[2024-01-24 13:54:04,284] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:54:04,287] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:54:04,287] [INFO] DQC Reference Directory: /var/lib/cwl/stg1a73c1af-903f-4b86-9967-257ac43c9c58/dqc_reference
[2024-01-24 13:54:05,807] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:54:05,808] [INFO] Task started: Prodigal
[2024-01-24 13:54:05,808] [INFO] Running command: gunzip -c /var/lib/cwl/stgb0d99ee4-ee16-43b5-ad55-3749d08dc338/GCF_000331025.1_ASM33102v1_genomic.fna.gz | prodigal -d GCF_000331025.1_ASM33102v1_genomic.fna/cds.fna -a GCF_000331025.1_ASM33102v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:54:15,711] [INFO] Task succeeded: Prodigal
[2024-01-24 13:54:15,712] [INFO] Task started: HMMsearch
[2024-01-24 13:54:15,712] [INFO] Running command: hmmsearch --tblout GCF_000331025.1_ASM33102v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1a73c1af-903f-4b86-9967-257ac43c9c58/dqc_reference/reference_markers.hmm GCF_000331025.1_ASM33102v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:54:16,028] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:54:16,030] [INFO] Found 6/6 markers.
[2024-01-24 13:54:16,083] [INFO] Query marker FASTA was written to GCF_000331025.1_ASM33102v1_genomic.fna/markers.fasta
[2024-01-24 13:54:16,083] [INFO] Task started: Blastn
[2024-01-24 13:54:16,083] [INFO] Running command: blastn -query GCF_000331025.1_ASM33102v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1a73c1af-903f-4b86-9967-257ac43c9c58/dqc_reference/reference_markers.fasta -out GCF_000331025.1_ASM33102v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:54:16,739] [INFO] Task succeeded: Blastn
[2024-01-24 13:54:16,743] [INFO] Selected 11 target genomes.
[2024-01-24 13:54:16,743] [INFO] Target genome list was writen to GCF_000331025.1_ASM33102v1_genomic.fna/target_genomes.txt
[2024-01-24 13:54:16,753] [INFO] Task started: fastANI
[2024-01-24 13:54:16,753] [INFO] Running command: fastANI --query /var/lib/cwl/stgb0d99ee4-ee16-43b5-ad55-3749d08dc338/GCF_000331025.1_ASM33102v1_genomic.fna.gz --refList GCF_000331025.1_ASM33102v1_genomic.fna/target_genomes.txt --output GCF_000331025.1_ASM33102v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:54:24,576] [INFO] Task succeeded: fastANI
[2024-01-24 13:54:24,576] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1a73c1af-903f-4b86-9967-257ac43c9c58/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:54:24,577] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1a73c1af-903f-4b86-9967-257ac43c9c58/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:54:24,588] [INFO] Found 6 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:54:24,588] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:54:24,588] [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
Maridesulfovibrio hydrothermalis	strain=AM13	GCA_000331025.1	191026	191026	type	True	100.0	1234	1235	95	conclusive
Maridesulfovibrio hydrothermalis	strain=DSM 14728	GCA_000425245.1	191026	191026	type	True	99.9749	1200	1235	95	conclusive
Maridesulfovibrio zosterae	strain=DSM 11974	GCA_000425265.1	82171	82171	type	True	79.4751	511	1235	95	below_threshold
Maridesulfovibrio salexigens	strain=DSM 2638	GCA_000023445.1	880	880	type	True	79.1917	507	1235	95	below_threshold
Maridesulfovibrio frigidus	strain=DSM 17176	GCA_000711735.1	340956	340956	type	True	77.8524	319	1235	95	below_threshold
Maridesulfovibrio bastinii	strain=DSM 16055	GCA_000429985.1	47157	47157	type	True	77.2671	156	1235	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:54:24,590] [INFO] DFAST Taxonomy check result was written to GCF_000331025.1_ASM33102v1_genomic.fna/tc_result.tsv
[2024-01-24 13:54:24,590] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:54:24,591] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:54:24,591] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1a73c1af-903f-4b86-9967-257ac43c9c58/dqc_reference/checkm_data
[2024-01-24 13:54:24,593] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:54:24,635] [INFO] Task started: CheckM
[2024-01-24 13:54:24,635] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000331025.1_ASM33102v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000331025.1_ASM33102v1_genomic.fna/checkm_input GCF_000331025.1_ASM33102v1_genomic.fna/checkm_result
[2024-01-24 13:54:59,041] [INFO] Task succeeded: CheckM
[2024-01-24 13:54:59,043] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:54:59,098] [INFO] ===== Completeness check finished =====
[2024-01-24 13:54:59,098] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:54:59,099] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000331025.1_ASM33102v1_genomic.fna/markers.fasta)
[2024-01-24 13:54:59,099] [INFO] Task started: Blastn
[2024-01-24 13:54:59,100] [INFO] Running command: blastn -query GCF_000331025.1_ASM33102v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1a73c1af-903f-4b86-9967-257ac43c9c58/dqc_reference/reference_markers_gtdb.fasta -out GCF_000331025.1_ASM33102v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:54:59,954] [INFO] Task succeeded: Blastn
[2024-01-24 13:54:59,957] [INFO] Selected 9 target genomes.
[2024-01-24 13:54:59,957] [INFO] Target genome list was writen to GCF_000331025.1_ASM33102v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:54:59,973] [INFO] Task started: fastANI
[2024-01-24 13:54:59,973] [INFO] Running command: fastANI --query /var/lib/cwl/stgb0d99ee4-ee16-43b5-ad55-3749d08dc338/GCF_000331025.1_ASM33102v1_genomic.fna.gz --refList GCF_000331025.1_ASM33102v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000331025.1_ASM33102v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:55:07,118] [INFO] Task succeeded: fastANI
[2024-01-24 13:55:07,131] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:55:07,131] [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_000331025.1	s__Maridesulfovibrio hydrothermalis	100.0	1235	1235	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Maridesulfovibrio	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_000425265.1	s__Maridesulfovibrio zosterae	79.4749	511	1235	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Maridesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004923195.1	s__Maridesulfovibrio sp004923195	79.2679	519	1235	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Maridesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010470675.1	s__Maridesulfovibrio sp010470675	79.2177	483	1235	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Maridesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010470665.1	s__Maridesulfovibrio sp010470665	79.1777	523	1235	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Maridesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000023445.1	s__Maridesulfovibrio salexigens	79.17	506	1235	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Maridesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101105.1	s__Maridesulfovibrio ferrireducens	78.3777	374	1235	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Maridesulfovibrio	95.0	95.27	95.27	0.87	0.87	2	-
GCA_006210265.1	s__Maridesulfovibrio sp006210265	77.6927	287	1235	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Maridesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:55:07,133] [INFO] GTDB search result was written to GCF_000331025.1_ASM33102v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:55:07,133] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:55:07,136] [INFO] DFAST_QC result json was written to GCF_000331025.1_ASM33102v1_genomic.fna/dqc_result.json
[2024-01-24 13:55:07,136] [INFO] DFAST_QC completed!
[2024-01-24 13:55:07,136] [INFO] Total running time: 0h1m3s