[2024-01-24 10:57:07,018] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:57:07,022] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:57:07,022] [INFO] DQC Reference Directory: /var/lib/cwl/stg606a0325-b61e-4ee3-9a81-e1ecc4b20602/dqc_reference
[2024-01-24 10:57:08,247] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:57:08,248] [INFO] Task started: Prodigal
[2024-01-24 10:57:08,248] [INFO] Running command: gunzip -c /var/lib/cwl/stgc322f526-4d3a-434c-9def-172e11743e60/GCF_014650495.1_ASM1465049v1_genomic.fna.gz | prodigal -d GCF_014650495.1_ASM1465049v1_genomic.fna/cds.fna -a GCF_014650495.1_ASM1465049v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:57:28,521] [INFO] Task succeeded: Prodigal
[2024-01-24 10:57:28,522] [INFO] Task started: HMMsearch
[2024-01-24 10:57:28,522] [INFO] Running command: hmmsearch --tblout GCF_014650495.1_ASM1465049v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg606a0325-b61e-4ee3-9a81-e1ecc4b20602/dqc_reference/reference_markers.hmm GCF_014650495.1_ASM1465049v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:57:28,853] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:57:28,855] [INFO] Found 6/6 markers.
[2024-01-24 10:57:28,908] [INFO] Query marker FASTA was written to GCF_014650495.1_ASM1465049v1_genomic.fna/markers.fasta
[2024-01-24 10:57:28,908] [INFO] Task started: Blastn
[2024-01-24 10:57:28,908] [INFO] Running command: blastn -query GCF_014650495.1_ASM1465049v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg606a0325-b61e-4ee3-9a81-e1ecc4b20602/dqc_reference/reference_markers.fasta -out GCF_014650495.1_ASM1465049v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:57:30,217] [INFO] Task succeeded: Blastn
[2024-01-24 10:57:30,221] [INFO] Selected 23 target genomes.
[2024-01-24 10:57:30,221] [INFO] Target genome list was writen to GCF_014650495.1_ASM1465049v1_genomic.fna/target_genomes.txt
[2024-01-24 10:57:30,230] [INFO] Task started: fastANI
[2024-01-24 10:57:30,230] [INFO] Running command: fastANI --query /var/lib/cwl/stgc322f526-4d3a-434c-9def-172e11743e60/GCF_014650495.1_ASM1465049v1_genomic.fna.gz --refList GCF_014650495.1_ASM1465049v1_genomic.fna/target_genomes.txt --output GCF_014650495.1_ASM1465049v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:58:07,855] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:07,856] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg606a0325-b61e-4ee3-9a81-e1ecc4b20602/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:58:07,856] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg606a0325-b61e-4ee3-9a81-e1ecc4b20602/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:58:07,884] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 10:58:07,884] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 10:58:07,884] [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
Streptomyces griseocarneus	strain=CGMCC4.1088	GCA_020093395.1	51201	51201	type	True	87.7515	1689	2329	95	below_threshold
Streptomyces griseocarneus	strain=JCM 4580	GCA_014655595.1	51201	51201	type	True	87.7486	1688	2329	95	below_threshold
Streptomyces olivoverticillatus	strain=CECT 3266	GCA_014203555.1	66427	66427	type	True	86.8728	1408	2329	95	below_threshold
Streptomyces abikoensis	strain=JCM 4002	GCA_014648775.1	97398	97398	type	True	86.7108	1604	2329	95	below_threshold
Streptomyces netropsis	strain=JCM 4063	GCA_014648835.1	55404	55404	type	True	85.4488	1601	2329	95	below_threshold
Streptomyces netropsis	strain=CECT 3265	GCA_014203545.1	55404	55404	type	True	85.3804	1641	2329	95	below_threshold
Streptomyces roseifaciens	strain=MBT76	GCA_001445655.1	1488406	1488406	type	True	85.3265	1630	2329	95	below_threshold
Streptomyces eurocidicus	strain=NRRL ISP-5604	GCA_015475845.1	66423	66423	type	True	85.149	1552	2329	95	below_threshold
Streptomyces eurocidicus	strain=ATCC 27428	GCA_002891295.1	66423	66423	type	True	85.1383	1552	2329	95	below_threshold
Streptomyces syringium	strain=DSM 41480	GCA_017876625.1	76729	76729	type	True	85.0726	1626	2329	95	below_threshold
Streptomyces albireticuli	strain=NRRL B-1670	GCA_002286695.1	1940	1940	type	True	85.0562	1410	2329	95	below_threshold
Streptomyces albireticuli	strain=NRRL B1670	GCA_021228125.1	1940	1940	type	True	84.9339	1594	2329	95	below_threshold
Streptomyces caatingaensis	strain=CMAA 1322	GCA_001187435.1	1678637	1678637	type	True	84.2803	1387	2329	95	below_threshold
Streptomyces mobaraensis	strain=DSM 40847	GCA_000342125.1	35621	35621	type	True	83.9902	1372	2329	95	below_threshold
Streptomyces mobaraensis	strain=DSM 40847	GCA_017916255.1	35621	35621	type	True	83.9857	1457	2329	95	below_threshold
Streptomyces huiliensis	strain=SCA2-4	GCA_020037025.1	2876027	2876027	type	True	83.9255	1344	2329	95	below_threshold
Streptomyces rapamycinicus	strain=NRRL 5491	GCA_024298965.1	1226757	1226757	type	True	81.324	1336	2329	95	below_threshold
Streptomyces panaciradicis	strain=NBRC 109811	GCA_023516615.1	1470261	1470261	type	True	80.9693	1182	2329	95	below_threshold
Oceanithermus profundus	strain=DSM 14977	GCA_000183745.1	187137	187137	type	True	74.8835	128	2329	95	below_threshold
Hymenobacter actinosclerus	strain=DSM 15310	GCA_900111515.1	82805	82805	type	True	74.8379	93	2329	95	below_threshold
Hymenobacter aerophilus	strain=DSM 13606	GCA_000382225.1	119644	119644	type	True	74.7812	91	2329	95	below_threshold
Hymenobacter lapidiphilus	strain=P5342	GCA_013377885.1	2608003	2608003	type	True	74.6979	65	2329	95	below_threshold
Hymenobacter piscis	strain=NST-14	GCA_018760735.1	2839984	2839984	type	True	74.6627	103	2329	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:58:07,886] [INFO] DFAST Taxonomy check result was written to GCF_014650495.1_ASM1465049v1_genomic.fna/tc_result.tsv
[2024-01-24 10:58:07,886] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:58:07,886] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:58:07,887] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg606a0325-b61e-4ee3-9a81-e1ecc4b20602/dqc_reference/checkm_data
[2024-01-24 10:58:07,888] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:58:07,953] [INFO] Task started: CheckM
[2024-01-24 10:58:07,953] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014650495.1_ASM1465049v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014650495.1_ASM1465049v1_genomic.fna/checkm_input GCF_014650495.1_ASM1465049v1_genomic.fna/checkm_result
[2024-01-24 10:59:39,856] [INFO] Task succeeded: CheckM
[2024-01-24 10:59:39,857] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 17.71%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:59:39,881] [INFO] ===== Completeness check finished =====
[2024-01-24 10:59:39,881] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:59:39,881] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014650495.1_ASM1465049v1_genomic.fna/markers.fasta)
[2024-01-24 10:59:39,882] [INFO] Task started: Blastn
[2024-01-24 10:59:39,882] [INFO] Running command: blastn -query GCF_014650495.1_ASM1465049v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg606a0325-b61e-4ee3-9a81-e1ecc4b20602/dqc_reference/reference_markers_gtdb.fasta -out GCF_014650495.1_ASM1465049v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:59:42,005] [INFO] Task succeeded: Blastn
[2024-01-24 10:59:42,009] [INFO] Selected 15 target genomes.
[2024-01-24 10:59:42,009] [INFO] Target genome list was writen to GCF_014650495.1_ASM1465049v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:59:42,020] [INFO] Task started: fastANI
[2024-01-24 10:59:42,020] [INFO] Running command: fastANI --query /var/lib/cwl/stgc322f526-4d3a-434c-9def-172e11743e60/GCF_014650495.1_ASM1465049v1_genomic.fna.gz --refList GCF_014650495.1_ASM1465049v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014650495.1_ASM1465049v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:00:08,209] [INFO] Task succeeded: fastANI
[2024-01-24 11:00:08,226] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:00:08,226] [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_014650495.1	s__Streptomyces cinnamoneus	100.0	2325	2329	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014655595.1	s__Streptomyces griseocarneus	87.7206	1692	2329	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017349075.1	s__Streptomyces triculaminicus_A	87.5081	1699	2329	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.73	99.73	0.98	0.98	3	-
GCF_002939475.1	s__Streptomyces cinnamoneus_A	87.0331	1595	2329	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.99	99.99	0.99	0.99	2	-
GCF_014203555.1	s__Streptomyces olivoverticillatus	86.8622	1409	2329	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648775.1	s__Streptomyces abikoensis	86.6891	1606	2329	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.57	96.57	0.89	0.89	2	-
GCF_014203545.1	s__Streptomyces netropsis	85.4293	1633	2329	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.99	99.99	1.00	1.00	2	-
GCF_003391135.1	s__Streptomyces olivoreticuli	85.1046	1514	2329	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017876625.1	s__Streptomyces syringium	85.046	1630	2329	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.60	99.60	0.98	0.98	2	-
GCF_017916255.1	s__Streptomyces mobaraensis	84.0007	1454	2329	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.59	99.19	0.96	0.92	3	-
GCF_014253015.1	s__Streptomyces sp014253015	83.9351	1421	2329	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001905905.1	s__Streptomyces sp001905905	81.2556	1141	2329	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.31	99.31	0.95	0.95	2	-
GCF_014084125.1	s__Streptacidiphilus sp014084125	79.2997	945	2329	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptacidiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001917585.1	s__40CM-68-15 sp001917585	74.8728	130	2329	d__Bacteria;p__Methylomirabilota;c__Methylomirabilia;o__Rokubacteriales;f__CSP1-6;g__40CM-68-15	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903897935.1	s__CAIUDO01 sp903897935	74.7521	200	2329	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__GCA-2862545;g__CAIUDO01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:00:08,228] [INFO] GTDB search result was written to GCF_014650495.1_ASM1465049v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:00:08,228] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:00:08,232] [INFO] DFAST_QC result json was written to GCF_014650495.1_ASM1465049v1_genomic.fna/dqc_result.json
[2024-01-24 11:00:08,233] [INFO] DFAST_QC completed!
[2024-01-24 11:00:08,233] [INFO] Total running time: 0h3m1s