[2024-01-24 13:31:35,484] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:31:35,487] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:31:35,487] [INFO] DQC Reference Directory: /var/lib/cwl/stg6c6602a4-b9b3-4d6e-9740-9c1bf31a1729/dqc_reference
[2024-01-24 13:31:36,890] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:31:36,891] [INFO] Task started: Prodigal
[2024-01-24 13:31:36,891] [INFO] Running command: gunzip -c /var/lib/cwl/stg46d33c9e-b01e-40fb-8436-765731531c17/GCF_025823105.1_ASM2582310v1_genomic.fna.gz | prodigal -d GCF_025823105.1_ASM2582310v1_genomic.fna/cds.fna -a GCF_025823105.1_ASM2582310v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:01,735] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:01,735] [INFO] Task started: HMMsearch
[2024-01-24 13:32:01,735] [INFO] Running command: hmmsearch --tblout GCF_025823105.1_ASM2582310v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6c6602a4-b9b3-4d6e-9740-9c1bf31a1729/dqc_reference/reference_markers.hmm GCF_025823105.1_ASM2582310v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:02,141] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:02,143] [INFO] Found 6/6 markers.
[2024-01-24 13:32:02,206] [INFO] Query marker FASTA was written to GCF_025823105.1_ASM2582310v1_genomic.fna/markers.fasta
[2024-01-24 13:32:02,207] [INFO] Task started: Blastn
[2024-01-24 13:32:02,207] [INFO] Running command: blastn -query GCF_025823105.1_ASM2582310v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6c6602a4-b9b3-4d6e-9740-9c1bf31a1729/dqc_reference/reference_markers.fasta -out GCF_025823105.1_ASM2582310v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:03,516] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:03,519] [INFO] Selected 16 target genomes.
[2024-01-24 13:32:03,519] [INFO] Target genome list was writen to GCF_025823105.1_ASM2582310v1_genomic.fna/target_genomes.txt
[2024-01-24 13:32:03,528] [INFO] Task started: fastANI
[2024-01-24 13:32:03,529] [INFO] Running command: fastANI --query /var/lib/cwl/stg46d33c9e-b01e-40fb-8436-765731531c17/GCF_025823105.1_ASM2582310v1_genomic.fna.gz --refList GCF_025823105.1_ASM2582310v1_genomic.fna/target_genomes.txt --output GCF_025823105.1_ASM2582310v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:29,612] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:29,613] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6c6602a4-b9b3-4d6e-9740-9c1bf31a1729/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:29,613] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6c6602a4-b9b3-4d6e-9740-9c1bf31a1729/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:29,629] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:32:29,629] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:32:29,629] [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
Mycolicibacterium boenickei	strain=JCM 15653	GCA_010731295.1	146017	146017	type	True	93.0338	1949	2305	95	below_threshold
Mycolicibacterium septicum	strain=ATCC 700731	GCA_012396425.1	98668	98668	type	True	88.8994	1796	2305	95	below_threshold
Mycolicibacterium septicum	strain=type strain: DSM 44393	GCA_000455325.1	98668	98668	type	True	88.8988	1792	2305	95	below_threshold
Mycolicibacterium nivoides	strain=DL90	GCA_003855255.1	2487344	2487344	type	True	88.8614	1890	2305	95	below_threshold
Mycolicibacterium neworleansense	strain=type strain: ATCC 49404	GCA_001245615.1	146018	146018	type	True	88.2301	1766	2305	95	below_threshold
Mycolicibacterium conceptionense	strain=CCUG 50187	GCA_002102065.1	451644	451644	suspected-type	True	88.2166	1712	2305	95	below_threshold
Mycolicibacterium setense	strain=DSM 45070	GCA_000805385.1	431269	431269	type	True	87.2248	1719	2305	95	below_threshold
Mycolicibacterium fortuitum subsp. fortuitum	strain=JCM 6387	GCA_022179545.1	144549	1766	type	True	87.0577	1687	2305	95	below_threshold
Mycolicibacterium fortuitum subsp. acetamidolyticum	strain=JCM6368	GCA_001570465.1	144550	1766	type	True	87.0291	1721	2305	95	below_threshold
Mycolicibacterium lutetiense	strain=DSM 46713	GCA_017876775.1	1641992	1641992	type	True	86.5179	1522	2305	95	below_threshold
Mycolicibacterium alvei	strain=JCM 12272	GCA_010727325.1	67081	67081	type	True	86.4715	1498	2305	95	below_threshold
Mycolicibacterium houstonense	strain=type strain: ATCC 49403	GCA_900078665.2	146021	146021	type	True	86.1932	1666	2305	95	below_threshold
Mycolicibacterium anyangense	strain=JCM 30275	GCA_010731855.1	1431246	1431246	type	True	79.8801	838	2305	95	below_threshold
Mycobacterium pallens	strain=JCM 16370	GCA_019456675.1	370524	370524	type	True	79.6167	908	2305	95	below_threshold
Mycobacterium crocinum	strain=JCM 16369	GCA_022370635.3	388459	388459	type	True	79.6091	891	2305	95	below_threshold
Mycolicibacterium vinylchloridicum	strain=CECT 8761	GCA_013404075.1	2736928	2736928	type	True	79.5769	895	2305	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:29,633] [INFO] DFAST Taxonomy check result was written to GCF_025823105.1_ASM2582310v1_genomic.fna/tc_result.tsv
[2024-01-24 13:32:29,633] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:29,634] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:29,634] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6c6602a4-b9b3-4d6e-9740-9c1bf31a1729/dqc_reference/checkm_data
[2024-01-24 13:32:29,635] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:29,705] [INFO] Task started: CheckM
[2024-01-24 13:32:29,705] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025823105.1_ASM2582310v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025823105.1_ASM2582310v1_genomic.fna/checkm_input GCF_025823105.1_ASM2582310v1_genomic.fna/checkm_result
[2024-01-24 13:33:44,475] [INFO] Task succeeded: CheckM
[2024-01-24 13:33:44,476] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:33:44,495] [INFO] ===== Completeness check finished =====
[2024-01-24 13:33:44,495] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:33:44,496] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025823105.1_ASM2582310v1_genomic.fna/markers.fasta)
[2024-01-24 13:33:44,496] [INFO] Task started: Blastn
[2024-01-24 13:33:44,496] [INFO] Running command: blastn -query GCF_025823105.1_ASM2582310v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6c6602a4-b9b3-4d6e-9740-9c1bf31a1729/dqc_reference/reference_markers_gtdb.fasta -out GCF_025823105.1_ASM2582310v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:46,636] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:46,639] [INFO] Selected 15 target genomes.
[2024-01-24 13:33:46,640] [INFO] Target genome list was writen to GCF_025823105.1_ASM2582310v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:33:46,670] [INFO] Task started: fastANI
[2024-01-24 13:33:46,670] [INFO] Running command: fastANI --query /var/lib/cwl/stg46d33c9e-b01e-40fb-8436-765731531c17/GCF_025823105.1_ASM2582310v1_genomic.fna.gz --refList GCF_025823105.1_ASM2582310v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025823105.1_ASM2582310v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:34:10,935] [INFO] Task succeeded: fastANI
[2024-01-24 13:34:10,960] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:34:10,960] [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_002086835.1	s__Mycobacterium porcinum	99.9812	2270	2305	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.47	97.32	0.92	0.87	9	conclusive
GCF_010731295.1	s__Mycobacterium boenickei	93.023	1950	2305	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.98	99.96	1.00	1.00	3	-
GCF_001942045.1	s__Mycobacterium porcinum_A	91.6882	1731	2305	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000455325.1	s__Mycobacterium septicum	88.8814	1795	2305	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	96.04	95.11	0.88	0.83	8	-
GCF_004762045.1	s__Mycobacterium sp004762045	88.7889	1753	2305	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001245615.1	s__Mycobacterium neworleansense	88.2247	1767	2305	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000723385.1	s__Mycobacterium farcinogenes	88.161	1696	2305	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.34	98.08	0.90	0.87	16	-
GCF_001942625.1	s__Mycobacterium syngnathidarum	87.7671	1630	2305	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.38	97.86	0.91	0.87	4	-
GCF_011745145.1	s__Mycobacterium sp011745145	87.3472	1697	2305	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000426065.1	s__Mycobacterium sp000426065	87.2839	1785	2305	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000805385.1	s__Mycobacterium setense	87.2248	1719	2305	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.09	98.47	0.95	0.89	4	-
GCF_000295855.1	s__Mycobacterium fortuitum	87.1017	1657	2305	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.13	96.41	0.93	0.89	30	-
GCF_009729095.1	s__Mycobacterium sp009729095	86.6207	1580	2305	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.96	1.00	1.00	6	-
GCF_900078665.2	s__Mycobacterium houstonense	86.1784	1668	2305	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001954135.1	s__Mycobacterium sp001954135	85.1474	1431	2305	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:34:10,962] [INFO] GTDB search result was written to GCF_025823105.1_ASM2582310v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:34:10,963] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:34:10,966] [INFO] DFAST_QC result json was written to GCF_025823105.1_ASM2582310v1_genomic.fna/dqc_result.json
[2024-01-24 13:34:10,966] [INFO] DFAST_QC completed!
[2024-01-24 13:34:10,967] [INFO] Total running time: 0h2m35s