[2024-01-24 14:14:20,239] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:14:20,243] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:14:20,243] [INFO] DQC Reference Directory: /var/lib/cwl/stgff96ba18-af49-4f45-b66e-c4465bea9fab/dqc_reference
[2024-01-24 14:14:21,532] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:14:21,533] [INFO] Task started: Prodigal
[2024-01-24 14:14:21,534] [INFO] Running command: gunzip -c /var/lib/cwl/stg8863f5ca-6b57-4a42-8760-6db331b2d9a5/GCF_004366555.1_ASM436655v1_genomic.fna.gz | prodigal -d GCF_004366555.1_ASM436655v1_genomic.fna/cds.fna -a GCF_004366555.1_ASM436655v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:14:38,636] [INFO] Task succeeded: Prodigal
[2024-01-24 14:14:38,636] [INFO] Task started: HMMsearch
[2024-01-24 14:14:38,636] [INFO] Running command: hmmsearch --tblout GCF_004366555.1_ASM436655v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgff96ba18-af49-4f45-b66e-c4465bea9fab/dqc_reference/reference_markers.hmm GCF_004366555.1_ASM436655v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:14:38,912] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:14:38,913] [INFO] Found 6/6 markers.
[2024-01-24 14:14:38,961] [INFO] Query marker FASTA was written to GCF_004366555.1_ASM436655v1_genomic.fna/markers.fasta
[2024-01-24 14:14:38,961] [INFO] Task started: Blastn
[2024-01-24 14:14:38,962] [INFO] Running command: blastn -query GCF_004366555.1_ASM436655v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgff96ba18-af49-4f45-b66e-c4465bea9fab/dqc_reference/reference_markers.fasta -out GCF_004366555.1_ASM436655v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:14:40,233] [INFO] Task succeeded: Blastn
[2024-01-24 14:14:40,236] [INFO] Selected 10 target genomes.
[2024-01-24 14:14:40,237] [INFO] Target genome list was writen to GCF_004366555.1_ASM436655v1_genomic.fna/target_genomes.txt
[2024-01-24 14:14:40,242] [INFO] Task started: fastANI
[2024-01-24 14:14:40,242] [INFO] Running command: fastANI --query /var/lib/cwl/stg8863f5ca-6b57-4a42-8760-6db331b2d9a5/GCF_004366555.1_ASM436655v1_genomic.fna.gz --refList GCF_004366555.1_ASM436655v1_genomic.fna/target_genomes.txt --output GCF_004366555.1_ASM436655v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:14:54,797] [INFO] Task succeeded: fastANI
[2024-01-24 14:14:54,798] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgff96ba18-af49-4f45-b66e-c4465bea9fab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:14:54,798] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgff96ba18-af49-4f45-b66e-c4465bea9fab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:14:54,807] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:14:54,807] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:14:54,807] [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 litorale	strain=CGMCC 4.5724	GCA_004366555.1	758802	758802	type	True	100.0	1839	1841	95	conclusive
Mycolicibacterium litorale	strain=JCM 17423	GCA_010731695.1	758802	758802	type	True	99.9968	1841	1841	95	conclusive
Mycolicibacterium baixiangningiae	strain=LJ126	GCA_014893035.1	2761578	2761578	type	True	87.4475	1494	1841	95	below_threshold
Mycolicibacterium baixiangningiae	strain=LJ126	GCA_016313185.1	2761578	2761578	type	True	87.4243	1496	1841	95	below_threshold
Mycolicibacterium monacense	strain=DSM 44395	GCA_009931355.1	85693	85693	type	True	86.781	1475	1841	95	below_threshold
Mycolicibacterium monacense	strain=DSM 44395	GCA_002086655.1	85693	85693	type	True	86.7697	1450	1841	95	below_threshold
Mycolicibacterium monacense	strain=JCM 15658	GCA_010731575.1	85693	85693	type	True	86.7264	1472	1841	95	below_threshold
Mycolicibacterium fortuitum subsp. fortuitum	strain=JCM 6387	GCA_022179545.1	144549	1766	type	True	80.2139	974	1841	95	below_threshold
Mycobacterium crocinum	strain=JCM 16369	GCA_022370635.3	388459	388459	type	True	79.8859	891	1841	95	below_threshold
Mycolicibacterium vinylchloridicum	strain=CECT 8761	GCA_013404075.1	2736928	2736928	type	True	79.8235	899	1841	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:14:54,809] [INFO] DFAST Taxonomy check result was written to GCF_004366555.1_ASM436655v1_genomic.fna/tc_result.tsv
[2024-01-24 14:14:54,809] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:14:54,810] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:14:54,810] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgff96ba18-af49-4f45-b66e-c4465bea9fab/dqc_reference/checkm_data
[2024-01-24 14:14:54,811] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:14:54,863] [INFO] Task started: CheckM
[2024-01-24 14:14:54,863] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004366555.1_ASM436655v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004366555.1_ASM436655v1_genomic.fna/checkm_input GCF_004366555.1_ASM436655v1_genomic.fna/checkm_result
[2024-01-24 14:15:54,659] [INFO] Task succeeded: CheckM
[2024-01-24 14:15:54,660] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:15:54,682] [INFO] ===== Completeness check finished =====
[2024-01-24 14:15:54,682] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:15:54,683] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004366555.1_ASM436655v1_genomic.fna/markers.fasta)
[2024-01-24 14:15:54,683] [INFO] Task started: Blastn
[2024-01-24 14:15:54,683] [INFO] Running command: blastn -query GCF_004366555.1_ASM436655v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgff96ba18-af49-4f45-b66e-c4465bea9fab/dqc_reference/reference_markers_gtdb.fasta -out GCF_004366555.1_ASM436655v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:15:56,756] [INFO] Task succeeded: Blastn
[2024-01-24 14:15:56,759] [INFO] Selected 12 target genomes.
[2024-01-24 14:15:56,759] [INFO] Target genome list was writen to GCF_004366555.1_ASM436655v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:15:56,772] [INFO] Task started: fastANI
[2024-01-24 14:15:56,773] [INFO] Running command: fastANI --query /var/lib/cwl/stg8863f5ca-6b57-4a42-8760-6db331b2d9a5/GCF_004366555.1_ASM436655v1_genomic.fna.gz --refList GCF_004366555.1_ASM436655v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004366555.1_ASM436655v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:16:12,692] [INFO] Task succeeded: fastANI
[2024-01-24 14:16:12,704] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:16:12,704] [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_010731695.1	s__Mycobacterium litorale	99.9968	1841	1841	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_014218295.1	s__Mycobacterium litorale_B	88.1293	1550	1841	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016313185.1	s__Mycobacterium sp016313185	87.4156	1497	1841	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.68	97.36	0.93	0.85	3	-
GCF_001499995.1	s__Mycobacterium sp001499995	86.9364	1411	1841	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001500125.1	s__Mycobacterium sp001500125	86.8197	1446	1841	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010731575.1	s__Mycobacterium monacense	86.7265	1472	1841	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.29	98.82	0.95	0.89	9	-
GCF_004570325.1	s__Mycobacterium sp004570325	84.252	1348	1841	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017352375.1	s__Mycobacterium sp017352375	82.7871	1275	1841	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	81.3983	1096	1841	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.53	98.42	0.88	0.88	3	-
GCF_002086815.1	s__Mycobacterium parafortuitum	81.1404	1100	1841	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900603025.1	s__Mycobacterium hassiacum	80.7823	1009	1841	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.99	1.00	1.00	3	-
GCF_001494595.1	s__Mycobacterium sp001494595	80.344	923	1841	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 14:16:12,706] [INFO] GTDB search result was written to GCF_004366555.1_ASM436655v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:16:12,706] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:16:12,709] [INFO] DFAST_QC result json was written to GCF_004366555.1_ASM436655v1_genomic.fna/dqc_result.json
[2024-01-24 14:16:12,709] [INFO] DFAST_QC completed!
[2024-01-24 14:16:12,709] [INFO] Total running time: 0h1m52s