[2024-01-24 11:05:28,029] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:05:28,031] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:05:28,032] [INFO] DQC Reference Directory: /var/lib/cwl/stgd92e5f40-165d-4baa-bad5-857b022b593c/dqc_reference
[2024-01-24 11:05:29,509] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:05:29,510] [INFO] Task started: Prodigal
[2024-01-24 11:05:29,510] [INFO] Running command: gunzip -c /var/lib/cwl/stg93f4205f-be43-4efe-8574-b78cb062edde/GCF_024171725.1_ASM2417172v1_genomic.fna.gz | prodigal -d GCF_024171725.1_ASM2417172v1_genomic.fna/cds.fna -a GCF_024171725.1_ASM2417172v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:05:47,548] [INFO] Task succeeded: Prodigal
[2024-01-24 11:05:47,549] [INFO] Task started: HMMsearch
[2024-01-24 11:05:47,549] [INFO] Running command: hmmsearch --tblout GCF_024171725.1_ASM2417172v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd92e5f40-165d-4baa-bad5-857b022b593c/dqc_reference/reference_markers.hmm GCF_024171725.1_ASM2417172v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:05:47,835] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:05:47,836] [INFO] Found 6/6 markers.
[2024-01-24 11:05:47,878] [INFO] Query marker FASTA was written to GCF_024171725.1_ASM2417172v1_genomic.fna/markers.fasta
[2024-01-24 11:05:47,878] [INFO] Task started: Blastn
[2024-01-24 11:05:47,878] [INFO] Running command: blastn -query GCF_024171725.1_ASM2417172v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd92e5f40-165d-4baa-bad5-857b022b593c/dqc_reference/reference_markers.fasta -out GCF_024171725.1_ASM2417172v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:05:49,225] [INFO] Task succeeded: Blastn
[2024-01-24 11:05:49,234] [INFO] Selected 11 target genomes.
[2024-01-24 11:05:49,235] [INFO] Target genome list was writen to GCF_024171725.1_ASM2417172v1_genomic.fna/target_genomes.txt
[2024-01-24 11:05:49,240] [INFO] Task started: fastANI
[2024-01-24 11:05:49,240] [INFO] Running command: fastANI --query /var/lib/cwl/stg93f4205f-be43-4efe-8574-b78cb062edde/GCF_024171725.1_ASM2417172v1_genomic.fna.gz --refList GCF_024171725.1_ASM2417172v1_genomic.fna/target_genomes.txt --output GCF_024171725.1_ASM2417172v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:06:01,472] [INFO] Task succeeded: fastANI
[2024-01-24 11:06:01,472] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd92e5f40-165d-4baa-bad5-857b022b593c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:06:01,473] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd92e5f40-165d-4baa-bad5-857b022b593c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:06:01,483] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:06:01,483] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:06:01,483] [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 serinedens	strain=DSM 45037	GCA_024171725.1	391736	391736	type	True	100.0	1529	1529	95	conclusive
Williamsia deligens	strain=DSM 44902	GCA_024171765.1	321325	321325	type	True	84.2835	1212	1529	95	below_threshold
Williamsia herbipolensis	strain=ARP1	GCA_000964005.1	1603258	1603258	type	True	81.1551	932	1529	95	below_threshold
Williamsia maris	strain=DSM 44693	GCA_024171815.1	72806	72806	type	True	80.6921	914	1529	95	below_threshold
Williamsia phyllosphaerae	strain=CCM 7855	GCA_014635305.1	885042	885042	type	True	80.5876	907	1529	95	below_threshold
Gordonia paraffinivorans	strain=NBRC 108238	GCA_000344155.1	175628	175628	type	True	79.5418	627	1529	95	below_threshold
Gordonia namibiensis	strain=NBRC 108229	GCA_000298235.1	168480	168480	type	True	79.5233	605	1529	95	below_threshold
Gordonia insulae	strain=MMS17-SY073	GCA_003855095.1	2420509	2420509	type	True	78.8159	613	1529	95	below_threshold
Gordonia phthalatica	strain=QH-11	GCA_001305675.1	1136941	1136941	type	True	78.5093	508	1529	95	below_threshold
Nocardia africana	strain=NBRC 100379	GCA_001612635.1	134964	134964	type	True	77.5352	436	1529	95	below_threshold
Nocardia africana	strain=FDAARGOS_1597	GCA_020731565.1	134964	134964	type	True	77.4831	429	1529	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:06:01,485] [INFO] DFAST Taxonomy check result was written to GCF_024171725.1_ASM2417172v1_genomic.fna/tc_result.tsv
[2024-01-24 11:06:01,486] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:06:01,486] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:06:01,486] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd92e5f40-165d-4baa-bad5-857b022b593c/dqc_reference/checkm_data
[2024-01-24 11:06:01,488] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:06:01,536] [INFO] Task started: CheckM
[2024-01-24 11:06:01,536] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024171725.1_ASM2417172v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024171725.1_ASM2417172v1_genomic.fna/checkm_input GCF_024171725.1_ASM2417172v1_genomic.fna/checkm_result
[2024-01-24 11:07:27,370] [INFO] Task succeeded: CheckM
[2024-01-24 11:07:27,372] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:07:27,392] [INFO] ===== Completeness check finished =====
[2024-01-24 11:07:27,393] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:07:27,393] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024171725.1_ASM2417172v1_genomic.fna/markers.fasta)
[2024-01-24 11:07:27,394] [INFO] Task started: Blastn
[2024-01-24 11:07:27,394] [INFO] Running command: blastn -query GCF_024171725.1_ASM2417172v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd92e5f40-165d-4baa-bad5-857b022b593c/dqc_reference/reference_markers_gtdb.fasta -out GCF_024171725.1_ASM2417172v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:07:29,378] [INFO] Task succeeded: Blastn
[2024-01-24 11:07:29,384] [INFO] Selected 18 target genomes.
[2024-01-24 11:07:29,384] [INFO] Target genome list was writen to GCF_024171725.1_ASM2417172v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:07:29,423] [INFO] Task started: fastANI
[2024-01-24 11:07:29,423] [INFO] Running command: fastANI --query /var/lib/cwl/stg93f4205f-be43-4efe-8574-b78cb062edde/GCF_024171725.1_ASM2417172v1_genomic.fna.gz --refList GCF_024171725.1_ASM2417172v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024171725.1_ASM2417172v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:07:47,894] [INFO] Task succeeded: fastANI
[2024-01-24 11:07:47,935] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 11:07:47,936] [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_000964005.1	s__Williamsia_A herbipolensis	81.1121	938	1529	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_014635305.1	s__Williamsia_A phyllosphaerae	80.6223	901	1529	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	80.4791	840	1529	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	79.5774	622	1529	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	98.97	98.74	0.93	0.90	12	-
GCF_000298235.1	s__Gordonia namibiensis	79.5316	604	1529	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	97.13	97.13	0.90	0.90	2	-
GCF_018474015.1	s__Williamsia_A sp018474015	79.4075	617	1529	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_000225505.1	s__Gordonia alkanivorans	79.3583	599	1529	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	98.26	97.87	0.90	0.88	6	-
GCF_001485495.1	s__Gordonia desulfuricans	79.0601	595	1529	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	99.37	98.77	0.95	0.92	3	-
GCA_013348785.1	s__Gordonia sp013348785	78.9561	490	1529	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003855095.1	s__Gordonia insulae	78.7768	618	1529	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	78.7691	580	1529	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_000334455.1	s__Gordonia soli	78.738	601	1529	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001305675.1	s__Gordonia phthalatica	78.5095	508	1529	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000333035.1	s__Gordonia sihwensis	78.3611	466	1529	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	99.38	98.97	0.93	0.88	4	-
GCF_001612635.1	s__Nocardia africana	77.5545	435	1529	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	99.93	99.93	0.99	0.99	2	-
GCF_004348515.1	s__Spirillospora sp004348515	76.0569	362	1529	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188445.1	s__Spirillospora meyerae	76.0297	417	1529	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000024025.1	s__Catenulispora acidiphila	75.861	352	1529	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Catenulisporaceae;g__Catenulispora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:07:47,937] [INFO] GTDB search result was written to GCF_024171725.1_ASM2417172v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:07:47,938] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:07:47,941] [INFO] DFAST_QC result json was written to GCF_024171725.1_ASM2417172v1_genomic.fna/dqc_result.json
[2024-01-24 11:07:47,942] [INFO] DFAST_QC completed!
[2024-01-24 11:07:47,942] [INFO] Total running time: 0h2m20s