[2024-01-24 13:56:27,582] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:56:27,638] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:56:27,638] [INFO] DQC Reference Directory: /var/lib/cwl/stga3651ad2-e757-4beb-83b7-2c86d0fd5ffa/dqc_reference
[2024-01-24 13:56:28,886] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:56:28,887] [INFO] Task started: Prodigal
[2024-01-24 13:56:28,887] [INFO] Running command: gunzip -c /var/lib/cwl/stge0133cb2-4c53-4380-8d7a-2dd117b45ae3/GCF_008124615.1_ASM812461v1_genomic.fna.gz | prodigal -d GCF_008124615.1_ASM812461v1_genomic.fna/cds.fna -a GCF_008124615.1_ASM812461v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:56:37,566] [INFO] Task succeeded: Prodigal
[2024-01-24 13:56:37,566] [INFO] Task started: HMMsearch
[2024-01-24 13:56:37,566] [INFO] Running command: hmmsearch --tblout GCF_008124615.1_ASM812461v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga3651ad2-e757-4beb-83b7-2c86d0fd5ffa/dqc_reference/reference_markers.hmm GCF_008124615.1_ASM812461v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:56:37,827] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:56:37,829] [INFO] Found 6/6 markers.
[2024-01-24 13:56:37,858] [INFO] Query marker FASTA was written to GCF_008124615.1_ASM812461v1_genomic.fna/markers.fasta
[2024-01-24 13:56:37,858] [INFO] Task started: Blastn
[2024-01-24 13:56:37,858] [INFO] Running command: blastn -query GCF_008124615.1_ASM812461v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga3651ad2-e757-4beb-83b7-2c86d0fd5ffa/dqc_reference/reference_markers.fasta -out GCF_008124615.1_ASM812461v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:56:38,610] [INFO] Task succeeded: Blastn
[2024-01-24 13:56:38,614] [INFO] Selected 17 target genomes.
[2024-01-24 13:56:38,614] [INFO] Target genome list was writen to GCF_008124615.1_ASM812461v1_genomic.fna/target_genomes.txt
[2024-01-24 13:56:38,627] [INFO] Task started: fastANI
[2024-01-24 13:56:38,628] [INFO] Running command: fastANI --query /var/lib/cwl/stge0133cb2-4c53-4380-8d7a-2dd117b45ae3/GCF_008124615.1_ASM812461v1_genomic.fna.gz --refList GCF_008124615.1_ASM812461v1_genomic.fna/target_genomes.txt --output GCF_008124615.1_ASM812461v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:56:49,466] [INFO] Task succeeded: fastANI
[2024-01-24 13:56:49,466] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga3651ad2-e757-4beb-83b7-2c86d0fd5ffa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:56:49,467] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga3651ad2-e757-4beb-83b7-2c86d0fd5ffa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:56:49,478] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:56:49,478] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:56:49,479] [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
Geothermobacter ehrlichii	strain=SS015	GCA_008124615.1	213224	213224	type	True	100.0	1063	1064	95	conclusive
Geothermobacter hydrogeniphilus	strain=EPR-M	GCA_002093115.1	1969733	1969733	type	True	80.0486	536	1064	95	below_threshold
Desulfuromonas versatilis	strain=NIT-T3	GCA_019704135.1	2802975	2802975	type	True	78.838	404	1064	95	below_threshold
Desulfuromonas soudanensis	strain=WTL	GCA_001278055.1	1603606	1603606	type	True	77.946	318	1064	95	below_threshold
Geoalkalibacter halelectricus	strain=SAP-1	GCA_025263685.1	2847045	2847045	type	True	77.5727	247	1064	95	below_threshold
Geoalkalibacter subterraneus	strain=Red1	GCA_000827125.1	483547	483547	type	True	77.1881	150	1064	95	below_threshold
Malonomonas rubra	strain=DSM 5091	GCA_900142125.1	57040	57040	type	True	77.0401	147	1064	95	below_threshold
Geoalkalibacter ferrihydriticus	strain=DSM 17813	GCA_900103065.1	392333	392333	type	True	76.9658	154	1064	95	below_threshold
Geoalkalibacter ferrihydriticus	strain=DSM 17813	GCA_000820505.1	392333	392333	type	True	76.9591	154	1064	95	below_threshold
Geobacter grbiciae	strain=DSM 13689	GCA_018531165.1	155042	155042	type	True	76.8429	130	1064	95	below_threshold
Geobacter metallireducens	strain=GS-15	GCA_000012925.1	28232	28232	type	True	76.8241	136	1064	95	below_threshold
Geobacter hydrogenophilus	strain=DSM 13691	GCA_018501225.1	40983	40983	type	True	76.7779	124	1064	95	below_threshold
Pseudomonas nitroreducens	strain=DSM 14399	GCA_012986245.1	46680	46680	suspected-type	True	75.8671	83	1064	95	below_threshold
Pseudomonas nitroreducens	strain=NBRC 12694	GCA_002091755.1	46680	46680	suspected-type	True	75.8286	82	1064	95	below_threshold
Klenkia soli	strain=DSM 45843	GCA_900103975.1	1052260	1052260	type	True	75.0607	83	1064	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:56:49,480] [INFO] DFAST Taxonomy check result was written to GCF_008124615.1_ASM812461v1_genomic.fna/tc_result.tsv
[2024-01-24 13:56:49,481] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:56:49,481] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:56:49,481] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga3651ad2-e757-4beb-83b7-2c86d0fd5ffa/dqc_reference/checkm_data
[2024-01-24 13:56:49,482] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:56:49,518] [INFO] Task started: CheckM
[2024-01-24 13:56:49,519] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008124615.1_ASM812461v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008124615.1_ASM812461v1_genomic.fna/checkm_input GCF_008124615.1_ASM812461v1_genomic.fna/checkm_result
[2024-01-24 13:57:20,390] [INFO] Task succeeded: CheckM
[2024-01-24 13:57:20,392] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:57:20,410] [INFO] ===== Completeness check finished =====
[2024-01-24 13:57:20,410] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:57:20,411] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008124615.1_ASM812461v1_genomic.fna/markers.fasta)
[2024-01-24 13:57:20,411] [INFO] Task started: Blastn
[2024-01-24 13:57:20,411] [INFO] Running command: blastn -query GCF_008124615.1_ASM812461v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga3651ad2-e757-4beb-83b7-2c86d0fd5ffa/dqc_reference/reference_markers_gtdb.fasta -out GCF_008124615.1_ASM812461v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:21,769] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:21,772] [INFO] Selected 17 target genomes.
[2024-01-24 13:57:21,773] [INFO] Target genome list was writen to GCF_008124615.1_ASM812461v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:57:21,803] [INFO] Task started: fastANI
[2024-01-24 13:57:21,803] [INFO] Running command: fastANI --query /var/lib/cwl/stge0133cb2-4c53-4380-8d7a-2dd117b45ae3/GCF_008124615.1_ASM812461v1_genomic.fna.gz --refList GCF_008124615.1_ASM812461v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008124615.1_ASM812461v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:57:32,332] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:32,347] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:57:32,347] [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_008124615.1	s__Geothermobacter ehrlichii	100.0	1063	1064	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Desulfuromonadales;f__Geothermobacteraceae;g__Geothermobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_003695205.1	s__Geothermobacter sp003695205	80.2769	317	1064	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Desulfuromonadales;f__Geothermobacteraceae;g__Geothermobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002898515.1	s__PPFX01 sp002898515	80.0778	533	1064	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Desulfuromonadales;f__Geothermobacteraceae;g__PPFX01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002093115.1	s__PPFX01 sp002093115	80.0187	538	1064	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Desulfuromonadales;f__Geothermobacteraceae;g__PPFX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005774545.1	s__VAUL01 sp005774545	78.615	298	1064	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Desulfuromonadales;f__BM103;g__VAUL01	95.0	99.97	99.97	0.96	0.96	2	-
GCF_001611275.1	s__DDH964 sp001611275	78.4747	331	1064	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Desulfuromonadales;f__DDH964;g__DDH964	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002868845.1	s__BM501 sp002868845	78.1991	296	1064	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Desulfuromonadales;f__BM501;g__BM501	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014860175.1	s__JACZKF01 sp014860175	77.7536	204	1064	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Desulfuromonadales;f__JACZKF01;g__JACZKF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002868925.1	s__BM707 sp002868925	77.6989	203	1064	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Desulfuromonadales;f__UBA2294;g__BM707	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000472285.1	s__ATBO01 sp000472285	77.6308	248	1064	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Desulfuromonadales;f__ATBO01;g__ATBO01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000175115.2	s__Geomonas sp000175115	77.2235	162	1064	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Geobacteraceae;g__Geomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003250235.1	s__SZUA-540 sp003250235	76.9837	99	1064	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Desulfuromonadales;f__SZUA-540;g__SZUA-540	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002841765.1	s__UBA2197 sp002841765	76.6594	95	1064	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Desulfuromonadales;f__UBA2197;g__UBA2197	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003664105.1	s__Leifsonia sp003664105	75.043	51	1064	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:57:32,349] [INFO] GTDB search result was written to GCF_008124615.1_ASM812461v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:57:32,350] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:57:32,353] [INFO] DFAST_QC result json was written to GCF_008124615.1_ASM812461v1_genomic.fna/dqc_result.json
[2024-01-24 13:57:32,353] [INFO] DFAST_QC completed!
[2024-01-24 13:57:32,353] [INFO] Total running time: 0h1m5s