[2024-01-24 10:57:13,196] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:57:13,198] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:57:13,198] [INFO] DQC Reference Directory: /var/lib/cwl/stg74e8c785-2014-474a-a28b-46a0fb2a1ad0/dqc_reference
[2024-01-24 10:57:14,678] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:57:14,679] [INFO] Task started: Prodigal
[2024-01-24 10:57:14,679] [INFO] Running command: gunzip -c /var/lib/cwl/stgfbb0c7c8-7cfd-4ece-9e42-b62d117ed517/GCF_003315035.1_ASM331503v1_genomic.fna.gz | prodigal -d GCF_003315035.1_ASM331503v1_genomic.fna/cds.fna -a GCF_003315035.1_ASM331503v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:57:47,775] [INFO] Task succeeded: Prodigal
[2024-01-24 10:57:47,775] [INFO] Task started: HMMsearch
[2024-01-24 10:57:47,775] [INFO] Running command: hmmsearch --tblout GCF_003315035.1_ASM331503v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg74e8c785-2014-474a-a28b-46a0fb2a1ad0/dqc_reference/reference_markers.hmm GCF_003315035.1_ASM331503v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:57:48,152] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:57:48,153] [INFO] Found 6/6 markers.
[2024-01-24 10:57:48,212] [INFO] Query marker FASTA was written to GCF_003315035.1_ASM331503v1_genomic.fna/markers.fasta
[2024-01-24 10:57:48,212] [INFO] Task started: Blastn
[2024-01-24 10:57:48,212] [INFO] Running command: blastn -query GCF_003315035.1_ASM331503v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg74e8c785-2014-474a-a28b-46a0fb2a1ad0/dqc_reference/reference_markers.fasta -out GCF_003315035.1_ASM331503v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:57:49,591] [INFO] Task succeeded: Blastn
[2024-01-24 10:57:49,594] [INFO] Selected 16 target genomes.
[2024-01-24 10:57:49,594] [INFO] Target genome list was writen to GCF_003315035.1_ASM331503v1_genomic.fna/target_genomes.txt
[2024-01-24 10:57:49,600] [INFO] Task started: fastANI
[2024-01-24 10:57:49,601] [INFO] Running command: fastANI --query /var/lib/cwl/stgfbb0c7c8-7cfd-4ece-9e42-b62d117ed517/GCF_003315035.1_ASM331503v1_genomic.fna.gz --refList GCF_003315035.1_ASM331503v1_genomic.fna/target_genomes.txt --output GCF_003315035.1_ASM331503v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:58:19,304] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:19,305] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg74e8c785-2014-474a-a28b-46a0fb2a1ad0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:58:19,306] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg74e8c785-2014-474a-a28b-46a0fb2a1ad0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:58:19,332] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:58:19,332] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:58:19,332] [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 puris	strain=DSM 44599	GCA_003315035.1	208602	208602	type	True	100.0	2535	2536	95	conclusive
Nocardia amikacinitolerans	strain=NBRC 108937	GCA_001612615.1	756689	756689	type	True	83.8923	1529	2536	95	below_threshold
Nocardia bhagyanarayanae	strain=DSM 103495	GCA_006716565.1	1215925	1215925	type	True	83.8644	1553	2536	95	below_threshold
Nocardia lijiangensis	strain=NBRC 108240	GCA_001613045.1	299618	299618	type	True	83.8394	1464	2536	95	below_threshold
Nocardia xishanensis	strain=NBRC 101358	GCA_001613365.1	238964	238964	type	True	83.7755	1443	2536	95	below_threshold
Nocardia amikacinitolerans	strain=DSM 45539	GCA_024172045.1	756689	756689	type	True	83.7692	1535	2536	95	below_threshold
Nocardia asiatica	strain=NBRC 100129	GCA_000308415.1	209252	209252	type	True	82.6029	1257	2536	95	below_threshold
Nocardia barduliensis	strain=335427	GCA_013315795.1	2736643	2736643	type	True	82.5027	1309	2536	95	below_threshold
Nocardia asteroides	strain=ATCC 19247	GCA_005863255.1	1824	1824	suspected-type	True	82.1135	1275	2536	95	below_threshold
Nocardia asteroides	strain=NBRC 15531	GCA_000308355.2	1824	1824	suspected-type	True	82.09	1306	2536	95	below_threshold
Nocardia asteroides	strain=DSM 43373	GCA_900114685.1	1824	1824	suspected-type	True	82.024	1301	2536	95	below_threshold
Nocardia asteroides	strain=NCTC11293	GCA_900637185.1	1824	1824	suspected-type	True	82.0179	1313	2536	95	below_threshold
Nocardia niwae	strain=NBRC 108934	GCA_001613465.1	626084	626084	type	True	81.889	1284	2536	95	below_threshold
Nocardia amamiensis	strain=NBRC 102102	GCA_001612745.1	404578	404578	type	True	81.7181	1164	2536	95	below_threshold
Nocardia colli	strain=CICC 11023	GCA_008704205.1	2545717	2545717	type	True	81.7021	1376	2536	95	below_threshold
Nocardia terpenica	strain=IFM 0706	GCA_013186535.1	455432	455432	type	True	80.9449	1155	2536	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:58:19,334] [INFO] DFAST Taxonomy check result was written to GCF_003315035.1_ASM331503v1_genomic.fna/tc_result.tsv
[2024-01-24 10:58:19,335] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:58:19,335] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:58:19,336] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg74e8c785-2014-474a-a28b-46a0fb2a1ad0/dqc_reference/checkm_data
[2024-01-24 10:58:19,338] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:58:19,411] [INFO] Task started: CheckM
[2024-01-24 10:58:19,411] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003315035.1_ASM331503v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003315035.1_ASM331503v1_genomic.fna/checkm_input GCF_003315035.1_ASM331503v1_genomic.fna/checkm_result
[2024-01-24 10:59:51,737] [INFO] Task succeeded: CheckM
[2024-01-24 10:59:51,739] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:59:51,760] [INFO] ===== Completeness check finished =====
[2024-01-24 10:59:51,760] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:59:51,761] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003315035.1_ASM331503v1_genomic.fna/markers.fasta)
[2024-01-24 10:59:51,761] [INFO] Task started: Blastn
[2024-01-24 10:59:51,761] [INFO] Running command: blastn -query GCF_003315035.1_ASM331503v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg74e8c785-2014-474a-a28b-46a0fb2a1ad0/dqc_reference/reference_markers_gtdb.fasta -out GCF_003315035.1_ASM331503v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:59:53,661] [INFO] Task succeeded: Blastn
[2024-01-24 10:59:53,666] [INFO] Selected 18 target genomes.
[2024-01-24 10:59:53,666] [INFO] Target genome list was writen to GCF_003315035.1_ASM331503v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:59:53,701] [INFO] Task started: fastANI
[2024-01-24 10:59:53,701] [INFO] Running command: fastANI --query /var/lib/cwl/stgfbb0c7c8-7cfd-4ece-9e42-b62d117ed517/GCF_003315035.1_ASM331503v1_genomic.fna.gz --refList GCF_003315035.1_ASM331503v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003315035.1_ASM331503v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:00:26,225] [INFO] Task succeeded: fastANI
[2024-01-24 11:00:26,252] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:00:26,252] [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_003315035.1	s__Nocardia puris	100.0	2535	2536	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	99.66	99.46	0.95	0.92	4	conclusive
GCF_001612615.1	s__Nocardia amikacinitolerans	83.8695	1532	2536	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	97.80	97.80	0.89	0.89	2	-
GCF_006716565.1	s__Nocardia bhagyanarayanae	83.8572	1554	2536	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001613045.1	s__Nocardia lijiangensis	83.7972	1472	2536	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001613365.1	s__Nocardia xishanensis	83.7493	1447	2536	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000308415.1	s__Nocardia asiatica	82.5906	1259	2536	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000284035.1	s__Nocardia cyriacigeorgica_B	82.1565	1276	2536	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	98.41	98.27	0.93	0.91	5	-
GCF_900637185.1	s__Nocardia asteroides	82.0132	1317	2536	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	100.00	100.00	1.00	1.00	5	-
GCF_011801125.1	s__Nocardia brasiliensis_C	81.9917	1313	2536	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001613465.1	s__Nocardia niwae	81.9282	1277	2536	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009829325.1	s__Nocardia sp009829325	81.8334	1273	2536	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	96.48	96.48	0.88	0.88	2	-
GCF_015477605.1	s__Nocardia amamiensis_A	81.7823	1244	2536	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008704205.1	s__Nocardia colli	81.7104	1375	2536	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001612745.1	s__Nocardia amamiensis	81.6687	1173	2536	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000250675.2	s__Nocardia brasiliensis_B	81.5189	1365	2536	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.2192	100.00	100.00	1.00	1.00	2	-
GCF_001886715.1	s__Nocardia mangyaensis	81.2448	1217	2536	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	81.0421	1298	2536	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013186535.1	s__Nocardia terpenica	80.9494	1154	2536	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	98.12	95.64	0.89	0.79	9	-
--------------------------------------------------------------------------------
[2024-01-24 11:00:26,253] [INFO] GTDB search result was written to GCF_003315035.1_ASM331503v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:00:26,254] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:00:26,258] [INFO] DFAST_QC result json was written to GCF_003315035.1_ASM331503v1_genomic.fna/dqc_result.json
[2024-01-24 11:00:26,258] [INFO] DFAST_QC completed!
[2024-01-24 11:00:26,258] [INFO] Total running time: 0h3m13s