[2024-01-25 18:58:05,724] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:58:05,726] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:58:05,726] [INFO] DQC Reference Directory: /var/lib/cwl/stgd03047f1-5f14-4f38-9b11-f27f589da42d/dqc_reference
[2024-01-25 18:58:06,886] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:58:06,887] [INFO] Task started: Prodigal
[2024-01-25 18:58:06,887] [INFO] Running command: gunzip -c /var/lib/cwl/stg7aad5165-d875-46e6-a786-c89b6206bbb4/GCF_014646135.1_ASM1464613v1_genomic.fna.gz | prodigal -d GCF_014646135.1_ASM1464613v1_genomic.fna/cds.fna -a GCF_014646135.1_ASM1464613v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:58:29,258] [INFO] Task succeeded: Prodigal
[2024-01-25 18:58:29,258] [INFO] Task started: HMMsearch
[2024-01-25 18:58:29,258] [INFO] Running command: hmmsearch --tblout GCF_014646135.1_ASM1464613v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd03047f1-5f14-4f38-9b11-f27f589da42d/dqc_reference/reference_markers.hmm GCF_014646135.1_ASM1464613v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:58:29,478] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:58:29,480] [INFO] Found 6/6 markers.
[2024-01-25 18:58:29,521] [INFO] Query marker FASTA was written to GCF_014646135.1_ASM1464613v1_genomic.fna/markers.fasta
[2024-01-25 18:58:29,522] [INFO] Task started: Blastn
[2024-01-25 18:58:29,522] [INFO] Running command: blastn -query GCF_014646135.1_ASM1464613v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd03047f1-5f14-4f38-9b11-f27f589da42d/dqc_reference/reference_markers.fasta -out GCF_014646135.1_ASM1464613v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:58:30,570] [INFO] Task succeeded: Blastn
[2024-01-25 18:58:30,572] [INFO] Selected 21 target genomes.
[2024-01-25 18:58:30,572] [INFO] Target genome list was writen to GCF_014646135.1_ASM1464613v1_genomic.fna/target_genomes.txt
[2024-01-25 18:58:30,582] [INFO] Task started: fastANI
[2024-01-25 18:58:30,582] [INFO] Running command: fastANI --query /var/lib/cwl/stg7aad5165-d875-46e6-a786-c89b6206bbb4/GCF_014646135.1_ASM1464613v1_genomic.fna.gz --refList GCF_014646135.1_ASM1464613v1_genomic.fna/target_genomes.txt --output GCF_014646135.1_ASM1464613v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:58:59,010] [INFO] Task succeeded: fastANI
[2024-01-25 18:58:59,011] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd03047f1-5f14-4f38-9b11-f27f589da42d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:58:59,011] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd03047f1-5f14-4f38-9b11-f27f589da42d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:58:59,023] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:58:59,023] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:58:59,024] [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
Nocardia camponoti	strain=CGMCC 4.7278	GCA_014646135.1	1616106	1616106	type	True	100.0	1733	1734	95	conclusive
Nocardia ignorata	strain=NBRC 108230	GCA_001612905.1	145285	145285	type	True	81.3511	983	1734	95	below_threshold
Nocardia rhizosphaerihabitans	strain=CGMCC 4.7329	GCA_014646295.1	1691570	1691570	type	True	81.343	1015	1734	95	below_threshold
Nocardia salmonicida	strain=NBRC 13393	GCA_001613085.1	53431	53431	type	True	81.2832	1022	1734	95	below_threshold
Nocardia ignorata	strain=DSM 44496	GCA_004362495.1	145285	145285	type	True	81.2593	1008	1734	95	below_threshold
Nocardia asteroides	strain=NCTC11293	GCA_900637185.1	1824	1824	suspected-type	True	81.1538	1045	1734	95	below_threshold
Nocardia asteroides	strain=ATCC 19247	GCA_005863255.1	1824	1824	suspected-type	True	81.1423	1035	1734	95	below_threshold
Nocardia asteroides	strain=DSM 43373	GCA_900114685.1	1824	1824	suspected-type	True	81.1376	1039	1734	95	below_threshold
Nocardia asteroides	strain=NBRC 15531	GCA_000308355.2	1824	1824	suspected-type	True	81.1295	1033	1734	95	below_threshold
Nocardia rosealba	strain=NEAU-G4	GCA_020216065.1	2878563	2878563	type	True	81.1274	985	1734	95	below_threshold
Nocardia caishijiensis	strain=DSM 44831	GCA_009858255.1	184756	184756	type	True	81.1118	993	1734	95	below_threshold
Nocardia salmonicida subsp. cummidelens	strain=NBRC 100378	GCA_001612865.1	2800120	53431	type	True	81.0983	1015	1734	95	below_threshold
Nocardia caishijiensis	strain=NBRC 108228	GCA_001612825.1	184756	184756	type	True	81.0167	991	1734	95	below_threshold
Nocardia mangyaensis	strain=Y48	GCA_001886715.1	2213200	2213200	type	True	80.9076	955	1734	95	below_threshold
Nocardia bhagyanarayanae	strain=DSM 103495	GCA_006716565.1	1215925	1215925	type	True	79.4015	749	1734	95	below_threshold
Nocardia higoensis	strain=NBRC 100133	GCA_000308595.1	228599	228599	type	True	79.1847	652	1734	95	below_threshold
Nocardia pseudovaccinii	strain=NBRC 100343	GCA_001613225.1	189540	189540	type	True	78.5977	624	1734	95	below_threshold
Nocardia mikamii	strain=NBRC 108933	GCA_001613505.1	508464	508464	type	True	78.3585	556	1734	95	below_threshold
Nocardia kruczakiae	strain=NBRC 101016	GCA_001612965.1	261477	261477	type	True	78.3455	566	1734	95	below_threshold
Nocardia miyunensis	strain=NBRC 108239	GCA_001613065.1	282684	282684	type	True	78.3194	538	1734	95	below_threshold
Nocardia vaccinii	strain=NBRC 15922	GCA_001613305.1	1822	1822	type	True	78.1374	499	1734	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:58:59,025] [INFO] DFAST Taxonomy check result was written to GCF_014646135.1_ASM1464613v1_genomic.fna/tc_result.tsv
[2024-01-25 18:58:59,026] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:58:59,026] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:58:59,026] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd03047f1-5f14-4f38-9b11-f27f589da42d/dqc_reference/checkm_data
[2024-01-25 18:58:59,027] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:58:59,078] [INFO] Task started: CheckM
[2024-01-25 18:58:59,078] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014646135.1_ASM1464613v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014646135.1_ASM1464613v1_genomic.fna/checkm_input GCF_014646135.1_ASM1464613v1_genomic.fna/checkm_result
[2024-01-25 18:59:59,525] [INFO] Task succeeded: CheckM
[2024-01-25 18:59:59,526] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 6.94%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:59:59,541] [INFO] ===== Completeness check finished =====
[2024-01-25 18:59:59,541] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:59:59,541] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014646135.1_ASM1464613v1_genomic.fna/markers.fasta)
[2024-01-25 18:59:59,542] [INFO] Task started: Blastn
[2024-01-25 18:59:59,542] [INFO] Running command: blastn -query GCF_014646135.1_ASM1464613v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd03047f1-5f14-4f38-9b11-f27f589da42d/dqc_reference/reference_markers_gtdb.fasta -out GCF_014646135.1_ASM1464613v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:00:01,143] [INFO] Task succeeded: Blastn
[2024-01-25 19:00:01,146] [INFO] Selected 20 target genomes.
[2024-01-25 19:00:01,146] [INFO] Target genome list was writen to GCF_014646135.1_ASM1464613v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:00:01,162] [INFO] Task started: fastANI
[2024-01-25 19:00:01,162] [INFO] Running command: fastANI --query /var/lib/cwl/stg7aad5165-d875-46e6-a786-c89b6206bbb4/GCF_014646135.1_ASM1464613v1_genomic.fna.gz --refList GCF_014646135.1_ASM1464613v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014646135.1_ASM1464613v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:00:28,869] [INFO] Task succeeded: fastANI
[2024-01-25 19:00:28,881] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:00:28,881] [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_014646135.1	s__Nocardia camponoti	100.0	1733	1734	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001612905.1	s__Nocardia ignorata	81.3485	985	1734	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	96.9719	100.00	100.00	1.00	1.00	2	-
GCF_014646295.1	s__Nocardia rhizosphaerihabitans	81.337	1017	1734	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001613085.1	s__Nocardia salmonicida	81.3187	1017	1734	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	97.01	95.63	0.88	0.85	5	-
GCF_003182135.1	s__Nocardia neocaledoniensis	81.2158	1011	1734	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900637185.1	s__Nocardia asteroides	81.1552	1044	1734	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	100.00	100.00	1.00	1.00	5	-
GCF_001612805.1	s__Nocardia coubleae	81.1173	1003	1734	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	96.9719	100.00	100.00	1.00	1.00	2	-
GCF_013839555.1	s__Nocardia sp013839555	81.1016	755	1734	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.2705	N/A	N/A	N/A	N/A	1	-
GCF_002846365.1	s__Nocardia fluminea	81.0642	1020	1734	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001612825.1	s__Nocardia caishijiensis	81.0152	993	1734	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001886715.1	s__Nocardia mangyaensis	80.908	953	1734	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001612665.1	s__Nocardia alba	80.8822	1001	1734	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000308595.1	s__Nocardia higoensis	79.2016	649	1734	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011801125.1	s__Nocardia brasiliensis_C	79.0227	755	1734	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011801145.1	s__Nocardia arthritidis_A	78.616	676	1734	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001613225.1	s__Nocardia pseudovaccinii	78.5916	625	1734	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002933465.1	s__Nocardia nova_B	78.3927	543	1734	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	99.92	99.92	0.99	0.99	2	-
GCF_001612965.1	s__Nocardia kruczakiae	78.3512	564	1734	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.6988	N/A	N/A	N/A	N/A	1	-
GCF_001613065.1	s__Nocardia miyunensis	78.3069	539	1734	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001613305.1	s__Nocardia vaccinii	78.1427	499	1734	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:00:28,884] [INFO] GTDB search result was written to GCF_014646135.1_ASM1464613v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:00:28,884] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:00:28,889] [INFO] DFAST_QC result json was written to GCF_014646135.1_ASM1464613v1_genomic.fna/dqc_result.json
[2024-01-25 19:00:28,889] [INFO] DFAST_QC completed!
[2024-01-25 19:00:28,889] [INFO] Total running time: 0h2m23s