[2024-01-25 18:48:50,489] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:48:50,490] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:48:50,490] [INFO] DQC Reference Directory: /var/lib/cwl/stg5be451d9-0cbd-4053-bac8-347db263df87/dqc_reference
[2024-01-25 18:48:51,688] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:48:51,689] [INFO] Task started: Prodigal
[2024-01-25 18:48:51,689] [INFO] Running command: gunzip -c /var/lib/cwl/stg350a8e77-3992-4a73-a30a-26a1fd8b7f23/GCF_002093115.1_ASM209311v1_genomic.fna.gz | prodigal -d GCF_002093115.1_ASM209311v1_genomic.fna/cds.fna -a GCF_002093115.1_ASM209311v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:49:00,499] [INFO] Task succeeded: Prodigal
[2024-01-25 18:49:00,500] [INFO] Task started: HMMsearch
[2024-01-25 18:49:00,500] [INFO] Running command: hmmsearch --tblout GCF_002093115.1_ASM209311v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5be451d9-0cbd-4053-bac8-347db263df87/dqc_reference/reference_markers.hmm GCF_002093115.1_ASM209311v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:49:00,726] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:49:00,727] [INFO] Found 6/6 markers.
[2024-01-25 18:49:00,755] [INFO] Query marker FASTA was written to GCF_002093115.1_ASM209311v1_genomic.fna/markers.fasta
[2024-01-25 18:49:00,755] [INFO] Task started: Blastn
[2024-01-25 18:49:00,755] [INFO] Running command: blastn -query GCF_002093115.1_ASM209311v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5be451d9-0cbd-4053-bac8-347db263df87/dqc_reference/reference_markers.fasta -out GCF_002093115.1_ASM209311v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:49:01,407] [INFO] Task succeeded: Blastn
[2024-01-25 18:49:01,409] [INFO] Selected 16 target genomes.
[2024-01-25 18:49:01,410] [INFO] Target genome list was writen to GCF_002093115.1_ASM209311v1_genomic.fna/target_genomes.txt
[2024-01-25 18:49:01,442] [INFO] Task started: fastANI
[2024-01-25 18:49:01,442] [INFO] Running command: fastANI --query /var/lib/cwl/stg350a8e77-3992-4a73-a30a-26a1fd8b7f23/GCF_002093115.1_ASM209311v1_genomic.fna.gz --refList GCF_002093115.1_ASM209311v1_genomic.fna/target_genomes.txt --output GCF_002093115.1_ASM209311v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:49:11,507] [INFO] Task succeeded: fastANI
[2024-01-25 18:49:11,507] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5be451d9-0cbd-4053-bac8-347db263df87/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:49:11,508] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5be451d9-0cbd-4053-bac8-347db263df87/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:49:11,516] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:49:11,516] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:49:11,516] [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 hydrogeniphilus	strain=EPR-M	GCA_002093115.1	1969733	1969733	type	True	100.0	1207	1212	95	conclusive
Geothermobacter ehrlichii	strain=SS015	GCA_008124615.1	213224	213224	type	True	79.8329	547	1212	95	below_threshold
Desulfuromonas versatilis	strain=NIT-T3	GCA_019704135.1	2802975	2802975	type	True	78.3558	325	1212	95	below_threshold
Desulfuromonas soudanensis	strain=WTL	GCA_001278055.1	1603606	1603606	type	True	77.6272	254	1212	95	below_threshold
Malonomonas rubra	strain=DSM 5091	GCA_900142125.1	57040	57040	type	True	77.3287	146	1212	95	below_threshold
Geoalkalibacter halelectricus	strain=SAP-1	GCA_025263685.1	2847045	2847045	type	True	77.1081	187	1212	95	below_threshold
Syntrophotalea acetylenica	strain=DSM 3246	GCA_001888165.1	29542	29542	type	True	77.0998	104	1212	95	below_threshold
Geoalkalibacter subterraneus	strain=Red1	GCA_000827125.1	483547	483547	type	True	77.0238	153	1212	95	below_threshold
Syntrophotalea acetylenivorans	strain=SFB93	GCA_001887775.1	1842532	1842532	type	True	76.8685	88	1212	95	below_threshold
Desulfuromonas thiophila	strain=DSM 8987	GCA_900101955.1	57664	57664	type	True	76.8672	131	1212	95	below_threshold
Geobacter sulfurreducens	strain=PCA	GCA_000007985.2	35554	35554	type	True	76.8289	72	1212	95	below_threshold
Geobacter metallireducens	strain=GS-15	GCA_000012925.1	28232	28232	type	True	76.64	91	1212	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:49:11,517] [INFO] DFAST Taxonomy check result was written to GCF_002093115.1_ASM209311v1_genomic.fna/tc_result.tsv
[2024-01-25 18:49:11,517] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:49:11,518] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:49:11,518] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5be451d9-0cbd-4053-bac8-347db263df87/dqc_reference/checkm_data
[2024-01-25 18:49:11,518] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:49:11,556] [INFO] Task started: CheckM
[2024-01-25 18:49:11,556] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002093115.1_ASM209311v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002093115.1_ASM209311v1_genomic.fna/checkm_input GCF_002093115.1_ASM209311v1_genomic.fna/checkm_result
[2024-01-25 18:49:41,297] [INFO] Task succeeded: CheckM
[2024-01-25 18:49:41,298] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:49:41,318] [INFO] ===== Completeness check finished =====
[2024-01-25 18:49:41,319] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:49:41,319] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002093115.1_ASM209311v1_genomic.fna/markers.fasta)
[2024-01-25 18:49:41,319] [INFO] Task started: Blastn
[2024-01-25 18:49:41,319] [INFO] Running command: blastn -query GCF_002093115.1_ASM209311v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5be451d9-0cbd-4053-bac8-347db263df87/dqc_reference/reference_markers_gtdb.fasta -out GCF_002093115.1_ASM209311v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:49:42,388] [INFO] Task succeeded: Blastn
[2024-01-25 18:49:42,392] [INFO] Selected 15 target genomes.
[2024-01-25 18:49:42,392] [INFO] Target genome list was writen to GCF_002093115.1_ASM209311v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:49:42,409] [INFO] Task started: fastANI
[2024-01-25 18:49:42,409] [INFO] Running command: fastANI --query /var/lib/cwl/stg350a8e77-3992-4a73-a30a-26a1fd8b7f23/GCF_002093115.1_ASM209311v1_genomic.fna.gz --refList GCF_002093115.1_ASM209311v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002093115.1_ASM209311v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:49:52,860] [INFO] Task succeeded: fastANI
[2024-01-25 18:49:52,869] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:49:52,869] [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_002093115.1	s__PPFX01 sp002093115	100.0	1207	1212	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Desulfuromonadales;f__Geothermobacteraceae;g__PPFX01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002898515.1	s__PPFX01 sp002898515	94.3829	1030	1212	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Desulfuromonadales;f__Geothermobacteraceae;g__PPFX01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008124615.1	s__Geothermobacter ehrlichii	79.8681	544	1212	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Desulfuromonadales;f__Geothermobacteraceae;g__Geothermobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003695205.1	s__Geothermobacter sp003695205	78.3224	220	1212	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Desulfuromonadales;f__Geothermobacteraceae;g__Geothermobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001611275.1	s__DDH964 sp001611275	78.0195	294	1212	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Desulfuromonadales;f__DDH964;g__DDH964	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002868925.1	s__BM707 sp002868925	77.5849	180	1212	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Desulfuromonadales;f__UBA2294;g__BM707	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002868845.1	s__BM501 sp002868845	77.3579	239	1212	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Desulfuromonadales;f__BM501;g__BM501	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142125.1	s__Malonomonas rubra	77.3287	146	1212	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Desulfuromonadales;f__Geopsychrobacteraceae;g__Malonomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014860175.1	s__JACZKF01 sp014860175	77.1362	172	1212	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Desulfuromonadales;f__JACZKF01;g__JACZKF01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001888165.1	s__Syntrophotalea acetylenica	77.0998	104	1212	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Desulfuromonadales;f__Syntrophotaleaceae;g__Syntrophotalea	95.0	99.99	99.99	1.00	1.00	2	-
GCA_002869605.1	s__SZUA-401 sp002869605	76.9349	179	1212	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Desulfuromonadales;f__SZUA-401;g__SZUA-401	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014197915.1	s__Rhodospira visakhapatnamensis	75.7408	63	1212	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Rhodospira	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:49:52,870] [INFO] GTDB search result was written to GCF_002093115.1_ASM209311v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:49:52,871] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:49:52,874] [INFO] DFAST_QC result json was written to GCF_002093115.1_ASM209311v1_genomic.fna/dqc_result.json
[2024-01-25 18:49:52,874] [INFO] DFAST_QC completed!
[2024-01-25 18:49:52,874] [INFO] Total running time: 0h1m2s