[2024-01-24 13:12:56,029] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:12:56,032] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:12:56,039] [INFO] DQC Reference Directory: /var/lib/cwl/stgf24b774c-1cac-434d-92ae-8eb597b582b5/dqc_reference
[2024-01-24 13:12:57,537] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:12:57,539] [INFO] Task started: Prodigal
[2024-01-24 13:12:57,539] [INFO] Running command: gunzip -c /var/lib/cwl/stg94d1acfa-f92a-4443-b9fb-f9a362f0b409/GCF_014873765.1_ASM1487376v1_genomic.fna.gz | prodigal -d GCF_014873765.1_ASM1487376v1_genomic.fna/cds.fna -a GCF_014873765.1_ASM1487376v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:13:11,417] [INFO] Task succeeded: Prodigal
[2024-01-24 13:13:11,417] [INFO] Task started: HMMsearch
[2024-01-24 13:13:11,417] [INFO] Running command: hmmsearch --tblout GCF_014873765.1_ASM1487376v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf24b774c-1cac-434d-92ae-8eb597b582b5/dqc_reference/reference_markers.hmm GCF_014873765.1_ASM1487376v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:13:11,733] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:13:11,734] [INFO] Found 6/6 markers.
[2024-01-24 13:13:11,772] [INFO] Query marker FASTA was written to GCF_014873765.1_ASM1487376v1_genomic.fna/markers.fasta
[2024-01-24 13:13:11,772] [INFO] Task started: Blastn
[2024-01-24 13:13:11,772] [INFO] Running command: blastn -query GCF_014873765.1_ASM1487376v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf24b774c-1cac-434d-92ae-8eb597b582b5/dqc_reference/reference_markers.fasta -out GCF_014873765.1_ASM1487376v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:12,432] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:12,435] [INFO] Selected 9 target genomes.
[2024-01-24 13:13:12,436] [INFO] Target genome list was writen to GCF_014873765.1_ASM1487376v1_genomic.fna/target_genomes.txt
[2024-01-24 13:13:12,443] [INFO] Task started: fastANI
[2024-01-24 13:13:12,443] [INFO] Running command: fastANI --query /var/lib/cwl/stg94d1acfa-f92a-4443-b9fb-f9a362f0b409/GCF_014873765.1_ASM1487376v1_genomic.fna.gz --refList GCF_014873765.1_ASM1487376v1_genomic.fna/target_genomes.txt --output GCF_014873765.1_ASM1487376v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:13:19,774] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:19,775] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf24b774c-1cac-434d-92ae-8eb597b582b5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:13:19,775] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf24b774c-1cac-434d-92ae-8eb597b582b5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:13:19,789] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:13:19,789] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:13:19,789] [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
Desulfomicrobium apsheronum	strain=DSM 5918	GCA_900114115.1	52560	52560	type	True	93.9293	1119	1446	95	below_threshold
Desulfomicrobium baculatum	strain=DSM 4028	GCA_000023225.1	899	899	type	True	87.4055	1010	1446	95	below_threshold
Desulfomicrobium escambiense	strain=DSM 10707	GCA_000428825.1	29503	29503	type	True	82.7654	826	1446	95	below_threshold
Desulfomicrobium orale	strain=DSM 12838	GCA_001553625.1	132132	132132	type	True	78.7095	346	1446	95	below_threshold
Desulfohalovibrio alkalitolerans	strain=DSM 16529	GCA_000422245.1	293256	293256	type	True	78.5504	192	1446	95	below_threshold
Pseudodesulfovibrio mercurii	strain=ND132	GCA_000189295.2	641491	641491	type	True	77.3455	220	1446	95	below_threshold
Pseudodesulfovibrio cashew	strain=SRB007	GCA_009762795.1	2678688	2678688	type	True	76.8961	150	1446	95	below_threshold
Pseudodesulfovibrio alkaliphilus	strain=F-1	GCA_009729555.1	2661613	2661613	type	True	76.6368	146	1446	95	below_threshold
Solidesulfovibrio fructosivorans	strain=JJ	GCA_000179555.1	878	878	type	True	76.4746	173	1446	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:13:19,795] [INFO] DFAST Taxonomy check result was written to GCF_014873765.1_ASM1487376v1_genomic.fna/tc_result.tsv
[2024-01-24 13:13:19,796] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:13:19,796] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:13:19,796] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf24b774c-1cac-434d-92ae-8eb597b582b5/dqc_reference/checkm_data
[2024-01-24 13:13:19,798] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:13:19,855] [INFO] Task started: CheckM
[2024-01-24 13:13:19,855] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014873765.1_ASM1487376v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014873765.1_ASM1487376v1_genomic.fna/checkm_input GCF_014873765.1_ASM1487376v1_genomic.fna/checkm_result
[2024-01-24 13:14:02,632] [INFO] Task succeeded: CheckM
[2024-01-24 13:14:02,633] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.44%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:14:02,653] [INFO] ===== Completeness check finished =====
[2024-01-24 13:14:02,654] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:14:02,654] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014873765.1_ASM1487376v1_genomic.fna/markers.fasta)
[2024-01-24 13:14:02,655] [INFO] Task started: Blastn
[2024-01-24 13:14:02,655] [INFO] Running command: blastn -query GCF_014873765.1_ASM1487376v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf24b774c-1cac-434d-92ae-8eb597b582b5/dqc_reference/reference_markers_gtdb.fasta -out GCF_014873765.1_ASM1487376v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:14:03,573] [INFO] Task succeeded: Blastn
[2024-01-24 13:14:03,578] [INFO] Selected 6 target genomes.
[2024-01-24 13:14:03,578] [INFO] Target genome list was writen to GCF_014873765.1_ASM1487376v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:14:03,588] [INFO] Task started: fastANI
[2024-01-24 13:14:03,588] [INFO] Running command: fastANI --query /var/lib/cwl/stg94d1acfa-f92a-4443-b9fb-f9a362f0b409/GCF_014873765.1_ASM1487376v1_genomic.fna.gz --refList GCF_014873765.1_ASM1487376v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014873765.1_ASM1487376v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:14:09,457] [INFO] Task succeeded: fastANI
[2024-01-24 13:14:09,464] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:14:09,464] [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_014873765.1	s__Desulfomicrobium macestii	100.0	1441	1446	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfomicrobiaceae;g__Desulfomicrobium	95.0	98.27	98.27	0.85	0.85	2	conclusive
GCF_900114115.1	s__Desulfomicrobium apsheronum	93.88	1122	1446	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfomicrobiaceae;g__Desulfomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002841885.1	s__Desulfomicrobium sp002841885	89.1005	1020	1446	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfomicrobiaceae;g__Desulfomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000023225.1	s__Desulfomicrobium baculatum	87.4119	1010	1446	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfomicrobiaceae;g__Desulfomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018902545.1	s__Desulfomicrobium sp018902545	84.3756	882	1446	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfomicrobiaceae;g__Desulfomicrobium	95.0	99.99	99.98	0.99	0.97	6	-
GCA_003542385.1	s__Desulfomicrobium sp003542385	82.4307	464	1446	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfomicrobiaceae;g__Desulfomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:14:09,467] [INFO] GTDB search result was written to GCF_014873765.1_ASM1487376v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:14:09,468] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:14:09,471] [INFO] DFAST_QC result json was written to GCF_014873765.1_ASM1487376v1_genomic.fna/dqc_result.json
[2024-01-24 13:14:09,471] [INFO] DFAST_QC completed!
[2024-01-24 13:14:09,471] [INFO] Total running time: 0h1m13s