[2024-01-24 10:48:09,494] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:48:09,496] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:48:09,497] [INFO] DQC Reference Directory: /var/lib/cwl/stg0c294819-48c7-4aa4-91b8-ab82d20b6784/dqc_reference
[2024-01-24 10:48:23,954] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:48:23,955] [INFO] Task started: Prodigal
[2024-01-24 10:48:23,956] [INFO] Running command: gunzip -c /var/lib/cwl/stg404a434d-4600-4dfc-ae1d-93894faabdb2/GCF_012396005.1_ASM1239600v1_genomic.fna.gz | prodigal -d GCF_012396005.1_ASM1239600v1_genomic.fna/cds.fna -a GCF_012396005.1_ASM1239600v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:48:46,077] [INFO] Task succeeded: Prodigal
[2024-01-24 10:48:46,078] [INFO] Task started: HMMsearch
[2024-01-24 10:48:46,078] [INFO] Running command: hmmsearch --tblout GCF_012396005.1_ASM1239600v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0c294819-48c7-4aa4-91b8-ab82d20b6784/dqc_reference/reference_markers.hmm GCF_012396005.1_ASM1239600v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:48:46,422] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:48:46,424] [INFO] Found 6/6 markers.
[2024-01-24 10:48:46,479] [INFO] Query marker FASTA was written to GCF_012396005.1_ASM1239600v1_genomic.fna/markers.fasta
[2024-01-24 10:48:46,480] [INFO] Task started: Blastn
[2024-01-24 10:48:46,480] [INFO] Running command: blastn -query GCF_012396005.1_ASM1239600v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0c294819-48c7-4aa4-91b8-ab82d20b6784/dqc_reference/reference_markers.fasta -out GCF_012396005.1_ASM1239600v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:47,634] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:47,638] [INFO] Selected 16 target genomes.
[2024-01-24 10:48:47,639] [INFO] Target genome list was writen to GCF_012396005.1_ASM1239600v1_genomic.fna/target_genomes.txt
[2024-01-24 10:48:47,668] [INFO] Task started: fastANI
[2024-01-24 10:48:47,668] [INFO] Running command: fastANI --query /var/lib/cwl/stg404a434d-4600-4dfc-ae1d-93894faabdb2/GCF_012396005.1_ASM1239600v1_genomic.fna.gz --refList GCF_012396005.1_ASM1239600v1_genomic.fna/target_genomes.txt --output GCF_012396005.1_ASM1239600v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:49:16,570] [INFO] Task succeeded: fastANI
[2024-01-24 10:49:16,571] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0c294819-48c7-4aa4-91b8-ab82d20b6784/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:49:16,571] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0c294819-48c7-4aa4-91b8-ab82d20b6784/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:49:16,589] [INFO] Found 16 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 10:49:16,589] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:49:16,589] [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 vermiculata	strain=JCM 12354	GCA_012396005.1	257274	257274	type	True	100.0	2205	2209	95	conclusive
Nocardia vermiculata	strain=NBRC 100427	GCA_001613265.1	257274	257274	type	True	99.9852	2177	2209	95	conclusive
Nocardia aobensis	strain=NBRC 100429	GCA_000308375.1	257277	257277	type	True	83.3753	1359	2209	95	below_threshold
Nocardia elegans	strain=NBRC 108235	GCA_001612845.1	300029	300029	type	True	83.3364	1380	2209	95	below_threshold
Nocardia africana	strain=NBRC 100379	GCA_001612635.1	134964	134964	type	True	83.3139	1382	2209	95	below_threshold
Nocardia kruczakiae	strain=NBRC 101016	GCA_001612965.1	261477	261477	type	True	83.2766	1397	2209	95	below_threshold
Nocardia africana	strain=FDAARGOS_1597	GCA_020731565.1	134964	134964	type	True	83.2661	1380	2209	95	below_threshold
Nocardia nova	strain=NBRC 15556	GCA_001613005.1	37330	37330	type	True	83.2476	1392	2209	95	below_threshold
Nocardia cerradoensis	strain=NBRC 101014	GCA_000308535.1	85688	85688	type	True	83.2164	1380	2209	95	below_threshold
Nocardia mikamii	strain=NBRC 108933	GCA_001613505.1	508464	508464	type	True	83.2101	1404	2209	95	below_threshold
Nocardia veterana	strain=NBRC 100344	GCA_000308855.1	132249	132249	type	True	82.935	1276	2209	95	below_threshold
Nocardia veterana	strain=DSM 44445	GCA_012396305.1	132249	132249	type	True	82.93	1305	2209	95	below_threshold
Nocardia mexicana	strain=NBRC 108244	GCA_001613165.1	279262	279262	type	True	80.4201	1073	2209	95	below_threshold
Nocardia miyunensis	strain=NBRC 108239	GCA_001613065.1	282684	282684	type	True	80.0481	1014	2209	95	below_threshold
Nocardia coffeae	strain=CA2R105	GCA_019890715.1	2873381	2873381	type	True	79.9831	1067	2209	95	below_threshold
Nocardia stercoris	strain=NEAU-LL90	GCA_003696265.1	2483361	2483361	type	True	79.3699	852	2209	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:49:16,591] [INFO] DFAST Taxonomy check result was written to GCF_012396005.1_ASM1239600v1_genomic.fna/tc_result.tsv
[2024-01-24 10:49:16,592] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:49:16,592] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:49:16,592] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0c294819-48c7-4aa4-91b8-ab82d20b6784/dqc_reference/checkm_data
[2024-01-24 10:49:16,594] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:49:16,656] [INFO] Task started: CheckM
[2024-01-24 10:49:16,656] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_012396005.1_ASM1239600v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_012396005.1_ASM1239600v1_genomic.fna/checkm_input GCF_012396005.1_ASM1239600v1_genomic.fna/checkm_result
[2024-01-24 10:50:21,598] [INFO] Task succeeded: CheckM
[2024-01-24 10:50:21,599] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:50:21,625] [INFO] ===== Completeness check finished =====
[2024-01-24 10:50:21,625] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:50:21,626] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_012396005.1_ASM1239600v1_genomic.fna/markers.fasta)
[2024-01-24 10:50:21,626] [INFO] Task started: Blastn
[2024-01-24 10:50:21,626] [INFO] Running command: blastn -query GCF_012396005.1_ASM1239600v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0c294819-48c7-4aa4-91b8-ab82d20b6784/dqc_reference/reference_markers_gtdb.fasta -out GCF_012396005.1_ASM1239600v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:50:23,322] [INFO] Task succeeded: Blastn
[2024-01-24 10:50:23,327] [INFO] Selected 15 target genomes.
[2024-01-24 10:50:23,328] [INFO] Target genome list was writen to GCF_012396005.1_ASM1239600v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:50:23,351] [INFO] Task started: fastANI
[2024-01-24 10:50:23,351] [INFO] Running command: fastANI --query /var/lib/cwl/stg404a434d-4600-4dfc-ae1d-93894faabdb2/GCF_012396005.1_ASM1239600v1_genomic.fna.gz --refList GCF_012396005.1_ASM1239600v1_genomic.fna/target_genomes_gtdb.txt --output GCF_012396005.1_ASM1239600v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:50:47,172] [INFO] Task succeeded: fastANI
[2024-01-24 10:50:47,188] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:50:47,188] [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_001613265.1	s__Nocardia vermiculata	99.9852	2177	2209	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_000308375.1	s__Nocardia aobensis	83.3587	1362	2209	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.6988	98.11	97.03	0.89	0.86	3	-
GCF_001612845.1	s__Nocardia elegans	83.3525	1376	2209	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	96.9334	99.79	99.59	0.97	0.94	3	-
GCF_001612635.1	s__Nocardia africana	83.2992	1384	2209	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	99.93	99.93	0.99	0.99	2	-
GCF_001612965.1	s__Nocardia kruczakiae	83.2639	1400	2209	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.6988	N/A	N/A	N/A	N/A	1	-
GCF_001613005.1	s__Nocardia nova	83.2634	1390	2209	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	96.9334	98.75	97.55	0.88	0.84	13	-
GCF_000308535.1	s__Nocardia cerradoensis	83.2219	1377	2209	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0231	99.71	99.43	1.00	0.99	3	-
GCF_001613505.1	s__Nocardia mikamii	83.2198	1402	2209	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015354405.1	s__Nocardia sp015354405	83.1751	1408	2209	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	83.0717	1295	2209	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	99.92	99.92	0.99	0.99	2	-
GCF_000523235.1	s__Nocardia nova_A	82.9822	1430	2209	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000308855.1	s__Nocardia veterana	82.9433	1275	2209	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	100.00	100.00	1.00	1.00	2	-
GCA_017354515.1	s__Nocardia sp017354515	81.1961	733	2209	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015477355.1	s__Nocardia blacklockiae	80.567	1112	2209	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001613065.1	s__Nocardia miyunensis	80.0249	1018	2209	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:50:47,190] [INFO] GTDB search result was written to GCF_012396005.1_ASM1239600v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:50:47,191] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:50:47,194] [INFO] DFAST_QC result json was written to GCF_012396005.1_ASM1239600v1_genomic.fna/dqc_result.json
[2024-01-24 10:50:47,195] [INFO] DFAST_QC completed!
[2024-01-24 10:50:47,195] [INFO] Total running time: 0h2m38s