[2024-01-24 13:40:46,002] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:46,004] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:46,005] [INFO] DQC Reference Directory: /var/lib/cwl/stgb2ac60fd-0171-451f-9f32-54ad08b8fdea/dqc_reference
[2024-01-24 13:40:47,294] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:47,295] [INFO] Task started: Prodigal
[2024-01-24 13:40:47,295] [INFO] Running command: gunzip -c /var/lib/cwl/stge61837f8-858e-4d36-9156-a97ea4139cf8/GCF_014646295.1_ASM1464629v1_genomic.fna.gz | prodigal -d GCF_014646295.1_ASM1464629v1_genomic.fna/cds.fna -a GCF_014646295.1_ASM1464629v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:14,527] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:14,527] [INFO] Task started: HMMsearch
[2024-01-24 13:41:14,527] [INFO] Running command: hmmsearch --tblout GCF_014646295.1_ASM1464629v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb2ac60fd-0171-451f-9f32-54ad08b8fdea/dqc_reference/reference_markers.hmm GCF_014646295.1_ASM1464629v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:14,885] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:14,887] [INFO] Found 6/6 markers.
[2024-01-24 13:41:14,949] [INFO] Query marker FASTA was written to GCF_014646295.1_ASM1464629v1_genomic.fna/markers.fasta
[2024-01-24 13:41:14,949] [INFO] Task started: Blastn
[2024-01-24 13:41:14,949] [INFO] Running command: blastn -query GCF_014646295.1_ASM1464629v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb2ac60fd-0171-451f-9f32-54ad08b8fdea/dqc_reference/reference_markers.fasta -out GCF_014646295.1_ASM1464629v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:16,308] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:16,312] [INFO] Selected 13 target genomes.
[2024-01-24 13:41:16,312] [INFO] Target genome list was writen to GCF_014646295.1_ASM1464629v1_genomic.fna/target_genomes.txt
[2024-01-24 13:41:16,417] [INFO] Task started: fastANI
[2024-01-24 13:41:16,417] [INFO] Running command: fastANI --query /var/lib/cwl/stge61837f8-858e-4d36-9156-a97ea4139cf8/GCF_014646295.1_ASM1464629v1_genomic.fna.gz --refList GCF_014646295.1_ASM1464629v1_genomic.fna/target_genomes.txt --output GCF_014646295.1_ASM1464629v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:41,408] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:41,409] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb2ac60fd-0171-451f-9f32-54ad08b8fdea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:41,409] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb2ac60fd-0171-451f-9f32-54ad08b8fdea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:41,420] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:41:41,420] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:41,420] [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 rhizosphaerihabitans	strain=CGMCC 4.7329	GCA_014646295.1	1691570	1691570	type	True	100.0	2544	2545	95	conclusive
Nocardia asteroides	strain=ATCC 19247	GCA_005863255.1	1824	1824	suspected-type	True	88.655	1790	2545	95	below_threshold
Nocardia asteroides	strain=NBRC 15531	GCA_000308355.2	1824	1824	suspected-type	True	88.557	1807	2545	95	below_threshold
Nocardia asteroides	strain=DSM 43373	GCA_900114685.1	1824	1824	suspected-type	True	88.5148	1814	2545	95	below_threshold
Nocardia asteroides	strain=NCTC11293	GCA_900637185.1	1824	1824	suspected-type	True	88.494	1814	2545	95	below_threshold
Nocardia neocaledoniensis	strain=NBRC 108232	GCA_007990735.1	236511	236511	type	True	87.9332	1634	2545	95	below_threshold
Nocardia neocaledoniensis	strain=DSM 44717	GCA_003182135.1	236511	236511	type	True	87.9003	1789	2545	95	below_threshold
Nocardia salmonicida subsp. cummidelens	strain=NBRC 100378	GCA_001612865.1	2800120	53431	type	True	85.9686	1726	2545	95	below_threshold
Nocardia salmonicida	strain=NBRC 13393	GCA_001613085.1	53431	53431	type	True	85.9387	1738	2545	95	below_threshold
Nocardia coubleae	strain=DSM 44960	GCA_012395945.1	356147	356147	type	True	85.6061	1591	2545	95	below_threshold
Nocardia coubleae	strain=NBRC 108252	GCA_001612805.1	356147	356147	type	True	85.5762	1577	2545	95	below_threshold
Nocardia caishijiensis	strain=NBRC 108228	GCA_001612825.1	184756	184756	type	True	85.4289	1509	2545	95	below_threshold
Nocardia caishijiensis	strain=DSM 44831	GCA_009858255.1	184756	184756	type	True	85.3739	1537	2545	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:41,422] [INFO] DFAST Taxonomy check result was written to GCF_014646295.1_ASM1464629v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:41,422] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:41,422] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:41,422] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb2ac60fd-0171-451f-9f32-54ad08b8fdea/dqc_reference/checkm_data
[2024-01-24 13:41:41,424] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:41,497] [INFO] Task started: CheckM
[2024-01-24 13:41:41,497] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014646295.1_ASM1464629v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014646295.1_ASM1464629v1_genomic.fna/checkm_input GCF_014646295.1_ASM1464629v1_genomic.fna/checkm_result
[2024-01-24 13:43:05,571] [INFO] Task succeeded: CheckM
[2024-01-24 13:43:05,572] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.78%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:43:05,599] [INFO] ===== Completeness check finished =====
[2024-01-24 13:43:05,599] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:43:05,599] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014646295.1_ASM1464629v1_genomic.fna/markers.fasta)
[2024-01-24 13:43:05,600] [INFO] Task started: Blastn
[2024-01-24 13:43:05,600] [INFO] Running command: blastn -query GCF_014646295.1_ASM1464629v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb2ac60fd-0171-451f-9f32-54ad08b8fdea/dqc_reference/reference_markers_gtdb.fasta -out GCF_014646295.1_ASM1464629v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:43:07,694] [INFO] Task succeeded: Blastn
[2024-01-24 13:43:07,699] [INFO] Selected 11 target genomes.
[2024-01-24 13:43:07,700] [INFO] Target genome list was writen to GCF_014646295.1_ASM1464629v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:43:07,869] [INFO] Task started: fastANI
[2024-01-24 13:43:07,870] [INFO] Running command: fastANI --query /var/lib/cwl/stge61837f8-858e-4d36-9156-a97ea4139cf8/GCF_014646295.1_ASM1464629v1_genomic.fna.gz --refList GCF_014646295.1_ASM1464629v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014646295.1_ASM1464629v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:43:29,064] [INFO] Task succeeded: fastANI
[2024-01-24 13:43:29,077] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:43:29,077] [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_014646295.1	s__Nocardia rhizosphaerihabitans	100.0	2544	2545	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_900637185.1	s__Nocardia asteroides	88.5208	1811	2545	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	100.00	100.00	1.00	1.00	5	-
GCF_003182135.1	s__Nocardia neocaledoniensis	87.8918	1790	2545	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	86.3473	1625	2545	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002846365.1	s__Nocardia fluminea	85.9321	1747	2545	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	85.9286	1741	2545	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	97.01	95.63	0.88	0.85	5	-
GCF_001612805.1	s__Nocardia coubleae	85.6024	1573	2545	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	96.9719	100.00	100.00	1.00	1.00	2	-
GCF_001612665.1	s__Nocardia alba	85.5773	1600	2545	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001612905.1	s__Nocardia ignorata	85.5187	1571	2545	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	96.9719	100.00	100.00	1.00	1.00	2	-
GCF_001612825.1	s__Nocardia caishijiensis	85.4334	1507	2545	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013839555.1	s__Nocardia sp013839555	85.1727	1248	2545	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.2705	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:43:29,079] [INFO] GTDB search result was written to GCF_014646295.1_ASM1464629v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:43:29,079] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:43:29,083] [INFO] DFAST_QC result json was written to GCF_014646295.1_ASM1464629v1_genomic.fna/dqc_result.json
[2024-01-24 13:43:29,083] [INFO] DFAST_QC completed!
[2024-01-24 13:43:29,083] [INFO] Total running time: 0h2m43s