[2024-01-24 13:12:56,019] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:12:56,021] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:12:56,021] [INFO] DQC Reference Directory: /var/lib/cwl/stg71415422-d972-4cf9-8a0a-902f5d1e82f7/dqc_reference
[2024-01-24 13:12:57,370] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:12:57,373] [INFO] Task started: Prodigal
[2024-01-24 13:12:57,374] [INFO] Running command: gunzip -c /var/lib/cwl/stg64c2eb8c-e221-4930-9f78-7bfcb543c789/GCF_003182135.1_ASM318213v1_genomic.fna.gz | prodigal -d GCF_003182135.1_ASM318213v1_genomic.fna/cds.fna -a GCF_003182135.1_ASM318213v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:13:23,003] [INFO] Task succeeded: Prodigal
[2024-01-24 13:13:23,003] [INFO] Task started: HMMsearch
[2024-01-24 13:13:23,003] [INFO] Running command: hmmsearch --tblout GCF_003182135.1_ASM318213v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg71415422-d972-4cf9-8a0a-902f5d1e82f7/dqc_reference/reference_markers.hmm GCF_003182135.1_ASM318213v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:13:23,359] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:13:23,360] [INFO] Found 6/6 markers.
[2024-01-24 13:13:23,416] [INFO] Query marker FASTA was written to GCF_003182135.1_ASM318213v1_genomic.fna/markers.fasta
[2024-01-24 13:13:23,417] [INFO] Task started: Blastn
[2024-01-24 13:13:23,417] [INFO] Running command: blastn -query GCF_003182135.1_ASM318213v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg71415422-d972-4cf9-8a0a-902f5d1e82f7/dqc_reference/reference_markers.fasta -out GCF_003182135.1_ASM318213v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:24,863] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:24,866] [INFO] Selected 6 target genomes.
[2024-01-24 13:13:24,866] [INFO] Target genome list was writen to GCF_003182135.1_ASM318213v1_genomic.fna/target_genomes.txt
[2024-01-24 13:13:24,872] [INFO] Task started: fastANI
[2024-01-24 13:13:24,873] [INFO] Running command: fastANI --query /var/lib/cwl/stg64c2eb8c-e221-4930-9f78-7bfcb543c789/GCF_003182135.1_ASM318213v1_genomic.fna.gz --refList GCF_003182135.1_ASM318213v1_genomic.fna/target_genomes.txt --output GCF_003182135.1_ASM318213v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:13:38,234] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:38,235] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg71415422-d972-4cf9-8a0a-902f5d1e82f7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:13:38,235] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg71415422-d972-4cf9-8a0a-902f5d1e82f7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:13:38,242] [INFO] Found 6 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:13:38,242] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:13:38,242] [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 neocaledoniensis	strain=DSM 44717	GCA_003182135.1	236511	236511	type	True	100.0	2426	2427	95	conclusive
Nocardia neocaledoniensis	strain=NBRC 108232	GCA_007990735.1	236511	236511	type	True	99.8802	2195	2427	95	conclusive
Nocardia asteroides	strain=ATCC 19247	GCA_005863255.1	1824	1824	suspected-type	True	87.8934	1778	2427	95	below_threshold
Nocardia asteroides	strain=DSM 43373	GCA_900114685.1	1824	1824	suspected-type	True	87.8382	1795	2427	95	below_threshold
Nocardia rhizosphaerihabitans	strain=CGMCC 4.7329	GCA_014646295.1	1691570	1691570	type	True	87.8381	1808	2427	95	below_threshold
Nocardia asteroides	strain=NBRC 15531	GCA_000308355.2	1824	1824	suspected-type	True	87.8303	1802	2427	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:13:38,244] [INFO] DFAST Taxonomy check result was written to GCF_003182135.1_ASM318213v1_genomic.fna/tc_result.tsv
[2024-01-24 13:13:38,244] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:13:38,245] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:13:38,245] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg71415422-d972-4cf9-8a0a-902f5d1e82f7/dqc_reference/checkm_data
[2024-01-24 13:13:38,246] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:13:38,312] [INFO] Task started: CheckM
[2024-01-24 13:13:38,312] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003182135.1_ASM318213v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003182135.1_ASM318213v1_genomic.fna/checkm_input GCF_003182135.1_ASM318213v1_genomic.fna/checkm_result
[2024-01-24 13:15:00,023] [INFO] Task succeeded: CheckM
[2024-01-24 13:15:00,025] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.78%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:15:00,059] [INFO] ===== Completeness check finished =====
[2024-01-24 13:15:00,060] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:15:00,060] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003182135.1_ASM318213v1_genomic.fna/markers.fasta)
[2024-01-24 13:15:00,061] [INFO] Task started: Blastn
[2024-01-24 13:15:00,061] [INFO] Running command: blastn -query GCF_003182135.1_ASM318213v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg71415422-d972-4cf9-8a0a-902f5d1e82f7/dqc_reference/reference_markers_gtdb.fasta -out GCF_003182135.1_ASM318213v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:15:02,209] [INFO] Task succeeded: Blastn
[2024-01-24 13:15:02,212] [INFO] Selected 10 target genomes.
[2024-01-24 13:15:02,212] [INFO] Target genome list was writen to GCF_003182135.1_ASM318213v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:15:02,230] [INFO] Task started: fastANI
[2024-01-24 13:15:02,230] [INFO] Running command: fastANI --query /var/lib/cwl/stg64c2eb8c-e221-4930-9f78-7bfcb543c789/GCF_003182135.1_ASM318213v1_genomic.fna.gz --refList GCF_003182135.1_ASM318213v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003182135.1_ASM318213v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:15:22,068] [INFO] Task succeeded: fastANI
[2024-01-24 13:15:22,077] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:15:22,078] [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_003182135.1	s__Nocardia neocaledoniensis	100.0	2426	2427	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_900637185.1	s__Nocardia asteroides	87.8516	1790	2427	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	100.00	100.00	1.00	1.00	5	-
GCF_014646295.1	s__Nocardia rhizosphaerihabitans	87.8455	1807	2427	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001886715.1	s__Nocardia mangyaensis	85.6905	1579	2427	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001612905.1	s__Nocardia ignorata	85.4723	1619	2427	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	96.9719	100.00	100.00	1.00	1.00	2	-
GCF_001612805.1	s__Nocardia coubleae	85.4501	1628	2427	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	85.3712	1553	2427	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002846365.1	s__Nocardia fluminea	85.2398	1701	2427	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013839555.1	s__Nocardia sp013839555	85.184	1227	2427	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.2705	N/A	N/A	N/A	N/A	1	-
GCF_000308555.1	s__Nocardia cyriacigeorgica	81.6147	1095	2427	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	96.94	96.19	0.91	0.88	19	-
--------------------------------------------------------------------------------
[2024-01-24 13:15:22,079] [INFO] GTDB search result was written to GCF_003182135.1_ASM318213v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:15:22,080] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:15:22,083] [INFO] DFAST_QC result json was written to GCF_003182135.1_ASM318213v1_genomic.fna/dqc_result.json
[2024-01-24 13:15:22,084] [INFO] DFAST_QC completed!
[2024-01-24 13:15:22,084] [INFO] Total running time: 0h2m26s