[2024-01-25 18:53:20,976] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:53:20,980] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:53:20,980] [INFO] DQC Reference Directory: /var/lib/cwl/stg652dfc55-baab-482f-a2ce-5d659eec2e8d/dqc_reference
[2024-01-25 18:53:22,144] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:53:22,146] [INFO] Task started: Prodigal
[2024-01-25 18:53:22,146] [INFO] Running command: gunzip -c /var/lib/cwl/stg523c1521-783b-4152-8c77-d4b5a50d82d2/GCF_016464305.1_ASM1646430v1_genomic.fna.gz | prodigal -d GCF_016464305.1_ASM1646430v1_genomic.fna/cds.fna -a GCF_016464305.1_ASM1646430v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:53:46,475] [INFO] Task succeeded: Prodigal
[2024-01-25 18:53:46,476] [INFO] Task started: HMMsearch
[2024-01-25 18:53:46,476] [INFO] Running command: hmmsearch --tblout GCF_016464305.1_ASM1646430v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg652dfc55-baab-482f-a2ce-5d659eec2e8d/dqc_reference/reference_markers.hmm GCF_016464305.1_ASM1646430v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:53:46,749] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:53:46,752] [INFO] Found 6/6 markers.
[2024-01-25 18:53:46,805] [INFO] Query marker FASTA was written to GCF_016464305.1_ASM1646430v1_genomic.fna/markers.fasta
[2024-01-25 18:53:46,805] [INFO] Task started: Blastn
[2024-01-25 18:53:46,805] [INFO] Running command: blastn -query GCF_016464305.1_ASM1646430v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg652dfc55-baab-482f-a2ce-5d659eec2e8d/dqc_reference/reference_markers.fasta -out GCF_016464305.1_ASM1646430v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:53:48,075] [INFO] Task succeeded: Blastn
[2024-01-25 18:53:48,078] [INFO] Selected 30 target genomes.
[2024-01-25 18:53:48,078] [INFO] Target genome list was writen to GCF_016464305.1_ASM1646430v1_genomic.fna/target_genomes.txt
[2024-01-25 18:53:48,097] [INFO] Task started: fastANI
[2024-01-25 18:53:48,097] [INFO] Running command: fastANI --query /var/lib/cwl/stg523c1521-783b-4152-8c77-d4b5a50d82d2/GCF_016464305.1_ASM1646430v1_genomic.fna.gz --refList GCF_016464305.1_ASM1646430v1_genomic.fna/target_genomes.txt --output GCF_016464305.1_ASM1646430v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:54:48,292] [INFO] Task succeeded: fastANI
[2024-01-25 18:54:48,292] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg652dfc55-baab-482f-a2ce-5d659eec2e8d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:54:48,293] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg652dfc55-baab-482f-a2ce-5d659eec2e8d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:54:48,310] [INFO] Found 30 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:54:48,310] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:54:48,311] [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
Saccharothrix coeruleofusca	strain=DSM 43679	GCA_017876325.1	33919	33919	type	True	81.9442	1318	2153	95	below_threshold
Saccharothrix coeruleofusca	strain=JCM 3313	GCA_014648515.1	33919	33919	type	True	81.8517	1315	2153	95	below_threshold
Saccharothrix texasensis	strain=DSM 44231	GCA_003752005.1	103734	103734	type	True	81.4224	1312	2153	95	below_threshold
Saccharothrix carnea	strain=CGMCC 4.7097	GCA_003014735.1	1280637	1280637	type	True	81.4153	1263	2153	95	below_threshold
Saccharothrix syringae	strain=NRRL B-16468	GCA_009498035.1	103733	103733	type	True	81.396	1367	2153	95	below_threshold
Saccharothrix algeriensis	strain=DSM 44581	GCA_016907655.1	173560	173560	type	True	81.3917	1176	2153	95	below_threshold
Saccharothrix saharensis	strain=DSM 45456	GCA_006716745.1	571190	571190	type	True	81.2953	1316	2153	95	below_threshold
Saccharothrix syringae	strain=NRRL B-16468	GCA_000716755.1	103733	103733	type	True	81.2891	1358	2153	95	below_threshold
Saccharothrix australiensis	strain=DSM 43800	GCA_003634935.1	2072	2072	type	True	81.2391	1186	2153	95	below_threshold
Saccharothrix tamanrassetensis	strain=CECT 8640	GCA_014203665.1	1051531	1051531	type	True	81.1423	1142	2153	95	below_threshold
Saccharothrix deserti	strain=BMP B8144	GCA_009769385.1	2593674	2593674	type	True	81.1355	1288	2153	95	below_threshold
Saccharothrix ecbatanensis	strain=DSM 45486	GCA_014205015.1	1105145	1105145	type	True	80.9484	1206	2153	95	below_threshold
Saccharothrix obliqua	strain=SC076	GCA_019375475.1	2861747	2861747	type	True	80.8552	1134	2153	95	below_threshold
Lentzea tibetensis	strain=FXJ1.1311	GCA_007845675.1	2591470	2591470	type	True	80.6109	1147	2153	95	below_threshold
Lentzea xinjiangensis	strain=CGMCC 4.3525	GCA_900110955.1	402600	402600	type	True	80.483	1189	2153	95	below_threshold
Lentzea flaviverrucosa	strain=DSM 44664	GCA_003350445.1	200379	200379	type	True	80.2371	1099	2153	95	below_threshold
Lentzea flava	strain=DSM 43885	GCA_024171845.1	103732	103732	type	True	80.1681	1096	2153	95	below_threshold
Lentzea flava	strain=JCM 3296	GCA_014648475.1	103732	103732	type	True	80.153	1097	2153	95	below_threshold
Lentzea californiensis	strain=DSM 43393	GCA_024648825.1	438851	438851	type	True	80.1368	1118	2153	95	below_threshold
Lentzea guizhouensis	strain=DHS C013	GCA_001701025.1	1586287	1586287	type	True	80.1257	1219	2153	95	below_threshold
Lentzea cavernae	strain=CGMCC 4.7367	GCA_014653695.1	2020703	2020703	type	True	80.1108	1149	2153	95	below_threshold
Lentzea kentuckyensis	strain=NRRL B-24416	GCA_002150765.1	360086	360086	type	True	80.0971	1049	2153	95	below_threshold
Lentzea aerocolonigenes	strain=DSM 40034	GCA_024171805.1	68170	68170	type	True	80.0774	1113	2153	95	below_threshold
Lentzea waywayandensis	strain=DSM 44232	GCA_900115955.1	84724	84724	type	True	80.0567	1107	2153	95	below_threshold
Lentzea atacamensis	strain=DSM 45479	GCA_003269295.1	531938	531938	type	True	80.0114	1101	2153	95	below_threshold
Lentzea aerocolonigenes	strain=NRRL B-3298	GCA_000719205.1	68170	68170	type	True	80.0005	1122	2153	95	below_threshold
Actinokineospora globicatena	strain=DSM 44256	GCA_024171945.1	103729	103729	type	True	78.9898	864	2153	95	below_threshold
Prauserella cavernicola	strain=ASG 168	GCA_016595675.1	2800127	2800127	type	True	78.4459	805	2153	95	below_threshold
Amycolatopsis camponoti	strain=A23	GCA_902497555.1	2606593	2606593	type	True	78.078	999	2153	95	below_threshold
Amycolatopsis aidingensis	strain=YIM 96748	GCA_018885265.1	2842453	2842453	type	True	77.7692	734	2153	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:54:48,312] [INFO] DFAST Taxonomy check result was written to GCF_016464305.1_ASM1646430v1_genomic.fna/tc_result.tsv
[2024-01-25 18:54:48,313] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:54:48,313] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:54:48,313] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg652dfc55-baab-482f-a2ce-5d659eec2e8d/dqc_reference/checkm_data
[2024-01-25 18:54:48,314] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:54:48,373] [INFO] Task started: CheckM
[2024-01-25 18:54:48,373] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016464305.1_ASM1646430v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016464305.1_ASM1646430v1_genomic.fna/checkm_input GCF_016464305.1_ASM1646430v1_genomic.fna/checkm_result
[2024-01-25 18:57:13,427] [INFO] Task succeeded: CheckM
[2024-01-25 18:57:13,428] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:57:13,449] [INFO] ===== Completeness check finished =====
[2024-01-25 18:57:13,449] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:57:13,450] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016464305.1_ASM1646430v1_genomic.fna/markers.fasta)
[2024-01-25 18:57:13,450] [INFO] Task started: Blastn
[2024-01-25 18:57:13,450] [INFO] Running command: blastn -query GCF_016464305.1_ASM1646430v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg652dfc55-baab-482f-a2ce-5d659eec2e8d/dqc_reference/reference_markers_gtdb.fasta -out GCF_016464305.1_ASM1646430v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:57:15,511] [INFO] Task succeeded: Blastn
[2024-01-25 18:57:15,514] [INFO] Selected 24 target genomes.
[2024-01-25 18:57:15,514] [INFO] Target genome list was writen to GCF_016464305.1_ASM1646430v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:57:15,533] [INFO] Task started: fastANI
[2024-01-25 18:57:15,534] [INFO] Running command: fastANI --query /var/lib/cwl/stg523c1521-783b-4152-8c77-d4b5a50d82d2/GCF_016464305.1_ASM1646430v1_genomic.fna.gz --refList GCF_016464305.1_ASM1646430v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016464305.1_ASM1646430v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:58:02,011] [INFO] Task succeeded: fastANI
[2024-01-25 18:58:02,025] [INFO] Found 24 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:58:02,025] [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_016464305.1	s__REN6 sp016464305	100.0	2151	2153	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__REN6	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014648515.1	s__Actinosynnema coeruleofuscum	81.8444	1316	2153	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	99.37	99.37	0.97	0.97	2	-
GCF_003002815.1	s__Umezawaea tangerina	81.4559	1365	2153	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Umezawaea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003752005.1	s__Actinosynnema texasense	81.4305	1312	2153	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	98.51	98.51	0.92	0.92	2	-
GCF_003014735.1	s__Actinosynnema carneum	81.4078	1265	2153	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	95.10	95.10	0.83	0.83	2	-
GCF_006716745.1	s__Actinosynnema saharense	81.2576	1324	2153	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001280085.1	s__Actinosynnema sp001280085	81.2569	1335	2153	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003634935.1	s__Actinosynnema australiense	81.2254	1188	2153	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000716595.1	s__Actinosynnema sp000716595	81.1483	1220	2153	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000023245.1	s__Actinosynnema mirum	80.9046	1208	2153	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	96.4703	99.51	99.51	0.95	0.95	3	-
GCF_007845675.1	s__Lentzea sp007845675	80.6175	1146	2153	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110955.1	s__Lentzea xinjiangensis	80.4998	1186	2153	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001279525.1	s__Lentzea sp001279525	80.2758	1173	2153	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003350445.1	s__Lentzea flaviverrucosa	80.2043	1105	2153	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014653695.1	s__Lentzea cavernae	80.1076	1151	2153	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008386585.1	s__AN110305 sp008386585	80.0947	1052	2153	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__AN110305	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000974445.1	s__Lentzea aerocolonigenes	80.0839	1117	2153	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	99.99	99.99	1.00	1.00	2	-
GCF_003269295.1	s__Lentzea atacamensis	80.0742	1088	2153	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	98.63	98.63	0.90	0.90	2	-
GCF_014646255.1	s__Lentzea pudingi	79.9892	1122	2153	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000715825.1	s__Goodfellowiella coeruleoviolacea	79.4103	1096	2153	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Goodfellowiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004214935.1	s__Amycolatopsis suaedae	78.3467	881	2153	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000716785.1	s__Amycolatopsis vancoresmycina	78.2022	978	2153	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	99.98	99.98	1.00	1.00	2	-
GCF_000308695.1	s__Nocardia takedensis	76.5136	555	2153	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001310275.1	s__Nocardia arizonensis	76.3908	444	2153	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	99.98	99.98	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-25 18:58:02,027] [INFO] GTDB search result was written to GCF_016464305.1_ASM1646430v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:58:02,027] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:58:02,032] [INFO] DFAST_QC result json was written to GCF_016464305.1_ASM1646430v1_genomic.fna/dqc_result.json
[2024-01-25 18:58:02,033] [INFO] DFAST_QC completed!
[2024-01-25 18:58:02,033] [INFO] Total running time: 0h4m41s