[2024-01-25 18:33:35,983] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:33:35,984] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:33:35,984] [INFO] DQC Reference Directory: /var/lib/cwl/stg97d29201-b212-4bc7-91a6-9d65fafe1375/dqc_reference
[2024-01-25 18:33:37,095] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:33:37,095] [INFO] Task started: Prodigal
[2024-01-25 18:33:37,096] [INFO] Running command: gunzip -c /var/lib/cwl/stg59a8fc95-1fc9-404f-ae55-846b34f78e91/GCF_025821955.1_ASM2582195v1_genomic.fna.gz | prodigal -d GCF_025821955.1_ASM2582195v1_genomic.fna/cds.fna -a GCF_025821955.1_ASM2582195v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:33:57,989] [INFO] Task succeeded: Prodigal
[2024-01-25 18:33:57,989] [INFO] Task started: HMMsearch
[2024-01-25 18:33:57,989] [INFO] Running command: hmmsearch --tblout GCF_025821955.1_ASM2582195v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg97d29201-b212-4bc7-91a6-9d65fafe1375/dqc_reference/reference_markers.hmm GCF_025821955.1_ASM2582195v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:33:58,288] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:33:58,289] [INFO] Found 6/6 markers.
[2024-01-25 18:33:58,353] [INFO] Query marker FASTA was written to GCF_025821955.1_ASM2582195v1_genomic.fna/markers.fasta
[2024-01-25 18:33:58,354] [INFO] Task started: Blastn
[2024-01-25 18:33:58,354] [INFO] Running command: blastn -query GCF_025821955.1_ASM2582195v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg97d29201-b212-4bc7-91a6-9d65fafe1375/dqc_reference/reference_markers.fasta -out GCF_025821955.1_ASM2582195v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:33:59,286] [INFO] Task succeeded: Blastn
[2024-01-25 18:33:59,289] [INFO] Selected 26 target genomes.
[2024-01-25 18:33:59,289] [INFO] Target genome list was writen to GCF_025821955.1_ASM2582195v1_genomic.fna/target_genomes.txt
[2024-01-25 18:33:59,341] [INFO] Task started: fastANI
[2024-01-25 18:33:59,342] [INFO] Running command: fastANI --query /var/lib/cwl/stg59a8fc95-1fc9-404f-ae55-846b34f78e91/GCF_025821955.1_ASM2582195v1_genomic.fna.gz --refList GCF_025821955.1_ASM2582195v1_genomic.fna/target_genomes.txt --output GCF_025821955.1_ASM2582195v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:34:34,960] [INFO] Task succeeded: fastANI
[2024-01-25 18:34:34,960] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg97d29201-b212-4bc7-91a6-9d65fafe1375/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:34:34,961] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg97d29201-b212-4bc7-91a6-9d65fafe1375/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:34:34,976] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:34:34,976] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:34:34,976] [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 angelicum	strain=DSM 45057	GCA_002086155.1	470074	470074	type	True	80.919	1163	2207	95	below_threshold
Mycobacterium heidelbergense	strain=JCM 14842	GCA_010730745.1	53376	53376	type	True	80.8749	998	2207	95	below_threshold
Mycobacterium shinjukuense	strain=CCUG 53584	GCA_002086755.1	398694	398694	type	True	80.7852	922	2207	95	below_threshold
Mycobacterium shinjukuense	strain=JCM 14233	GCA_010730055.1	398694	398694	type	True	80.747	970	2207	95	below_threshold
Mycobacterium paraense	strain=IEC26	GCA_002101815.1	767916	767916	type	True	80.7318	1095	2207	95	below_threshold
Mycobacterium kubicae	strain=JCM 13573	GCA_010723135.1	120959	120959	type	True	80.4268	1038	2207	95	below_threshold
Mycobacterium riyadhense	strain=DSM 45176	GCA_002101845.1	486698	486698	type	True	80.4168	1104	2207	95	below_threshold
Mycobacterium simulans	strain=FI-09026	GCA_900232995.1	627089	627089	type	True	80.3629	1124	2207	95	below_threshold
Mycobacterium colombiense	strain=CECT 3035	GCA_002105755.1	339268	339268	suspected-type	True	80.3528	1043	2207	95	below_threshold
Mycobacterium gordonae	strain=DSM 44160	GCA_002101675.1	1778	1778	type	True	80.3516	1221	2207	95	below_threshold
Mycobacterium asiaticum	strain=DSM 44297	GCA_002086545.1	1790	1790	suspected-type	True	80.3354	1202	2207	95	below_threshold
Mycobacterium asiaticum	strain=DSM 44297	GCA_000613245.1	1790	1790	suspected-type	True	80.3311	1211	2207	95	below_threshold
Mycobacterium innocens	strain=MK13	GCA_900566055.1	2341083	2341083	type	True	80.3245	994	2207	95	below_threshold
Mycobacterium colombiense	strain=CECT 3035	GCA_000222105.4	339268	339268	suspected-type	True	80.3008	1051	2207	95	below_threshold
Mycobacterium ostraviense	strain=241/15	GCA_002705925.1	2738409	2738409	type	True	80.2369	1058	2207	95	below_threshold
Mycobacterium intracellulare subsp. yongonense	strain=05-1390	GCA_000418535.2	1203599	1767	type	True	80.2295	1020	2207	95	below_threshold
Mycobacterium persicum	strain=AFPC-000227	GCA_002086675.1	1487726	1487726	type	True	80.213	1002	2207	95	below_threshold
Mycobacterium pseudokansasii	strain=MK142	GCA_900566075.1	2341080	2341080	type	True	80.2037	1023	2207	95	below_threshold
Mycobacterium parmense	strain=DSM 44553	GCA_002102335.1	185642	185642	type	True	79.9701	977	2207	95	below_threshold
Mycobacterium vicinigordonae	strain=24	GCA_013466425.1	1719132	1719132	type	True	79.9017	1063	2207	95	below_threshold
Mycobacterium haemophilum	strain=ATCC 29548	GCA_000340435.3	29311	29311	type	True	79.5239	736	2207	95	below_threshold
Mycolicibacterium baixiangningiae	strain=LJ126	GCA_016313185.1	2761578	2761578	type	True	78.4202	635	2207	95	below_threshold
Mycolicibacterium fortuitum subsp. fortuitum	strain=JCM 6387	GCA_022179545.1	144549	1766	type	True	78.3685	615	2207	95	below_threshold
Mycolicibacterium baixiangningiae	strain=LJ126	GCA_014893035.1	2761578	2761578	type	True	78.3557	625	2207	95	below_threshold
Mycobacterium pallens	strain=JCM 16370	GCA_019456675.1	370524	370524	type	True	78.3424	697	2207	95	below_threshold
Mycolicibacterium stellerae	strain=CECT 8783	GCA_003719305.1	2358193	2358193	type	True	78.1315	660	2207	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:34:34,977] [INFO] DFAST Taxonomy check result was written to GCF_025821955.1_ASM2582195v1_genomic.fna/tc_result.tsv
[2024-01-25 18:34:34,978] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:34:34,978] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:34:34,978] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg97d29201-b212-4bc7-91a6-9d65fafe1375/dqc_reference/checkm_data
[2024-01-25 18:34:34,979] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:34:35,043] [INFO] Task started: CheckM
[2024-01-25 18:34:35,043] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025821955.1_ASM2582195v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025821955.1_ASM2582195v1_genomic.fna/checkm_input GCF_025821955.1_ASM2582195v1_genomic.fna/checkm_result
[2024-01-25 18:35:35,207] [INFO] Task succeeded: CheckM
[2024-01-25 18:35:35,208] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:35:35,239] [INFO] ===== Completeness check finished =====
[2024-01-25 18:35:35,239] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:35:35,239] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025821955.1_ASM2582195v1_genomic.fna/markers.fasta)
[2024-01-25 18:35:35,239] [INFO] Task started: Blastn
[2024-01-25 18:35:35,240] [INFO] Running command: blastn -query GCF_025821955.1_ASM2582195v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg97d29201-b212-4bc7-91a6-9d65fafe1375/dqc_reference/reference_markers_gtdb.fasta -out GCF_025821955.1_ASM2582195v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:35:36,596] [INFO] Task succeeded: Blastn
[2024-01-25 18:35:36,600] [INFO] Selected 23 target genomes.
[2024-01-25 18:35:36,600] [INFO] Target genome list was writen to GCF_025821955.1_ASM2582195v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:35:36,685] [INFO] Task started: fastANI
[2024-01-25 18:35:36,685] [INFO] Running command: fastANI --query /var/lib/cwl/stg59a8fc95-1fc9-404f-ae55-846b34f78e91/GCF_025821955.1_ASM2582195v1_genomic.fna.gz --refList GCF_025821955.1_ASM2582195v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025821955.1_ASM2582195v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:36:12,312] [INFO] Task succeeded: fastANI
[2024-01-25 18:36:12,325] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:36:12,326] [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	99.9844	2204	2207	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	92.0019	1888	2207	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.91	99.88	0.97	0.95	3	-
GCF_002086155.1	s__Mycobacterium angelicum	80.9126	1166	2207	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010730055.1	s__Mycobacterium shinjukuense	80.7708	967	2207	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.98	99.98	1.00	1.00	2	-
GCF_001673535.1	s__Mycobacterium sp001673535	80.7608	1062	2207	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	80.6986	1100	2207	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.85	98.84	0.95	0.95	4	-
GCF_001667015.1	s__Mycobacterium sp001667015	80.6267	1072	2207	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	80.572	1097	2207	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	80.5688	1176	2207	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	80.5596	1162	2207	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	80.5514	1084	2207	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	80.408	1106	2207	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.42	99.30	0.97	0.96	10	-
GCF_017086405.1	s__Mycobacterium gordonae_D	80.3375	1194	2207	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900566055.1	s__Mycobacterium innocens	80.3163	997	2207	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.27	98.57	0.94	0.90	3	-
GCF_002101675.1	s__Mycobacterium gordonae	80.3045	1235	2207	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	80.2505	994	2207	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	80.1558	1009	2207	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	79.999	1024	2207	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	79.6421	762	2207	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	79.546	733	2207	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.07	99.06	0.94	0.94	5	-
GCF_000382405.1	s__Mycobacterium sp000382405	78.4435	473	2207	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000612725.1	s__Mycobacterium austroafricanum	78.4382	662	2207	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.53	98.42	0.88	0.88	3	-
GCA_011620645.1	s__Mycobacterium sp011620645	78.1343	447	2207	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 18:36:12,328] [INFO] GTDB search result was written to GCF_025821955.1_ASM2582195v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:36:12,328] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:36:12,332] [INFO] DFAST_QC result json was written to GCF_025821955.1_ASM2582195v1_genomic.fna/dqc_result.json
[2024-01-25 18:36:12,332] [INFO] DFAST_QC completed!
[2024-01-25 18:36:12,333] [INFO] Total running time: 0h2m36s