[2024-01-24 14:39:34,338] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:39:34,340] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:39:34,340] [INFO] DQC Reference Directory: /var/lib/cwl/stgf86f219b-af6f-4767-bb71-824794ccbc95/dqc_reference
[2024-01-24 14:39:36,894] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:39:36,895] [INFO] Task started: Prodigal
[2024-01-24 14:39:36,895] [INFO] Running command: gunzip -c /var/lib/cwl/stg3a312aaf-267d-465c-8f16-d08c6dabbf56/GCF_014203495.1_ASM1420349v1_genomic.fna.gz | prodigal -d GCF_014203495.1_ASM1420349v1_genomic.fna/cds.fna -a GCF_014203495.1_ASM1420349v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:40:05,285] [INFO] Task succeeded: Prodigal
[2024-01-24 14:40:05,285] [INFO] Task started: HMMsearch
[2024-01-24 14:40:05,286] [INFO] Running command: hmmsearch --tblout GCF_014203495.1_ASM1420349v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf86f219b-af6f-4767-bb71-824794ccbc95/dqc_reference/reference_markers.hmm GCF_014203495.1_ASM1420349v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:40:05,680] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:40:05,681] [INFO] Found 6/6 markers.
[2024-01-24 14:40:05,753] [INFO] Query marker FASTA was written to GCF_014203495.1_ASM1420349v1_genomic.fna/markers.fasta
[2024-01-24 14:40:05,753] [INFO] Task started: Blastn
[2024-01-24 14:40:05,754] [INFO] Running command: blastn -query GCF_014203495.1_ASM1420349v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf86f219b-af6f-4767-bb71-824794ccbc95/dqc_reference/reference_markers.fasta -out GCF_014203495.1_ASM1420349v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:40:07,178] [INFO] Task succeeded: Blastn
[2024-01-24 14:40:07,182] [INFO] Selected 22 target genomes.
[2024-01-24 14:40:07,183] [INFO] Target genome list was writen to GCF_014203495.1_ASM1420349v1_genomic.fna/target_genomes.txt
[2024-01-24 14:40:07,206] [INFO] Task started: fastANI
[2024-01-24 14:40:07,206] [INFO] Running command: fastANI --query /var/lib/cwl/stg3a312aaf-267d-465c-8f16-d08c6dabbf56/GCF_014203495.1_ASM1420349v1_genomic.fna.gz --refList GCF_014203495.1_ASM1420349v1_genomic.fna/target_genomes.txt --output GCF_014203495.1_ASM1420349v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:40:51,390] [INFO] Task succeeded: fastANI
[2024-01-24 14:40:51,391] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf86f219b-af6f-4767-bb71-824794ccbc95/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:40:51,392] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf86f219b-af6f-4767-bb71-824794ccbc95/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:40:51,415] [INFO] Found 22 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:40:51,415] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:40:51,415] [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 albaduncus	strain=CECT 3226	GCA_014203495.1	68172	68172	type	True	100.0	2614	2618	95	conclusive
Streptomyces albaduncus	strain=JCM 4715	GCA_014650615.1	68172	68172	type	True	99.9796	2577	2618	95	conclusive
Streptomyces capillispiralis	strain=JCM 5075	GCA_014656315.1	68182	68182	type	True	92.91	2168	2618	95	below_threshold
Streptomyces capillispiralis	strain=DSM 41695	GCA_007829875.1	68182	68182	type	True	92.8866	2180	2618	95	below_threshold
Streptomyces calvus	strain=CECT 3271	GCA_014138735.1	67282	67282	type	True	91.1638	2069	2618	95	below_threshold
Streptomyces griseostramineus	strain=JCM 4385	GCA_014649635.1	66898	66898	suspected-type	True	90.0011	1879	2618	95	below_threshold
Streptomyces griseostramineus	strain=CECT 3273	GCA_014203535.1	66898	66898	suspected-type	True	89.9796	1882	2618	95	below_threshold
Streptomyces viridosporus	strain=NRRL 2414	GCA_002078235.1	67581	67581	type	True	89.3754	1519	2618	95	below_threshold
Streptomyces griseoflavus	strain=JCM 4479	GCA_014649995.1	35619	35619	type	True	89.1513	1810	2618	95	below_threshold
Streptomyces lomondensis	strain=DSM 41428	GCA_021440105.1	68229	68229	type	True	86.4757	1790	2618	95	below_threshold
Streptomyces griseicoloratus	strain=TRM S81-3	GCA_014534645.1	2752516	2752516	type	True	86.3901	1729	2618	95	below_threshold
Streptomyces purpurascens	strain=DSM 40310	GCA_021390235.1	1924	1924	type	True	86.1761	1764	2618	95	below_threshold
Streptomyces flaveolus	strain=JCM 4032	GCA_014648815.1	67297	67297	type	True	86.1427	1714	2618	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	85.6812	1466	2618	95	below_threshold
Streptomyces daghestanicus	strain=NBRC 12762	GCA_020521275.1	66885	66885	suspected-type	True	85.2389	1684	2618	95	below_threshold
Streptomyces daghestanicus	strain=JCM 4365	GCA_014649475.1	66885	66885	suspected-type	True	85.208	1650	2618	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	85.0277	1520	2618	95	below_threshold
Streptomyces nymphaeiformis	strain=SFB5A	GCA_014203895.1	2663842	2663842	type	True	81.5196	1366	2618	95	below_threshold
Marmoricola aurantiacus	strain=DSM 12652	GCA_003752505.1	86796	86796	type	True	76.7544	430	2618	95	below_threshold
Motilibacter deserti	strain=E257	GCA_011250635.1	2714956	2714956	type	True	76.7251	457	2618	95	below_threshold
Marmoricola aequoreus	strain=NRRL B-24464	GCA_000720335.1	397278	397278	type	True	76.5582	443	2618	95	below_threshold
Cellulomonas rhizosphaerae	strain=NEAU-TCZ24	GCA_003470205.1	2293719	2293719	type	True	76.4772	361	2618	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:40:51,417] [INFO] DFAST Taxonomy check result was written to GCF_014203495.1_ASM1420349v1_genomic.fna/tc_result.tsv
[2024-01-24 14:40:51,418] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:40:51,418] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:40:51,418] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf86f219b-af6f-4767-bb71-824794ccbc95/dqc_reference/checkm_data
[2024-01-24 14:40:51,419] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:40:51,499] [INFO] Task started: CheckM
[2024-01-24 14:40:51,500] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014203495.1_ASM1420349v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014203495.1_ASM1420349v1_genomic.fna/checkm_input GCF_014203495.1_ASM1420349v1_genomic.fna/checkm_result
[2024-01-24 14:42:52,157] [INFO] Task succeeded: CheckM
[2024-01-24 14:42:52,159] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.21%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:42:52,180] [INFO] ===== Completeness check finished =====
[2024-01-24 14:42:52,180] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:42:52,181] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014203495.1_ASM1420349v1_genomic.fna/markers.fasta)
[2024-01-24 14:42:52,181] [INFO] Task started: Blastn
[2024-01-24 14:42:52,181] [INFO] Running command: blastn -query GCF_014203495.1_ASM1420349v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf86f219b-af6f-4767-bb71-824794ccbc95/dqc_reference/reference_markers_gtdb.fasta -out GCF_014203495.1_ASM1420349v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:42:54,273] [INFO] Task succeeded: Blastn
[2024-01-24 14:42:54,279] [INFO] Selected 21 target genomes.
[2024-01-24 14:42:54,279] [INFO] Target genome list was writen to GCF_014203495.1_ASM1420349v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:42:54,303] [INFO] Task started: fastANI
[2024-01-24 14:42:54,304] [INFO] Running command: fastANI --query /var/lib/cwl/stg3a312aaf-267d-465c-8f16-d08c6dabbf56/GCF_014203495.1_ASM1420349v1_genomic.fna.gz --refList GCF_014203495.1_ASM1420349v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014203495.1_ASM1420349v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:43:40,551] [INFO] Task succeeded: fastANI
[2024-01-24 14:43:40,568] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:43:40,569] [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_014650015.1	s__Streptomyces griseoloalbus	99.1593	2440	2618	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.17	99.17	0.94	0.94	3	conclusive
GCF_007829875.1	s__Streptomyces capillispiralis	92.8794	2181	2618	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	100.00	100.00	1.00	1.00	2	-
GCF_006782915.1	s__Streptomyces calvus	91.1296	2053	2618	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.66	99.31	0.97	0.96	5	-
GCF_019049255.1	s__Streptomyces sp019049255	90.7659	2011	2618	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001905725.1	s__Streptomyces sp001905725	90.6107	1966	2618	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000721605.1	s__Streptomyces sp000721605	90.4792	1975	2618	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008312835.1	s__Streptomyces marokkonensis	90.462	1886	2618	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009852415.1	s__Streptomyces sp009852415	90.1029	1961	2618	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003665435.1	s__Streptomyces fungicidicus_A	90.028	1914	2618	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.86	98.42	0.93	0.90	4	-
GCF_000718785.1	s__Streptomyces sp000718785	89.3662	1852	2618	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014649995.1	s__Streptomyces griseoflavus	89.1351	1812	2618	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018638295.1	s__Streptomyces sp018638295	88.7239	1731	2618	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648815.1	s__Streptomyces flaveolus	86.1333	1717	2618	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000717055.1	s__Streptomyces iakyrus	86.1122	1758	2618	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.3776	96.00	95.60	0.85	0.85	3	-
GCF_000931445.1	s__Streptomyces cyaneogriseus	85.6768	1684	2618	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.603	N/A	N/A	N/A	N/A	1	-
GCF_018614415.1	s__Streptomyces sp018614415	85.4169	1628	2618	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002291145.1	s__Streptomyces sp002291145	85.3746	1698	2618	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014649155.1	s__Streptomyces griseoviridis	85.2728	1643	2618	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.52	99.48	0.96	0.96	3	-
GCF_900103455.1	s__Streptomyces wuyuanensis	81.5868	1313	2618	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001704635.1	s__Streptomyces sparsogenes	80.8167	1279	2618	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.81	99.81	0.87	0.87	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:43:40,570] [INFO] GTDB search result was written to GCF_014203495.1_ASM1420349v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:43:40,571] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:43:40,575] [INFO] DFAST_QC result json was written to GCF_014203495.1_ASM1420349v1_genomic.fna/dqc_result.json
[2024-01-24 14:43:40,576] [INFO] DFAST_QC completed!
[2024-01-24 14:43:40,576] [INFO] Total running time: 0h4m6s