[2023-06-27 14:02:59,224] [INFO] DFAST_QC pipeline started.
[2023-06-27 14:02:59,233] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 14:02:59,233] [INFO] DQC Reference Directory: /var/lib/cwl/stg3062b4f5-abac-46c0-bf64-b1adad28ea74/dqc_reference
[2023-06-27 14:03:01,074] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 14:03:01,075] [INFO] Task started: Prodigal
[2023-06-27 14:03:01,076] [INFO] Running command: gunzip -c /var/lib/cwl/stg0f8767d2-7bf7-45eb-85d7-48c22756feae/GCA_026708005.1_ASM2670800v1_genomic.fna.gz | prodigal -d GCA_026708005.1_ASM2670800v1_genomic.fna/cds.fna -a GCA_026708005.1_ASM2670800v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 14:03:10,474] [INFO] Task succeeded: Prodigal
[2023-06-27 14:03:10,475] [INFO] Task started: HMMsearch
[2023-06-27 14:03:10,475] [INFO] Running command: hmmsearch --tblout GCA_026708005.1_ASM2670800v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3062b4f5-abac-46c0-bf64-b1adad28ea74/dqc_reference/reference_markers.hmm GCA_026708005.1_ASM2670800v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 14:03:10,660] [INFO] Task succeeded: HMMsearch
[2023-06-27 14:03:10,662] [INFO] Found 6/6 markers.
[2023-06-27 14:03:10,692] [INFO] Query marker FASTA was written to GCA_026708005.1_ASM2670800v1_genomic.fna/markers.fasta
[2023-06-27 14:03:10,692] [INFO] Task started: Blastn
[2023-06-27 14:03:10,692] [INFO] Running command: blastn -query GCA_026708005.1_ASM2670800v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3062b4f5-abac-46c0-bf64-b1adad28ea74/dqc_reference/reference_markers.fasta -out GCA_026708005.1_ASM2670800v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 14:03:11,320] [INFO] Task succeeded: Blastn
[2023-06-27 14:03:11,323] [INFO] Selected 19 target genomes.
[2023-06-27 14:03:11,324] [INFO] Target genome list was writen to GCA_026708005.1_ASM2670800v1_genomic.fna/target_genomes.txt
[2023-06-27 14:03:11,330] [INFO] Task started: fastANI
[2023-06-27 14:03:11,330] [INFO] Running command: fastANI --query /var/lib/cwl/stg0f8767d2-7bf7-45eb-85d7-48c22756feae/GCA_026708005.1_ASM2670800v1_genomic.fna.gz --refList GCA_026708005.1_ASM2670800v1_genomic.fna/target_genomes.txt --output GCA_026708005.1_ASM2670800v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 14:03:26,871] [INFO] Task succeeded: fastANI
[2023-06-27 14:03:26,871] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3062b4f5-abac-46c0-bf64-b1adad28ea74/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 14:03:26,871] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3062b4f5-abac-46c0-bf64-b1adad28ea74/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 14:03:26,884] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 14:03:26,884] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-27 14:03:26,884] [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
Gaiella occulta	strain=F2-233	GCA_003351045.1	1002870	1002870	type	True	76.3105	159	1146	95	below_threshold
Miltoncostaea oceani	strain=SCSIO 61214	GCA_018141545.1	2843216	2843216	type	True	75.648	108	1146	95	below_threshold
Capillimicrobium parvum	strain=0166_1	GCA_021172045.1	2884022	2884022	type	True	75.5929	170	1146	95	below_threshold
Patulibacter minatonensis	strain=DSM 18081	GCA_000519325.1	298163	298163	type	True	75.5705	95	1146	95	below_threshold
Solirubrobacter pauli	strain=DSM 14954	GCA_003633755.1	166793	166793	type	True	75.4006	150	1146	95	below_threshold
Conexibacter woesei	strain=DSM 14684	GCA_000025265.1	191495	191495	type	True	75.3826	155	1146	95	below_threshold
Paraconexibacter algicola	strain=Seoho-28	GCA_003044185.1	2133960	2133960	type	True	75.2808	122	1146	95	below_threshold
Micromonospora parathelypteridis	strain=DSM 103125	GCA_014201145.1	1839617	1839617	type	True	75.051	63	1146	95	below_threshold
Actinomycetospora corticicola	strain=DSM 45772	GCA_013409505.1	663602	663602	type	True	75.0468	108	1146	95	below_threshold
Actinomycetospora soli	strain=SF1	GCA_021026295.1	2893887	2893887	type	True	75.032	122	1146	95	below_threshold
Acrocarpospora pleiomorpha	strain=NBRC 16267	GCA_009687885.1	90975	90975	type	True	74.9913	74	1146	95	below_threshold
Acrocarpospora macrocephala	strain=NBRC 16266	GCA_009687865.1	150177	150177	type	True	74.9429	89	1146	95	below_threshold
Micromonospora parathelypteridis	strain=CGMCC 4.7347	GCA_014646315.1	1839617	1839617	type	True	74.9127	60	1146	95	below_threshold
Acrocarpospora phusangensis	strain=NBRC 108782	GCA_016862995.1	1070424	1070424	type	True	74.9023	85	1146	95	below_threshold
Micromonospora aurantiaca	strain=ATCC 27029	GCA_003721415.1	47850	47850	type	True	74.7866	88	1146	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 14:03:26,886] [INFO] DFAST Taxonomy check result was written to GCA_026708005.1_ASM2670800v1_genomic.fna/tc_result.tsv
[2023-06-27 14:03:26,887] [INFO] ===== Taxonomy check completed =====
[2023-06-27 14:03:26,887] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 14:03:26,887] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3062b4f5-abac-46c0-bf64-b1adad28ea74/dqc_reference/checkm_data
[2023-06-27 14:03:26,888] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 14:03:26,925] [INFO] Task started: CheckM
[2023-06-27 14:03:26,925] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026708005.1_ASM2670800v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026708005.1_ASM2670800v1_genomic.fna/checkm_input GCA_026708005.1_ASM2670800v1_genomic.fna/checkm_result
[2023-06-27 14:03:56,713] [INFO] Task succeeded: CheckM
[2023-06-27 14:03:56,714] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 14:03:56,732] [INFO] ===== Completeness check finished =====
[2023-06-27 14:03:56,733] [INFO] ===== Start GTDB Search =====
[2023-06-27 14:03:56,733] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026708005.1_ASM2670800v1_genomic.fna/markers.fasta)
[2023-06-27 14:03:56,733] [INFO] Task started: Blastn
[2023-06-27 14:03:56,733] [INFO] Running command: blastn -query GCA_026708005.1_ASM2670800v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3062b4f5-abac-46c0-bf64-b1adad28ea74/dqc_reference/reference_markers_gtdb.fasta -out GCA_026708005.1_ASM2670800v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 14:03:57,663] [INFO] Task succeeded: Blastn
[2023-06-27 14:03:57,680] [INFO] Selected 21 target genomes.
[2023-06-27 14:03:57,681] [INFO] Target genome list was writen to GCA_026708005.1_ASM2670800v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 14:03:57,696] [INFO] Task started: fastANI
[2023-06-27 14:03:57,697] [INFO] Running command: fastANI --query /var/lib/cwl/stg0f8767d2-7bf7-45eb-85d7-48c22756feae/GCA_026708005.1_ASM2670800v1_genomic.fna.gz --refList GCA_026708005.1_ASM2670800v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026708005.1_ASM2670800v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 14:04:06,645] [INFO] Task succeeded: fastANI
[2023-06-27 14:04:06,660] [INFO] Found 19 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-27 14:04:06,660] [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_003139545.1	s__Palsa-739 sp003139545	76.5427	118	1146	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Gaiellales;f__Gaiellaceae;g__Palsa-739	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005883335.1	s__AC-32 sp005883335	76.5133	101	1146	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Gaiellales;f__Gaiellaceae;g__AC-32	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019236545.1	s__Palsa-739 sp019236545	76.4971	114	1146	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Gaiellales;f__Gaiellaceae;g__Palsa-739	95.0	98.19	98.19	0.82	0.82	2	-
GCA_005883365.1	s__Palsa-739 sp005883365	76.4751	86	1146	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Gaiellales;f__Gaiellaceae;g__Palsa-739	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005883955.1	s__13-2-20CM-68-14 sp005883955	76.4693	106	1146	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Gaiellales;f__Gaiellaceae;g__13-2-20CM-68-14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005884155.1	s__AC-32 sp005884155	76.4523	102	1146	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Gaiellales;f__Gaiellaceae;g__AC-32	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005884575.1	s__AC-16 sp005884575	76.4123	161	1146	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Gaiellales;f__Gaiellaceae;g__AC-16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013696185.1	s__JACCZA01 sp013696185	76.3985	117	1146	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Gaiellales;f__Gaiellaceae;g__JACCZA01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003161615.1	s__Palsa-739 sp003161615	76.3799	102	1146	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Gaiellales;f__Gaiellaceae;g__Palsa-739	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005885245.1	s__3-1-20CM-4-69-9 sp005885245	76.3655	106	1146	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Gaiellales;f__Gaiellaceae;g__3-1-20CM-4-69-9	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003351045.1	s__Gaiella occulta	76.3219	158	1146	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Gaiellales;f__Gaiellaceae;g__Gaiella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013816275.1	s__JACDER01 sp013816275	76.3138	60	1146	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Gaiellales;f__Gaiellaceae;g__JACDER01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016870235.1	s__Gaiella sp016870235	76.3106	128	1146	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Gaiellales;f__Gaiellaceae;g__Gaiella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005885565.1	s__AC-50 sp005885565	76.238	132	1146	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Gaiellales;f__Gaiellaceae;g__AC-50	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013812265.1	s__JACCTQ01 sp013812265	76.0928	100	1146	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Gaiellales;f__Gaiellaceae;g__JACCTQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001920085.1	s__3-1-20CM-4-69-9 sp001920085	76.0732	72	1146	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Gaiellales;f__Gaiellaceae;g__3-1-20CM-4-69-9	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005883235.1	s__AC-50 sp005883235	76.0253	77	1146	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Gaiellales;f__Gaiellaceae;g__AC-50	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014534155.1	s__JACVSB01 sp014534155	75.6664	76	1146	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Gaiellales;f__Gaiellaceae;g__JACVSB01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003152275.1	s__Palsa-739 sp003152275	75.6482	86	1146	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Gaiellales;f__Gaiellaceae;g__Palsa-739	95.0	96.63	96.63	0.81	0.81	2	-
--------------------------------------------------------------------------------
[2023-06-27 14:04:06,666] [INFO] GTDB search result was written to GCA_026708005.1_ASM2670800v1_genomic.fna/result_gtdb.tsv
[2023-06-27 14:04:06,666] [INFO] ===== GTDB Search completed =====
[2023-06-27 14:04:06,670] [INFO] DFAST_QC result json was written to GCA_026708005.1_ASM2670800v1_genomic.fna/dqc_result.json
[2023-06-27 14:04:06,670] [INFO] DFAST_QC completed!
[2023-06-27 14:04:06,670] [INFO] Total running time: 0h1m7s