[2024-01-24 13:32:40,483] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:32:40,484] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:32:40,485] [INFO] DQC Reference Directory: /var/lib/cwl/stg978c2913-7fea-4020-9a29-a628b78e2cca/dqc_reference
[2024-01-24 13:32:41,859] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:32:41,860] [INFO] Task started: Prodigal
[2024-01-24 13:32:41,860] [INFO] Running command: gunzip -c /var/lib/cwl/stg9d32ec10-4c83-4d2c-8846-c4cd489baae7/GCF_014649895.1_ASM1464989v1_genomic.fna.gz | prodigal -d GCF_014649895.1_ASM1464989v1_genomic.fna/cds.fna -a GCF_014649895.1_ASM1464989v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:33:03,452] [INFO] Task succeeded: Prodigal
[2024-01-24 13:33:03,452] [INFO] Task started: HMMsearch
[2024-01-24 13:33:03,453] [INFO] Running command: hmmsearch --tblout GCF_014649895.1_ASM1464989v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg978c2913-7fea-4020-9a29-a628b78e2cca/dqc_reference/reference_markers.hmm GCF_014649895.1_ASM1464989v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:33:03,827] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:33:03,828] [INFO] Found 6/6 markers.
[2024-01-24 13:33:03,887] [INFO] Query marker FASTA was written to GCF_014649895.1_ASM1464989v1_genomic.fna/markers.fasta
[2024-01-24 13:33:03,887] [INFO] Task started: Blastn
[2024-01-24 13:33:03,888] [INFO] Running command: blastn -query GCF_014649895.1_ASM1464989v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg978c2913-7fea-4020-9a29-a628b78e2cca/dqc_reference/reference_markers.fasta -out GCF_014649895.1_ASM1464989v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:05,277] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:05,280] [INFO] Selected 25 target genomes.
[2024-01-24 13:33:05,281] [INFO] Target genome list was writen to GCF_014649895.1_ASM1464989v1_genomic.fna/target_genomes.txt
[2024-01-24 13:33:05,293] [INFO] Task started: fastANI
[2024-01-24 13:33:05,293] [INFO] Running command: fastANI --query /var/lib/cwl/stg9d32ec10-4c83-4d2c-8846-c4cd489baae7/GCF_014649895.1_ASM1464989v1_genomic.fna.gz --refList GCF_014649895.1_ASM1464989v1_genomic.fna/target_genomes.txt --output GCF_014649895.1_ASM1464989v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:33:50,426] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:50,427] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg978c2913-7fea-4020-9a29-a628b78e2cca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:33:50,428] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg978c2913-7fea-4020-9a29-a628b78e2cca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:33:50,450] [INFO] Found 25 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:33:50,450] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:33:50,450] [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 malachitofuscus	strain=JCM 4493	GCA_014650055.1	67322	67322	type	True	88.1978	1855	2393	95	below_threshold
Streptomyces griseoflavus	strain=JCM 4479	GCA_014649995.1	35619	35619	type	True	88.0597	1784	2393	95	below_threshold
Streptomyces capillispiralis	strain=JCM 5075	GCA_014656315.1	68182	68182	type	True	88.0509	1811	2393	95	below_threshold
Streptomyces capillispiralis	strain=DSM 41695	GCA_007829875.1	68182	68182	type	True	88.0425	1838	2393	95	below_threshold
Streptomyces calvus	strain=JCM 4326	GCA_014649315.1	67282	67282	type	True	87.9877	1862	2393	95	below_threshold
Streptomyces calvus	strain=CECT 3271	GCA_014138735.1	67282	67282	type	True	87.9467	1855	2393	95	below_threshold
Streptomyces pilosus	strain=JCM 4403	GCA_014649835.1	28893	28893	type	True	87.8068	1821	2393	95	below_threshold
Streptomyces albaduncus	strain=CECT 3226	GCA_014203495.1	68172	68172	type	True	87.7302	1805	2393	95	below_threshold
Streptomyces griseostramineus	strain=JCM 4385	GCA_014649635.1	66898	66898	suspected-type	True	87.6448	1798	2393	95	below_threshold
Streptomyces griseostramineus	strain=CECT 3273	GCA_014203535.1	66898	66898	suspected-type	True	87.597	1807	2393	95	below_threshold
Streptomyces viridosporus	strain=NRRL 2414	GCA_002078235.1	67581	67581	type	True	87.3932	1417	2393	95	below_threshold
Streptomyces lomondensis	strain=DSM 41428	GCA_021440105.1	68229	68229	type	True	85.6814	1673	2393	95	below_threshold
Streptomyces solaniscabiei	strain=FS70	GCA_020312315.1	2683255	2683255	type	True	85.6795	1647	2393	95	below_threshold
Streptomyces griseicoloratus	strain=TRM S81-3	GCA_014534645.1	2752516	2752516	type	True	85.6384	1670	2393	95	below_threshold
Streptomyces viridiviolaceus	strain=JCM 4855	GCA_014650995.1	68282	68282	type	True	85.5835	1673	2393	95	below_threshold
Streptomyces flaveolus	strain=JCM 4032	GCA_014648815.1	67297	67297	type	True	85.5818	1669	2393	95	below_threshold
Streptomyces indiaensis	strain=DSM 43803	GCA_021474405.1	284033	284033	type	True	85.5471	1535	2393	95	below_threshold
Streptomyces purpurascens	strain=DSM 40310	GCA_021390235.1	1924	1924	type	True	85.2742	1656	2393	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	85.2612	1432	2393	95	below_threshold
Streptomyces mutabilis	strain=JCM 4400	GCA_014649815.1	67332	67332	type	True	85.2257	1637	2393	95	below_threshold
Streptomyces sennicomposti	strain=RCPT1-4	GCA_019890635.1	2873384	2873384	type	True	84.8679	1460	2393	95	below_threshold
Galactobacter valiniphilus	strain=JZ R-35	GCA_003575975.1	2676122	2676122	type	True	76.4258	236	2393	95	below_threshold
Pseudarthrobacter enclensis	strain=NIO-1008	GCA_900094675.1	993070	993070	type	True	76.3188	228	2393	95	below_threshold
Pseudarthrobacter enclensis	strain=NIO-1008	GCA_001457025.1	993070	993070	type	True	76.3188	228	2393	95	below_threshold
Galactobacter caseinivorans	strain=JZ R-183	GCA_003640665.1	2676123	2676123	type	True	75.8361	129	2393	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:33:50,452] [INFO] DFAST Taxonomy check result was written to GCF_014649895.1_ASM1464989v1_genomic.fna/tc_result.tsv
[2024-01-24 13:33:50,453] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:33:50,453] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:33:50,453] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg978c2913-7fea-4020-9a29-a628b78e2cca/dqc_reference/checkm_data
[2024-01-24 13:33:50,454] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:33:50,521] [INFO] Task started: CheckM
[2024-01-24 13:33:50,522] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014649895.1_ASM1464989v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014649895.1_ASM1464989v1_genomic.fna/checkm_input GCF_014649895.1_ASM1464989v1_genomic.fna/checkm_result
[2024-01-24 13:35:30,754] [INFO] Task succeeded: CheckM
[2024-01-24 13:35:30,756] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:35:30,780] [INFO] ===== Completeness check finished =====
[2024-01-24 13:35:30,780] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:35:30,781] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014649895.1_ASM1464989v1_genomic.fna/markers.fasta)
[2024-01-24 13:35:30,781] [INFO] Task started: Blastn
[2024-01-24 13:35:30,781] [INFO] Running command: blastn -query GCF_014649895.1_ASM1464989v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg978c2913-7fea-4020-9a29-a628b78e2cca/dqc_reference/reference_markers_gtdb.fasta -out GCF_014649895.1_ASM1464989v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:35:32,971] [INFO] Task succeeded: Blastn
[2024-01-24 13:35:32,976] [INFO] Selected 12 target genomes.
[2024-01-24 13:35:32,977] [INFO] Target genome list was writen to GCF_014649895.1_ASM1464989v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:35:33,035] [INFO] Task started: fastANI
[2024-01-24 13:35:33,035] [INFO] Running command: fastANI --query /var/lib/cwl/stg9d32ec10-4c83-4d2c-8846-c4cd489baae7/GCF_014649895.1_ASM1464989v1_genomic.fna.gz --refList GCF_014649895.1_ASM1464989v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014649895.1_ASM1464989v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:35:57,711] [INFO] Task succeeded: fastANI
[2024-01-24 13:35:57,724] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:35:57,724] [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_002154585.1	s__Streptomyces pseudogriseolus	99.2161	1844	2393	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.58	96.58	0.90	0.87	9	conclusive
GCA_014650475.1	s__Streptomyces albogriseolus	93.6359	2012	2393	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.59	97.23	0.93	0.90	7	-
GCA_014656175.1	s__Streptomyces werraensis	93.5077	2015	2393	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014655195.1	s__Streptomyces cellulosae	93.2963	1992	2393	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.05	95.87	0.87	0.85	11	-
GCA_014649575.1	s__Streptomyces griseoincarnatus	93.1583	1990	2393	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.374	98.24	97.52	0.91	0.85	21	-
GCA_014649355.1	s__Streptomyces althioticus	93.0764	2009	2393	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.374	98.43	96.72	0.91	0.83	9	-
GCF_002899455.1	s__Streptomyces sp002899455	92.5052	1865	2393	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000725125.1	s__Streptomyces toyocaensis	88.0228	1695	2393	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002005565.1	s__Streptomyces sp002005565	85.7887	1578	2393	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007176755.1	s__Streptomyces sp007176755	84.6305	1609	2393	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019049245.1	s__Streptomyces sp019049245	84.298	1648	2393	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014203595.1	s__Streptomyces echinatus	84.2849	1594	2393	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:35:57,726] [INFO] GTDB search result was written to GCF_014649895.1_ASM1464989v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:35:57,726] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:35:57,730] [INFO] DFAST_QC result json was written to GCF_014649895.1_ASM1464989v1_genomic.fna/dqc_result.json
[2024-01-24 13:35:57,731] [INFO] DFAST_QC completed!
[2024-01-24 13:35:57,731] [INFO] Total running time: 0h3m17s