[2024-01-24 12:23:50,025] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:23:50,027] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:23:50,027] [INFO] DQC Reference Directory: /var/lib/cwl/stg236f0d9a-94e6-42d6-8427-889f837ea21a/dqc_reference
[2024-01-24 12:23:51,394] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:23:51,395] [INFO] Task started: Prodigal
[2024-01-24 12:23:51,396] [INFO] Running command: gunzip -c /var/lib/cwl/stg4aa10d56-818e-41a3-aaad-5049e10f5281/GCF_022808885.1_ASM2280888v1_genomic.fna.gz | prodigal -d GCF_022808885.1_ASM2280888v1_genomic.fna/cds.fna -a GCF_022808885.1_ASM2280888v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:24:01,684] [INFO] Task succeeded: Prodigal
[2024-01-24 12:24:01,685] [INFO] Task started: HMMsearch
[2024-01-24 12:24:01,685] [INFO] Running command: hmmsearch --tblout GCF_022808885.1_ASM2280888v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg236f0d9a-94e6-42d6-8427-889f837ea21a/dqc_reference/reference_markers.hmm GCF_022808885.1_ASM2280888v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:24:01,949] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:24:01,951] [INFO] Found 6/6 markers.
[2024-01-24 12:24:01,984] [INFO] Query marker FASTA was written to GCF_022808885.1_ASM2280888v1_genomic.fna/markers.fasta
[2024-01-24 12:24:01,985] [INFO] Task started: Blastn
[2024-01-24 12:24:01,985] [INFO] Running command: blastn -query GCF_022808885.1_ASM2280888v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg236f0d9a-94e6-42d6-8427-889f837ea21a/dqc_reference/reference_markers.fasta -out GCF_022808885.1_ASM2280888v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:24:02,692] [INFO] Task succeeded: Blastn
[2024-01-24 12:24:02,697] [INFO] Selected 18 target genomes.
[2024-01-24 12:24:02,698] [INFO] Target genome list was writen to GCF_022808885.1_ASM2280888v1_genomic.fna/target_genomes.txt
[2024-01-24 12:24:02,705] [INFO] Task started: fastANI
[2024-01-24 12:24:02,705] [INFO] Running command: fastANI --query /var/lib/cwl/stg4aa10d56-818e-41a3-aaad-5049e10f5281/GCF_022808885.1_ASM2280888v1_genomic.fna.gz --refList GCF_022808885.1_ASM2280888v1_genomic.fna/target_genomes.txt --output GCF_022808885.1_ASM2280888v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:24:15,954] [INFO] Task succeeded: fastANI
[2024-01-24 12:24:15,954] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg236f0d9a-94e6-42d6-8427-889f837ea21a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:24:15,955] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg236f0d9a-94e6-42d6-8427-889f837ea21a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:24:15,969] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:24:15,969] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:24:15,969] [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
Geothrix fermentans	strain=DSM 14018	GCA_000428885.1	44676	44676	type	True	88.7496	884	1133	95	below_threshold
Holophaga foetida	strain=DSM 6591	GCA_000242615.3	35839	35839	type	True	78.7279	266	1133	95	below_threshold
Thioalbus denitrificans	strain=DSM 26407	GCA_003337735.1	547122	547122	type	True	75.961	100	1133	95	below_threshold
Thioalkalivibrio sulfidiphilus	strain=HL-EbGR7	GCA_000021985.1	1033854	1033854	type	True	75.8192	81	1133	95	below_threshold
Melaminivora alkalimesophila	strain=CY1	GCA_000282995.1	1165852	1165852	type	True	75.7462	60	1133	95	below_threshold
Dissulfurirhabdus thermomarina	strain=DSM 100025	GCA_010499435.1	1765737	1765737	type	True	75.4737	55	1133	95	below_threshold
Corallococcus sicarius	strain=CA040B	GCA_003611735.1	2316726	2316726	type	True	75.4336	149	1133	95	below_threshold
Streptosporangium violaceochromogenes	strain=JCM 3281	GCA_014654615.1	46188	46188	type	True	75.3905	71	1133	95	below_threshold
Stigmatella erecta	strain=DSM 16858	GCA_900111745.1	83460	83460	type	True	75.3663	160	1133	95	below_threshold
Archangium gephyra	strain=DSM 2261	GCA_003387095.1	48	48	type	True	75.3377	163	1133	95	below_threshold
Thioalkalivibrio thiocyanodenitrificans	strain=ARhD 1	GCA_000378965.1	243063	243063	type	True	75.1067	61	1133	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:24:15,971] [INFO] DFAST Taxonomy check result was written to GCF_022808885.1_ASM2280888v1_genomic.fna/tc_result.tsv
[2024-01-24 12:24:15,972] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:24:15,972] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:24:15,972] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg236f0d9a-94e6-42d6-8427-889f837ea21a/dqc_reference/checkm_data
[2024-01-24 12:24:15,973] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:24:16,014] [INFO] Task started: CheckM
[2024-01-24 12:24:16,015] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_022808885.1_ASM2280888v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_022808885.1_ASM2280888v1_genomic.fna/checkm_input GCF_022808885.1_ASM2280888v1_genomic.fna/checkm_result
[2024-01-24 12:24:51,415] [INFO] Task succeeded: CheckM
[2024-01-24 12:24:51,417] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:24:51,437] [INFO] ===== Completeness check finished =====
[2024-01-24 12:24:51,438] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:24:51,438] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_022808885.1_ASM2280888v1_genomic.fna/markers.fasta)
[2024-01-24 12:24:51,439] [INFO] Task started: Blastn
[2024-01-24 12:24:51,439] [INFO] Running command: blastn -query GCF_022808885.1_ASM2280888v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg236f0d9a-94e6-42d6-8427-889f837ea21a/dqc_reference/reference_markers_gtdb.fasta -out GCF_022808885.1_ASM2280888v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:24:52,582] [INFO] Task succeeded: Blastn
[2024-01-24 12:24:52,587] [INFO] Selected 11 target genomes.
[2024-01-24 12:24:52,587] [INFO] Target genome list was writen to GCF_022808885.1_ASM2280888v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:24:52,596] [INFO] Task started: fastANI
[2024-01-24 12:24:52,597] [INFO] Running command: fastANI --query /var/lib/cwl/stg4aa10d56-818e-41a3-aaad-5049e10f5281/GCF_022808885.1_ASM2280888v1_genomic.fna.gz --refList GCF_022808885.1_ASM2280888v1_genomic.fna/target_genomes_gtdb.txt --output GCF_022808885.1_ASM2280888v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:25:01,310] [INFO] Task succeeded: fastANI
[2024-01-24 12:25:01,324] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:25:01,325] [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_000428885.1	s__Geothrix fermentans	88.7389	885	1133	d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Holophagales;f__Holophagaceae;g__Geothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003538615.1	s__Geothrix sp003538615	85.8843	583	1133	d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Holophagales;f__Holophagaceae;g__Geothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013390615.1	s__Geothrix sp013390615	84.687	773	1133	d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Holophagales;f__Holophagaceae;g__Geothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016714685.1	s__Geothrix sp016714685	84.4713	744	1133	d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Holophagales;f__Holophagaceae;g__Geothrix	95.0	98.39	97.91	0.89	0.88	4	-
GCA_013334395.1	s__Geothrix sp013334395	83.8579	566	1133	d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Holophagales;f__Holophagaceae;g__Geothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016721195.1	s__Geothrix sp016721195	83.5695	745	1133	d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Holophagales;f__Holophagaceae;g__Geothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903937385.1	s__Geothrix sp903937385	83.4474	676	1133	d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Holophagales;f__Holophagaceae;g__Geothrix	95.0	99.84	98.90	0.96	0.91	10	-
GCA_016195985.1	s__Geothrix sp016195985	83.0803	741	1133	d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Holophagales;f__Holophagaceae;g__Geothrix	95.0	99.98	99.98	0.99	0.99	2	-
GCA_903843705.1	s__Geothrix sp903843705	82.5432	601	1133	d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Holophagales;f__Holophagaceae;g__Geothrix	95.0	99.09	98.86	0.88	0.85	6	-
GCA_003158505.1	s__Geothrix sp003158505	81.9462	577	1133	d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Holophagales;f__Holophagaceae;g__Geothrix	95.0	99.60	99.60	0.90	0.90	2	-
GCA_903873655.1	s__Geothrix sp903873655	81.5777	555	1133	d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Holophagales;f__Holophagaceae;g__Geothrix	95.0	99.34	99.01	0.91	0.87	6	-
--------------------------------------------------------------------------------
[2024-01-24 12:25:01,327] [INFO] GTDB search result was written to GCF_022808885.1_ASM2280888v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:25:01,327] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:25:01,330] [INFO] DFAST_QC result json was written to GCF_022808885.1_ASM2280888v1_genomic.fna/dqc_result.json
[2024-01-24 12:25:01,331] [INFO] DFAST_QC completed!
[2024-01-24 12:25:01,331] [INFO] Total running time: 0h1m11s