[2024-01-25 18:08:20,617] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:08:20,630] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:08:20,631] [INFO] DQC Reference Directory: /var/lib/cwl/stg05dae8d9-8cae-4972-8536-7c832c4e0bde/dqc_reference
[2024-01-25 18:08:21,831] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:08:21,832] [INFO] Task started: Prodigal
[2024-01-25 18:08:21,832] [INFO] Running command: gunzip -c /var/lib/cwl/stgc6a3dd71-be50-43b2-8ca0-5a4f0342072f/GCF_002086635.1_ASM208663v1_genomic.fna.gz | prodigal -d GCF_002086635.1_ASM208663v1_genomic.fna/cds.fna -a GCF_002086635.1_ASM208663v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:08:36,776] [INFO] Task succeeded: Prodigal
[2024-01-25 18:08:36,777] [INFO] Task started: HMMsearch
[2024-01-25 18:08:36,777] [INFO] Running command: hmmsearch --tblout GCF_002086635.1_ASM208663v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg05dae8d9-8cae-4972-8536-7c832c4e0bde/dqc_reference/reference_markers.hmm GCF_002086635.1_ASM208663v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:08:37,082] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:08:37,083] [INFO] Found 6/6 markers.
[2024-01-25 18:08:37,139] [INFO] Query marker FASTA was written to GCF_002086635.1_ASM208663v1_genomic.fna/markers.fasta
[2024-01-25 18:08:37,139] [INFO] Task started: Blastn
[2024-01-25 18:08:37,139] [INFO] Running command: blastn -query GCF_002086635.1_ASM208663v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg05dae8d9-8cae-4972-8536-7c832c4e0bde/dqc_reference/reference_markers.fasta -out GCF_002086635.1_ASM208663v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:08:38,268] [INFO] Task succeeded: Blastn
[2024-01-25 18:08:38,271] [INFO] Selected 17 target genomes.
[2024-01-25 18:08:38,271] [INFO] Target genome list was writen to GCF_002086635.1_ASM208663v1_genomic.fna/target_genomes.txt
[2024-01-25 18:08:38,283] [INFO] Task started: fastANI
[2024-01-25 18:08:38,283] [INFO] Running command: fastANI --query /var/lib/cwl/stgc6a3dd71-be50-43b2-8ca0-5a4f0342072f/GCF_002086635.1_ASM208663v1_genomic.fna.gz --refList GCF_002086635.1_ASM208663v1_genomic.fna/target_genomes.txt --output GCF_002086635.1_ASM208663v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:08:59,489] [INFO] Task succeeded: fastANI
[2024-01-25 18:08:59,489] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg05dae8d9-8cae-4972-8536-7c832c4e0bde/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:08:59,489] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg05dae8d9-8cae-4972-8536-7c832c4e0bde/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:08:59,500] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:08:59,500] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:08:59,500] [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 paraense	strain=IEC26	GCA_002101815.1	767916	767916	type	True	86.3818	1427	1831	95	below_threshold
Mycobacterium heidelbergense	strain=DSM 44471	GCA_002086215.1	53376	53376	type	True	85.9727	1200	1831	95	below_threshold
Mycobacterium heidelbergense	strain=JCM 14842	GCA_010730745.1	53376	53376	type	True	85.9305	1226	1831	95	below_threshold
Mycobacterium palustre	strain=DSM 44572	GCA_002101785.1	153971	153971	type	True	85.2663	1272	1831	95	below_threshold
Mycobacterium paraintracellulare	strain=JCM 30622	GCA_010731935.1	1138383	1138383	suspected-type	True	83.8477	1298	1831	95	below_threshold
Mycobacterium intracellulare	strain=ATCC 13950	GCA_000172115.1	1767	1767	suspected-type	True	83.8232	1153	1831	95	below_threshold
Mycobacterium paraintracellulare	strain=MOTT64	GCA_000276825.1	1138383	1138383	suspected-type	True	83.8064	1300	1831	95	below_threshold
Mycobacterium bohemicum	strain=DSM 44277	GCA_002102025.1	56425	56425	type	True	83.7092	1257	1831	95	below_threshold
Mycobacterium helveticum	strain=16-83	GCA_007714205.1	2592811	2592811	type	True	83.6849	1089	1831	95	below_threshold
Mycobacterium bohemicum	strain=DSM 44277	GCA_001053185.1	56425	56425	type	True	83.6424	1221	1831	95	below_threshold
Mycobacterium colombiense	strain=CECT 3035	GCA_002105755.1	339268	339268	suspected-type	True	83.5858	1287	1831	95	below_threshold
Mycobacterium conspicuum	strain=DSM 44136	GCA_002102095.1	44010	44010	type	True	82.8612	1264	1831	95	below_threshold
Mycobacterium conspicuum	strain=JCM 14738	GCA_010730195.1	44010	44010	type	True	82.8323	1285	1831	95	below_threshold
Mycobacterium lacus	strain=DSM 44577	GCA_002102215.1	169765	169765	type	True	82.3301	1014	1831	95	below_threshold
Mycobacterium lacus	strain=JCM 15657	GCA_010731535.1	169765	169765	type	True	82.2178	1045	1831	95	below_threshold
Mycobacterium riyadhense	strain=DSM 45176	GCA_002101845.1	486698	486698	type	True	81.1247	1014	1831	95	below_threshold
Mycobacterium tuberculosis variant africanum	strain=ATCC 25420	GCA_002982335.1	33894	1773	type	True	80.9848	860	1831	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:08:59,501] [INFO] DFAST Taxonomy check result was written to GCF_002086635.1_ASM208663v1_genomic.fna/tc_result.tsv
[2024-01-25 18:08:59,502] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:08:59,502] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:08:59,502] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg05dae8d9-8cae-4972-8536-7c832c4e0bde/dqc_reference/checkm_data
[2024-01-25 18:08:59,503] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:08:59,554] [INFO] Task started: CheckM
[2024-01-25 18:08:59,555] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002086635.1_ASM208663v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002086635.1_ASM208663v1_genomic.fna/checkm_input GCF_002086635.1_ASM208663v1_genomic.fna/checkm_result
[2024-01-25 18:09:46,748] [INFO] Task succeeded: CheckM
[2024-01-25 18:09:46,749] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:09:46,762] [INFO] ===== Completeness check finished =====
[2024-01-25 18:09:46,762] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:09:46,763] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002086635.1_ASM208663v1_genomic.fna/markers.fasta)
[2024-01-25 18:09:46,763] [INFO] Task started: Blastn
[2024-01-25 18:09:46,764] [INFO] Running command: blastn -query GCF_002086635.1_ASM208663v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg05dae8d9-8cae-4972-8536-7c832c4e0bde/dqc_reference/reference_markers_gtdb.fasta -out GCF_002086635.1_ASM208663v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:09:48,455] [INFO] Task succeeded: Blastn
[2024-01-25 18:09:48,464] [INFO] Selected 18 target genomes.
[2024-01-25 18:09:48,464] [INFO] Target genome list was writen to GCF_002086635.1_ASM208663v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:09:48,488] [INFO] Task started: fastANI
[2024-01-25 18:09:48,488] [INFO] Running command: fastANI --query /var/lib/cwl/stgc6a3dd71-be50-43b2-8ca0-5a4f0342072f/GCF_002086635.1_ASM208663v1_genomic.fna.gz --refList GCF_002086635.1_ASM208663v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002086635.1_ASM208663v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:10:15,102] [INFO] Task succeeded: fastANI
[2024-01-25 18:10:15,113] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:10:15,113] [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_002086635.1	s__Mycobacterium alsense	100.0	1825	1831	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	96.76	96.71	0.91	0.90	3	conclusive
GCF_002101815.1	s__Mycobacterium paraense	86.3744	1429	1831	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.85	98.84	0.95	0.95	4	-
GCA_002102225.1	s__Mycobacterium interjectum_B	86.2956	1433	1831	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001673535.1	s__Mycobacterium sp001673535	86.2853	1345	1831	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900157385.1	s__Mycobacterium terramassiliense	86.1902	1443	1831	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001667015.1	s__Mycobacterium sp001667015	86.1581	1392	1831	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900078675.2	s__Mycobacterium interjectum	86.1564	1411	1831	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001672915.1	s__Mycobacterium sp001672915	86.0803	1362	1831	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010730745.1	s__Mycobacterium heidelbergense	85.9472	1224	1831	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001665295.1	s__Mycobacterium sp001665295	85.9316	1357	1831	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000455205.1	s__Mycobacterium sp000455205	85.6354	1357	1831	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	96.16	95.96	0.85	0.84	3	-
GCF_001672815.1	s__Mycobacterium sp001672815	85.6032	1314	1831	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002101785.1	s__Mycobacterium palustre	85.2852	1270	1831	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002086305.1	s__Mycobacterium malmoense_B	85.2257	1231	1831	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.01	99.01	0.95	0.95	2	-
GCF_001053185.1	s__Mycobacterium bohemicum	83.6819	1214	1831	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.81	99.81	0.97	0.97	2	-
GCF_007714205.1	s__Mycobacterium helveticum	83.6772	1090	1831	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.98	99.98	0.99	0.99	2	-
GCF_002101845.1	s__Mycobacterium riyadhense	81.1427	1012	1831	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.42	99.30	0.97	0.96	10	-
GCF_010723735.1	s__Mycobacterium hippocampi_B	79.0706	766	1831	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:10:15,118] [INFO] GTDB search result was written to GCF_002086635.1_ASM208663v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:10:15,118] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:10:15,122] [INFO] DFAST_QC result json was written to GCF_002086635.1_ASM208663v1_genomic.fna/dqc_result.json
[2024-01-25 18:10:15,122] [INFO] DFAST_QC completed!
[2024-01-25 18:10:15,122] [INFO] Total running time: 0h1m55s