[2024-01-24 11:34:41,258] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:34:41,262] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:34:41,263] [INFO] DQC Reference Directory: /var/lib/cwl/stgaef99290-8e71-4975-b7f7-79d3d486794f/dqc_reference
[2024-01-24 11:34:42,628] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:34:42,629] [INFO] Task started: Prodigal
[2024-01-24 11:34:42,629] [INFO] Running command: gunzip -c /var/lib/cwl/stgf8515d64-d1f6-4d8d-92f5-ce8e327fa244/GCF_000830005.1_ASM83000v1_genomic.fna.gz | prodigal -d GCF_000830005.1_ASM83000v1_genomic.fna/cds.fna -a GCF_000830005.1_ASM83000v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:35:08,290] [INFO] Task succeeded: Prodigal
[2024-01-24 11:35:08,290] [INFO] Task started: HMMsearch
[2024-01-24 11:35:08,290] [INFO] Running command: hmmsearch --tblout GCF_000830005.1_ASM83000v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaef99290-8e71-4975-b7f7-79d3d486794f/dqc_reference/reference_markers.hmm GCF_000830005.1_ASM83000v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:35:08,727] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:35:08,728] [INFO] Found 6/6 markers.
[2024-01-24 11:35:08,793] [INFO] Query marker FASTA was written to GCF_000830005.1_ASM83000v1_genomic.fna/markers.fasta
[2024-01-24 11:35:08,793] [INFO] Task started: Blastn
[2024-01-24 11:35:08,793] [INFO] Running command: blastn -query GCF_000830005.1_ASM83000v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaef99290-8e71-4975-b7f7-79d3d486794f/dqc_reference/reference_markers.fasta -out GCF_000830005.1_ASM83000v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:10,284] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:10,288] [INFO] Selected 18 target genomes.
[2024-01-24 11:35:10,289] [INFO] Target genome list was writen to GCF_000830005.1_ASM83000v1_genomic.fna/target_genomes.txt
[2024-01-24 11:35:10,295] [INFO] Task started: fastANI
[2024-01-24 11:35:10,295] [INFO] Running command: fastANI --query /var/lib/cwl/stgf8515d64-d1f6-4d8d-92f5-ce8e327fa244/GCF_000830005.1_ASM83000v1_genomic.fna.gz --refList GCF_000830005.1_ASM83000v1_genomic.fna/target_genomes.txt --output GCF_000830005.1_ASM83000v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:52,605] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:52,605] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaef99290-8e71-4975-b7f7-79d3d486794f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:52,606] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaef99290-8e71-4975-b7f7-79d3d486794f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:52,619] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:35:52,619] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:35:52,620] [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 vietnamensis	strain=GIM4.0001	GCA_000830005.1	362257	362257	type	True	100.0	3048	3050	95	conclusive
Streptomyces nymphaeiformis	strain=SFB5A	GCA_014203895.1	2663842	2663842	type	True	92.6366	2292	3050	95	below_threshold
Streptomyces tanashiensis	strain=JCM 4086	GCA_014648895.1	67367	67367	type	True	92.609	2210	3050	95	below_threshold
Streptomyces nashvillensis	strain=JCM 4498	GCA_014650095.1	67334	67334	type	True	92.5838	2179	3050	95	below_threshold
Streptomyces litmocidini	strain=JCM 4394	GCA_014649755.1	67318	67318	type	True	92.2173	2098	3050	95	below_threshold
Streptomyces venezuelae	strain=ATCC 10712	GCA_021432215.1	54571	54571	type	True	89.3181	1560	3050	95	below_threshold
Streptomyces cinereoruber	strain=JCM4205	GCA_019880525.1	67260	67260	type	True	89.2729	1787	3050	95	below_threshold
Streptomyces cinereoruber	strain=JCM 4205	GCA_014649095.1	67260	67260	type	True	89.2208	1758	3050	95	below_threshold
Streptomyces omiyaensis	strain=JCM 4806	GCA_014650895.1	68247	68247	type	True	86.7384	1871	3050	95	below_threshold
Streptomyces genisteinicus	strain=CRPJ-33	GCA_014489615.1	2768068	2768068	type	True	82.7329	1515	3050	95	below_threshold
Streptomyces lichenis	strain=LCR6-01	GCA_023218175.1	2306967	2306967	type	True	82.5384	1405	3050	95	below_threshold
Streptomyces subrutilus	strain=ATCC 27467	GCA_008704535.1	36818	36818	type	True	82.4036	1503	3050	95	below_threshold
Streptomyces subrutilus	strain=JCM 4834	GCA_014650935.1	36818	36818	type	True	82.2716	1495	3050	95	below_threshold
Streptomyces sennicomposti	strain=RCPT1-4	GCA_019890635.1	2873384	2873384	type	True	81.8944	1359	3050	95	below_threshold
Streptomyces viridiviolaceus	strain=JCM 4855	GCA_014650995.1	68282	68282	type	True	81.7986	1477	3050	95	below_threshold
Streptomyces griseostramineus	strain=JCM 4385	GCA_014649635.1	66898	66898	suspected-type	True	81.704	1437	3050	95	below_threshold
Streptomyces justiciae	strain=3R004	GCA_015163075.1	2780140	2780140	type	True	81.657	1558	3050	95	below_threshold
Streptomyces griseostramineus	strain=CECT 3273	GCA_014203535.1	66898	66898	suspected-type	True	81.5753	1465	3050	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:35:52,622] [INFO] DFAST Taxonomy check result was written to GCF_000830005.1_ASM83000v1_genomic.fna/tc_result.tsv
[2024-01-24 11:35:52,622] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:52,622] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:52,622] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaef99290-8e71-4975-b7f7-79d3d486794f/dqc_reference/checkm_data
[2024-01-24 11:35:52,624] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:35:52,704] [INFO] Task started: CheckM
[2024-01-24 11:35:52,704] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000830005.1_ASM83000v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000830005.1_ASM83000v1_genomic.fna/checkm_input GCF_000830005.1_ASM83000v1_genomic.fna/checkm_result
[2024-01-24 11:38:13,738] [INFO] Task succeeded: CheckM
[2024-01-24 11:38:13,739] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:38:13,765] [INFO] ===== Completeness check finished =====
[2024-01-24 11:38:13,765] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:38:13,765] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000830005.1_ASM83000v1_genomic.fna/markers.fasta)
[2024-01-24 11:38:13,765] [INFO] Task started: Blastn
[2024-01-24 11:38:13,765] [INFO] Running command: blastn -query GCF_000830005.1_ASM83000v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaef99290-8e71-4975-b7f7-79d3d486794f/dqc_reference/reference_markers_gtdb.fasta -out GCF_000830005.1_ASM83000v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:38:15,989] [INFO] Task succeeded: Blastn
[2024-01-24 11:38:15,992] [INFO] Selected 15 target genomes.
[2024-01-24 11:38:15,992] [INFO] Target genome list was writen to GCF_000830005.1_ASM83000v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:38:16,035] [INFO] Task started: fastANI
[2024-01-24 11:38:16,035] [INFO] Running command: fastANI --query /var/lib/cwl/stgf8515d64-d1f6-4d8d-92f5-ce8e327fa244/GCF_000830005.1_ASM83000v1_genomic.fna.gz --refList GCF_000830005.1_ASM83000v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000830005.1_ASM83000v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:38:50,851] [INFO] Task succeeded: fastANI
[2024-01-24 11:38:50,864] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:38:50,864] [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_000830005.1	s__Streptomyces vietnamensis	100.0	3047	3050	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_900105415.1	s__Streptomyces sp900105415	92.7399	2291	3050	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.65	95.65	0.85	0.85	2	-
GCF_014648895.1	s__Streptomyces tanashiensis	92.614	2209	3050	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.78	97.78	0.91	0.91	2	-
GCF_003386135.1	s__Streptomyces sp003386135	92.5888	2299	3050	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.57	99.57	0.94	0.94	2	-
GCF_014649755.1	s__Streptomyces litmocidini	92.2086	2099	3050	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.07	95.07	0.85	0.85	2	-
GCF_001426405.1	s__Streptomyces sp001426405	89.7327	1990	3050	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000716445.1	s__Streptomyces wedmorensis	89.4077	2092	3050	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.81	97.63	0.94	0.88	3	-
GCA_000716465.1	s__Streptomyces bikiniensis	89.1156	1763	3050	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.67	95.67	0.86	0.82	10	-
GCF_001905825.1	s__Streptomyces sp001905825	89.0827	2081	3050	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.90	96.90	0.90	0.90	2	-
GCF_001008345.1	s__Streptomyces showdoensis	86.949	1866	3050	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001865245.1	s__Streptomyces sp001865245	82.4969	1314	3050	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.88	98.02	0.87	0.86	3	-
GCF_002028425.1	s__Streptomyces katrae_A	82.3916	1525	3050	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.60	99.44	0.97	0.94	4	-
GCF_019049245.1	s__Streptomyces sp019049245	81.3783	1448	3050	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003143855.1	s__Streptomyces sp003143855	81.2719	1333	3050	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.17	95.17	0.79	0.79	2	-
GCF_014647675.1	s__Streptomyces flaveus	81.0412	1420	3050	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.63	96.63	0.83	0.83	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:38:50,865] [INFO] GTDB search result was written to GCF_000830005.1_ASM83000v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:38:50,866] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:38:50,869] [INFO] DFAST_QC result json was written to GCF_000830005.1_ASM83000v1_genomic.fna/dqc_result.json
[2024-01-24 11:38:50,869] [INFO] DFAST_QC completed!
[2024-01-24 11:38:50,869] [INFO] Total running time: 0h4m10s