[2024-01-24 10:57:06,462] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:57:06,466] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:57:06,466] [INFO] DQC Reference Directory: /var/lib/cwl/stg725b33f2-3ce8-4d7a-875e-1fcbc34d7f2c/dqc_reference
[2024-01-24 10:57:07,706] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:57:07,707] [INFO] Task started: Prodigal
[2024-01-24 10:57:07,707] [INFO] Running command: gunzip -c /var/lib/cwl/stgd4315db5-55df-4558-ab9e-f3e2fbe758a7/GCF_002086165.1_ASM208616v1_genomic.fna.gz | prodigal -d GCF_002086165.1_ASM208616v1_genomic.fna/cds.fna -a GCF_002086165.1_ASM208616v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:57:25,193] [INFO] Task succeeded: Prodigal
[2024-01-24 10:57:25,193] [INFO] Task started: HMMsearch
[2024-01-24 10:57:25,194] [INFO] Running command: hmmsearch --tblout GCF_002086165.1_ASM208616v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg725b33f2-3ce8-4d7a-875e-1fcbc34d7f2c/dqc_reference/reference_markers.hmm GCF_002086165.1_ASM208616v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:57:25,505] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:57:25,506] [INFO] Found 6/6 markers.
[2024-01-24 10:57:25,560] [INFO] Query marker FASTA was written to GCF_002086165.1_ASM208616v1_genomic.fna/markers.fasta
[2024-01-24 10:57:25,560] [INFO] Task started: Blastn
[2024-01-24 10:57:25,560] [INFO] Running command: blastn -query GCF_002086165.1_ASM208616v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg725b33f2-3ce8-4d7a-875e-1fcbc34d7f2c/dqc_reference/reference_markers.fasta -out GCF_002086165.1_ASM208616v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:57:26,810] [INFO] Task succeeded: Blastn
[2024-01-24 10:57:26,815] [INFO] Selected 30 target genomes.
[2024-01-24 10:57:26,815] [INFO] Target genome list was writen to GCF_002086165.1_ASM208616v1_genomic.fna/target_genomes.txt
[2024-01-24 10:57:26,840] [INFO] Task started: fastANI
[2024-01-24 10:57:26,840] [INFO] Running command: fastANI --query /var/lib/cwl/stgd4315db5-55df-4558-ab9e-f3e2fbe758a7/GCF_002086165.1_ASM208616v1_genomic.fna.gz --refList GCF_002086165.1_ASM208616v1_genomic.fna/target_genomes.txt --output GCF_002086165.1_ASM208616v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:58:02,278] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:02,279] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg725b33f2-3ce8-4d7a-875e-1fcbc34d7f2c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:58:02,279] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg725b33f2-3ce8-4d7a-875e-1fcbc34d7f2c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:58:02,304] [INFO] Found 30 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 10:58:02,305] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:58:02,305] [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
Mycobacterium avium subsp. avium	strain=DSM 44156	GCA_009741445.1	44454	1764	type	True	98.8356	1494	1865	95	conclusive
Mycobacterium avium subsp. avium	strain=ATCC 25291	GCA_000174035.1	44454	1764	type	True	98.7446	1382	1865	95	conclusive
Mycobacterium intracellulare	strain=ATCC 13950	GCA_023278525.1	1767	1767	suspected-type	True	87.446	1412	1865	95	below_threshold
Mycobacterium intracellulare	strain=ATCC 13950	GCA_000277125.1	1767	1767	suspected-type	True	87.4312	1413	1865	95	below_threshold
Mycobacterium paraintracellulare	strain=JCM 30622	GCA_010731935.1	1138383	1138383	suspected-type	True	87.3542	1397	1865	95	below_threshold
Mycobacterium intracellulare	strain=ATCC 13950	GCA_000172115.1	1767	1767	suspected-type	True	87.3393	1242	1865	95	below_threshold
Mycobacterium paraintracellulare	strain=MOTT64	GCA_000276825.1	1138383	1138383	suspected-type	True	87.2945	1410	1865	95	below_threshold
Mycobacterium paraintracellulare	strain=KCTC 29084	GCA_002104735.1	1138383	1138383	suspected-type	True	87.2929	1392	1865	95	below_threshold
Mycobacterium marseillense	strain=JCM 17324	GCA_010731675.1	701042	701042	type	True	87.1573	1354	1865	95	below_threshold
Mycobacterium colombiense	strain=CECT 3035	GCA_002105755.1	339268	339268	suspected-type	True	87.1258	1394	1865	95	below_threshold
Mycobacterium marseillense	strain=DSM 45437	GCA_002086345.1	701042	701042	type	True	87.0704	1341	1865	95	below_threshold
Mycobacterium colombiense	strain=CECT 3035	GCA_000222105.4	339268	339268	suspected-type	True	87.0597	1404	1865	95	below_threshold
Mycobacterium mantenii	strain=JCM 18113	GCA_010731775.1	560555	560555	type	True	86.5896	1430	1865	95	below_threshold
Mycobacterium arosiense	strain=DSM 45069	GCA_002086125.1	425468	425468	type	True	86.1905	1297	1865	95	below_threshold
Mycobacterium parmense	strain=DSM 44553	GCA_002102335.1	185642	185642	type	True	83.6761	1214	1865	95	below_threshold
Mycobacterium kyorinense	strain=DSM 45166	GCA_002101735.1	487514	487514	type	True	83.1475	1077	1865	95	below_threshold
Mycobacterium kyorinense	strain=KUM060204T	GCA_000759695.1	487514	487514	type	True	82.2206	998	1865	95	below_threshold
Mycobacterium xenopi	strain=NCTC10042	GCA_900453395.1	1789	1789	type	True	80.9944	943	1865	95	below_threshold
Mycobacterium fragae	strain=DSM 45731	GCA_002102185.1	1260918	1260918	type	True	80.9571	948	1865	95	below_threshold
Mycobacterium xenopi	strain=JCM 15661T	GCA_009936235.1	1789	1789	type	True	80.5824	897	1865	95	below_threshold
Mycobacterium xenopi	strain=DSM 43995	GCA_002102015.1	1789	1789	type	True	80.5814	883	1865	95	below_threshold
Mycobacterium heckeshornense	strain=JCM 15655	GCA_016592155.1	110505	110505	type	True	80.4571	898	1865	95	below_threshold
Mycolicibacterium hassiacum	strain=DSM 44199	GCA_000379865.1	46351	46351	type	True	80.3528	835	1865	95	below_threshold
Mycolicibacterium hassiacum	strain=DSM 44199	GCA_000300375.1	46351	46351	type	True	80.3454	823	1865	95	below_threshold
Mycolicibacterium thermoresistibile	strain=ATCC 19527	GCA_000234585.2	1797	1797	type	True	80.2076	782	1865	95	below_threshold
Mycolicibacterium thermoresistibile	strain=NCTC10409	GCA_900187065.1	1797	1797	type	True	80.1439	792	1865	95	below_threshold
Mycolicibacter engbaekii	strain=ATCC 27353	GCA_002101585.1	188915	188915	type	True	79.9421	754	1865	95	below_threshold
Mycolicibacterium fortuitum subsp. fortuitum	strain=JCM 6387	GCA_022179545.1	144549	1766	type	True	79.3792	755	1865	95	below_threshold
Mycolicibacterium fortuitum subsp. acetamidolyticum	strain=JCM6368	GCA_001570465.1	144550	1766	type	True	79.3524	812	1865	95	below_threshold
Mycolicibacterium fortuitum subsp. fortuitum	strain=DSM 46621	GCA_000295855.1	144549	1766	type	True	79.3104	754	1865	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:58:02,306] [INFO] DFAST Taxonomy check result was written to GCF_002086165.1_ASM208616v1_genomic.fna/tc_result.tsv
[2024-01-24 10:58:02,307] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:58:02,307] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:58:02,307] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg725b33f2-3ce8-4d7a-875e-1fcbc34d7f2c/dqc_reference/checkm_data
[2024-01-24 10:58:02,308] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:58:02,361] [INFO] Task started: CheckM
[2024-01-24 10:58:02,361] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002086165.1_ASM208616v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002086165.1_ASM208616v1_genomic.fna/checkm_input GCF_002086165.1_ASM208616v1_genomic.fna/checkm_result
[2024-01-24 10:58:57,492] [INFO] Task succeeded: CheckM
[2024-01-24 10:58:57,494] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:58:57,518] [INFO] ===== Completeness check finished =====
[2024-01-24 10:58:57,518] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:58:57,519] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002086165.1_ASM208616v1_genomic.fna/markers.fasta)
[2024-01-24 10:58:57,519] [INFO] Task started: Blastn
[2024-01-24 10:58:57,519] [INFO] Running command: blastn -query GCF_002086165.1_ASM208616v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg725b33f2-3ce8-4d7a-875e-1fcbc34d7f2c/dqc_reference/reference_markers_gtdb.fasta -out GCF_002086165.1_ASM208616v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:59,400] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:59,403] [INFO] Selected 30 target genomes.
[2024-01-24 10:58:59,404] [INFO] Target genome list was writen to GCF_002086165.1_ASM208616v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:58:59,426] [INFO] Task started: fastANI
[2024-01-24 10:58:59,426] [INFO] Running command: fastANI --query /var/lib/cwl/stgd4315db5-55df-4558-ab9e-f3e2fbe758a7/GCF_002086165.1_ASM208616v1_genomic.fna.gz --refList GCF_002086165.1_ASM208616v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002086165.1_ASM208616v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:59:38,095] [INFO] Task succeeded: fastANI
[2024-01-24 10:59:38,123] [INFO] Found 30 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:59:38,124] [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_009741445.1	s__Mycobacterium avium	98.8454	1493	1865	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	96.9043	98.75	98.29	0.92	0.84	206	conclusive
GCA_002291465.1	s__Mycobacterium lepraemurium	96.8818	1278	1865	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	96.9043	N/A	N/A	N/A	N/A	1	-
GCF_000277125.1	s__Mycobacterium intracellulare	87.4235	1414	1865	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.48	95.71	0.93	0.84	82	-
GCF_010731675.1	s__Mycobacterium marseillense	87.1624	1354	1865	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.64	95.51	0.95	0.90	6	-
GCF_002105755.1	s__Mycobacterium colombiense	87.1133	1396	1865	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.60	97.75	0.94	0.91	4	-
GCF_001672755.1	s__Mycobacterium colombiense_C	86.9008	1346	1865	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003284935.1	s__Mycobacterium arosiense_A	86.8839	1298	1865	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001667315.1	s__Mycobacterium sp001667315	86.8654	1316	1865	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001665835.1	s__Mycobacterium colombiense_A	86.8536	1363	1865	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003284975.1	s__Mycobacterium europaeum_A	86.7453	1256	1865	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	95.84	95.70	0.84	0.79	6	-
GCA_004298145.1	s__Mycobacterium sp004298145	86.6913	1327	1865	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001667145.1	s__Mycobacterium sp001667145	85.6996	1294	1865	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002086735.1	s__Mycobacterium scrofulaceum	84.6797	1309	1865	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900240975.1	s__Mycobacterium sp900240975	84.5656	1265	1865	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	97.65	95.35	0.92	0.88	4	-
GCF_001667735.1	s__Mycobacterium sp001667735	84.4868	1212	1865	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.41	99.16	0.95	0.92	6	-
GCF_001666835.1	s__Mycobacterium sp001666835	84.2647	1233	1865	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.04	99.01	0.94	0.94	3	-
GCA_002102225.1	s__Mycobacterium interjectum_B	84.076	1210	1865	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001665295.1	s__Mycobacterium sp001665295	83.9413	1199	1865	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010730575.1	s__Mycobacterium parmense	83.6432	1241	1865	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002101735.1	s__Mycobacterium kyorinense	83.1913	1071	1865	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.84	99.84	0.96	0.94	3	-
GCF_002102185.1	s__Mycobacterium fragae	80.9341	950	1865	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016592155.1	s__Mycobacterium heckeshornense	80.4502	902	1865	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.54	99.17	0.94	0.93	4	-
GCF_900603025.1	s__Mycobacterium hassiacum	80.3425	856	1865	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.99	1.00	1.00	3	-
GCA_008709575.1	s__Mycobacterium sp008709575	80.3169	706	1865	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002592005.1	s__Mycobacterium palauense	80.2825	832	1865	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008370645.1	s__Mycobacterium simiae_A	80.1925	762	1865	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003347205.1	s__Mycobacterium moriokaense_B	79.9325	856	1865	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003284965.1	s__Mycobacterium sp003284965	79.5572	744	1865	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001570485.1	s__Mycobacterium novocastrense	79.5473	814	1865	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	97.10	95.11	0.87	0.87	5	-
GCF_001907655.1	s__Mycobacterium diernhoferi	79.5285	787	1865	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.97	99.94	1.00	1.00	3	-
--------------------------------------------------------------------------------
[2024-01-24 10:59:38,125] [INFO] GTDB search result was written to GCF_002086165.1_ASM208616v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:59:38,126] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:59:38,131] [INFO] DFAST_QC result json was written to GCF_002086165.1_ASM208616v1_genomic.fna/dqc_result.json
[2024-01-24 10:59:38,131] [INFO] DFAST_QC completed!
[2024-01-24 10:59:38,131] [INFO] Total running time: 0h2m32s