[2024-01-24 13:51:12,209] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:51:12,211] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:51:12,211] [INFO] DQC Reference Directory: /var/lib/cwl/stg243225ef-4354-4fb5-bad4-73d5d3ccc35e/dqc_reference
[2024-01-24 13:51:13,463] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:51:13,464] [INFO] Task started: Prodigal
[2024-01-24 13:51:13,464] [INFO] Running command: gunzip -c /var/lib/cwl/stgfdab983a-d841-4ccb-a357-e7079b192595/GCF_005670655.1_ASM567065v1_genomic.fna.gz | prodigal -d GCF_005670655.1_ASM567065v1_genomic.fna/cds.fna -a GCF_005670655.1_ASM567065v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:51:34,648] [INFO] Task succeeded: Prodigal
[2024-01-24 13:51:34,648] [INFO] Task started: HMMsearch
[2024-01-24 13:51:34,649] [INFO] Running command: hmmsearch --tblout GCF_005670655.1_ASM567065v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg243225ef-4354-4fb5-bad4-73d5d3ccc35e/dqc_reference/reference_markers.hmm GCF_005670655.1_ASM567065v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:51:34,978] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:51:34,979] [INFO] Found 6/6 markers.
[2024-01-24 13:51:35,036] [INFO] Query marker FASTA was written to GCF_005670655.1_ASM567065v1_genomic.fna/markers.fasta
[2024-01-24 13:51:35,037] [INFO] Task started: Blastn
[2024-01-24 13:51:35,037] [INFO] Running command: blastn -query GCF_005670655.1_ASM567065v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg243225ef-4354-4fb5-bad4-73d5d3ccc35e/dqc_reference/reference_markers.fasta -out GCF_005670655.1_ASM567065v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:51:36,299] [INFO] Task succeeded: Blastn
[2024-01-24 13:51:36,303] [INFO] Selected 14 target genomes.
[2024-01-24 13:51:36,303] [INFO] Target genome list was writen to GCF_005670655.1_ASM567065v1_genomic.fna/target_genomes.txt
[2024-01-24 13:51:36,310] [INFO] Task started: fastANI
[2024-01-24 13:51:36,310] [INFO] Running command: fastANI --query /var/lib/cwl/stgfdab983a-d841-4ccb-a357-e7079b192595/GCF_005670655.1_ASM567065v1_genomic.fna.gz --refList GCF_005670655.1_ASM567065v1_genomic.fna/target_genomes.txt --output GCF_005670655.1_ASM567065v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:51:55,409] [INFO] Task succeeded: fastANI
[2024-01-24 13:51:55,410] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg243225ef-4354-4fb5-bad4-73d5d3ccc35e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:51:55,410] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg243225ef-4354-4fb5-bad4-73d5d3ccc35e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:51:55,431] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:51:55,431] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:51:55,431] [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 phocaicum	strain=DSM 45104	GCA_005670655.1	319706	319706	type	True	100.0	1880	1884	95	conclusive
Mycolicibacterium phocaicum	strain=JCM 15301	GCA_010731115.1	319706	319706	type	True	99.9922	1883	1884	95	conclusive
Mycolicibacterium llatzerense	strain=MG13	GCA_025331195.1	280871	280871	type	True	89.5455	1546	1884	95	below_threshold
Mycolicibacterium aubagnense	strain=DSM 45150	GCA_005670695.1	319707	319707	type	True	88.5757	1452	1884	95	below_threshold
Mycolicibacterium cosmeticum	strain=DSM 44829	GCA_005670675.1	258533	258533	type	True	80.8206	929	1884	95	below_threshold
Mycolicibacterium boenickei	strain=JCM 15653	GCA_010731295.1	146017	146017	type	True	80.5284	929	1884	95	below_threshold
Mycolicibacterium canariasense	strain=JCM15298	GCA_001570445.1	228230	228230	type	True	80.5205	902	1884	95	below_threshold
Mycolicibacterium fortuitum subsp. fortuitum	strain=JCM 6387	GCA_022179545.1	144549	1766	type	True	80.3743	875	1884	95	below_threshold
Mycolicibacterium mageritense	strain=CIP 104973	GCA_000612825.1	53462	53462	type	True	80.1343	947	1884	95	below_threshold
Mycolicibacterium litorale	strain=CGMCC 4.5724	GCA_004366555.1	758802	758802	type	True	80.0857	802	1884	95	below_threshold
Mycolicibacterium anyangense	strain=JCM 30275	GCA_010731855.1	1431246	1431246	type	True	79.729	762	1884	95	below_threshold
Mycobacterium pallens	strain=JCM 16370	GCA_019456675.1	370524	370524	type	True	79.6982	788	1884	95	below_threshold
Mycobacterium crocinum	strain=JCM 16369	GCA_022370635.3	388459	388459	type	True	79.5338	787	1884	95	below_threshold
Mycolicibacterium vinylchloridicum	strain=CECT 8761	GCA_013404075.1	2736928	2736928	type	True	79.4742	745	1884	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:51:55,433] [INFO] DFAST Taxonomy check result was written to GCF_005670655.1_ASM567065v1_genomic.fna/tc_result.tsv
[2024-01-24 13:51:55,434] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:51:55,434] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:51:55,435] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg243225ef-4354-4fb5-bad4-73d5d3ccc35e/dqc_reference/checkm_data
[2024-01-24 13:51:55,436] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:51:55,494] [INFO] Task started: CheckM
[2024-01-24 13:51:55,495] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005670655.1_ASM567065v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005670655.1_ASM567065v1_genomic.fna/checkm_input GCF_005670655.1_ASM567065v1_genomic.fna/checkm_result
[2024-01-24 13:53:00,852] [INFO] Task succeeded: CheckM
[2024-01-24 13:53:00,854] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:53:00,877] [INFO] ===== Completeness check finished =====
[2024-01-24 13:53:00,877] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:53:00,877] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005670655.1_ASM567065v1_genomic.fna/markers.fasta)
[2024-01-24 13:53:00,878] [INFO] Task started: Blastn
[2024-01-24 13:53:00,878] [INFO] Running command: blastn -query GCF_005670655.1_ASM567065v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg243225ef-4354-4fb5-bad4-73d5d3ccc35e/dqc_reference/reference_markers_gtdb.fasta -out GCF_005670655.1_ASM567065v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:53:02,771] [INFO] Task succeeded: Blastn
[2024-01-24 13:53:02,775] [INFO] Selected 8 target genomes.
[2024-01-24 13:53:02,775] [INFO] Target genome list was writen to GCF_005670655.1_ASM567065v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:53:02,784] [INFO] Task started: fastANI
[2024-01-24 13:53:02,784] [INFO] Running command: fastANI --query /var/lib/cwl/stgfdab983a-d841-4ccb-a357-e7079b192595/GCF_005670655.1_ASM567065v1_genomic.fna.gz --refList GCF_005670655.1_ASM567065v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005670655.1_ASM567065v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:53:15,654] [INFO] Task succeeded: fastANI
[2024-01-24 13:53:15,668] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:53:15,668] [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_010731115.1	s__Mycobacterium phocaicum	99.9922	1883	1884	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	96.06	95.24	0.87	0.80	8	conclusive
GCF_018326285.1	s__Mycobacterium sp018326285	92.7745	1653	1884	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_005670685.2	s__Mycobacterium mucogenicum_B	91.841	1600	1884	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.72	96.94	0.94	0.86	7	-
GCF_001905655.1	s__Mycobacterium sp001905655	90.3637	1471	1884	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000878195.1	s__Mycobacterium llatzerense	89.4476	1498	1884	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.29	97.98	0.87	0.81	4	-
GCF_009729075.1	s__Mycobacterium sp009729075	89.2564	1478	1884	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004363795.1	s__Mycobacterium sp004363795	89.0894	1491	1884	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_010730955.1	s__Mycobacterium aubagnense	88.5216	1482	1884	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.98	99.98	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:53:15,670] [INFO] GTDB search result was written to GCF_005670655.1_ASM567065v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:53:15,671] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:53:15,674] [INFO] DFAST_QC result json was written to GCF_005670655.1_ASM567065v1_genomic.fna/dqc_result.json
[2024-01-24 13:53:15,674] [INFO] DFAST_QC completed!
[2024-01-24 13:53:15,674] [INFO] Total running time: 0h2m3s