[2024-01-24 12:48:20,344] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:48:20,347] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:48:20,347] [INFO] DQC Reference Directory: /var/lib/cwl/stg4f12674e-81a1-4400-993c-cb180035dd59/dqc_reference
[2024-01-24 12:48:21,610] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:48:21,611] [INFO] Task started: Prodigal
[2024-01-24 12:48:21,612] [INFO] Running command: gunzip -c /var/lib/cwl/stg3d24c236-bafa-4bda-9b67-63654d51a027/GCF_000420085.1_ASM42008v1_genomic.fna.gz | prodigal -d GCF_000420085.1_ASM42008v1_genomic.fna/cds.fna -a GCF_000420085.1_ASM42008v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:48:38,807] [INFO] Task succeeded: Prodigal
[2024-01-24 12:48:38,807] [INFO] Task started: HMMsearch
[2024-01-24 12:48:38,808] [INFO] Running command: hmmsearch --tblout GCF_000420085.1_ASM42008v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4f12674e-81a1-4400-993c-cb180035dd59/dqc_reference/reference_markers.hmm GCF_000420085.1_ASM42008v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:48:39,161] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:48:39,162] [INFO] Found 6/6 markers.
[2024-01-24 12:48:39,215] [INFO] Query marker FASTA was written to GCF_000420085.1_ASM42008v1_genomic.fna/markers.fasta
[2024-01-24 12:48:39,215] [INFO] Task started: Blastn
[2024-01-24 12:48:39,215] [INFO] Running command: blastn -query GCF_000420085.1_ASM42008v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4f12674e-81a1-4400-993c-cb180035dd59/dqc_reference/reference_markers.fasta -out GCF_000420085.1_ASM42008v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:48:39,796] [INFO] Task succeeded: Blastn
[2024-01-24 12:48:39,799] [INFO] Selected 15 target genomes.
[2024-01-24 12:48:39,799] [INFO] Target genome list was writen to GCF_000420085.1_ASM42008v1_genomic.fna/target_genomes.txt
[2024-01-24 12:48:39,809] [INFO] Task started: fastANI
[2024-01-24 12:48:39,809] [INFO] Running command: fastANI --query /var/lib/cwl/stg3d24c236-bafa-4bda-9b67-63654d51a027/GCF_000420085.1_ASM42008v1_genomic.fna.gz --refList GCF_000420085.1_ASM42008v1_genomic.fna/target_genomes.txt --output GCF_000420085.1_ASM42008v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:48:53,441] [INFO] Task succeeded: fastANI
[2024-01-24 12:48:53,442] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4f12674e-81a1-4400-993c-cb180035dd59/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:48:53,443] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4f12674e-81a1-4400-993c-cb180035dd59/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:48:53,453] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:48:53,454] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:48:53,454] [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
Desulfospira joergensenii	strain=DSM 10085	GCA_000420085.1	53329	53329	type	True	100.0	2037	2038	95	conclusive
Desulfotignum balticum	strain=DSM 7044	GCA_000421285.1	115781	115781	type	True	77.6205	347	2038	95	below_threshold
Desulfotignum phosphitoxidans	strain=DSM 13687	GCA_000350545.1	190898	190898	type	True	77.5333	337	2038	95	below_threshold
Desulfobacter vibrioformis	strain=DSM 8776	GCA_000745975.1	34031	34031	type	True	77.5111	234	2038	95	below_threshold
Desulfobacter curvatus	strain=DSM 3379	GCA_000373985.1	2290	2290	type	True	76.8246	211	2038	95	below_threshold
Desulfocicer vacuolatum	strain=DSM 3385	GCA_900176365.1	2298	2298	type	True	76.4727	156	2038	95	below_threshold
Desulforapulum autotrophicum	strain=HRM2	GCA_000020365.1	2296	2296	type	True	76.3761	167	2038	95	below_threshold
Desulfosarcina ovata subsp. ovata	strain=oXyS1	GCA_009689005.1	2752305	83564	type	True	75.8658	90	2038	95	below_threshold
Desulfosarcina ovata subsp. sediminis	strain=28bB2T	GCA_009688985.1	885957	83564	type	True	75.8611	85	2038	95	below_threshold
Desulfosarcina widdelii	strain=PP31	GCA_009688965.1	947919	947919	type	True	75.8318	96	2038	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:48:53,555] [INFO] DFAST Taxonomy check result was written to GCF_000420085.1_ASM42008v1_genomic.fna/tc_result.tsv
[2024-01-24 12:48:53,556] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:48:53,556] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:48:53,556] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4f12674e-81a1-4400-993c-cb180035dd59/dqc_reference/checkm_data
[2024-01-24 12:48:53,558] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:48:53,616] [INFO] Task started: CheckM
[2024-01-24 12:48:53,616] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000420085.1_ASM42008v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000420085.1_ASM42008v1_genomic.fna/checkm_input GCF_000420085.1_ASM42008v1_genomic.fna/checkm_result
[2024-01-24 12:49:44,578] [INFO] Task succeeded: CheckM
[2024-01-24 12:49:44,580] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:49:44,604] [INFO] ===== Completeness check finished =====
[2024-01-24 12:49:44,604] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:49:44,605] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000420085.1_ASM42008v1_genomic.fna/markers.fasta)
[2024-01-24 12:49:44,605] [INFO] Task started: Blastn
[2024-01-24 12:49:44,605] [INFO] Running command: blastn -query GCF_000420085.1_ASM42008v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4f12674e-81a1-4400-993c-cb180035dd59/dqc_reference/reference_markers_gtdb.fasta -out GCF_000420085.1_ASM42008v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:49:45,412] [INFO] Task succeeded: Blastn
[2024-01-24 12:49:45,417] [INFO] Selected 21 target genomes.
[2024-01-24 12:49:45,417] [INFO] Target genome list was writen to GCF_000420085.1_ASM42008v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:49:45,443] [INFO] Task started: fastANI
[2024-01-24 12:49:45,444] [INFO] Running command: fastANI --query /var/lib/cwl/stg3d24c236-bafa-4bda-9b67-63654d51a027/GCF_000420085.1_ASM42008v1_genomic.fna.gz --refList GCF_000420085.1_ASM42008v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000420085.1_ASM42008v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:50:01,673] [INFO] Task succeeded: fastANI
[2024-01-24 12:50:01,695] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:50:01,695] [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_000420085.1	s__Desulfospira joergensenii	100.0	2036	2038	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfobacteraceae;g__Desulfospira	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_011390335.1	s__Desulfotignum sp011390335	77.6494	374	2038	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfobacteraceae;g__Desulfotignum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000421285.1	s__Desulfotignum balticum	77.6288	349	2038	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfobacteraceae;g__Desulfotignum	96.875	N/A	N/A	N/A	N/A	1	-
GCA_011390615.1	s__Desulfotignum sp011390615	77.626	275	2038	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfobacteraceae;g__Desulfotignum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011390635.1	s__Desulfotignum sp011390635	77.5744	377	2038	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfobacteraceae;g__Desulfotignum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013792075.1	s__NBML01 sp013792075	77.4552	390	2038	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfobacteraceae;g__NBML01	95.0	99.85	99.75	0.95	0.94	3	-
GCA_011389555.1	s__Desulfotignum sp011389555	77.4361	309	2038	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfobacteraceae;g__Desulfotignum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012031875.1	s__Desulfobacula sp012031875	77.4153	338	2038	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfobacteraceae;g__Desulfobacula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011389575.1	s__Desulfotignum sp011389575	77.4059	310	2038	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfobacteraceae;g__Desulfotignum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018816605.1	s__NBML01 sp018816605	77.3529	330	2038	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfobacteraceae;g__NBML01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016743945.1	s__NBML01 sp016743945	77.3064	353	2038	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfobacteraceae;g__NBML01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018399285.1	s__Desulfotignum sp018399285	77.3007	275	2038	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfobacteraceae;g__Desulfotignum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011389715.1	s__Desulfotignum sp011389715	77.1181	206	2038	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfobacteraceae;g__Desulfotignum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004796375.1	s__MADRE2 sp004796375	76.9558	214	2038	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfobacteraceae;g__MADRE2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011390085.1	s__Desulfobacula sp011390085	76.8413	145	2038	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfobacteraceae;g__Desulfobacula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000373985.1	s__Desulfobacter curvatus	76.8143	212	2038	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfobacteraceae;g__Desulfobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011390695.1	s__Desulfotignum sp011390695	76.7379	164	2038	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfobacteraceae;g__Desulfotignum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900176365.1	s__Desulfobacterium_A vacuolatum	76.4769	157	2038	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfobacteraceae;g__Desulfobacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009689005.1	s__Desulfosarcina ovata	75.935	91	2038	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfosarcinaceae;g__Desulfosarcina	95.0	97.03	97.03	0.77	0.77	2	-
GCA_011390345.1	s__JAABSP01 sp011390345	75.6976	72	2038	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfococcaceae;g__JAABSP01	95.0	95.08	95.08	0.82	0.82	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:50:01,697] [INFO] GTDB search result was written to GCF_000420085.1_ASM42008v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:50:01,697] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:50:01,701] [INFO] DFAST_QC result json was written to GCF_000420085.1_ASM42008v1_genomic.fna/dqc_result.json
[2024-01-24 12:50:01,701] [INFO] DFAST_QC completed!
[2024-01-24 12:50:01,701] [INFO] Total running time: 0h1m41s