[2024-01-24 12:36:58,392] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:36:58,399] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:36:58,400] [INFO] DQC Reference Directory: /var/lib/cwl/stg6d48c9f6-16e3-4554-a517-dfed97008726/dqc_reference
[2024-01-24 12:36:59,804] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:36:59,805] [INFO] Task started: Prodigal
[2024-01-24 12:36:59,805] [INFO] Running command: gunzip -c /var/lib/cwl/stgd11c9543-7ea7-4ef4-9b6f-6e6b943e641c/GCF_014648815.1_ASM1464881v1_genomic.fna.gz | prodigal -d GCF_014648815.1_ASM1464881v1_genomic.fna/cds.fna -a GCF_014648815.1_ASM1464881v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:37:24,589] [INFO] Task succeeded: Prodigal
[2024-01-24 12:37:24,590] [INFO] Task started: HMMsearch
[2024-01-24 12:37:24,590] [INFO] Running command: hmmsearch --tblout GCF_014648815.1_ASM1464881v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6d48c9f6-16e3-4554-a517-dfed97008726/dqc_reference/reference_markers.hmm GCF_014648815.1_ASM1464881v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:37:25,051] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:37:25,052] [INFO] Found 6/6 markers.
[2024-01-24 12:37:25,127] [INFO] Query marker FASTA was written to GCF_014648815.1_ASM1464881v1_genomic.fna/markers.fasta
[2024-01-24 12:37:25,127] [INFO] Task started: Blastn
[2024-01-24 12:37:25,128] [INFO] Running command: blastn -query GCF_014648815.1_ASM1464881v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6d48c9f6-16e3-4554-a517-dfed97008726/dqc_reference/reference_markers.fasta -out GCF_014648815.1_ASM1464881v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:26,472] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:26,476] [INFO] Selected 17 target genomes.
[2024-01-24 12:37:26,476] [INFO] Target genome list was writen to GCF_014648815.1_ASM1464881v1_genomic.fna/target_genomes.txt
[2024-01-24 12:37:26,487] [INFO] Task started: fastANI
[2024-01-24 12:37:26,487] [INFO] Running command: fastANI --query /var/lib/cwl/stgd11c9543-7ea7-4ef4-9b6f-6e6b943e641c/GCF_014648815.1_ASM1464881v1_genomic.fna.gz --refList GCF_014648815.1_ASM1464881v1_genomic.fna/target_genomes.txt --output GCF_014648815.1_ASM1464881v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:38:03,142] [INFO] Task succeeded: fastANI
[2024-01-24 12:38:03,143] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6d48c9f6-16e3-4554-a517-dfed97008726/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:38:03,143] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6d48c9f6-16e3-4554-a517-dfed97008726/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:38:03,164] [INFO] Found 17 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:38:03,164] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 12:38:03,164] [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 flaveolus	strain=JCM 4032	GCA_014648815.1	67297	67297	type	True	100.0	2600	2600	95	inconclusive
Streptomyces solaniscabiei	strain=FS70	GCA_020312315.1	2683255	2683255	type	True	97.2303	2276	2600	95	inconclusive
Streptomyces ambofaciens	strain=ATCC 23877	GCA_001267885.1	1889	1889	type	True	89.3609	1947	2600	95	below_threshold
Streptomyces mutabilis	strain=JCM 4400	GCA_014649815.1	67332	67332	type	True	89.1664	1823	2600	95	below_threshold
Streptomyces rubrogriseus	strain=NBRC 15455	GCA_003112595.1	194673	194673	type	True	89.1577	1902	2600	95	below_threshold
Streptomyces griseicoloratus	strain=TRM S81-3	GCA_014534645.1	2752516	2752516	type	True	89.0855	1933	2600	95	below_threshold
Streptomyces parvulus	strain=JCM 4068	GCA_014648855.1	146923	146923	type	True	88.7325	1796	2600	95	below_threshold
Streptomyces olivaceus	strain=NRRL B-3009	GCA_015645455.1	47716	47716	type	True	88.4039	1755	2600	95	below_threshold
Streptomyces olivaceus	strain=NRRL B-3009	GCA_000721235.1	47716	47716	type	True	88.3241	1775	2600	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	86.7055	1528	2600	95	below_threshold
Streptomyces lomondensis	strain=DSM 41428	GCA_021440105.1	68229	68229	type	True	86.3559	1744	2600	95	below_threshold
Streptomyces albaduncus	strain=CECT 3226	GCA_014203495.1	68172	68172	type	True	86.1817	1721	2600	95	below_threshold
Streptomyces albaduncus	strain=JCM 4715	GCA_014650615.1	68172	68172	type	True	86.0945	1707	2600	95	below_threshold
Streptomyces coeruleorubidus	strain=ATCC 13740	GCA_008705135.1	116188	116188	suspected-type	True	85.8893	1779	2600	95	below_threshold
Streptomyces swartbergensis	strain=HMC13	GCA_002148965.1	487165	487165	type	True	85.8872	1543	2600	95	below_threshold
Streptomyces sennicomposti	strain=RCPT1-4	GCA_019890635.1	2873384	2873384	type	True	85.5031	1533	2600	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	85.1027	1540	2600	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:38:03,167] [INFO] DFAST Taxonomy check result was written to GCF_014648815.1_ASM1464881v1_genomic.fna/tc_result.tsv
[2024-01-24 12:38:03,168] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:38:03,168] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:38:03,168] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6d48c9f6-16e3-4554-a517-dfed97008726/dqc_reference/checkm_data
[2024-01-24 12:38:03,170] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:38:03,254] [INFO] Task started: CheckM
[2024-01-24 12:38:03,255] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014648815.1_ASM1464881v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014648815.1_ASM1464881v1_genomic.fna/checkm_input GCF_014648815.1_ASM1464881v1_genomic.fna/checkm_result
[2024-01-24 12:39:57,075] [INFO] Task succeeded: CheckM
[2024-01-24 12:39:57,076] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:39:57,101] [INFO] ===== Completeness check finished =====
[2024-01-24 12:39:57,102] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:39:57,102] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014648815.1_ASM1464881v1_genomic.fna/markers.fasta)
[2024-01-24 12:39:57,103] [INFO] Task started: Blastn
[2024-01-24 12:39:57,103] [INFO] Running command: blastn -query GCF_014648815.1_ASM1464881v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6d48c9f6-16e3-4554-a517-dfed97008726/dqc_reference/reference_markers_gtdb.fasta -out GCF_014648815.1_ASM1464881v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:39:59,336] [INFO] Task succeeded: Blastn
[2024-01-24 12:39:59,339] [INFO] Selected 20 target genomes.
[2024-01-24 12:39:59,339] [INFO] Target genome list was writen to GCF_014648815.1_ASM1464881v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:39:59,351] [INFO] Task started: fastANI
[2024-01-24 12:39:59,352] [INFO] Running command: fastANI --query /var/lib/cwl/stgd11c9543-7ea7-4ef4-9b6f-6e6b943e641c/GCF_014648815.1_ASM1464881v1_genomic.fna.gz --refList GCF_014648815.1_ASM1464881v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014648815.1_ASM1464881v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:40:41,678] [INFO] Task succeeded: fastANI
[2024-01-24 12:40:41,694] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:40:41,694] [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_014648815.1	s__Streptomyces flaveolus	100.0	2600	2600	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_002005565.1	s__Streptomyces sp002005565	93.2117	1846	2600	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002005225.1	s__Streptomyces pactum_A	89.6945	1911	2600	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.96	99.96	0.98	0.98	2	-
GCF_001905385.1	s__Streptomyces sp001905385	89.3933	1895	2600	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.01	96.01	0.83	0.83	2	-
GCF_001267885.1	s__Streptomyces ambofaciens	89.3773	1945	2600	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.23	99.23	0.92	0.92	2	-
GCF_002939385.1	s__Streptomyces sp002939385	89.3249	1825	2600	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.14	95.04	0.81	0.78	6	-
GCF_014649815.1	s__Streptomyces mutabilis	89.1481	1826	2600	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.69	95.91	0.82	0.76	4	-
GCF_003112595.1	s__Streptomyces rubrogriseus	89.1467	1904	2600	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.9168	N/A	N/A	N/A	N/A	1	-
GCA_002155895.1	s__Streptomyces rochei	89.0794	1646	2600	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.80	98.25	0.91	0.79	28	-
GCF_014650995.1	s__Streptomyces viridiviolaceus	89.0546	1949	2600	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014534645.1	s__Streptomyces sp014534645	89.0416	1939	2600	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003112555.1	s__Streptomyces coelicoflavus	88.8995	1904	2600	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.84	97.03	0.90	0.86	6	-
GCF_004364245.1	s__Streptomyces sp004364245	88.8427	1888	2600	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648855.1	s__Streptomyces parvulus	88.677	1803	2600	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.39	95.93	0.93	0.87	4	-
GCF_000721235.1	s__Streptomyces olivaceus	88.3139	1776	2600	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.53	98.10	0.91	0.89	6	-
GCF_018982965.1	s__Streptomyces sp018982965	88.1575	1717	2600	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014650015.1	s__Streptomyces griseoloalbus	86.2381	1711	2600	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.17	99.17	0.94	0.94	3	-
GCF_900236475.1	s__Streptomyces chartreusis_D	86.0989	1764	2600	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.99	99.98	1.00	1.00	4	-
GCF_008705135.1	s__Streptomyces coeruleorubidus	85.8737	1781	2600	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.68	95.03	0.91	0.83	4	-
GCF_003143855.1	s__Streptomyces sp003143855	85.1956	1628	2600	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.17	95.17	0.79	0.79	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:40:41,696] [INFO] GTDB search result was written to GCF_014648815.1_ASM1464881v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:40:41,697] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:40:41,701] [INFO] DFAST_QC result json was written to GCF_014648815.1_ASM1464881v1_genomic.fna/dqc_result.json
[2024-01-24 12:40:41,702] [INFO] DFAST_QC completed!
[2024-01-24 12:40:41,702] [INFO] Total running time: 0h3m43s