[2024-01-24 14:19:17,348] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:19:17,349] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:19:17,349] [INFO] DQC Reference Directory: /var/lib/cwl/stg815fe158-0d0e-42c8-ae4e-5955ccae4473/dqc_reference
[2024-01-24 14:19:18,683] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:19:18,684] [INFO] Task started: Prodigal
[2024-01-24 14:19:18,684] [INFO] Running command: gunzip -c /var/lib/cwl/stgc9fc17d3-51a1-4cdd-bd69-e318e8402d33/GCF_000341895.1_ASM34189v1_genomic.fna.gz | prodigal -d GCF_000341895.1_ASM34189v1_genomic.fna/cds.fna -a GCF_000341895.1_ASM34189v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:19:30,642] [INFO] Task succeeded: Prodigal
[2024-01-24 14:19:30,643] [INFO] Task started: HMMsearch
[2024-01-24 14:19:30,643] [INFO] Running command: hmmsearch --tblout GCF_000341895.1_ASM34189v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg815fe158-0d0e-42c8-ae4e-5955ccae4473/dqc_reference/reference_markers.hmm GCF_000341895.1_ASM34189v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:19:30,961] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:19:30,962] [INFO] Found 6/6 markers.
[2024-01-24 14:19:30,996] [INFO] Query marker FASTA was written to GCF_000341895.1_ASM34189v1_genomic.fna/markers.fasta
[2024-01-24 14:19:30,997] [INFO] Task started: Blastn
[2024-01-24 14:19:30,997] [INFO] Running command: blastn -query GCF_000341895.1_ASM34189v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg815fe158-0d0e-42c8-ae4e-5955ccae4473/dqc_reference/reference_markers.fasta -out GCF_000341895.1_ASM34189v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:19:31,654] [INFO] Task succeeded: Blastn
[2024-01-24 14:19:31,657] [INFO] Selected 13 target genomes.
[2024-01-24 14:19:31,658] [INFO] Target genome list was writen to GCF_000341895.1_ASM34189v1_genomic.fna/target_genomes.txt
[2024-01-24 14:19:31,699] [INFO] Task started: fastANI
[2024-01-24 14:19:31,700] [INFO] Running command: fastANI --query /var/lib/cwl/stgc9fc17d3-51a1-4cdd-bd69-e318e8402d33/GCF_000341895.1_ASM34189v1_genomic.fna.gz --refList GCF_000341895.1_ASM34189v1_genomic.fna/target_genomes.txt --output GCF_000341895.1_ASM34189v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:19:39,967] [INFO] Task succeeded: fastANI
[2024-01-24 14:19:39,968] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg815fe158-0d0e-42c8-ae4e-5955ccae4473/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:19:39,969] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg815fe158-0d0e-42c8-ae4e-5955ccae4473/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:19:39,983] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:19:39,983] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:19:39,983] [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
Pseudodesulfovibrio piezophilus	strain=type strain: C1TLV30	GCA_000341895.1	879567	879567	type	True	100.0	1214	1215	95	conclusive
Pseudodesulfovibrio profundus	strain=500-1	GCA_900217235.1	57320	57320	type	True	78.9227	255	1215	95	below_threshold
Pseudodesulfovibrio cashew	strain=SRB007	GCA_009762795.1	2678688	2678688	type	True	78.6955	228	1215	95	below_threshold
Pseudodesulfovibrio sediminis	strain=SF6	GCA_020886695.1	2810563	2810563	type	True	78.4492	188	1215	95	below_threshold
Pseudodesulfovibrio hydrargyri	strain=BerOc1	GCA_001874525.1	2125990	2125990	type	True	77.9378	154	1215	95	below_threshold
Pseudodesulfovibrio mercurii	strain=ND132	GCA_000189295.2	641491	641491	type	True	77.904	161	1215	95	below_threshold
Pseudodesulfovibrio indicus	strain=J2	GCA_001563225.1	1716143	1716143	type	True	77.7782	172	1215	95	below_threshold
Pseudodesulfovibrio indicus	strain=DSM 101483	GCA_004365595.1	1716143	1716143	type	True	77.6908	172	1215	95	below_threshold
Pseudodesulfovibrio alkaliphilus	strain=F-1	GCA_009729555.1	2661613	2661613	type	True	77.5974	136	1215	95	below_threshold
Maridesulfovibrio salexigens	strain=DSM 2638	GCA_000023445.1	880	880	type	True	77.4866	57	1215	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:19:39,985] [INFO] DFAST Taxonomy check result was written to GCF_000341895.1_ASM34189v1_genomic.fna/tc_result.tsv
[2024-01-24 14:19:39,986] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:19:39,986] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:19:39,986] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg815fe158-0d0e-42c8-ae4e-5955ccae4473/dqc_reference/checkm_data
[2024-01-24 14:19:39,987] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:19:40,035] [INFO] Task started: CheckM
[2024-01-24 14:19:40,035] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000341895.1_ASM34189v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000341895.1_ASM34189v1_genomic.fna/checkm_input GCF_000341895.1_ASM34189v1_genomic.fna/checkm_result
[2024-01-24 14:20:21,235] [INFO] Task succeeded: CheckM
[2024-01-24 14:20:21,237] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:20:21,261] [INFO] ===== Completeness check finished =====
[2024-01-24 14:20:21,261] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:20:21,262] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000341895.1_ASM34189v1_genomic.fna/markers.fasta)
[2024-01-24 14:20:21,262] [INFO] Task started: Blastn
[2024-01-24 14:20:21,262] [INFO] Running command: blastn -query GCF_000341895.1_ASM34189v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg815fe158-0d0e-42c8-ae4e-5955ccae4473/dqc_reference/reference_markers_gtdb.fasta -out GCF_000341895.1_ASM34189v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:20:22,098] [INFO] Task succeeded: Blastn
[2024-01-24 14:20:22,102] [INFO] Selected 13 target genomes.
[2024-01-24 14:20:22,103] [INFO] Target genome list was writen to GCF_000341895.1_ASM34189v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:20:22,132] [INFO] Task started: fastANI
[2024-01-24 14:20:22,132] [INFO] Running command: fastANI --query /var/lib/cwl/stgc9fc17d3-51a1-4cdd-bd69-e318e8402d33/GCF_000341895.1_ASM34189v1_genomic.fna.gz --refList GCF_000341895.1_ASM34189v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000341895.1_ASM34189v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:20:30,985] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:31,004] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:20:31,005] [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_000341895.1	s__Pseudodesulfovibrio piezophilus	100.0	1215	1215	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Pseudodesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900217235.1	s__Pseudodesulfovibrio profundus	79.017	254	1215	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Pseudodesulfovibrio	95.0	98.02	97.98	0.88	0.83	5	-
GCF_009762795.1	s__Pseudodesulfovibrio cashew	78.6984	228	1215	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Pseudodesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012516435.1	s__Pseudodesulfovibrio sp012516435	78.6353	236	1215	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Pseudodesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016744135.1	s__Pseudodesulfovibrio sp016744135	78.1083	203	1215	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Pseudodesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004025585.1	s__Pseudodesulfovibrio sp004025585	77.959	205	1215	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Pseudodesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001874525.1	s__Pseudodesulfovibrio hydrargyri	77.9436	153	1215	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Pseudodesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017351175.1	s__Pseudodesulfovibrio sp017351175	77.924	170	1215	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Pseudodesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010468615.1	s__Pseudodesulfovibrio sp010468615	77.8251	169	1215	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Pseudodesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009729555.1	s__Pseudodesulfovibrio sp009729555	77.5952	136	1215	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Pseudodesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016342345.1	s__Pseudodesulfovibrio sp016342345	77.5791	202	1215	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Pseudodesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000023445.1	s__Maridesulfovibrio salexigens	77.5309	58	1215	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 14:20:31,007] [INFO] GTDB search result was written to GCF_000341895.1_ASM34189v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:20:31,007] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:20:31,011] [INFO] DFAST_QC result json was written to GCF_000341895.1_ASM34189v1_genomic.fna/dqc_result.json
[2024-01-24 14:20:31,011] [INFO] DFAST_QC completed!
[2024-01-24 14:20:31,011] [INFO] Total running time: 0h1m14s