[2024-01-24 15:02:33,324] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:02:33,326] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:02:33,326] [INFO] DQC Reference Directory: /var/lib/cwl/stg4e8b2fd7-91f0-4539-b9a8-69e46df99a28/dqc_reference
[2024-01-24 15:02:34,570] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:02:34,570] [INFO] Task started: Prodigal
[2024-01-24 15:02:34,571] [INFO] Running command: gunzip -c /var/lib/cwl/stgf3a9c5da-0287-4643-98b9-7e62f5f3f40e/GCF_007990735.1_ASM799073v1_genomic.fna.gz | prodigal -d GCF_007990735.1_ASM799073v1_genomic.fna/cds.fna -a GCF_007990735.1_ASM799073v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:02:57,462] [INFO] Task succeeded: Prodigal
[2024-01-24 15:02:57,463] [INFO] Task started: HMMsearch
[2024-01-24 15:02:57,463] [INFO] Running command: hmmsearch --tblout GCF_007990735.1_ASM799073v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4e8b2fd7-91f0-4539-b9a8-69e46df99a28/dqc_reference/reference_markers.hmm GCF_007990735.1_ASM799073v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:02:57,917] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:02:57,918] [INFO] Found 6/6 markers.
[2024-01-24 15:02:57,987] [INFO] Query marker FASTA was written to GCF_007990735.1_ASM799073v1_genomic.fna/markers.fasta
[2024-01-24 15:02:57,988] [INFO] Task started: Blastn
[2024-01-24 15:02:57,988] [INFO] Running command: blastn -query GCF_007990735.1_ASM799073v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4e8b2fd7-91f0-4539-b9a8-69e46df99a28/dqc_reference/reference_markers.fasta -out GCF_007990735.1_ASM799073v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:02:59,414] [INFO] Task succeeded: Blastn
[2024-01-24 15:02:59,419] [INFO] Selected 6 target genomes.
[2024-01-24 15:02:59,420] [INFO] Target genome list was writen to GCF_007990735.1_ASM799073v1_genomic.fna/target_genomes.txt
[2024-01-24 15:02:59,423] [INFO] Task started: fastANI
[2024-01-24 15:02:59,423] [INFO] Running command: fastANI --query /var/lib/cwl/stgf3a9c5da-0287-4643-98b9-7e62f5f3f40e/GCF_007990735.1_ASM799073v1_genomic.fna.gz --refList GCF_007990735.1_ASM799073v1_genomic.fna/target_genomes.txt --output GCF_007990735.1_ASM799073v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:03:12,086] [INFO] Task succeeded: fastANI
[2024-01-24 15:03:12,086] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4e8b2fd7-91f0-4539-b9a8-69e46df99a28/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:03:12,087] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4e8b2fd7-91f0-4539-b9a8-69e46df99a28/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:03:12,095] [INFO] Found 6 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 15:03:12,095] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:03:12,095] [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=NBRC 108232	GCA_007990735.1	236511	236511	type	True	100.0	2215	2222	95	conclusive
Nocardia neocaledoniensis	strain=DSM 44717	GCA_003182135.1	236511	236511	type	True	99.9984	2218	2222	95	conclusive
Nocardia asteroides	strain=ATCC 19247	GCA_005863255.1	1824	1824	suspected-type	True	87.9131	1620	2222	95	below_threshold
Nocardia rhizosphaerihabitans	strain=CGMCC 4.7329	GCA_014646295.1	1691570	1691570	type	True	87.8803	1639	2222	95	below_threshold
Nocardia asteroides	strain=NBRC 15531	GCA_000308355.2	1824	1824	suspected-type	True	87.8572	1647	2222	95	below_threshold
Nocardia asteroides	strain=DSM 43373	GCA_900114685.1	1824	1824	suspected-type	True	87.8082	1660	2222	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:03:12,097] [INFO] DFAST Taxonomy check result was written to GCF_007990735.1_ASM799073v1_genomic.fna/tc_result.tsv
[2024-01-24 15:03:12,098] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:03:12,098] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:03:12,098] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4e8b2fd7-91f0-4539-b9a8-69e46df99a28/dqc_reference/checkm_data
[2024-01-24 15:03:12,100] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:03:12,172] [INFO] Task started: CheckM
[2024-01-24 15:03:12,173] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007990735.1_ASM799073v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007990735.1_ASM799073v1_genomic.fna/checkm_input GCF_007990735.1_ASM799073v1_genomic.fna/checkm_result
[2024-01-24 15:04:20,549] [INFO] Task succeeded: CheckM
[2024-01-24 15:04:20,551] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.78%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:04:20,577] [INFO] ===== Completeness check finished =====
[2024-01-24 15:04:20,577] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:04:20,578] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007990735.1_ASM799073v1_genomic.fna/markers.fasta)
[2024-01-24 15:04:20,578] [INFO] Task started: Blastn
[2024-01-24 15:04:20,578] [INFO] Running command: blastn -query GCF_007990735.1_ASM799073v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4e8b2fd7-91f0-4539-b9a8-69e46df99a28/dqc_reference/reference_markers_gtdb.fasta -out GCF_007990735.1_ASM799073v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:04:22,516] [INFO] Task succeeded: Blastn
[2024-01-24 15:04:22,520] [INFO] Selected 10 target genomes.
[2024-01-24 15:04:22,521] [INFO] Target genome list was writen to GCF_007990735.1_ASM799073v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:04:22,528] [INFO] Task started: fastANI
[2024-01-24 15:04:22,528] [INFO] Running command: fastANI --query /var/lib/cwl/stgf3a9c5da-0287-4643-98b9-7e62f5f3f40e/GCF_007990735.1_ASM799073v1_genomic.fna.gz --refList GCF_007990735.1_ASM799073v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007990735.1_ASM799073v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:04:42,046] [INFO] Task succeeded: fastANI
[2024-01-24 15:04:42,055] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:04:42,056] [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	99.9984	2218	2222	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_014646295.1	s__Nocardia rhizosphaerihabitans	87.8714	1640	2222	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900637185.1	s__Nocardia asteroides	87.8214	1648	2222	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	100.00	100.00	1.00	1.00	5	-
GCF_001886715.1	s__Nocardia mangyaensis	85.635	1467	2222	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	85.5357	1478	2222	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	85.4906	1498	2222	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	85.3503	1438	2222	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	85.2425	1569	2222	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	84.9575	1152	2222	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	81.4143	1052	2222	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 15:04:42,057] [INFO] GTDB search result was written to GCF_007990735.1_ASM799073v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:04:42,058] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:04:42,061] [INFO] DFAST_QC result json was written to GCF_007990735.1_ASM799073v1_genomic.fna/dqc_result.json
[2024-01-24 15:04:42,061] [INFO] DFAST_QC completed!
[2024-01-24 15:04:42,062] [INFO] Total running time: 0h2m9s