[2024-01-24 10:57:38,494] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:57:38,495] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:57:38,496] [INFO] DQC Reference Directory: /var/lib/cwl/stg2cb84c1f-0ec4-4c9d-83d2-811d3ad1b786/dqc_reference
[2024-01-24 10:57:39,935] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:57:39,936] [INFO] Task started: Prodigal
[2024-01-24 10:57:39,936] [INFO] Running command: gunzip -c /var/lib/cwl/stg95c79cb1-0e8f-4d4b-b182-09774002a3fa/GCF_014295035.1_ASM1429503v1_genomic.fna.gz | prodigal -d GCF_014295035.1_ASM1429503v1_genomic.fna/cds.fna -a GCF_014295035.1_ASM1429503v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:58:10,542] [INFO] Task succeeded: Prodigal
[2024-01-24 10:58:10,543] [INFO] Task started: HMMsearch
[2024-01-24 10:58:10,543] [INFO] Running command: hmmsearch --tblout GCF_014295035.1_ASM1429503v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2cb84c1f-0ec4-4c9d-83d2-811d3ad1b786/dqc_reference/reference_markers.hmm GCF_014295035.1_ASM1429503v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:58:10,914] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:58:10,916] [INFO] Found 6/6 markers.
[2024-01-24 10:58:10,973] [INFO] Query marker FASTA was written to GCF_014295035.1_ASM1429503v1_genomic.fna/markers.fasta
[2024-01-24 10:58:10,974] [INFO] Task started: Blastn
[2024-01-24 10:58:10,974] [INFO] Running command: blastn -query GCF_014295035.1_ASM1429503v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2cb84c1f-0ec4-4c9d-83d2-811d3ad1b786/dqc_reference/reference_markers.fasta -out GCF_014295035.1_ASM1429503v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:12,455] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:12,458] [INFO] Selected 29 target genomes.
[2024-01-24 10:58:12,459] [INFO] Target genome list was writen to GCF_014295035.1_ASM1429503v1_genomic.fna/target_genomes.txt
[2024-01-24 10:58:12,466] [INFO] Task started: fastANI
[2024-01-24 10:58:12,466] [INFO] Running command: fastANI --query /var/lib/cwl/stg95c79cb1-0e8f-4d4b-b182-09774002a3fa/GCF_014295035.1_ASM1429503v1_genomic.fna.gz --refList GCF_014295035.1_ASM1429503v1_genomic.fna/target_genomes.txt --output GCF_014295035.1_ASM1429503v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:59:11,090] [INFO] Task succeeded: fastANI
[2024-01-24 10:59:11,090] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2cb84c1f-0ec4-4c9d-83d2-811d3ad1b786/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:59:11,091] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2cb84c1f-0ec4-4c9d-83d2-811d3ad1b786/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:59:11,111] [INFO] Found 29 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:59:11,111] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:59:11,111] [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 buecherae	strain=AC541	GCA_014295035.1	2763006	2763006	type	True	100.0	2804	2805	95	conclusive
Streptomyces zagrosensis	strain=CECT 8305	GCA_014203645.1	1042984	1042984	type	True	84.8304	1986	2805	95	below_threshold
Streptomyces pactum	strain=ATCC 27456	GCA_016031615.1	68249	68249	type	True	81.4536	1515	2805	95	below_threshold
Streptomyces netropsis	strain=JCM 4063	GCA_014648835.1	55404	55404	type	True	81.2306	1324	2805	95	below_threshold
Streptomyces chrestomyceticus	strain=NBRC 13444	GCA_003865135.1	68185	68185	type	True	81.2211	1446	2805	95	below_threshold
Streptomyces netropsis	strain=CECT 3265	GCA_014203545.1	55404	55404	type	True	81.2048	1327	2805	95	below_threshold
Streptomyces rimosus subsp. rimosus	strain=R7	GCA_022760195.1	132474	1927	type	True	81.202	1423	2805	95	below_threshold
Streptomyces antimycoticus	strain=NBRC 12839	GCA_005405925.1	68175	68175	type	True	81.1953	1490	2805	95	below_threshold
Streptomyces rimosus subsp. rimosus	strain=NRRL ISP-5260	GCA_000717285.1	132474	1927	type	True	81.1616	1393	2805	95	below_threshold
Streptomyces albofaciens	strain=ATCC 23873	GCA_008634025.1	66866	66866	type	True	81.1388	1446	2805	95	below_threshold
Streptomyces mashuensis	strain=JCM 4059	GCA_014654785.1	33904	33904	type	True	81.097	1246	2805	95	below_threshold
Streptomyces benahoarensis	strain=MZ03-37	GCA_007280575.1	2595054	2595054	type	True	81.0828	1032	2805	95	below_threshold
Streptomyces albospinus	strain=JCM 3399	GCA_014648695.1	285515	285515	type	True	81.0015	1239	2805	95	below_threshold
Streptomyces mobaraensis	strain=DSM 40847	GCA_017916255.1	35621	35621	type	True	80.7974	1318	2805	95	below_threshold
Streptomyces mobaraensis	strain=DSM 40847	GCA_000342125.1	35621	35621	type	True	80.792	1236	2805	95	below_threshold
Streptomyces huiliensis	strain=SCA2-4	GCA_020037025.1	2876027	2876027	type	True	80.7414	1194	2805	95	below_threshold
Streptomyces lichenis	strain=LCR6-01	GCA_023218175.1	2306967	2306967	type	True	80.7329	1190	2805	95	below_threshold
Streptomyces melanogenes	strain=JCM 4398	GCA_014649795.1	67326	67326	type	True	80.658	1292	2805	95	below_threshold
Streptomyces violascens	strain=NBRC 12920	GCA_020521295.1	67381	67381	type	True	80.6479	1217	2805	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	80.5014	1182	2805	95	below_threshold
Streptomyces durbertensis	strain=DSM 104538	GCA_014156695.1	2448886	2448886	type	True	80.3309	872	2805	95	below_threshold
Streptomyces durmitorensis	strain=MS405	GCA_023498005.1	319947	319947	type	True	80.3079	1299	2805	95	below_threshold
Streptomyces roseolilacinus	strain=JCM 4335	GCA_014649335.1	66904	66904	type	True	80.2827	1208	2805	95	below_threshold
Streptomyces spinosus	strain=SBTS01	GCA_020400655.1	2872623	2872623	type	True	80.1689	1290	2805	95	below_threshold
Actinacidiphila glaucinigra	strain=CGMCC 4.1858	GCA_900188405.1	235986	235986	type	True	80.0479	1226	2805	95	below_threshold
Streptomyces goshikiensis	strain=JCM 4640	GCA_014650555.1	1942	1942	type	True	79.9293	1254	2805	95	below_threshold
Streptomyces cyaneus	strain=CGMCC 4.1671	GCA_004028635.1	1904	1904	type	True	79.8391	1221	2805	95	below_threshold
Streptomyces aurantiacus	strain=NRRL ISP-5412	GCA_001418335.1	47760	47760	type	True	79.8368	1093	2805	95	below_threshold
Streptomyces panaciradicis	strain=NBRC 109811	GCA_023516615.1	1470261	1470261	type	True	79.822	1240	2805	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:59:11,113] [INFO] DFAST Taxonomy check result was written to GCF_014295035.1_ASM1429503v1_genomic.fna/tc_result.tsv
[2024-01-24 10:59:11,113] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:59:11,114] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:59:11,114] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2cb84c1f-0ec4-4c9d-83d2-811d3ad1b786/dqc_reference/checkm_data
[2024-01-24 10:59:11,115] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:59:11,189] [INFO] Task started: CheckM
[2024-01-24 10:59:11,189] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014295035.1_ASM1429503v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014295035.1_ASM1429503v1_genomic.fna/checkm_input GCF_014295035.1_ASM1429503v1_genomic.fna/checkm_result
[2024-01-24 11:01:12,463] [INFO] Task succeeded: CheckM
[2024-01-24 11:01:12,465] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:01:12,488] [INFO] ===== Completeness check finished =====
[2024-01-24 11:01:12,488] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:01:12,489] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014295035.1_ASM1429503v1_genomic.fna/markers.fasta)
[2024-01-24 11:01:12,489] [INFO] Task started: Blastn
[2024-01-24 11:01:12,489] [INFO] Running command: blastn -query GCF_014295035.1_ASM1429503v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2cb84c1f-0ec4-4c9d-83d2-811d3ad1b786/dqc_reference/reference_markers_gtdb.fasta -out GCF_014295035.1_ASM1429503v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:01:14,941] [INFO] Task succeeded: Blastn
[2024-01-24 11:01:14,945] [INFO] Selected 20 target genomes.
[2024-01-24 11:01:14,946] [INFO] Target genome list was writen to GCF_014295035.1_ASM1429503v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:01:14,976] [INFO] Task started: fastANI
[2024-01-24 11:01:14,976] [INFO] Running command: fastANI --query /var/lib/cwl/stg95c79cb1-0e8f-4d4b-b182-09774002a3fa/GCF_014295035.1_ASM1429503v1_genomic.fna.gz --refList GCF_014295035.1_ASM1429503v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014295035.1_ASM1429503v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:01:56,362] [INFO] Task succeeded: fastANI
[2024-01-24 11:01:56,384] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:01:56,385] [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_014295035.1	s__Streptomyces buecherae	100.0	2804	2805	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.71	96.93	0.96	0.94	7	conclusive
GCA_018114805.1	s__Streptomyces philanthi	93.8466	2153	2805	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014203645.1	s__Streptomyces zagrosensis	84.8621	1980	2805	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007595705.1	s__Streptomyces sp007595705	81.7505	1431	2805	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001417735.1	s__Streptomyces sp001417735	81.4903	1349	2805	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016031615.1	s__Streptomyces pactum	81.4421	1519	2805	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	81.3952	1298	2805	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.60	99.60	0.98	0.98	2	-
GCF_014203545.1	s__Streptomyces netropsis	81.1838	1330	2805	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.99	99.99	1.00	1.00	2	-
GCF_008634025.1	s__Streptomyces albofaciens	81.1242	1454	2805	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000373585.1	s__Streptomyces sp000373585	80.9803	1267	2805	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014648695.1	s__Streptomyces albospinus	80.96	1247	2805	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013055795.1	s__Streptomyces sp013055795	80.9141	1205	2805	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009769735.1	s__Streptomyces sp009769735	80.2617	1285	2805	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002941025.1	s__Streptomyces sp002941025	80.1863	1201	2805	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014646115.1	s__Streptomyces camponoticapitis	80.0239	1196	2805	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188405.1	s__Streptomyces glauciniger	80.0093	1234	2805	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.09	95.09	0.86	0.86	3	-
GCF_014650555.1	s__Streptomyces goshikiensis	79.9413	1252	2805	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.27	96.91	0.89	0.81	10	-
GCF_004028635.1	s__Streptomyces cyaneus	79.8409	1221	2805	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900103585.1	s__Streptomyces sp900103585	79.7779	1254	2805	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008905045.1	s__Streptomyces albicerus	79.734	1274	2805	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:01:56,386] [INFO] GTDB search result was written to GCF_014295035.1_ASM1429503v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:01:56,387] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:01:56,392] [INFO] DFAST_QC result json was written to GCF_014295035.1_ASM1429503v1_genomic.fna/dqc_result.json
[2024-01-24 11:01:56,392] [INFO] DFAST_QC completed!
[2024-01-24 11:01:56,392] [INFO] Total running time: 0h4m18s