[2024-01-24 13:28:29,183] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:28:29,185] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:28:29,186] [INFO] DQC Reference Directory: /var/lib/cwl/stg4dcc88bf-3b30-48ed-b77c-c1fd011743e8/dqc_reference
[2024-01-24 13:28:30,510] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:28:30,511] [INFO] Task started: Prodigal
[2024-01-24 13:28:30,511] [INFO] Running command: gunzip -c /var/lib/cwl/stg93e16047-917f-4cb1-ac74-9d8bfab3a195/GCF_014650175.1_ASM1465017v1_genomic.fna.gz | prodigal -d GCF_014650175.1_ASM1465017v1_genomic.fna/cds.fna -a GCF_014650175.1_ASM1465017v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:48,378] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:48,379] [INFO] Task started: HMMsearch
[2024-01-24 13:28:48,379] [INFO] Running command: hmmsearch --tblout GCF_014650175.1_ASM1465017v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4dcc88bf-3b30-48ed-b77c-c1fd011743e8/dqc_reference/reference_markers.hmm GCF_014650175.1_ASM1465017v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:48,709] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:48,711] [INFO] Found 6/6 markers.
[2024-01-24 13:28:48,774] [INFO] Query marker FASTA was written to GCF_014650175.1_ASM1465017v1_genomic.fna/markers.fasta
[2024-01-24 13:28:48,775] [INFO] Task started: Blastn
[2024-01-24 13:28:48,775] [INFO] Running command: blastn -query GCF_014650175.1_ASM1465017v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4dcc88bf-3b30-48ed-b77c-c1fd011743e8/dqc_reference/reference_markers.fasta -out GCF_014650175.1_ASM1465017v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:50,140] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:50,144] [INFO] Selected 17 target genomes.
[2024-01-24 13:28:50,145] [INFO] Target genome list was writen to GCF_014650175.1_ASM1465017v1_genomic.fna/target_genomes.txt
[2024-01-24 13:28:50,157] [INFO] Task started: fastANI
[2024-01-24 13:28:50,158] [INFO] Running command: fastANI --query /var/lib/cwl/stg93e16047-917f-4cb1-ac74-9d8bfab3a195/GCF_014650175.1_ASM1465017v1_genomic.fna.gz --refList GCF_014650175.1_ASM1465017v1_genomic.fna/target_genomes.txt --output GCF_014650175.1_ASM1465017v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:29:21,045] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:21,046] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4dcc88bf-3b30-48ed-b77c-c1fd011743e8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:29:21,046] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4dcc88bf-3b30-48ed-b77c-c1fd011743e8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:29:21,061] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:29:21,061] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:29:21,061] [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 termitum	strain=JCM 4518	GCA_014650175.1	67368	67368	type	True	100.0	2348	2351	95	conclusive
Streptomyces filamentosus	strain=JCM 4122	GCA_014654895.1	67294	67294	type	True	90.0518	1871	2351	95	below_threshold
Streptomyces hydrogenans	strain=NBRC 13475	GCA_020521255.1	1873719	1873719	type	True	89.7586	1858	2351	95	below_threshold
Streptomyces omiyaensis	strain=JCM 4806	GCA_014650895.1	68247	68247	type	True	89.721	1856	2351	95	below_threshold
Streptomyces hydrogenans	strain=JCM 4771	GCA_014656075.1	1873719	1873719	type	True	89.6019	1810	2351	95	below_threshold
Streptomyces roseolus	strain=JCM 4411	GCA_014649855.1	67358	67358	type	True	89.349	1753	2351	95	below_threshold
Streptomyces nymphaeiformis	strain=SFB5A	GCA_014203895.1	2663842	2663842	type	True	86.5999	1743	2351	95	below_threshold
Streptomyces vietnamensis	strain=GIM4.0001	GCA_000830005.1	362257	362257	type	True	86.5713	1719	2351	95	below_threshold
Streptomyces venezuelae	strain=ATCC 10712	GCA_021432215.1	54571	54571	type	True	86.4574	1375	2351	95	below_threshold
Streptomyces lichenis	strain=LCR6-01	GCA_023218175.1	2306967	2306967	type	True	82.8919	1377	2351	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	82.0159	1200	2351	95	below_threshold
Streptomyces spinosus	strain=SBTS01	GCA_020400655.1	2872623	2872623	type	True	81.7542	1352	2351	95	below_threshold
Alicyclobacillus macrosporangiidus	strain=DSM 17980	GCA_900116805.1	392015	392015	type	True	74.7655	76	2351	95	below_threshold
Aminomonas paucivorans	strain=DSM 12260	GCA_000165795.1	81412	81412	type	True	74.7113	60	2351	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:29:21,063] [INFO] DFAST Taxonomy check result was written to GCF_014650175.1_ASM1465017v1_genomic.fna/tc_result.tsv
[2024-01-24 13:29:21,063] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:29:21,063] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:29:21,064] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4dcc88bf-3b30-48ed-b77c-c1fd011743e8/dqc_reference/checkm_data
[2024-01-24 13:29:21,065] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:29:21,136] [INFO] Task started: CheckM
[2024-01-24 13:29:21,137] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014650175.1_ASM1465017v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014650175.1_ASM1465017v1_genomic.fna/checkm_input GCF_014650175.1_ASM1465017v1_genomic.fna/checkm_result
[2024-01-24 13:30:46,634] [INFO] Task succeeded: CheckM
[2024-01-24 13:30:46,635] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.21%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:30:46,660] [INFO] ===== Completeness check finished =====
[2024-01-24 13:30:46,661] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:30:46,661] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014650175.1_ASM1465017v1_genomic.fna/markers.fasta)
[2024-01-24 13:30:46,661] [INFO] Task started: Blastn
[2024-01-24 13:30:46,662] [INFO] Running command: blastn -query GCF_014650175.1_ASM1465017v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4dcc88bf-3b30-48ed-b77c-c1fd011743e8/dqc_reference/reference_markers_gtdb.fasta -out GCF_014650175.1_ASM1465017v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:30:48,937] [INFO] Task succeeded: Blastn
[2024-01-24 13:30:48,944] [INFO] Selected 12 target genomes.
[2024-01-24 13:30:48,945] [INFO] Target genome list was writen to GCF_014650175.1_ASM1465017v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:30:48,981] [INFO] Task started: fastANI
[2024-01-24 13:30:48,981] [INFO] Running command: fastANI --query /var/lib/cwl/stg93e16047-917f-4cb1-ac74-9d8bfab3a195/GCF_014650175.1_ASM1465017v1_genomic.fna.gz --refList GCF_014650175.1_ASM1465017v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014650175.1_ASM1465017v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:31:15,306] [INFO] Task succeeded: fastANI
[2024-01-24 13:31:15,319] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:31:15,320] [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_014650175.1	s__Streptomyces termitum	100.0	2348	2351	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_014654895.1	s__Streptomyces filamentosus	90.0267	1874	2351	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.28	96.27	0.93	0.92	4	-
GCF_014650895.1	s__Streptomyces omiyaensis	89.735	1855	2351	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014656075.1	s__Streptomyces hydrogenans	89.6414	1805	2351	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.17	97.53	0.88	0.87	3	-
GCF_000719555.1	s__Streptomyces sp000719555	89.6374	1701	2351	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012927245.1	s__Streptomyces sp012927245	89.5195	1758	2351	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	100.00	100.00	1.00	1.00	2	-
GCA_000721275.1	s__Streptomyces sp000721275	89.3888	1728	2351	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014649855.1	s__Streptomyces roseolus	89.3545	1753	2351	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014649335.1	s__Streptomyces roseolilacinus	83.3559	1363	2351	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000720535.1	s__Streptomyces halstedii	82.0707	1298	2351	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.49	96.54	0.92	0.83	17	-
GCF_000719865.1	s__Streptomyces albus_E	80.9257	1137	2351	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016717595.1	s__JADKFE01 sp016717595	74.7924	315	2351	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__CAJQPC01;g__JADKFE01	95.0	98.32	98.16	0.91	0.88	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:31:15,322] [INFO] GTDB search result was written to GCF_014650175.1_ASM1465017v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:31:15,322] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:31:15,326] [INFO] DFAST_QC result json was written to GCF_014650175.1_ASM1465017v1_genomic.fna/dqc_result.json
[2024-01-24 13:31:15,326] [INFO] DFAST_QC completed!
[2024-01-24 13:31:15,326] [INFO] Total running time: 0h2m46s