[2024-01-24 12:44:51,879] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:44:51,881] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:44:51,881] [INFO] DQC Reference Directory: /var/lib/cwl/stg833bf800-9450-478a-a99f-b42a0f85413d/dqc_reference
[2024-01-24 12:44:53,100] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:44:53,101] [INFO] Task started: Prodigal
[2024-01-24 12:44:53,101] [INFO] Running command: gunzip -c /var/lib/cwl/stg185346c4-7f1f-4070-ac51-39113740d557/GCF_010731875.1_ASM1073187v1_genomic.fna.gz | prodigal -d GCF_010731875.1_ASM1073187v1_genomic.fna/cds.fna -a GCF_010731875.1_ASM1073187v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:45:08,867] [INFO] Task succeeded: Prodigal
[2024-01-24 12:45:08,867] [INFO] Task started: HMMsearch
[2024-01-24 12:45:08,867] [INFO] Running command: hmmsearch --tblout GCF_010731875.1_ASM1073187v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg833bf800-9450-478a-a99f-b42a0f85413d/dqc_reference/reference_markers.hmm GCF_010731875.1_ASM1073187v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:45:09,175] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:45:09,177] [INFO] Found 6/6 markers.
[2024-01-24 12:45:09,224] [INFO] Query marker FASTA was written to GCF_010731875.1_ASM1073187v1_genomic.fna/markers.fasta
[2024-01-24 12:45:09,224] [INFO] Task started: Blastn
[2024-01-24 12:45:09,225] [INFO] Running command: blastn -query GCF_010731875.1_ASM1073187v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg833bf800-9450-478a-a99f-b42a0f85413d/dqc_reference/reference_markers.fasta -out GCF_010731875.1_ASM1073187v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:45:10,295] [INFO] Task succeeded: Blastn
[2024-01-24 12:45:10,300] [INFO] Selected 13 target genomes.
[2024-01-24 12:45:10,300] [INFO] Target genome list was writen to GCF_010731875.1_ASM1073187v1_genomic.fna/target_genomes.txt
[2024-01-24 12:45:10,312] [INFO] Task started: fastANI
[2024-01-24 12:45:10,312] [INFO] Running command: fastANI --query /var/lib/cwl/stg185346c4-7f1f-4070-ac51-39113740d557/GCF_010731875.1_ASM1073187v1_genomic.fna.gz --refList GCF_010731875.1_ASM1073187v1_genomic.fna/target_genomes.txt --output GCF_010731875.1_ASM1073187v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:45:28,319] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:28,319] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg833bf800-9450-478a-a99f-b42a0f85413d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:45:28,320] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg833bf800-9450-478a-a99f-b42a0f85413d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:45:28,331] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:45:28,332] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:45:28,332] [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 sarraceniae	strain=JCM 30395	GCA_010731875.1	1534348	1534348	type	True	100.0	1609	1609	95	conclusive
Mycolicibacterium helvum	strain=JCM 30396	GCA_010731895.1	1534349	1534349	type	True	86.8216	1296	1609	95	below_threshold
Mycolicibacterium sphagni	strain=ATCC 33027	GCA_002250655.1	1786	1786	type	True	85.3461	1259	1609	95	below_threshold
Mycolicibacterium vinylchloridicum	strain=CECT 8761	GCA_013404075.1	2736928	2736928	type	True	85.1756	1237	1609	95	below_threshold
Mycobacterium pallens	strain=JCM 16370	GCA_019456675.1	370524	370524	type	True	83.8362	1203	1609	95	below_threshold
Mycobacterium crocinum	strain=JCM 16369	GCA_022370635.3	388459	388459	type	True	83.737	1197	1609	95	below_threshold
Mycolicibacterium aichiense	strain=NCTC10820	GCA_900453085.1	1799	1799	type	True	83.6004	1202	1609	95	below_threshold
Mycolicibacterium aromaticivorans	strain=JS19b1	GCA_000559085.2	318425	318425	type	True	83.4289	1192	1609	95	below_threshold
Mycolicibacterium rhodesiae	strain=DSM 44223	GCA_002086695.1	36814	36814	type	True	83.4115	1191	1609	95	below_threshold
Mycolicibacterium anyangense	strain=JCM 30275	GCA_010731855.1	1431246	1431246	type	True	81.4149	983	1609	95	below_threshold
Mycolicibacterium fortuitum subsp. fortuitum	strain=JCM 6387	GCA_022179545.1	144549	1766	type	True	79.2537	713	1609	95	below_threshold
Mycolicibacterium lacusdiani	strain=JXJ CY 35	GCA_021916785.1	2895283	2895283	type	True	79.1514	689	1609	95	below_threshold
Mycolicibacterium arabiense	strain=JCM 18538	GCA_010731815.2	1286181	1286181	type	True	79.15	721	1609	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:45:28,334] [INFO] DFAST Taxonomy check result was written to GCF_010731875.1_ASM1073187v1_genomic.fna/tc_result.tsv
[2024-01-24 12:45:28,334] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:45:28,334] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:45:28,335] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg833bf800-9450-478a-a99f-b42a0f85413d/dqc_reference/checkm_data
[2024-01-24 12:45:28,336] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:45:28,386] [INFO] Task started: CheckM
[2024-01-24 12:45:28,386] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_010731875.1_ASM1073187v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_010731875.1_ASM1073187v1_genomic.fna/checkm_input GCF_010731875.1_ASM1073187v1_genomic.fna/checkm_result
[2024-01-24 12:46:14,721] [INFO] Task succeeded: CheckM
[2024-01-24 12:46:14,722] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:46:14,748] [INFO] ===== Completeness check finished =====
[2024-01-24 12:46:14,748] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:46:14,749] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_010731875.1_ASM1073187v1_genomic.fna/markers.fasta)
[2024-01-24 12:46:14,749] [INFO] Task started: Blastn
[2024-01-24 12:46:14,750] [INFO] Running command: blastn -query GCF_010731875.1_ASM1073187v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg833bf800-9450-478a-a99f-b42a0f85413d/dqc_reference/reference_markers_gtdb.fasta -out GCF_010731875.1_ASM1073187v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:46:16,250] [INFO] Task succeeded: Blastn
[2024-01-24 12:46:16,256] [INFO] Selected 11 target genomes.
[2024-01-24 12:46:16,256] [INFO] Target genome list was writen to GCF_010731875.1_ASM1073187v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:46:16,273] [INFO] Task started: fastANI
[2024-01-24 12:46:16,273] [INFO] Running command: fastANI --query /var/lib/cwl/stg185346c4-7f1f-4070-ac51-39113740d557/GCF_010731875.1_ASM1073187v1_genomic.fna.gz --refList GCF_010731875.1_ASM1073187v1_genomic.fna/target_genomes_gtdb.txt --output GCF_010731875.1_ASM1073187v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:46:32,048] [INFO] Task succeeded: fastANI
[2024-01-24 12:46:32,064] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:46:32,065] [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_010731875.1	s__Mycobacterium sarraceniae	100.0	1609	1609	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_013337765.1	s__Mycobacterium sp003053865	87.2888	1261	1609	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	95.43	95.41	0.83	0.83	3	-
GCA_900078375.1	s__Mycobacterium sp900078375	87.1258	1257	1609	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010731895.1	s__Mycobacterium helvum	86.8103	1299	1609	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004362315.1	s__Mycobacterium sp004362315	85.4339	1268	1609	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.02	98.99	0.96	0.96	6	-
GCF_002250655.1	s__Mycobacterium sphagni	85.3468	1259	1609	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000230935.1	s__Mycobacterium rhodesiae_B	85.2122	1232	1609	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013404075.1	s__Mycobacterium sp013404075	85.1837	1235	1609	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001886515.1	s__Mycobacterium sp001886515	83.9396	1183	1609	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.54	98.54	0.94	0.94	2	-
GCF_002887815.1	s__Mycobacterium sp002887815	83.6129	1191	1609	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010729305.1	s__Mycobacterium psychrotolerans	79.5303	772	1609	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	96.53	96.53	0.90	0.90	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:46:32,066] [INFO] GTDB search result was written to GCF_010731875.1_ASM1073187v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:46:32,067] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:46:32,070] [INFO] DFAST_QC result json was written to GCF_010731875.1_ASM1073187v1_genomic.fna/dqc_result.json
[2024-01-24 12:46:32,070] [INFO] DFAST_QC completed!
[2024-01-24 12:46:32,070] [INFO] Total running time: 0h1m40s