[2024-01-24 13:56:26,304] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:56:26,306] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:56:26,306] [INFO] DQC Reference Directory: /var/lib/cwl/stg801e99fe-41bc-4259-bac8-fc6386b7fd13/dqc_reference
[2024-01-24 13:56:27,517] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:56:27,518] [INFO] Task started: Prodigal
[2024-01-24 13:56:27,518] [INFO] Running command: gunzip -c /var/lib/cwl/stg0df56532-46d6-4096-91e4-defdaf98ac2a/GCF_000423665.1_ASM42366v1_genomic.fna.gz | prodigal -d GCF_000423665.1_ASM42366v1_genomic.fna/cds.fna -a GCF_000423665.1_ASM42366v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:56:51,808] [INFO] Task succeeded: Prodigal
[2024-01-24 13:56:51,809] [INFO] Task started: HMMsearch
[2024-01-24 13:56:51,809] [INFO] Running command: hmmsearch --tblout GCF_000423665.1_ASM42366v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg801e99fe-41bc-4259-bac8-fc6386b7fd13/dqc_reference/reference_markers.hmm GCF_000423665.1_ASM42366v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:56:52,193] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:56:52,195] [INFO] Found 6/6 markers.
[2024-01-24 13:56:52,268] [INFO] Query marker FASTA was written to GCF_000423665.1_ASM42366v1_genomic.fna/markers.fasta
[2024-01-24 13:56:52,269] [INFO] Task started: Blastn
[2024-01-24 13:56:52,269] [INFO] Running command: blastn -query GCF_000423665.1_ASM42366v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg801e99fe-41bc-4259-bac8-fc6386b7fd13/dqc_reference/reference_markers.fasta -out GCF_000423665.1_ASM42366v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:56:53,017] [INFO] Task succeeded: Blastn
[2024-01-24 13:56:53,021] [INFO] Selected 9 target genomes.
[2024-01-24 13:56:53,022] [INFO] Target genome list was writen to GCF_000423665.1_ASM42366v1_genomic.fna/target_genomes.txt
[2024-01-24 13:56:53,027] [INFO] Task started: fastANI
[2024-01-24 13:56:53,028] [INFO] Running command: fastANI --query /var/lib/cwl/stg0df56532-46d6-4096-91e4-defdaf98ac2a/GCF_000423665.1_ASM42366v1_genomic.fna.gz --refList GCF_000423665.1_ASM42366v1_genomic.fna/target_genomes.txt --output GCF_000423665.1_ASM42366v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:57:06,285] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:06,285] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg801e99fe-41bc-4259-bac8-fc6386b7fd13/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:57:06,286] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg801e99fe-41bc-4259-bac8-fc6386b7fd13/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:57:06,300] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:57:06,301] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:57:06,301] [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
Solirubrobacter pauli	strain=DSM 14954	GCA_003633755.1	166793	166793	type	True	81.463	1534	3080	95	below_threshold
Capillimicrobium parvum	strain=0166_1	GCA_021172045.1	2884022	2884022	type	True	77.1225	896	3080	95	below_threshold
Conexibacter arvalis	strain=DSM 23288	GCA_014199525.1	912552	912552	type	True	77.0626	969	3080	95	below_threshold
Baekduia soli	strain=BR7-21	GCA_007970665.1	496014	496014	type	True	76.999	827	3080	95	below_threshold
Conexibacter woesei	strain=DSM 14684	GCA_000025265.1	191495	191495	type	True	76.9509	1011	3080	95	below_threshold
Paraconexibacter algicola	strain=Seoho-28	GCA_003044185.1	2133960	2133960	type	True	76.785	786	3080	95	below_threshold
Patulibacter medicamentivorans	strain=I11	GCA_000240225.2	1097667	1097667	type	True	76.5937	699	3080	95	below_threshold
Patulibacter minatonensis	strain=DSM 18081	GCA_000519325.1	298163	298163	type	True	76.1864	743	3080	95	below_threshold
Pseudokineococcus marinus	strain=JCM 14547	GCA_013004605.1	351215	351215	type	True	75.0608	385	3080	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:57:06,303] [INFO] DFAST Taxonomy check result was written to GCF_000423665.1_ASM42366v1_genomic.fna/tc_result.tsv
[2024-01-24 13:57:06,303] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:57:06,304] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:57:06,304] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg801e99fe-41bc-4259-bac8-fc6386b7fd13/dqc_reference/checkm_data
[2024-01-24 13:57:06,306] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:57:06,390] [INFO] Task started: CheckM
[2024-01-24 13:57:06,391] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000423665.1_ASM42366v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000423665.1_ASM42366v1_genomic.fna/checkm_input GCF_000423665.1_ASM42366v1_genomic.fna/checkm_result
[2024-01-24 13:58:56,863] [INFO] Task succeeded: CheckM
[2024-01-24 13:58:56,864] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:58:56,887] [INFO] ===== Completeness check finished =====
[2024-01-24 13:58:56,887] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:58:56,888] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000423665.1_ASM42366v1_genomic.fna/markers.fasta)
[2024-01-24 13:58:56,888] [INFO] Task started: Blastn
[2024-01-24 13:58:56,888] [INFO] Running command: blastn -query GCF_000423665.1_ASM42366v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg801e99fe-41bc-4259-bac8-fc6386b7fd13/dqc_reference/reference_markers_gtdb.fasta -out GCF_000423665.1_ASM42366v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:58,179] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:58,185] [INFO] Selected 10 target genomes.
[2024-01-24 13:58:58,186] [INFO] Target genome list was writen to GCF_000423665.1_ASM42366v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:58:58,204] [INFO] Task started: fastANI
[2024-01-24 13:58:58,204] [INFO] Running command: fastANI --query /var/lib/cwl/stg0df56532-46d6-4096-91e4-defdaf98ac2a/GCF_000423665.1_ASM42366v1_genomic.fna.gz --refList GCF_000423665.1_ASM42366v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000423665.1_ASM42366v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:59:15,515] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:15,527] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:59:15,527] [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_000423665.1	s__Solirubrobacter soli	100.0	3076	3080	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__Solirubrobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003633755.1	s__Solirubrobacter pauli	81.4676	1534	3080	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__Solirubrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003344625.1	s__Solirubrobacter sp003344625	81.3624	1488	3080	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__Solirubrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000425945.1	s__Solirubrobacter sp000425945	80.6489	1341	3080	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__Solirubrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018268595.1	s__Conexibacter sp018268595	77.4295	683	3080	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__Conexibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902806175.1	s__CADCVQ01 sp902806175	77.1862	624	3080	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__CADCVQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016781085.1	s__LC5-1 sp016781085	77.0635	236	3080	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__LC5-1	95.0	99.49	99.49	0.89	0.89	2	-
GCA_005888335.1	s__VAWY01 sp005888335	76.9632	886	3080	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__VAWY01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902806215.1	s__CADCVT01 sp902806215	76.5574	549	3080	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__CADCVT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015655225.1	s__Conexibacter sp015655225	76.3017	519	3080	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__Conexibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:59:15,529] [INFO] GTDB search result was written to GCF_000423665.1_ASM42366v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:59:15,529] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:59:15,534] [INFO] DFAST_QC result json was written to GCF_000423665.1_ASM42366v1_genomic.fna/dqc_result.json
[2024-01-24 13:59:15,534] [INFO] DFAST_QC completed!
[2024-01-24 13:59:15,534] [INFO] Total running time: 0h2m49s