[2024-01-25 19:47:20,517] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:47:20,519] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:47:20,519] [INFO] DQC Reference Directory: /var/lib/cwl/stga72ec3a2-97e7-48a0-9c2a-a36591ad4b49/dqc_reference
[2024-01-25 19:47:21,690] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:47:21,691] [INFO] Task started: Prodigal
[2024-01-25 19:47:21,691] [INFO] Running command: gunzip -c /var/lib/cwl/stg4ee99d21-f595-4157-b75c-6edf9322e282/GCF_031348265.1_ASM3134826v1_genomic.fna.gz | prodigal -d GCF_031348265.1_ASM3134826v1_genomic.fna/cds.fna -a GCF_031348265.1_ASM3134826v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:47:43,882] [INFO] Task succeeded: Prodigal
[2024-01-25 19:47:43,882] [INFO] Task started: HMMsearch
[2024-01-25 19:47:43,882] [INFO] Running command: hmmsearch --tblout GCF_031348265.1_ASM3134826v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga72ec3a2-97e7-48a0-9c2a-a36591ad4b49/dqc_reference/reference_markers.hmm GCF_031348265.1_ASM3134826v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:47:44,204] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:47:44,205] [INFO] Found 6/6 markers.
[2024-01-25 19:47:44,280] [INFO] Query marker FASTA was written to GCF_031348265.1_ASM3134826v1_genomic.fna/markers.fasta
[2024-01-25 19:47:44,280] [INFO] Task started: Blastn
[2024-01-25 19:47:44,280] [INFO] Running command: blastn -query GCF_031348265.1_ASM3134826v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga72ec3a2-97e7-48a0-9c2a-a36591ad4b49/dqc_reference/reference_markers.fasta -out GCF_031348265.1_ASM3134826v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:47:45,530] [INFO] Task succeeded: Blastn
[2024-01-25 19:47:45,533] [INFO] Selected 17 target genomes.
[2024-01-25 19:47:45,534] [INFO] Target genome list was writen to GCF_031348265.1_ASM3134826v1_genomic.fna/target_genomes.txt
[2024-01-25 19:47:45,536] [INFO] Task started: fastANI
[2024-01-25 19:47:45,536] [INFO] Running command: fastANI --query /var/lib/cwl/stg4ee99d21-f595-4157-b75c-6edf9322e282/GCF_031348265.1_ASM3134826v1_genomic.fna.gz --refList GCF_031348265.1_ASM3134826v1_genomic.fna/target_genomes.txt --output GCF_031348265.1_ASM3134826v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:48:23,221] [INFO] Task succeeded: fastANI
[2024-01-25 19:48:23,222] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga72ec3a2-97e7-48a0-9c2a-a36591ad4b49/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:48:23,223] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga72ec3a2-97e7-48a0-9c2a-a36591ad4b49/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:48:23,235] [INFO] Found 17 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 19:48:23,235] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-25 19:48:23,235] [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 violaceochromogenes	strain=JCM 4530	GCA_014650235.1	67377	67377	type	True	99.3598	2761	2955	95	inconclusive
Streptomyces iakyrus	strain=NRRL ISP-5482	GCA_000717055.1	68219	68219	type	True	95.3159	2362	2955	95	inconclusive
Streptomyces cahuitamycinicus	strain=13K301	GCA_002891435.1	2070367	2070367	type	True	93.7526	1921	2955	95	below_threshold
Streptomyces hawaiiensis	strain=ATCC 12236	GCA_004803895.1	67305	67305	type	True	93.2121	2349	2955	95	below_threshold
Streptomyces massasporeus	strain=JCM 4139	GCA_014648995.1	67324	67324	type	True	93.1546	2400	2955	95	below_threshold
Streptomyces flavovariabilis	strain=NRRL B-16367	GCA_000725785.1	284031	284031	type	True	93.0666	2344	2955	95	below_threshold
Streptomyces luteogriseus	strain=DSM 40483	GCA_014205055.1	68233	68233	type	True	92.9245	2381	2955	95	below_threshold
Streptomyces tuirus	strain=JCM 4255	GCA_014701095.1	68278	68278	type	True	92.9033	2167	2955	95	below_threshold
Streptomyces tibetensis	strain=XZ 46	GCA_005869865.1	2382123	2382123	type	True	92.4328	2343	2955	95	below_threshold
Streptomyces tibetensis	strain=XZ 46	GCA_007655005.1	2382123	2382123	type	True	92.4242	2344	2955	95	below_threshold
Streptomyces indiaensis	strain=DSM 43803	GCA_021474405.1	284033	284033	type	True	91.8895	2049	2955	95	below_threshold
Streptomyces lomondensis	strain=DSM 41428	GCA_021440105.1	68229	68229	type	True	90.9698	2217	2955	95	below_threshold
Streptomyces purpurascens	strain=DSM 40310	GCA_021390235.1	1924	1924	type	True	90.8184	2280	2955	95	below_threshold
Streptomyces resistomycificus	strain=DSM 40133	GCA_001514265.1	67356	67356	type	True	85.7702	2080	2955	95	below_threshold
Streptomyces resistomycificus	strain=NRRL ISP-5133	GCA_000716215.1	67356	67356	type	True	85.764	2060	2955	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	85.2832	1516	2955	95	below_threshold
Streptomyces kebangsaanensis	strain=SUK12	GCA_001906585.1	864058	864058	type	True	84.9787	1605	2955	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:48:23,237] [INFO] DFAST Taxonomy check result was written to GCF_031348265.1_ASM3134826v1_genomic.fna/tc_result.tsv
[2024-01-25 19:48:23,237] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:48:23,237] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:48:23,237] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga72ec3a2-97e7-48a0-9c2a-a36591ad4b49/dqc_reference/checkm_data
[2024-01-25 19:48:23,240] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:48:23,326] [INFO] Task started: CheckM
[2024-01-25 19:48:23,326] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_031348265.1_ASM3134826v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_031348265.1_ASM3134826v1_genomic.fna/checkm_input GCF_031348265.1_ASM3134826v1_genomic.fna/checkm_result
[2024-01-25 19:51:29,735] [INFO] Task succeeded: CheckM
[2024-01-25 19:51:29,736] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:51:29,763] [INFO] ===== Completeness check finished =====
[2024-01-25 19:51:29,764] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:51:29,764] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_031348265.1_ASM3134826v1_genomic.fna/markers.fasta)
[2024-01-25 19:51:29,765] [INFO] Task started: Blastn
[2024-01-25 19:51:29,765] [INFO] Running command: blastn -query GCF_031348265.1_ASM3134826v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga72ec3a2-97e7-48a0-9c2a-a36591ad4b49/dqc_reference/reference_markers_gtdb.fasta -out GCF_031348265.1_ASM3134826v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:51:31,808] [INFO] Task succeeded: Blastn
[2024-01-25 19:51:31,811] [INFO] Selected 10 target genomes.
[2024-01-25 19:51:31,811] [INFO] Target genome list was writen to GCF_031348265.1_ASM3134826v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:51:31,824] [INFO] Task started: fastANI
[2024-01-25 19:51:31,825] [INFO] Running command: fastANI --query /var/lib/cwl/stg4ee99d21-f595-4157-b75c-6edf9322e282/GCF_031348265.1_ASM3134826v1_genomic.fna.gz --refList GCF_031348265.1_ASM3134826v1_genomic.fna/target_genomes_gtdb.txt --output GCF_031348265.1_ASM3134826v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:51:56,258] [INFO] Task succeeded: fastANI
[2024-01-25 19:51:56,266] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:51:56,266] [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_014204745.1	s__Streptomyces collinus	99.9992	2948	2955	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.3776	99.36	99.36	0.94	0.94	2	conclusive
GCF_000717055.1	s__Streptomyces iakyrus	95.3512	2358	2955	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.3776	96.00	95.60	0.85	0.85	3	-
GCF_001611795.1	s__Streptomyces qaidamensis	95.2921	2467	2955	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.3368	N/A	N/A	N/A	N/A	1	-
GCF_014202475.1	s__Streptomyces paradoxus	94.7906	2456	2955	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004803895.1	s__Streptomyces hawaiiensis	93.2223	2347	2955	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.39	95.39	0.84	0.84	3	-
GCF_014648995.1	s__Streptomyces massasporeus	93.1483	2401	2955	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.09	95.23	0.86	0.83	4	-
GCF_014205055.1	s__Streptomyces luteogriseus	92.902	2384	2955	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.10	95.50	0.87	0.84	3	-
GCF_007655005.1	s__Streptomyces tibetensis	92.4088	2346	2955	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	100.00	100.00	1.00	1.00	3	-
GCF_014649375.1	s__Streptomyces aurantiogriseus	85.5948	2070	2955	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004187715.1	s__Streptomyces sp004187715	85.5755	1874	2955	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:51:56,267] [INFO] GTDB search result was written to GCF_031348265.1_ASM3134826v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:51:56,268] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:51:56,271] [INFO] DFAST_QC result json was written to GCF_031348265.1_ASM3134826v1_genomic.fna/dqc_result.json
[2024-01-25 19:51:56,271] [INFO] DFAST_QC completed!
[2024-01-25 19:51:56,271] [INFO] Total running time: 0h4m36s