[2024-01-25 20:03:50,645] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:03:50,646] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:03:50,646] [INFO] DQC Reference Directory: /var/lib/cwl/stgc04d6fb3-5e88-4e42-93c1-dacd8b0c778f/dqc_reference
[2024-01-25 20:03:51,757] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:03:51,757] [INFO] Task started: Prodigal
[2024-01-25 20:03:51,758] [INFO] Running command: gunzip -c /var/lib/cwl/stg700ca188-6277-4114-b0ad-10d9056b7fc0/GCF_014635305.1_ASM1463530v1_genomic.fna.gz | prodigal -d GCF_014635305.1_ASM1463530v1_genomic.fna/cds.fna -a GCF_014635305.1_ASM1463530v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:04:05,208] [INFO] Task succeeded: Prodigal
[2024-01-25 20:04:05,209] [INFO] Task started: HMMsearch
[2024-01-25 20:04:05,209] [INFO] Running command: hmmsearch --tblout GCF_014635305.1_ASM1463530v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc04d6fb3-5e88-4e42-93c1-dacd8b0c778f/dqc_reference/reference_markers.hmm GCF_014635305.1_ASM1463530v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:04:05,457] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:04:05,458] [INFO] Found 6/6 markers.
[2024-01-25 20:04:05,507] [INFO] Query marker FASTA was written to GCF_014635305.1_ASM1463530v1_genomic.fna/markers.fasta
[2024-01-25 20:04:05,507] [INFO] Task started: Blastn
[2024-01-25 20:04:05,507] [INFO] Running command: blastn -query GCF_014635305.1_ASM1463530v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc04d6fb3-5e88-4e42-93c1-dacd8b0c778f/dqc_reference/reference_markers.fasta -out GCF_014635305.1_ASM1463530v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:04:06,693] [INFO] Task succeeded: Blastn
[2024-01-25 20:04:06,698] [INFO] Selected 7 target genomes.
[2024-01-25 20:04:06,698] [INFO] Target genome list was writen to GCF_014635305.1_ASM1463530v1_genomic.fna/target_genomes.txt
[2024-01-25 20:04:06,703] [INFO] Task started: fastANI
[2024-01-25 20:04:06,704] [INFO] Running command: fastANI --query /var/lib/cwl/stg700ca188-6277-4114-b0ad-10d9056b7fc0/GCF_014635305.1_ASM1463530v1_genomic.fna.gz --refList GCF_014635305.1_ASM1463530v1_genomic.fna/target_genomes.txt --output GCF_014635305.1_ASM1463530v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:04:15,224] [INFO] Task succeeded: fastANI
[2024-01-25 20:04:15,225] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc04d6fb3-5e88-4e42-93c1-dacd8b0c778f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:04:15,225] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc04d6fb3-5e88-4e42-93c1-dacd8b0c778f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:04:15,231] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:04:15,231] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:04:15,231] [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
Williamsia phyllosphaerae	strain=CCM 7855	GCA_014635305.1	885042	885042	type	True	100.0	1600	1600	95	conclusive
Williamsia maris	strain=DSM 44693	GCA_024171815.1	72806	72806	type	True	91.1721	1422	1600	95	below_threshold
Williamsia herbipolensis	strain=ARP1	GCA_000964005.1	1603258	1603258	type	True	82.3967	1038	1600	95	below_threshold
Williamsia serinedens	strain=DSM 45037	GCA_024171725.1	391736	391736	type	True	80.6645	881	1600	95	below_threshold
Williamsia deligens	strain=DSM 44902	GCA_024171765.1	321325	321325	type	True	80.6189	871	1600	95	below_threshold
Gordonia terrae	strain=NRRL B-16283	GCA_003183825.1	2055	2055	suspected-type	True	78.9656	597	1600	95	below_threshold
Nocardia harenae	strain=NBRC 108248	GCA_001612885.1	358707	358707	type	True	77.6648	438	1600	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:04:15,232] [INFO] DFAST Taxonomy check result was written to GCF_014635305.1_ASM1463530v1_genomic.fna/tc_result.tsv
[2024-01-25 20:04:15,233] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:04:15,233] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:04:15,233] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc04d6fb3-5e88-4e42-93c1-dacd8b0c778f/dqc_reference/checkm_data
[2024-01-25 20:04:15,234] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:04:15,278] [INFO] Task started: CheckM
[2024-01-25 20:04:15,279] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014635305.1_ASM1463530v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014635305.1_ASM1463530v1_genomic.fna/checkm_input GCF_014635305.1_ASM1463530v1_genomic.fna/checkm_result
[2024-01-25 20:05:14,399] [INFO] Task succeeded: CheckM
[2024-01-25 20:05:14,400] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:05:14,416] [INFO] ===== Completeness check finished =====
[2024-01-25 20:05:14,416] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:05:14,416] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014635305.1_ASM1463530v1_genomic.fna/markers.fasta)
[2024-01-25 20:05:14,416] [INFO] Task started: Blastn
[2024-01-25 20:05:14,417] [INFO] Running command: blastn -query GCF_014635305.1_ASM1463530v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc04d6fb3-5e88-4e42-93c1-dacd8b0c778f/dqc_reference/reference_markers_gtdb.fasta -out GCF_014635305.1_ASM1463530v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:05:16,252] [INFO] Task succeeded: Blastn
[2024-01-25 20:05:16,257] [INFO] Selected 14 target genomes.
[2024-01-25 20:05:16,257] [INFO] Target genome list was writen to GCF_014635305.1_ASM1463530v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:05:16,280] [INFO] Task started: fastANI
[2024-01-25 20:05:16,280] [INFO] Running command: fastANI --query /var/lib/cwl/stg700ca188-6277-4114-b0ad-10d9056b7fc0/GCF_014635305.1_ASM1463530v1_genomic.fna.gz --refList GCF_014635305.1_ASM1463530v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014635305.1_ASM1463530v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:05:31,670] [INFO] Task succeeded: fastANI
[2024-01-25 20:05:31,679] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:05:31,679] [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_014635305.1	s__Williamsia_A phyllosphaerae	100.0	1600	1600	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Williamsia_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016462415.1	s__Williamsia_A sp016462415	90.3054	1280	1600	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Williamsia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000964005.1	s__Williamsia_A herbipolensis	82.3849	1039	1600	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Williamsia_A	95.0	95.03	95.03	0.89	0.89	2	-
GCF_018474015.1	s__Williamsia_A sp018474015	79.7688	672	1600	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Williamsia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011290605.1	s__Gordonia sp002009645	78.9888	561	1600	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	97.70	97.37	0.91	0.88	14	-
GCF_003855095.1	s__Gordonia insulae	78.8963	582	1600	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002149015.1	s__Gordonia lacunae	78.8662	599	1600	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000143885.2	s__Gordonia sp000143885	78.8439	595	1600	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	97.85	97.53	0.90	0.88	3	-
GCF_003797825.1	s__Gordonia sp003797825	78.7285	612	1600	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003202005.1	s__Williamsia faeni	78.5911	518	1600	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Williamsia	95.0	97.44	97.44	0.90	0.90	2	-
GCF_009914535.1	s__Gordonia pseudoamarae	78.1963	493	1600	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	99.95	99.95	1.00	1.00	2	-
GCF_001646785.1	s__Rhodococcus phenolicus	78.0123	441	1600	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001612885.1	s__Nocardia harenae	77.6548	438	1600	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016907655.1	s__Actinosynnema algeriensis	76.5705	364	1600	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:05:31,681] [INFO] GTDB search result was written to GCF_014635305.1_ASM1463530v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:05:31,681] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:05:31,684] [INFO] DFAST_QC result json was written to GCF_014635305.1_ASM1463530v1_genomic.fna/dqc_result.json
[2024-01-25 20:05:31,684] [INFO] DFAST_QC completed!
[2024-01-25 20:05:31,684] [INFO] Total running time: 0h1m41s