[2024-01-24 13:57:14,331] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:14,332] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:14,333] [INFO] DQC Reference Directory: /var/lib/cwl/stgb814591c-2999-46b8-93da-238944b49e2f/dqc_reference
[2024-01-24 13:57:15,689] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:15,691] [INFO] Task started: Prodigal
[2024-01-24 13:57:15,691] [INFO] Running command: gunzip -c /var/lib/cwl/stg9dd6f6ea-b715-4938-977a-41da25dcadc8/GCF_024171815.1_ASM2417181v1_genomic.fna.gz | prodigal -d GCF_024171815.1_ASM2417181v1_genomic.fna/cds.fna -a GCF_024171815.1_ASM2417181v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:57:38,658] [INFO] Task succeeded: Prodigal
[2024-01-24 13:57:38,658] [INFO] Task started: HMMsearch
[2024-01-24 13:57:38,658] [INFO] Running command: hmmsearch --tblout GCF_024171815.1_ASM2417181v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb814591c-2999-46b8-93da-238944b49e2f/dqc_reference/reference_markers.hmm GCF_024171815.1_ASM2417181v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:57:38,980] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:57:38,981] [INFO] Found 6/6 markers.
[2024-01-24 13:57:39,032] [INFO] Query marker FASTA was written to GCF_024171815.1_ASM2417181v1_genomic.fna/markers.fasta
[2024-01-24 13:57:39,032] [INFO] Task started: Blastn
[2024-01-24 13:57:39,032] [INFO] Running command: blastn -query GCF_024171815.1_ASM2417181v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb814591c-2999-46b8-93da-238944b49e2f/dqc_reference/reference_markers.fasta -out GCF_024171815.1_ASM2417181v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:40,385] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:40,389] [INFO] Selected 9 target genomes.
[2024-01-24 13:57:40,389] [INFO] Target genome list was writen to GCF_024171815.1_ASM2417181v1_genomic.fna/target_genomes.txt
[2024-01-24 13:57:40,393] [INFO] Task started: fastANI
[2024-01-24 13:57:40,394] [INFO] Running command: fastANI --query /var/lib/cwl/stg9dd6f6ea-b715-4938-977a-41da25dcadc8/GCF_024171815.1_ASM2417181v1_genomic.fna.gz --refList GCF_024171815.1_ASM2417181v1_genomic.fna/target_genomes.txt --output GCF_024171815.1_ASM2417181v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:57:51,181] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:51,182] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb814591c-2999-46b8-93da-238944b49e2f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:57:51,182] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb814591c-2999-46b8-93da-238944b49e2f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:57:51,194] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:57:51,194] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:57:51,194] [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 maris	strain=DSM 44693	GCA_024171815.1	72806	72806	type	True	100.0	1641	1641	95	conclusive
Williamsia phyllosphaerae	strain=CCM 7855	GCA_014635305.1	885042	885042	type	True	91.0867	1415	1641	95	below_threshold
Williamsia herbipolensis	strain=ARP1	GCA_000964005.1	1603258	1603258	type	True	82.3169	1062	1641	95	below_threshold
Williamsia deligens	strain=DSM 44902	GCA_024171765.1	321325	321325	type	True	80.6559	897	1641	95	below_threshold
Williamsia serinedens	strain=DSM 45037	GCA_024171725.1	391736	391736	type	True	80.6278	905	1641	95	below_threshold
Gordonia lacunae	strain=BS2	GCA_002149015.1	417102	417102	type	True	78.8228	609	1641	95	below_threshold
Gordonia crocea	strain=NBRC 107697	GCA_009932435.1	589162	589162	type	True	78.5132	475	1641	95	below_threshold
Nocardia harenae	strain=NBRC 108248	GCA_001612885.1	358707	358707	type	True	77.4013	455	1641	95	below_threshold
Mycolicibacterium elephantis	strain=DSM 44368	GCA_004014805.1	81858	81858	type	True	77.3683	383	1641	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:57:51,195] [INFO] DFAST Taxonomy check result was written to GCF_024171815.1_ASM2417181v1_genomic.fna/tc_result.tsv
[2024-01-24 13:57:51,196] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:57:51,196] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:57:51,196] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb814591c-2999-46b8-93da-238944b49e2f/dqc_reference/checkm_data
[2024-01-24 13:57:51,197] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:57:51,265] [INFO] Task started: CheckM
[2024-01-24 13:57:51,265] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024171815.1_ASM2417181v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024171815.1_ASM2417181v1_genomic.fna/checkm_input GCF_024171815.1_ASM2417181v1_genomic.fna/checkm_result
[2024-01-24 13:59:07,757] [INFO] Task succeeded: CheckM
[2024-01-24 13:59:07,758] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:59:07,778] [INFO] ===== Completeness check finished =====
[2024-01-24 13:59:07,778] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:59:07,778] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024171815.1_ASM2417181v1_genomic.fna/markers.fasta)
[2024-01-24 13:59:07,779] [INFO] Task started: Blastn
[2024-01-24 13:59:07,779] [INFO] Running command: blastn -query GCF_024171815.1_ASM2417181v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb814591c-2999-46b8-93da-238944b49e2f/dqc_reference/reference_markers_gtdb.fasta -out GCF_024171815.1_ASM2417181v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:09,782] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:09,786] [INFO] Selected 13 target genomes.
[2024-01-24 13:59:09,786] [INFO] Target genome list was writen to GCF_024171815.1_ASM2417181v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:59:09,824] [INFO] Task started: fastANI
[2024-01-24 13:59:09,824] [INFO] Running command: fastANI --query /var/lib/cwl/stg9dd6f6ea-b715-4938-977a-41da25dcadc8/GCF_024171815.1_ASM2417181v1_genomic.fna.gz --refList GCF_024171815.1_ASM2417181v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024171815.1_ASM2417181v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:59:23,779] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:23,790] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:59:23,790] [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	91.0867	1415	1641	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Williamsia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016462415.1	s__Williamsia_A sp016462415	90.3358	1293	1641	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	82.3276	1060	1641	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	79.6152	708	1641	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_000344155.1	s__Gordonia paraffinivorans	79.3165	595	1641	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	98.97	98.74	0.93	0.90	12	-
GCF_001698225.1	s__Gordonia terrae	78.8352	617	1641	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	99.37	97.67	0.96	0.87	7	-
GCF_002149015.1	s__Gordonia lacunae	78.8232	609	1641	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156495.1	s__Williamsia_B sterculiae	78.8049	636	1641	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Williamsia_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003797825.1	s__Gordonia sp003797825	78.661	631	1641	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009932435.1	s__Gordonia crocea	78.529	473	1641	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001894985.1	s__Rhodococcus tukisamuensis	78.3415	497	1641	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	99.99	99.99	0.99	0.99	2	-
GCF_001612885.1	s__Nocardia harenae	77.4154	452	1641	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004014805.1	s__Mycobacterium elephantis	77.3744	382	1641	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	96.23	96.21	0.87	0.85	6	-
--------------------------------------------------------------------------------
[2024-01-24 13:59:23,792] [INFO] GTDB search result was written to GCF_024171815.1_ASM2417181v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:59:23,793] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:59:23,798] [INFO] DFAST_QC result json was written to GCF_024171815.1_ASM2417181v1_genomic.fna/dqc_result.json
[2024-01-24 13:59:23,798] [INFO] DFAST_QC completed!
[2024-01-24 13:59:23,798] [INFO] Total running time: 0h2m9s