[2024-01-24 13:21:40,132] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:21:40,134] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:21:40,134] [INFO] DQC Reference Directory: /var/lib/cwl/stg33069ba7-52ef-48f8-9cb9-2f5d1e95db74/dqc_reference
[2024-01-24 13:21:41,301] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:21:41,301] [INFO] Task started: Prodigal
[2024-01-24 13:21:41,302] [INFO] Running command: gunzip -c /var/lib/cwl/stg63959946-d935-4543-bdfa-3bbd8d324941/GCF_010723575.1_ASM1072357v1_genomic.fna.gz | prodigal -d GCF_010723575.1_ASM1072357v1_genomic.fna/cds.fna -a GCF_010723575.1_ASM1072357v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:22:08,752] [INFO] Task succeeded: Prodigal
[2024-01-24 13:22:08,753] [INFO] Task started: HMMsearch
[2024-01-24 13:22:08,753] [INFO] Running command: hmmsearch --tblout GCF_010723575.1_ASM1072357v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg33069ba7-52ef-48f8-9cb9-2f5d1e95db74/dqc_reference/reference_markers.hmm GCF_010723575.1_ASM1072357v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:22:09,115] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:22:09,117] [INFO] Found 6/6 markers.
[2024-01-24 13:22:09,172] [INFO] Query marker FASTA was written to GCF_010723575.1_ASM1072357v1_genomic.fna/markers.fasta
[2024-01-24 13:22:09,173] [INFO] Task started: Blastn
[2024-01-24 13:22:09,173] [INFO] Running command: blastn -query GCF_010723575.1_ASM1072357v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg33069ba7-52ef-48f8-9cb9-2f5d1e95db74/dqc_reference/reference_markers.fasta -out GCF_010723575.1_ASM1072357v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:10,152] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:10,157] [INFO] Selected 26 target genomes.
[2024-01-24 13:22:10,157] [INFO] Target genome list was writen to GCF_010723575.1_ASM1072357v1_genomic.fna/target_genomes.txt
[2024-01-24 13:22:10,197] [INFO] Task started: fastANI
[2024-01-24 13:22:10,198] [INFO] Running command: fastANI --query /var/lib/cwl/stg63959946-d935-4543-bdfa-3bbd8d324941/GCF_010723575.1_ASM1072357v1_genomic.fna.gz --refList GCF_010723575.1_ASM1072357v1_genomic.fna/target_genomes.txt --output GCF_010723575.1_ASM1072357v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:22:44,626] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:44,626] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg33069ba7-52ef-48f8-9cb9-2f5d1e95db74/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:22:44,627] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg33069ba7-52ef-48f8-9cb9-2f5d1e95db74/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:22:44,657] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:22:44,657] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:22:44,657] [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 shinjukuense	strain=JCM 14233	GCA_010730055.1	398694	398694	type	True	80.8676	963	2304	95	below_threshold
Mycobacterium shinjukuense	strain=CCUG 53584	GCA_002086755.1	398694	398694	type	True	80.8647	923	2304	95	below_threshold
Mycobacterium heidelbergense	strain=JCM 14842	GCA_010730745.1	53376	53376	type	True	80.8241	1013	2304	95	below_threshold
Mycobacterium angelicum	strain=DSM 45057	GCA_002086155.1	470074	470074	type	True	80.8188	1176	2304	95	below_threshold
Mycobacterium paraense	strain=IEC26	GCA_002101815.1	767916	767916	type	True	80.795	1100	2304	95	below_threshold
Mycobacterium riyadhense	strain=DSM 45176	GCA_002101845.1	486698	486698	type	True	80.4816	1098	2304	95	below_threshold
Mycobacterium innocens	strain=MK13	GCA_900566055.1	2341083	2341083	type	True	80.4562	1011	2304	95	below_threshold
Mycobacterium kubicae	strain=JCM 13573	GCA_010723135.1	120959	120959	type	True	80.4243	1039	2304	95	below_threshold
Mycobacterium colombiense	strain=CECT 3035	GCA_002105755.1	339268	339268	suspected-type	True	80.4012	1024	2304	95	below_threshold
Mycobacterium colombiense	strain=CECT 3035	GCA_000222105.4	339268	339268	suspected-type	True	80.3951	1035	2304	95	below_threshold
Mycobacterium asiaticum	strain=DSM 44297	GCA_000613245.1	1790	1790	suspected-type	True	80.3234	1199	2304	95	below_threshold
Mycobacterium simulans	strain=FI-09026	GCA_900232995.1	627089	627089	type	True	80.3124	1146	2304	95	below_threshold
Mycobacterium asiaticum	strain=DSM 44297	GCA_002086545.1	1790	1790	suspected-type	True	80.2974	1215	2304	95	below_threshold
Mycobacterium ostraviense	strain=241/15	GCA_002705925.1	2738409	2738409	type	True	80.2824	1066	2304	95	below_threshold
Mycobacterium gordonae	strain=DSM 44160	GCA_002101675.1	1778	1778	type	True	80.2585	1241	2304	95	below_threshold
Mycobacterium persicum	strain=AFPC-000227	GCA_002086675.1	1487726	1487726	type	True	80.2503	995	2304	95	below_threshold
Mycobacterium intracellulare subsp. yongonense	strain=05-1390	GCA_000418535.2	1203599	1767	type	True	80.2397	1038	2304	95	below_threshold
Mycobacterium pseudokansasii	strain=MK142	GCA_900566075.1	2341080	2341080	type	True	80.0796	1077	2304	95	below_threshold
Mycobacterium parmense	strain=DSM 44553	GCA_002102335.1	185642	185642	type	True	80.0555	987	2304	95	below_threshold
Mycobacterium vicinigordonae	strain=24	GCA_013466425.1	1719132	1719132	type	True	79.9367	1066	2304	95	below_threshold
Mycobacterium haemophilum	strain=ATCC 29548	GCA_000340435.3	29311	29311	type	True	79.4921	748	2304	95	below_threshold
Mycobacterium pallens	strain=JCM 16370	GCA_019456675.1	370524	370524	type	True	78.363	702	2304	95	below_threshold
Mycolicibacterium fortuitum subsp. fortuitum	strain=JCM 6387	GCA_022179545.1	144549	1766	type	True	78.3471	634	2304	95	below_threshold
Mycolicibacterium baixiangningiae	strain=LJ126	GCA_014893035.1	2761578	2761578	type	True	78.2613	650	2304	95	below_threshold
Mycolicibacterium baixiangningiae	strain=LJ126	GCA_016313185.1	2761578	2761578	type	True	78.2533	659	2304	95	below_threshold
Mycolicibacterium stellerae	strain=CECT 8783	GCA_003719305.1	2358193	2358193	type	True	78.1562	664	2304	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:22:44,659] [INFO] DFAST Taxonomy check result was written to GCF_010723575.1_ASM1072357v1_genomic.fna/tc_result.tsv
[2024-01-24 13:22:44,659] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:22:44,660] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:22:44,660] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg33069ba7-52ef-48f8-9cb9-2f5d1e95db74/dqc_reference/checkm_data
[2024-01-24 13:22:44,661] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:22:44,721] [INFO] Task started: CheckM
[2024-01-24 13:22:44,721] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_010723575.1_ASM1072357v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_010723575.1_ASM1072357v1_genomic.fna/checkm_input GCF_010723575.1_ASM1072357v1_genomic.fna/checkm_result
[2024-01-24 13:24:01,955] [INFO] Task succeeded: CheckM
[2024-01-24 13:24:01,956] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:24:01,982] [INFO] ===== Completeness check finished =====
[2024-01-24 13:24:01,982] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:24:01,983] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_010723575.1_ASM1072357v1_genomic.fna/markers.fasta)
[2024-01-24 13:24:01,983] [INFO] Task started: Blastn
[2024-01-24 13:24:01,983] [INFO] Running command: blastn -query GCF_010723575.1_ASM1072357v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg33069ba7-52ef-48f8-9cb9-2f5d1e95db74/dqc_reference/reference_markers_gtdb.fasta -out GCF_010723575.1_ASM1072357v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:24:03,319] [INFO] Task succeeded: Blastn
[2024-01-24 13:24:03,324] [INFO] Selected 23 target genomes.
[2024-01-24 13:24:03,324] [INFO] Target genome list was writen to GCF_010723575.1_ASM1072357v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:24:03,533] [INFO] Task started: fastANI
[2024-01-24 13:24:03,534] [INFO] Running command: fastANI --query /var/lib/cwl/stg63959946-d935-4543-bdfa-3bbd8d324941/GCF_010723575.1_ASM1072357v1_genomic.fna.gz --refList GCF_010723575.1_ASM1072357v1_genomic.fna/target_genomes_gtdb.txt --output GCF_010723575.1_ASM1072357v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:24:37,394] [INFO] Task succeeded: fastANI
[2024-01-24 13:24:37,415] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:24:37,415] [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_010723575.1	s__Mycobacterium bourgelatii	100.0	2303	2304	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002086275.1	s__Mycobacterium intermedium	91.9281	1898	2304	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.91	99.88	0.97	0.95	3	-
GCF_010730055.1	s__Mycobacterium shinjukuense	80.8562	964	2304	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.98	99.98	1.00	1.00	2	-
GCF_002086155.1	s__Mycobacterium angelicum	80.8186	1178	2304	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002101815.1	s__Mycobacterium paraense	80.7815	1100	2304	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.85	98.84	0.95	0.95	4	-
GCF_001673535.1	s__Mycobacterium sp001673535	80.7055	1077	2304	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	80.6854	1067	2304	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001673635.1	s__Mycobacterium asiaticum_C	80.6287	1187	2304	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.07	99.07	0.94	0.94	2	-
GCF_001668675.1	s__Mycobacterium asiaticum_D	80.6051	1172	2304	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	80.5532	1098	2304	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	80.5426	1085	2304	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002101845.1	s__Mycobacterium riyadhense	80.4775	1103	2304	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.42	99.30	0.97	0.96	10	-
GCF_900566055.1	s__Mycobacterium innocens	80.4482	1013	2304	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.27	98.57	0.94	0.90	3	-
GCF_017086405.1	s__Mycobacterium gordonae_D	80.3796	1199	2304	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002101675.1	s__Mycobacterium gordonae	80.2677	1237	2304	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.22	98.97	0.90	0.87	6	-
GCF_002086675.1	s__Mycobacterium persicum	80.2348	999	2304	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.71	99.58	0.97	0.95	12	-
GCF_001667115.1	s__Mycobacterium sp001667115	80.0821	1025	2304	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001665395.1	s__Mycobacterium sp001665395	79.9674	1036	2304	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	79.5904	773	2304	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000340435.2	s__Mycobacterium haemophilum	79.5094	745	2304	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.07	99.06	0.94	0.94	5	-
GCF_000612725.1	s__Mycobacterium austroafricanum	78.4378	678	2304	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.53	98.42	0.88	0.88	3	-
GCF_000382405.1	s__Mycobacterium sp000382405	78.3882	468	2304	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011620645.1	s__Mycobacterium sp011620645	77.9636	453	2304	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 13:24:37,416] [INFO] GTDB search result was written to GCF_010723575.1_ASM1072357v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:24:37,417] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:24:37,421] [INFO] DFAST_QC result json was written to GCF_010723575.1_ASM1072357v1_genomic.fna/dqc_result.json
[2024-01-24 13:24:37,421] [INFO] DFAST_QC completed!
[2024-01-24 13:24:37,422] [INFO] Total running time: 0h2m57s