[2024-01-24 12:13:41,954] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:13:41,957] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:13:41,957] [INFO] DQC Reference Directory: /var/lib/cwl/stg0941f7fd-ce28-4892-aba0-481cc1c8abd8/dqc_reference
[2024-01-24 12:13:43,294] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:13:43,294] [INFO] Task started: Prodigal
[2024-01-24 12:13:43,295] [INFO] Running command: gunzip -c /var/lib/cwl/stg0dd82d8b-bad6-4f3a-baa5-b2fc364227e9/GCF_019599405.1_ASM1959940v1_genomic.fna.gz | prodigal -d GCF_019599405.1_ASM1959940v1_genomic.fna/cds.fna -a GCF_019599405.1_ASM1959940v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:14:04,370] [INFO] Task succeeded: Prodigal
[2024-01-24 12:14:04,370] [INFO] Task started: HMMsearch
[2024-01-24 12:14:04,370] [INFO] Running command: hmmsearch --tblout GCF_019599405.1_ASM1959940v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0941f7fd-ce28-4892-aba0-481cc1c8abd8/dqc_reference/reference_markers.hmm GCF_019599405.1_ASM1959940v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:14:04,698] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:14:04,699] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg0dd82d8b-bad6-4f3a-baa5-b2fc364227e9/GCF_019599405.1_ASM1959940v1_genomic.fna.gz]
[2024-01-24 12:14:04,735] [INFO] Query marker FASTA was written to GCF_019599405.1_ASM1959940v1_genomic.fna/markers.fasta
[2024-01-24 12:14:04,736] [INFO] Task started: Blastn
[2024-01-24 12:14:04,736] [INFO] Running command: blastn -query GCF_019599405.1_ASM1959940v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0941f7fd-ce28-4892-aba0-481cc1c8abd8/dqc_reference/reference_markers.fasta -out GCF_019599405.1_ASM1959940v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:05,288] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:05,291] [INFO] Selected 7 target genomes.
[2024-01-24 12:14:05,292] [INFO] Target genome list was writen to GCF_019599405.1_ASM1959940v1_genomic.fna/target_genomes.txt
[2024-01-24 12:14:05,295] [INFO] Task started: fastANI
[2024-01-24 12:14:05,295] [INFO] Running command: fastANI --query /var/lib/cwl/stg0dd82d8b-bad6-4f3a-baa5-b2fc364227e9/GCF_019599405.1_ASM1959940v1_genomic.fna.gz --refList GCF_019599405.1_ASM1959940v1_genomic.fna/target_genomes.txt --output GCF_019599405.1_ASM1959940v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:14:12,157] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:12,157] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0941f7fd-ce28-4892-aba0-481cc1c8abd8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:14:12,158] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0941f7fd-ce28-4892-aba0-481cc1c8abd8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:14:12,165] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:14:12,165] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:14:12,165] [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
Halomicroarcula salinisoli	strain=F24A	GCA_019599405.1	2487746	2487746	type	True	100.0	1336	1337	95	conclusive
Halomicroarcula rubra	strain=F13	GCA_019599465.1	2487747	2487747	type	True	82.544	756	1337	95	below_threshold
Halomicroarcula pellucida	strain=CECT 7537	GCA_019599515.1	1427151	1427151	type	True	81.7295	688	1337	95	below_threshold
Halomicroarcula pellucida	strain=JCM 17820	GCA_014647235.1	1427151	1427151	type	True	81.7123	687	1337	95	below_threshold
Halomicroarcula nitratireducens	strain=F27	GCA_019599505.1	2487749	2487749	type	True	81.2329	709	1337	95	below_threshold
Halomicroarcula salina	strain=YGHS18	GCA_010119195.1	1429914	1429914	type	True	80.8083	635	1337	95	below_threshold
Halomicroarcula salina	strain=JCM 18369	GCA_019061225.1	1429914	1429914	type	True	80.7728	632	1337	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:14:12,167] [INFO] DFAST Taxonomy check result was written to GCF_019599405.1_ASM1959940v1_genomic.fna/tc_result.tsv
[2024-01-24 12:14:12,168] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:14:12,168] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:14:12,168] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0941f7fd-ce28-4892-aba0-481cc1c8abd8/dqc_reference/checkm_data
[2024-01-24 12:14:12,169] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:14:12,211] [INFO] Task started: CheckM
[2024-01-24 12:14:12,211] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019599405.1_ASM1959940v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019599405.1_ASM1959940v1_genomic.fna/checkm_input GCF_019599405.1_ASM1959940v1_genomic.fna/checkm_result
[2024-01-24 12:15:11,092] [INFO] Task succeeded: CheckM
[2024-01-24 12:15:11,096] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:15:11,123] [INFO] ===== Completeness check finished =====
[2024-01-24 12:15:11,124] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:15:11,124] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019599405.1_ASM1959940v1_genomic.fna/markers.fasta)
[2024-01-24 12:15:11,125] [INFO] Task started: Blastn
[2024-01-24 12:15:11,125] [INFO] Running command: blastn -query GCF_019599405.1_ASM1959940v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0941f7fd-ce28-4892-aba0-481cc1c8abd8/dqc_reference/reference_markers_gtdb.fasta -out GCF_019599405.1_ASM1959940v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:11,651] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:11,655] [INFO] Selected 8 target genomes.
[2024-01-24 12:15:11,655] [INFO] Target genome list was writen to GCF_019599405.1_ASM1959940v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:15:11,671] [INFO] Task started: fastANI
[2024-01-24 12:15:11,671] [INFO] Running command: fastANI --query /var/lib/cwl/stg0dd82d8b-bad6-4f3a-baa5-b2fc364227e9/GCF_019599405.1_ASM1959940v1_genomic.fna.gz --refList GCF_019599405.1_ASM1959940v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019599405.1_ASM1959940v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:15:18,591] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:18,599] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:15:18,599] [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
GCA_003021755.1	s__Halomicroarcula sp003021755	86.3269	468	1337	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halomicroarcula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003020925.1	s__Halomicroarcula sp003020925	86.1758	612	1337	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halomicroarcula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014647235.1	s__Halomicroarcula pellucida	81.6608	692	1337	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halomicroarcula	95.0	96.63	96.63	0.87	0.87	2	-
GCF_010119205.1	s__Halomicroarcula limicola	81.4521	678	1337	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halomicroarcula	95.0	100.00	100.00	1.00	1.00	2	-
GCF_010119195.1	s__Haloarcula salina	80.7986	637	1337	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Haloarcula	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000336615.1	s__Haloarcula amylolytica	80.4553	593	1337	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Haloarcula	95.3005	N/A	N/A	N/A	N/A	1	-
GCF_002844335.1	s__Haloarcula taiwanensis	80.2294	565	1337	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Haloarcula	95.0	99.00	98.44	0.94	0.92	4	-
GCF_004698125.1	s__Halosimplex halophilum	78.5898	545	1337	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halosimplex	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:15:18,601] [INFO] GTDB search result was written to GCF_019599405.1_ASM1959940v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:15:18,602] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:15:18,606] [INFO] DFAST_QC result json was written to GCF_019599405.1_ASM1959940v1_genomic.fna/dqc_result.json
[2024-01-24 12:15:18,606] [INFO] DFAST_QC completed!
[2024-01-24 12:15:18,606] [INFO] Total running time: 0h1m37s