[2024-01-25 19:40:06,040] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:40:06,042] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:40:06,042] [INFO] DQC Reference Directory: /var/lib/cwl/stgb822949d-4f89-4f3f-9800-3fa25936de0f/dqc_reference
[2024-01-25 19:40:07,235] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:40:07,236] [INFO] Task started: Prodigal
[2024-01-25 19:40:07,236] [INFO] Running command: gunzip -c /var/lib/cwl/stg76f426a4-4c4e-4060-bb63-7b9c3ab390d3/GCF_001552315.1_ASM155231v1_genomic.fna.gz | prodigal -d GCF_001552315.1_ASM155231v1_genomic.fna/cds.fna -a GCF_001552315.1_ASM155231v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:40:30,880] [INFO] Task succeeded: Prodigal
[2024-01-25 19:40:30,881] [INFO] Task started: HMMsearch
[2024-01-25 19:40:30,881] [INFO] Running command: hmmsearch --tblout GCF_001552315.1_ASM155231v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb822949d-4f89-4f3f-9800-3fa25936de0f/dqc_reference/reference_markers.hmm GCF_001552315.1_ASM155231v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:40:31,186] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:40:31,187] [INFO] Found 6/6 markers.
[2024-01-25 19:40:31,252] [INFO] Query marker FASTA was written to GCF_001552315.1_ASM155231v1_genomic.fna/markers.fasta
[2024-01-25 19:40:31,252] [INFO] Task started: Blastn
[2024-01-25 19:40:31,252] [INFO] Running command: blastn -query GCF_001552315.1_ASM155231v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb822949d-4f89-4f3f-9800-3fa25936de0f/dqc_reference/reference_markers.fasta -out GCF_001552315.1_ASM155231v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:40:32,392] [INFO] Task succeeded: Blastn
[2024-01-25 19:40:32,395] [INFO] Selected 16 target genomes.
[2024-01-25 19:40:32,396] [INFO] Target genome list was writen to GCF_001552315.1_ASM155231v1_genomic.fna/target_genomes.txt
[2024-01-25 19:40:32,406] [INFO] Task started: fastANI
[2024-01-25 19:40:32,407] [INFO] Running command: fastANI --query /var/lib/cwl/stg76f426a4-4c4e-4060-bb63-7b9c3ab390d3/GCF_001552315.1_ASM155231v1_genomic.fna.gz --refList GCF_001552315.1_ASM155231v1_genomic.fna/target_genomes.txt --output GCF_001552315.1_ASM155231v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:40:55,946] [INFO] Task succeeded: fastANI
[2024-01-25 19:40:55,947] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb822949d-4f89-4f3f-9800-3fa25936de0f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:40:55,947] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb822949d-4f89-4f3f-9800-3fa25936de0f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:40:55,957] [INFO] Found 16 fastANI hits (5 hits with ANI > threshold)
[2024-01-25 19:40:55,957] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-25 19:40:55,957] [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 chlorophenolicum	strain=NBRC 15527	GCA_001552315.1	37916	37916	type	True	100.0	2386	2392	95	inconclusive
Mycolicibacterium chlorophenolicum	strain=DSM 43826	GCA_001044235.1	37916	37916	type	True	99.9926	2378	2392	95	inconclusive
Mycolicibacterium chubuense	strain=DSM 44219	GCA_002086595.1	1800	1800	type	True	95.8646	1755	2392	95	inconclusive
Mycolicibacterium chubuense	strain=DSM 44219	GCA_001044255.1	1800	1800	type	True	95.84	1732	2392	95	inconclusive
Mycolicibacterium chubuense	strain=NCTC10819	GCA_900453455.1	1800	1800	type	True	95.7518	1791	2392	95	inconclusive
Mycolicibacterium psychrotolerans	strain=JCM 13323	GCA_010729305.1	216929	216929	type	True	91.3519	1616	2392	95	below_threshold
Mycolicibacterium arabiense	strain=JCM 18538	GCA_010731815.2	1286181	1286181	type	True	80.6315	1109	2392	95	below_threshold
Mycolicibacterium lacusdiani	strain=JXJ CY 35	GCA_021916785.1	2895283	2895283	type	True	80.4939	1137	2392	95	below_threshold
Mycobacterium dioxanotrophicus	strain=PH-06	GCA_002157835.1	482462	482462	type	True	80.2646	1038	2392	95	below_threshold
Mycolicibacterium anyangense	strain=JCM 30275	GCA_010731855.1	1431246	1431246	type	True	80.1318	923	2392	95	below_threshold
Mycolicibacterium fortuitum subsp. fortuitum	strain=JCM 6387	GCA_022179545.1	144549	1766	type	True	80.061	965	2392	95	below_threshold
Mycolicibacterium fluoranthenivorans	strain=DSM 44556	GCA_011758805.1	258505	258505	type	True	79.9732	1004	2392	95	below_threshold
Mycolicibacterium vinylchloridicum	strain=CECT 8761	GCA_013404075.1	2736928	2736928	type	True	79.8927	957	2392	95	below_threshold
Mycobacteroides saopaulense	strain=EPM10906	GCA_001456355.1	1578165	1578165	type	True	78.4254	470	2392	95	below_threshold
Pseudonocardia thermophila	strain=DSM 43832	GCA_900142365.1	1848	1848	type	True	76.7787	526	2392	95	below_threshold
Actinokineospora spheciospongiae	strain=EG49	GCA_000564855.1	909613	909613	type	True	76.6174	513	2392	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:40:55,959] [INFO] DFAST Taxonomy check result was written to GCF_001552315.1_ASM155231v1_genomic.fna/tc_result.tsv
[2024-01-25 19:40:55,959] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:40:55,959] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:40:55,959] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb822949d-4f89-4f3f-9800-3fa25936de0f/dqc_reference/checkm_data
[2024-01-25 19:40:55,960] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:40:56,028] [INFO] Task started: CheckM
[2024-01-25 19:40:56,028] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001552315.1_ASM155231v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001552315.1_ASM155231v1_genomic.fna/checkm_input GCF_001552315.1_ASM155231v1_genomic.fna/checkm_result
[2024-01-25 19:42:21,961] [INFO] Task succeeded: CheckM
[2024-01-25 19:42:21,962] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:42:21,986] [INFO] ===== Completeness check finished =====
[2024-01-25 19:42:21,987] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:42:21,988] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001552315.1_ASM155231v1_genomic.fna/markers.fasta)
[2024-01-25 19:42:21,988] [INFO] Task started: Blastn
[2024-01-25 19:42:21,988] [INFO] Running command: blastn -query GCF_001552315.1_ASM155231v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb822949d-4f89-4f3f-9800-3fa25936de0f/dqc_reference/reference_markers_gtdb.fasta -out GCF_001552315.1_ASM155231v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:42:23,728] [INFO] Task succeeded: Blastn
[2024-01-25 19:42:23,736] [INFO] Selected 13 target genomes.
[2024-01-25 19:42:23,736] [INFO] Target genome list was writen to GCF_001552315.1_ASM155231v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:42:23,757] [INFO] Task started: fastANI
[2024-01-25 19:42:23,758] [INFO] Running command: fastANI --query /var/lib/cwl/stg76f426a4-4c4e-4060-bb63-7b9c3ab390d3/GCF_001552315.1_ASM155231v1_genomic.fna.gz --refList GCF_001552315.1_ASM155231v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001552315.1_ASM155231v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:42:43,947] [INFO] Task succeeded: fastANI
[2024-01-25 19:42:43,956] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:42:43,956] [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_001044235.1	s__Mycobacterium chlorophenolicum	99.9926	2378	2392	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.8643	98.88	97.93	0.94	0.90	4	conclusive
GCF_001044255.1	s__Mycobacterium chubuense	95.8524	1731	2392	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.8643	99.98	99.97	0.99	0.98	3	-
GCF_010729305.1	s__Mycobacterium psychrotolerans	91.353	1616	2392	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	96.53	96.53	0.90	0.90	2	-
GCA_000762985.1	s__Mycobacterium rufum_A	89.3154	1706	2392	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001044245.1	s__Mycobacterium obuense	84.3925	1388	2392	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	97.74	96.27	0.88	0.86	5	-
GCF_007096635.1	s__Mycobacterium sp007096635	84.2511	1373	2392	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001545925.1	s__Mycobacterium sp001545925	82.9206	1067	2392	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001050035.1	s__Mycobacterium komanii	81.0094	984	2392	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002723835.1	s__Mycobacterium sp002723835	80.7214	1051	2392	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000328565.1	s__Mycobacterium sp000328565	80.6719	1031	2392	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010729665.1	s__Mycobacterium madagascariense	80.4827	1008	2392	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000243415.2	s__Mycobacterium tusciae_A	80.3106	1004	2392	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002157835.1	s__Mycobacterium dioxanotrophicus	80.2643	1040	2392	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 19:42:43,957] [INFO] GTDB search result was written to GCF_001552315.1_ASM155231v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:42:43,958] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:42:43,961] [INFO] DFAST_QC result json was written to GCF_001552315.1_ASM155231v1_genomic.fna/dqc_result.json
[2024-01-25 19:42:43,961] [INFO] DFAST_QC completed!
[2024-01-25 19:42:43,961] [INFO] Total running time: 0h2m38s