[2024-01-24 15:18:05,087] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:18:05,089] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:18:05,089] [INFO] DQC Reference Directory: /var/lib/cwl/stg49e54924-bb82-4063-a727-ffb55095664c/dqc_reference
[2024-01-24 15:18:07,532] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:18:07,533] [INFO] Task started: Prodigal
[2024-01-24 15:18:07,534] [INFO] Running command: gunzip -c /var/lib/cwl/stg420eb534-d85a-4a54-a36b-f86fa222000b/GCF_003024195.1_ASM302419v1_genomic.fna.gz | prodigal -d GCF_003024195.1_ASM302419v1_genomic.fna/cds.fna -a GCF_003024195.1_ASM302419v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:18:39,812] [INFO] Task succeeded: Prodigal
[2024-01-24 15:18:39,813] [INFO] Task started: HMMsearch
[2024-01-24 15:18:39,813] [INFO] Running command: hmmsearch --tblout GCF_003024195.1_ASM302419v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg49e54924-bb82-4063-a727-ffb55095664c/dqc_reference/reference_markers.hmm GCF_003024195.1_ASM302419v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:18:40,298] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:18:40,300] [INFO] Found 6/6 markers.
[2024-01-24 15:18:40,373] [INFO] Query marker FASTA was written to GCF_003024195.1_ASM302419v1_genomic.fna/markers.fasta
[2024-01-24 15:18:40,374] [INFO] Task started: Blastn
[2024-01-24 15:18:40,374] [INFO] Running command: blastn -query GCF_003024195.1_ASM302419v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg49e54924-bb82-4063-a727-ffb55095664c/dqc_reference/reference_markers.fasta -out GCF_003024195.1_ASM302419v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:18:41,622] [INFO] Task succeeded: Blastn
[2024-01-24 15:18:41,626] [INFO] Selected 23 target genomes.
[2024-01-24 15:18:41,626] [INFO] Target genome list was writen to GCF_003024195.1_ASM302419v1_genomic.fna/target_genomes.txt
[2024-01-24 15:18:41,653] [INFO] Task started: fastANI
[2024-01-24 15:18:41,653] [INFO] Running command: fastANI --query /var/lib/cwl/stg420eb534-d85a-4a54-a36b-f86fa222000b/GCF_003024195.1_ASM302419v1_genomic.fna.gz --refList GCF_003024195.1_ASM302419v1_genomic.fna/target_genomes.txt --output GCF_003024195.1_ASM302419v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:19:31,022] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:31,023] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg49e54924-bb82-4063-a727-ffb55095664c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:19:31,023] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg49e54924-bb82-4063-a727-ffb55095664c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:19:31,046] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 15:19:31,047] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 15:19:31,047] [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 aurantiacus	strain=NRRL ISP-5412	GCA_001418335.1	47760	47760	type	True	89.6789	2035	3388	95	below_threshold
Streptomyces umbrinus	strain=JCM 4521	GCA_014650195.1	67370	67370	type	True	87.8761	2386	3388	95	below_threshold
Streptomyces phaeochromogenes	strain=NRRL B-1248	GCA_001418655.1	1923	1923	type	True	87.741	2132	3388	95	below_threshold
Streptomyces fructofermentans	strain=JCM 4956	GCA_014651055.1	152141	152141	type	True	86.0515	2093	3388	95	below_threshold
Streptomyces scabichelini	strain=HC44	GCA_011045015.1	2711217	2711217	type	True	85.1658	1907	3388	95	below_threshold
Streptomyces avermitilis	strain=DSM 46492	GCA_001514135.1	33903	33903	type	True	84.4758	1888	3388	95	below_threshold
Streptomyces avermitilis	strain=MA-4680	GCA_000009765.2	33903	33903	type	True	84.4635	1890	3388	95	below_threshold
Streptomyces avermitilis	strain=NBRC 14893	GCA_005405965.1	33903	33903	type	True	84.3421	1974	3388	95	below_threshold
Streptomyces avermitilis	strain=MA-4680	GCA_000968255.1	33903	33903	type	True	84.3042	1965	3388	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	83.3762	1646	3388	95	below_threshold
Streptomyces prunicolor	strain=NBRC 13075	GCA_000367365.1	67348	67348	type	True	83.3037	1919	3388	95	below_threshold
Streptomyces indiaensis	strain=DSM 43803	GCA_021474405.1	284033	284033	type	True	83.262	1609	3388	95	below_threshold
Streptomyces cahuitamycinicus	strain=13K301	GCA_002891435.1	2070367	2070367	type	True	83.2427	1471	3388	95	below_threshold
Streptomyces viridiviolaceus	strain=JCM 4855	GCA_014650995.1	68282	68282	type	True	83.0856	1731	3388	95	below_threshold
Streptomyces sennicomposti	strain=RCPT1-4	GCA_019890635.1	2873384	2873384	type	True	82.8161	1507	3388	95	below_threshold
Streptomyces kanamyceticus	strain=NRRL B-2535	GCA_001418465.1	1967	1967	type	True	82.6473	1507	3388	95	below_threshold
Streptomyces kanamyceticus	strain=ATCC 12853	GCA_008704495.1	1967	1967	type	True	82.5632	1726	3388	95	below_threshold
Streptomyces durmitorensis	strain=MS405	GCA_023498005.1	319947	319947	type	True	82.4521	1795	3388	95	below_threshold
Streptomyces xanthii	strain=CRXT-Y-14	GCA_014621695.1	2768069	2768069	type	True	82.3542	1600	3388	95	below_threshold
Streptomyces boluensis	strain=YC537	GCA_009908195.1	1775135	1775135	type	True	82.0432	1343	3388	95	below_threshold
Streptomyces rhizosphaericola	strain=1AS2c	GCA_004794175.1	2564098	2564098	type	True	81.3825	1197	3388	95	below_threshold
Streptomyces cavourensis	strain=DSM 41795	GCA_006788935.1	67258	67258	type	True	81.1378	1403	3388	95	below_threshold
Streptomyces cavourensis	strain=JCM 4298	GCA_014649215.1	67258	67258	type	True	81.0911	1403	3388	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:19:31,049] [INFO] DFAST Taxonomy check result was written to GCF_003024195.1_ASM302419v1_genomic.fna/tc_result.tsv
[2024-01-24 15:19:31,049] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:19:31,049] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:19:31,049] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg49e54924-bb82-4063-a727-ffb55095664c/dqc_reference/checkm_data
[2024-01-24 15:19:31,050] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:19:31,140] [INFO] Task started: CheckM
[2024-01-24 15:19:31,140] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003024195.1_ASM302419v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003024195.1_ASM302419v1_genomic.fna/checkm_input GCF_003024195.1_ASM302419v1_genomic.fna/checkm_result
[2024-01-24 15:21:23,856] [INFO] Task succeeded: CheckM
[2024-01-24 15:21:23,857] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.21%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:21:23,885] [INFO] ===== Completeness check finished =====
[2024-01-24 15:21:23,885] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:21:23,886] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003024195.1_ASM302419v1_genomic.fna/markers.fasta)
[2024-01-24 15:21:23,886] [INFO] Task started: Blastn
[2024-01-24 15:21:23,886] [INFO] Running command: blastn -query GCF_003024195.1_ASM302419v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg49e54924-bb82-4063-a727-ffb55095664c/dqc_reference/reference_markers_gtdb.fasta -out GCF_003024195.1_ASM302419v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:21:25,898] [INFO] Task succeeded: Blastn
[2024-01-24 15:21:25,902] [INFO] Selected 11 target genomes.
[2024-01-24 15:21:25,902] [INFO] Target genome list was writen to GCF_003024195.1_ASM302419v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:21:25,910] [INFO] Task started: fastANI
[2024-01-24 15:21:25,910] [INFO] Running command: fastANI --query /var/lib/cwl/stg420eb534-d85a-4a54-a36b-f86fa222000b/GCF_003024195.1_ASM302419v1_genomic.fna.gz --refList GCF_003024195.1_ASM302419v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003024195.1_ASM302419v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:21:56,567] [INFO] Task succeeded: fastANI
[2024-01-24 15:21:56,584] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:21:56,584] [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_003024195.1	s__Streptomyces dioscori	100.0	3388	3388	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_018070025.1	s__Streptomyces sp018070025	94.5467	2925	3388	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014650955.1	s__Streptomyces tauricus	93.562	2699	3388	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001418335.1	s__Streptomyces aurantiacus	89.6943	2033	3388	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.25	99.25	0.97	0.97	2	-
GCF_008369065.1	s__Streptomyces sp008369065	89.3557	2286	3388	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019090165.1	s__Streptomyces sp019090165	88.9668	2199	3388	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001418655.1	s__Streptomyces phaeochromogenes	87.7282	2135	3388	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.97	95.89	0.88	0.87	3	-
GCF_008905045.1	s__Streptomyces albicerus	87.5276	2232	3388	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014651055.1	s__Streptomyces fructofermentans	86.0653	2090	3388	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002082585.1	s__Streptomyces albolongus	81.0288	1428	3388	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003268675.1	s__Streptomyces bacillaris	81.0115	1443	3388	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.84	95.80	0.88	0.83	37	-
--------------------------------------------------------------------------------
[2024-01-24 15:21:56,586] [INFO] GTDB search result was written to GCF_003024195.1_ASM302419v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:21:56,586] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:21:56,590] [INFO] DFAST_QC result json was written to GCF_003024195.1_ASM302419v1_genomic.fna/dqc_result.json
[2024-01-24 15:21:56,591] [INFO] DFAST_QC completed!
[2024-01-24 15:21:56,591] [INFO] Total running time: 0h3m52s