[2024-01-24 13:55:44,835] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:55:44,840] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:55:44,841] [INFO] DQC Reference Directory: /var/lib/cwl/stgaf60af54-c812-4a1c-9a26-ff0e58315c21/dqc_reference
[2024-01-24 13:55:46,110] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:55:46,111] [INFO] Task started: Prodigal
[2024-01-24 13:55:46,111] [INFO] Running command: gunzip -c /var/lib/cwl/stg0b190e9e-0a5a-4ca9-bd48-430a221bfbcd/GCF_014649995.1_ASM1464999v1_genomic.fna.gz | prodigal -d GCF_014649995.1_ASM1464999v1_genomic.fna/cds.fna -a GCF_014649995.1_ASM1464999v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:56:06,967] [INFO] Task succeeded: Prodigal
[2024-01-24 13:56:06,968] [INFO] Task started: HMMsearch
[2024-01-24 13:56:06,968] [INFO] Running command: hmmsearch --tblout GCF_014649995.1_ASM1464999v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaf60af54-c812-4a1c-9a26-ff0e58315c21/dqc_reference/reference_markers.hmm GCF_014649995.1_ASM1464999v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:56:07,314] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:56:07,315] [INFO] Found 6/6 markers.
[2024-01-24 13:56:07,378] [INFO] Query marker FASTA was written to GCF_014649995.1_ASM1464999v1_genomic.fna/markers.fasta
[2024-01-24 13:56:07,378] [INFO] Task started: Blastn
[2024-01-24 13:56:07,378] [INFO] Running command: blastn -query GCF_014649995.1_ASM1464999v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaf60af54-c812-4a1c-9a26-ff0e58315c21/dqc_reference/reference_markers.fasta -out GCF_014649995.1_ASM1464999v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:56:08,681] [INFO] Task succeeded: Blastn
[2024-01-24 13:56:08,685] [INFO] Selected 24 target genomes.
[2024-01-24 13:56:08,685] [INFO] Target genome list was writen to GCF_014649995.1_ASM1464999v1_genomic.fna/target_genomes.txt
[2024-01-24 13:56:08,716] [INFO] Task started: fastANI
[2024-01-24 13:56:08,716] [INFO] Running command: fastANI --query /var/lib/cwl/stg0b190e9e-0a5a-4ca9-bd48-430a221bfbcd/GCF_014649995.1_ASM1464999v1_genomic.fna.gz --refList GCF_014649995.1_ASM1464999v1_genomic.fna/target_genomes.txt --output GCF_014649995.1_ASM1464999v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:56:51,893] [INFO] Task succeeded: fastANI
[2024-01-24 13:56:51,894] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaf60af54-c812-4a1c-9a26-ff0e58315c21/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:56:51,894] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaf60af54-c812-4a1c-9a26-ff0e58315c21/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:56:51,923] [INFO] Found 24 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:56:51,923] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:56:51,924] [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 griseoflavus	strain=JCM 4479	GCA_014649995.1	35619	35619	type	True	100.0	2497	2500	95	conclusive
Streptomyces pilosus	strain=JCM 4403	GCA_014649835.1	28893	28893	type	True	93.6478	2006	2500	95	below_threshold
Streptomyces malachitofuscus	strain=JCM 4493	GCA_014650055.1	67322	67322	type	True	90.0995	1875	2500	95	below_threshold
Streptomyces albaduncus	strain=JCM 4715	GCA_014650615.1	68172	68172	type	True	89.239	1782	2500	95	below_threshold
Streptomyces capillispiralis	strain=DSM 41695	GCA_007829875.1	68182	68182	type	True	89.236	1811	2500	95	below_threshold
Streptomyces albaduncus	strain=CECT 3226	GCA_014203495.1	68172	68172	type	True	89.2191	1813	2500	95	below_threshold
Streptomyces capillispiralis	strain=JCM 5075	GCA_014656315.1	68182	68182	type	True	89.1475	1820	2500	95	below_threshold
Streptomyces griseostramineus	strain=JCM 4385	GCA_014649635.1	66898	66898	suspected-type	True	88.8303	1848	2500	95	below_threshold
Streptomyces griseostramineus	strain=CECT 3273	GCA_014203535.1	66898	66898	suspected-type	True	88.7264	1863	2500	95	below_threshold
Streptomyces viridosporus	strain=NRRL 2414	GCA_002078235.1	67581	67581	type	True	88.5057	1552	2500	95	below_threshold
Streptomyces lomondensis	strain=DSM 41428	GCA_021440105.1	68229	68229	type	True	85.9927	1678	2500	95	below_threshold
Streptomyces solaniscabiei	strain=FS70	GCA_020312315.1	2683255	2683255	type	True	85.9397	1626	2500	95	below_threshold
Streptomyces flaveolus	strain=JCM 4032	GCA_014648815.1	67297	67297	type	True	85.8687	1660	2500	95	below_threshold
Streptomyces tuirus	strain=JCM 4255	GCA_014701095.1	68278	68278	type	True	85.8416	1637	2500	95	below_threshold
Streptomyces griseicoloratus	strain=TRM S81-3	GCA_014534645.1	2752516	2752516	type	True	85.7262	1674	2500	95	below_threshold
Streptomyces indiaensis	strain=DSM 43803	GCA_021474405.1	284033	284033	type	True	85.6148	1538	2500	95	below_threshold
Streptomyces ambofaciens	strain=ATCC 23877	GCA_001267885.1	1889	1889	type	True	85.5084	1708	2500	95	below_threshold
Streptomyces sennicomposti	strain=RCPT1-4	GCA_019890635.1	2873384	2873384	type	True	84.8441	1433	2500	95	below_threshold
Streptomyces barringtoniae	strain=JA03	GCA_020819595.1	2892029	2892029	type	True	84.2275	1548	2500	95	below_threshold
Actinacidiphila oryziradicis	strain=NEAU-C40	GCA_005047355.1	2571141	2571141	type	True	79.5643	1077	2500	95	below_threshold
Actinomadura rubrobrunea	strain=NBRC 15275	GCA_001552235.1	115335	115335	type	True	76.9055	660	2500	95	below_threshold
Thermomonospora catenispora	strain=3-22-3	GCA_006363815.1	2493090	2493090	type	True	76.8196	564	2500	95	below_threshold
Thermopolyspora flexuosa	strain=JCM 3056	GCA_014647775.1	103836	103836	type	True	76.7453	601	2500	95	below_threshold
Thermopolyspora flexuosa	strain=DSM 43186	GCA_006716785.1	103836	103836	type	True	76.7299	600	2500	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:56:51,926] [INFO] DFAST Taxonomy check result was written to GCF_014649995.1_ASM1464999v1_genomic.fna/tc_result.tsv
[2024-01-24 13:56:51,927] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:56:51,927] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:56:51,927] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaf60af54-c812-4a1c-9a26-ff0e58315c21/dqc_reference/checkm_data
[2024-01-24 13:56:51,928] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:56:51,998] [INFO] Task started: CheckM
[2024-01-24 13:56:51,999] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014649995.1_ASM1464999v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014649995.1_ASM1464999v1_genomic.fna/checkm_input GCF_014649995.1_ASM1464999v1_genomic.fna/checkm_result
[2024-01-24 13:58:40,567] [INFO] Task succeeded: CheckM
[2024-01-24 13:58:40,569] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:58:40,591] [INFO] ===== Completeness check finished =====
[2024-01-24 13:58:40,592] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:58:40,592] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014649995.1_ASM1464999v1_genomic.fna/markers.fasta)
[2024-01-24 13:58:40,592] [INFO] Task started: Blastn
[2024-01-24 13:58:40,593] [INFO] Running command: blastn -query GCF_014649995.1_ASM1464999v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaf60af54-c812-4a1c-9a26-ff0e58315c21/dqc_reference/reference_markers_gtdb.fasta -out GCF_014649995.1_ASM1464999v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:42,725] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:42,728] [INFO] Selected 15 target genomes.
[2024-01-24 13:58:42,729] [INFO] Target genome list was writen to GCF_014649995.1_ASM1464999v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:58:42,743] [INFO] Task started: fastANI
[2024-01-24 13:58:42,744] [INFO] Running command: fastANI --query /var/lib/cwl/stg0b190e9e-0a5a-4ca9-bd48-430a221bfbcd/GCF_014649995.1_ASM1464999v1_genomic.fna.gz --refList GCF_014649995.1_ASM1464999v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014649995.1_ASM1464999v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:59:12,280] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:12,298] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:59:12,299] [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_014649995.1	s__Streptomyces griseoflavus	100.0	2497	2500	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_014649835.1	s__Streptomyces pilosus	93.6451	2007	2500	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.43	99.43	0.94	0.94	2	-
GCF_008312835.1	s__Streptomyces marokkonensis	90.3623	1870	2500	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	90.0609	1840	2500	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	89.9129	1795	2500	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	89.8252	1944	2500	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019049255.1	s__Streptomyces sp019049255	89.796	1866	2500	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	89.7316	1846	2500	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	89.5958	1913	2500	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	88.8395	1802	2500	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014203535.1	s__Streptomyces griseostramineus	88.7291	1863	2500	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.88	99.76	0.99	0.98	3	-
GCF_000931445.1	s__Streptomyces cyaneogriseus	85.3959	1578	2500	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.603	N/A	N/A	N/A	N/A	1	-
GCF_002155905.1	s__Streptomyces tricolor	84.4663	1352	2500	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.81	98.00	0.86	0.72	5	-
GCF_900103455.1	s__Streptomyces wuyuanensis	81.625	1332	2500	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 13:59:12,300] [INFO] GTDB search result was written to GCF_014649995.1_ASM1464999v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:59:12,301] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:59:12,305] [INFO] DFAST_QC result json was written to GCF_014649995.1_ASM1464999v1_genomic.fna/dqc_result.json
[2024-01-24 13:59:12,305] [INFO] DFAST_QC completed!
[2024-01-24 13:59:12,305] [INFO] Total running time: 0h3m27s