[2023-06-29 22:59:48,798] [INFO] DFAST_QC pipeline started.
[2023-06-29 22:59:48,800] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 22:59:48,801] [INFO] DQC Reference Directory: /var/lib/cwl/stg51e3c5d2-2528-4680-96b7-57adc882a78e/dqc_reference
[2023-06-29 22:59:50,164] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 22:59:50,165] [INFO] Task started: Prodigal
[2023-06-29 22:59:50,165] [INFO] Running command: gunzip -c /var/lib/cwl/stgb0a1d172-7f1b-472c-b788-058b28230170/GCA_019351995.1_ASM1935199v1_genomic.fna.gz | prodigal -d GCA_019351995.1_ASM1935199v1_genomic.fna/cds.fna -a GCA_019351995.1_ASM1935199v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 22:59:58,334] [INFO] Task succeeded: Prodigal
[2023-06-29 22:59:58,334] [INFO] Task started: HMMsearch
[2023-06-29 22:59:58,334] [INFO] Running command: hmmsearch --tblout GCA_019351995.1_ASM1935199v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg51e3c5d2-2528-4680-96b7-57adc882a78e/dqc_reference/reference_markers.hmm GCA_019351995.1_ASM1935199v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 22:59:58,593] [INFO] Task succeeded: HMMsearch
[2023-06-29 22:59:58,594] [INFO] Found 6/6 markers.
[2023-06-29 22:59:58,629] [INFO] Query marker FASTA was written to GCA_019351995.1_ASM1935199v1_genomic.fna/markers.fasta
[2023-06-29 22:59:58,629] [INFO] Task started: Blastn
[2023-06-29 22:59:58,629] [INFO] Running command: blastn -query GCA_019351995.1_ASM1935199v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg51e3c5d2-2528-4680-96b7-57adc882a78e/dqc_reference/reference_markers.fasta -out GCA_019351995.1_ASM1935199v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 22:59:59,722] [INFO] Task succeeded: Blastn
[2023-06-29 22:59:59,726] [INFO] Selected 24 target genomes.
[2023-06-29 22:59:59,726] [INFO] Target genome list was writen to GCA_019351995.1_ASM1935199v1_genomic.fna/target_genomes.txt
[2023-06-29 22:59:59,729] [INFO] Task started: fastANI
[2023-06-29 22:59:59,729] [INFO] Running command: fastANI --query /var/lib/cwl/stgb0a1d172-7f1b-472c-b788-058b28230170/GCA_019351995.1_ASM1935199v1_genomic.fna.gz --refList GCA_019351995.1_ASM1935199v1_genomic.fna/target_genomes.txt --output GCA_019351995.1_ASM1935199v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 23:00:14,194] [INFO] Task succeeded: fastANI
[2023-06-29 23:00:14,194] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg51e3c5d2-2528-4680-96b7-57adc882a78e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 23:00:14,194] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg51e3c5d2-2528-4680-96b7-57adc882a78e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 23:00:14,213] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 23:00:14,213] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 23:00:14,213] [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
Protaetiibacter larvae	strain=KACC 19322	GCA_008365275.1	2592654	2592654	type	True	79.2803	321	915	95	below_threshold
Protaetiibacter intestinalis	strain=2DFWR-13	GCA_003627075.1	2419774	2419774	type	True	79.1864	341	915	95	below_threshold
Herbiconiux flava	strain=DSM 26474	GCA_013409865.1	881268	881268	type	True	78.3446	277	915	95	below_threshold
Chryseoglobus frigidaquae	strain=DSM 23889	GCA_009664385.2	424758	424758	type	True	78.1792	258	915	95	below_threshold
Chryseoglobus frigidaquae	strain=DSM 23889	GCA_014200395.1	424758	424758	type	True	78.1027	267	915	95	below_threshold
Conyzicola nivalis	strain=CGMCC 1.12813	GCA_014639655.1	1477021	1477021	type	True	78.0691	256	915	95	below_threshold
Clavibacter michiganensis subsp. tessellarius	strain=ATCC 33566	GCA_002240635.1	31965	28447	type	True	77.9552	225	915	95	below_threshold
Clavibacter zhangzhiyongii	strain=DM1	GCA_014775655.1	2768071	2768071	type	True	77.9504	237	915	95	below_threshold
Leifsonia shinshuensis	strain=DSM 15165	GCA_013410375.1	150026	150026	type	True	77.9432	284	915	95	below_threshold
Conyzicola lurida	strain=DSM 105784	GCA_014204935.1	1172621	1172621	type	True	77.9399	274	915	95	below_threshold
Herbiconiux moechotypicola	strain=KCTC 19653	GCA_024979255.1	637393	637393	type	True	77.9094	261	915	95	below_threshold
Clavibacter michiganensis subsp. tessellarius	strain=ATCC 33566	GCA_021922985.1	31965	28447	type	True	77.9074	232	915	95	below_threshold
Herbiconiux ginsengi	strain=CGMCC 4.3491	GCA_900107435.1	381665	381665	type	True	77.9006	259	915	95	below_threshold
Agromyces allii	strain=JCM 13584	GCA_009749385.1	393607	393607	type	True	77.8361	272	915	95	below_threshold
Clavibacter phaseoli	strain=LPPA 982	GCA_021922925.1	1734031	1734031	type	True	77.8121	244	915	95	below_threshold
Agromyces albus	strain=DSM 15934	GCA_004134825.1	205332	205332	type	True	77.8039	245	915	95	below_threshold
Agromyces humatus	strain=JCM 14319	GCA_021228295.1	279573	279573	type	True	77.7763	248	915	95	below_threshold
Plantibacter flavus	strain=VKM Ac-2504	GCA_900177615.1	150123	150123	type	True	77.6906	216	915	95	below_threshold
Cryobacterium psychrotolerans	strain=CGMCC 1.5382	GCA_900101115.1	386301	386301	type	True	77.6209	224	915	95	below_threshold
Microbacterium atlanticum	strain=WY121	GCA_015277815.1	2782168	2782168	type	True	77.5744	207	915	95	below_threshold
Cryobacterium psychrotolerans	strain=CGMCC 1.5382	GCA_004564325.1	386301	386301	type	True	77.5603	224	915	95	below_threshold
Microbacterium pullorum	strain=Sa4CUA7	GCA_014836535.1	2762236	2762236	type	True	77.46	202	915	95	below_threshold
Microbacterium gallinarum	strain=Sa1CUA4	GCA_014837165.1	2762209	2762209	type	True	77.4596	217	915	95	below_threshold
Microbacterium mangrovi	strain=MUSC 115	GCA_000802305.1	1348253	1348253	type	True	77.2849	216	915	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 23:00:14,216] [INFO] DFAST Taxonomy check result was written to GCA_019351995.1_ASM1935199v1_genomic.fna/tc_result.tsv
[2023-06-29 23:00:14,216] [INFO] ===== Taxonomy check completed =====
[2023-06-29 23:00:14,217] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 23:00:14,217] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg51e3c5d2-2528-4680-96b7-57adc882a78e/dqc_reference/checkm_data
[2023-06-29 23:00:14,218] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 23:00:14,249] [INFO] Task started: CheckM
[2023-06-29 23:00:14,249] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_019351995.1_ASM1935199v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_019351995.1_ASM1935199v1_genomic.fna/checkm_input GCA_019351995.1_ASM1935199v1_genomic.fna/checkm_result
[2023-06-29 23:00:56,360] [INFO] Task succeeded: CheckM
[2023-06-29 23:00:56,361] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 90.51%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 23:00:56,387] [INFO] ===== Completeness check finished =====
[2023-06-29 23:00:56,388] [INFO] ===== Start GTDB Search =====
[2023-06-29 23:00:56,388] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_019351995.1_ASM1935199v1_genomic.fna/markers.fasta)
[2023-06-29 23:00:56,388] [INFO] Task started: Blastn
[2023-06-29 23:00:56,388] [INFO] Running command: blastn -query GCA_019351995.1_ASM1935199v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg51e3c5d2-2528-4680-96b7-57adc882a78e/dqc_reference/reference_markers_gtdb.fasta -out GCA_019351995.1_ASM1935199v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 23:00:58,066] [INFO] Task succeeded: Blastn
[2023-06-29 23:00:58,071] [INFO] Selected 18 target genomes.
[2023-06-29 23:00:58,071] [INFO] Target genome list was writen to GCA_019351995.1_ASM1935199v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 23:00:58,081] [INFO] Task started: fastANI
[2023-06-29 23:00:58,082] [INFO] Running command: fastANI --query /var/lib/cwl/stgb0a1d172-7f1b-472c-b788-058b28230170/GCA_019351995.1_ASM1935199v1_genomic.fna.gz --refList GCA_019351995.1_ASM1935199v1_genomic.fna/target_genomes_gtdb.txt --output GCA_019351995.1_ASM1935199v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 23:01:08,217] [INFO] Task succeeded: fastANI
[2023-06-29 23:01:08,237] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 23:01:08,237] [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_011620705.1	s__Pseudolysinimonas sp011620705	80.6134	351	915	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Pseudolysinimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008365275.1	s__Protaetiibacter larvae	79.2803	321	915	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Protaetiibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003627075.1	s__Protaetiibacter intestinalis	79.2002	340	915	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Protaetiibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004216815.1	s__Protaetiibacter sp004216815	79.149	341	915	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Protaetiibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014653215.1	s__Pseudolysinimonas yzui	79.0828	326	915	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Pseudolysinimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002325245.1	s__Pseudolysinimonas sp002325245	79.0679	307	915	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Pseudolysinimonas	95.0	99.78	99.17	0.96	0.89	14	-
GCA_003852775.1	s__Protaetiibacter sp003852775	79.0277	295	915	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Protaetiibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006517435.1	s__Schumannella sp006517435	78.8485	341	915	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Schumannella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001898835.1	s__Protaetiibacter sp001898835	78.7792	346	915	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Protaetiibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014483895.1	s__Protaetiibacter sp014483895	78.691	336	915	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Protaetiibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905479755.1	s__Pseudolysinimonas sp905479755	78.6451	282	915	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Pseudolysinimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017308515.1	s__Pseudolysinimonas sp017308515	78.5587	321	915	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Pseudolysinimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013409865.1	s__Herbiconiux flava	78.3109	280	915	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Herbiconiux	95.0	95.35	95.35	0.90	0.90	2	-
GCA_001898805.1	s__Leifsonia sp001898805	78.1385	269	915	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107435.1	s__Herbiconiux ginsengi	77.887	260	915	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Herbiconiux	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004134825.1	s__Agromyces albus	77.79	246	915	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014378715.1	s__Marisediminicola sp014378715	77.604	244	915	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Marisediminicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015751965.1	s__Lacisediminihabitans sp015751965	76.9918	142	915	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Lacisediminihabitans	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 23:01:08,291] [INFO] GTDB search result was written to GCA_019351995.1_ASM1935199v1_genomic.fna/result_gtdb.tsv
[2023-06-29 23:01:08,292] [INFO] ===== GTDB Search completed =====
[2023-06-29 23:01:08,299] [INFO] DFAST_QC result json was written to GCA_019351995.1_ASM1935199v1_genomic.fna/dqc_result.json
[2023-06-29 23:01:08,299] [INFO] DFAST_QC completed!
[2023-06-29 23:01:08,299] [INFO] Total running time: 0h1m20s