[2024-01-24 14:25:04,183] [INFO] Task succeeded: CheckM
[2024-01-24 14:25:04,184] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:25:04,210] [INFO] ===== Completeness check finished =====
[2024-01-24 14:25:04,210] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:25:04,211] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003965815.1_ASM396581v1_genomic.fna/markers.fasta)
[2024-01-24 14:25:04,211] [INFO] Task started: Blastn
[2024-01-24 14:25:04,211] [INFO] Running command: blastn -query GCF_003965815.1_ASM396581v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg68fb10b6-683c-4bd7-adfa-7e957d880227/dqc_reference/reference_markers_gtdb.fasta -out GCF_003965815.1_ASM396581v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:25:05,868] [INFO] Task succeeded: Blastn
[2024-01-24 14:25:05,871] [INFO] Selected 7 target genomes.
[2024-01-24 14:25:05,871] [INFO] Target genome list was writen to GCF_003965815.1_ASM396581v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:25:05,939] [INFO] Task started: fastANI
[2024-01-24 14:25:05,939] [INFO] Running command: fastANI --query /var/lib/cwl/stgb0089357-819e-4f94-a7c7-f738e2784818/GCF_003965815.1_ASM396581v1_genomic.fna.gz --refList GCF_003965815.1_ASM396581v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003965815.1_ASM396581v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:25:19,295] [INFO] Task succeeded: fastANI
[2024-01-24 14:25:19,307] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:25:19,308] [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_003965815.1	s__Variovorax gossypii	100.0	2092	2093	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	98.17	98.16	0.90	0.89	6	conclusive
GCF_003952185.1	s__Variovorax sp003952185	93.3077	1635	2093	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	99.99	99.98	0.99	0.99	3	-
GCF_013376045.1	s__Variovorax sp013376045	93.2054	1620	2093	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003952165.1	s__Variovorax guangxiensis	92.2152	1548	2093	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	97.91	97.91	0.87	0.87	2	-
GCF_000382045.1	s__Variovorax paradoxus_A	91.7034	1576	2093	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	98.57	98.47	0.92	0.91	6	-
GCF_004216615.1	s__Variovorax sp004216615	90.6766	1392	2093	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900106655.1	s__Variovorax sp900106655	90.5405	1564	2093	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	98.15	98.06	0.92	0.90	4	-
--------------------------------------------------------------------------------
[2024-01-24 14:25:19,310] [INFO] GTDB search result was written to GCF_003965815.1_ASM396581v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:25:19,311] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:25:19,314] [INFO] DFAST_QC result json was written to GCF_003965815.1_ASM396581v1_genomic.fna/dqc_result.json
[2024-01-24 14:25:19,314] [INFO] DFAST_QC completed!
[2024-01-24 14:25:19,314] [INFO] Total running time: 0h2m17s