[2024-01-24 14:10:16,100] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:10:16,102] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:10:16,102] [INFO] DQC Reference Directory: /var/lib/cwl/stgde7024e8-beee-48f6-9dfc-6a967643aa20/dqc_reference
[2024-01-24 14:10:17,427] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:10:17,427] [INFO] Task started: Prodigal
[2024-01-24 14:10:17,428] [INFO] Running command: gunzip -c /var/lib/cwl/stg556988ac-55e8-4731-a502-8e241f0a4f47/GCF_000429985.1_ASM42998v1_genomic.fna.gz | prodigal -d GCF_000429985.1_ASM42998v1_genomic.fna/cds.fna -a GCF_000429985.1_ASM42998v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:10:26,466] [INFO] Task succeeded: Prodigal
[2024-01-24 14:10:26,467] [INFO] Task started: HMMsearch
[2024-01-24 14:10:26,467] [INFO] Running command: hmmsearch --tblout GCF_000429985.1_ASM42998v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgde7024e8-beee-48f6-9dfc-6a967643aa20/dqc_reference/reference_markers.hmm GCF_000429985.1_ASM42998v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:10:26,776] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:10:26,778] [INFO] Found 6/6 markers.
[2024-01-24 14:10:26,814] [INFO] Query marker FASTA was written to GCF_000429985.1_ASM42998v1_genomic.fna/markers.fasta
[2024-01-24 14:10:26,814] [INFO] Task started: Blastn
[2024-01-24 14:10:26,814] [INFO] Running command: blastn -query GCF_000429985.1_ASM42998v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgde7024e8-beee-48f6-9dfc-6a967643aa20/dqc_reference/reference_markers.fasta -out GCF_000429985.1_ASM42998v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:10:27,459] [INFO] Task succeeded: Blastn
[2024-01-24 14:10:27,462] [INFO] Selected 19 target genomes.
[2024-01-24 14:10:27,462] [INFO] Target genome list was writen to GCF_000429985.1_ASM42998v1_genomic.fna/target_genomes.txt
[2024-01-24 14:10:27,478] [INFO] Task started: fastANI
[2024-01-24 14:10:27,479] [INFO] Running command: fastANI --query /var/lib/cwl/stg556988ac-55e8-4731-a502-8e241f0a4f47/GCF_000429985.1_ASM42998v1_genomic.fna.gz --refList GCF_000429985.1_ASM42998v1_genomic.fna/target_genomes.txt --output GCF_000429985.1_ASM42998v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:10:39,066] [INFO] Task succeeded: fastANI
[2024-01-24 14:10:39,067] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgde7024e8-beee-48f6-9dfc-6a967643aa20/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:10:39,067] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgde7024e8-beee-48f6-9dfc-6a967643aa20/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:10:39,079] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:10:39,079] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:10:39,080] [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 bastinii	strain=DSM 16055	GCA_000429985.1	47157	47157	type	True	100.0	1286	1287	95	conclusive
Maridesulfovibrio salexigens	strain=DSM 2638	GCA_000023445.1	880	880	type	True	77.6214	163	1287	95	below_threshold
Maridesulfovibrio zosterae	strain=DSM 11974	GCA_000425265.1	82171	82171	type	True	77.285	174	1287	95	below_threshold
Maridesulfovibrio hydrothermalis	strain=AM13	GCA_000331025.1	191026	191026	type	True	77.1249	170	1287	95	below_threshold
Maridesulfovibrio hydrothermalis	strain=DSM 14728	GCA_000425245.1	191026	191026	type	True	77.0764	165	1287	95	below_threshold
Maridesulfovibrio frigidus	strain=DSM 17176	GCA_000711735.1	340956	340956	type	True	76.8458	128	1287	95	below_threshold
Pseudodesulfovibrio profundus	strain=500-1	GCA_900217235.1	57320	57320	type	True	76.36	51	1287	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:10:39,082] [INFO] DFAST Taxonomy check result was written to GCF_000429985.1_ASM42998v1_genomic.fna/tc_result.tsv
[2024-01-24 14:10:39,082] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:10:39,083] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:10:39,083] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgde7024e8-beee-48f6-9dfc-6a967643aa20/dqc_reference/checkm_data
[2024-01-24 14:10:39,085] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:10:39,128] [INFO] Task started: CheckM
[2024-01-24 14:10:39,128] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000429985.1_ASM42998v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000429985.1_ASM42998v1_genomic.fna/checkm_input GCF_000429985.1_ASM42998v1_genomic.fna/checkm_result
[2024-01-24 14:11:11,258] [INFO] Task succeeded: CheckM
[2024-01-24 14:11:11,259] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:11:11,281] [INFO] ===== Completeness check finished =====
[2024-01-24 14:11:11,281] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:11:11,282] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000429985.1_ASM42998v1_genomic.fna/markers.fasta)
[2024-01-24 14:11:11,282] [INFO] Task started: Blastn
[2024-01-24 14:11:11,282] [INFO] Running command: blastn -query GCF_000429985.1_ASM42998v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgde7024e8-beee-48f6-9dfc-6a967643aa20/dqc_reference/reference_markers_gtdb.fasta -out GCF_000429985.1_ASM42998v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:11:12,113] [INFO] Task succeeded: Blastn
[2024-01-24 14:11:12,116] [INFO] Selected 25 target genomes.
[2024-01-24 14:11:12,116] [INFO] Target genome list was writen to GCF_000429985.1_ASM42998v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:11:12,187] [INFO] Task started: fastANI
[2024-01-24 14:11:12,188] [INFO] Running command: fastANI --query /var/lib/cwl/stg556988ac-55e8-4731-a502-8e241f0a4f47/GCF_000429985.1_ASM42998v1_genomic.fna.gz --refList GCF_000429985.1_ASM42998v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000429985.1_ASM42998v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:11:27,507] [INFO] Task succeeded: fastANI
[2024-01-24 14:11:27,523] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:11:27,523] [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_000429985.1	s__Maridesulfovibrio bastinii	100.0	1286	1287	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Maridesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000023445.1	s__Maridesulfovibrio salexigens	77.6079	165	1287	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	77.5813	162	1287	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	77.57	154	1287	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	77.4492	166	1287	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	77.3342	149	1287	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Maridesulfovibrio	95.0	95.27	95.27	0.87	0.87	2	-
GCF_000425265.1	s__Maridesulfovibrio zosterae	77.2709	173	1287	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Maridesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006210265.1	s__Maridesulfovibrio sp006210265	77.1609	133	1287	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_900177375.1	s__Maridesulfovibrio gilichinskyi	77.1415	150	1287	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_000331025.1	s__Maridesulfovibrio hydrothermalis	77.1249	170	1287	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Maridesulfovibrio	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000711735.1	s__Maridesulfovibrio frigidus	76.8458	128	1287	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 14:11:27,535] [INFO] GTDB search result was written to GCF_000429985.1_ASM42998v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:11:27,536] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:11:27,541] [INFO] DFAST_QC result json was written to GCF_000429985.1_ASM42998v1_genomic.fna/dqc_result.json
[2024-01-24 14:11:27,541] [INFO] DFAST_QC completed!
[2024-01-24 14:11:27,542] [INFO] Total running time: 0h1m11s