[2024-01-24 11:43:53,260] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:43:53,261] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:43:53,261] [INFO] DQC Reference Directory: /var/lib/cwl/stg16832262-9a2d-4012-83c8-840adac5bddc/dqc_reference
[2024-01-24 11:43:54,527] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:43:54,528] [INFO] Task started: Prodigal
[2024-01-24 11:43:54,528] [INFO] Running command: gunzip -c /var/lib/cwl/stg923beaad-ee59-4abf-8d3b-0dafe99db832/GCF_019430945.1_ASM1943094v1_genomic.fna.gz | prodigal -d GCF_019430945.1_ASM1943094v1_genomic.fna/cds.fna -a GCF_019430945.1_ASM1943094v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:44:13,819] [INFO] Task succeeded: Prodigal
[2024-01-24 11:44:13,819] [INFO] Task started: HMMsearch
[2024-01-24 11:44:13,820] [INFO] Running command: hmmsearch --tblout GCF_019430945.1_ASM1943094v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg16832262-9a2d-4012-83c8-840adac5bddc/dqc_reference/reference_markers.hmm GCF_019430945.1_ASM1943094v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:44:14,100] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:44:14,101] [INFO] Found 6/6 markers.
[2024-01-24 11:44:14,151] [INFO] Query marker FASTA was written to GCF_019430945.1_ASM1943094v1_genomic.fna/markers.fasta
[2024-01-24 11:44:14,151] [INFO] Task started: Blastn
[2024-01-24 11:44:14,151] [INFO] Running command: blastn -query GCF_019430945.1_ASM1943094v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg16832262-9a2d-4012-83c8-840adac5bddc/dqc_reference/reference_markers.fasta -out GCF_019430945.1_ASM1943094v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:15,116] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:15,119] [INFO] Selected 14 target genomes.
[2024-01-24 11:44:15,120] [INFO] Target genome list was writen to GCF_019430945.1_ASM1943094v1_genomic.fna/target_genomes.txt
[2024-01-24 11:44:15,125] [INFO] Task started: fastANI
[2024-01-24 11:44:15,125] [INFO] Running command: fastANI --query /var/lib/cwl/stg923beaad-ee59-4abf-8d3b-0dafe99db832/GCF_019430945.1_ASM1943094v1_genomic.fna.gz --refList GCF_019430945.1_ASM1943094v1_genomic.fna/target_genomes.txt --output GCF_019430945.1_ASM1943094v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:44:34,157] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:34,157] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg16832262-9a2d-4012-83c8-840adac5bddc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:44:34,157] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg16832262-9a2d-4012-83c8-840adac5bddc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:44:34,168] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:44:34,168] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:44:34,169] [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
Rhizobium populisoli	strain=XQZ8	GCA_019430945.1	2859785	2859785	type	True	100.0	2257	2258	95	conclusive
Neorhizobium vignae	strain=CCBAU 05176	GCA_000732195.1	690585	690585	type	True	83.4204	1326	2258	95	below_threshold
Neorhizobium galegae	strain=HAMBI 540	GCA_000731315.1	399	399	suspected-type	True	83.2849	1328	2258	95	below_threshold
Rhizobium petrolearium	strain=DSM 26482	GCA_017873175.1	515361	515361	type	True	81.8323	1215	2258	95	below_threshold
Neorhizobium alkalisoli	strain=DSM 21826	GCA_002968635.1	528178	528178	type	True	81.5788	1099	2258	95	below_threshold
Neorhizobium huautlense	strain=DSM 21817	GCA_002968575.1	67774	67774	type	True	81.2366	1064	2258	95	below_threshold
Rhizobium smilacinae	strain=PTYR-5	GCA_006335145.1	1395944	1395944	type	True	80.8482	939	2258	95	below_threshold
Rhizobium wenxiniae	strain=DSM 100734	GCA_014201355.1	1737357	1737357	type	True	80.7529	955	2258	95	below_threshold
Rhizobium wenxiniae	strain=CGMCC 1.15279	GCA_014641515.1	1737357	1737357	type	True	80.7001	952	2258	95	below_threshold
Neorhizobium lilium	strain=24NR	GCA_004053875.1	2503024	2503024	type	True	80.3243	853	2258	95	below_threshold
Rhizobium viscosum	strain=DSM 7307	GCA_014873945.1	1673	1673	type	True	79.5121	825	2258	95	below_threshold
Pseudorhizobium flavum	strain=YW14	GCA_002000045.1	1335061	1335061	type	True	79.2612	666	2258	95	below_threshold
Rhizobium dioscoreae	strain=S-93	GCA_009176305.1	2653122	2653122	type	True	79.0524	713	2258	95	below_threshold
Ciceribacter ferrooxidans	strain=F8825	GCA_004137355.1	2509717	2509717	type	True	78.9685	623	2258	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:44:34,170] [INFO] DFAST Taxonomy check result was written to GCF_019430945.1_ASM1943094v1_genomic.fna/tc_result.tsv
[2024-01-24 11:44:34,170] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:44:34,171] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:44:34,171] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg16832262-9a2d-4012-83c8-840adac5bddc/dqc_reference/checkm_data
[2024-01-24 11:44:34,172] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:44:34,233] [INFO] Task started: CheckM
[2024-01-24 11:44:34,233] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019430945.1_ASM1943094v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019430945.1_ASM1943094v1_genomic.fna/checkm_input GCF_019430945.1_ASM1943094v1_genomic.fna/checkm_result
[2024-01-24 11:45:27,930] [INFO] Task succeeded: CheckM
[2024-01-24 11:45:27,931] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:45:27,949] [INFO] ===== Completeness check finished =====
[2024-01-24 11:45:27,949] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:45:27,950] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019430945.1_ASM1943094v1_genomic.fna/markers.fasta)
[2024-01-24 11:45:27,950] [INFO] Task started: Blastn
[2024-01-24 11:45:27,950] [INFO] Running command: blastn -query GCF_019430945.1_ASM1943094v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg16832262-9a2d-4012-83c8-840adac5bddc/dqc_reference/reference_markers_gtdb.fasta -out GCF_019430945.1_ASM1943094v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:45:29,824] [INFO] Task succeeded: Blastn
[2024-01-24 11:45:29,827] [INFO] Selected 16 target genomes.
[2024-01-24 11:45:29,827] [INFO] Target genome list was writen to GCF_019430945.1_ASM1943094v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:45:29,856] [INFO] Task started: fastANI
[2024-01-24 11:45:29,857] [INFO] Running command: fastANI --query /var/lib/cwl/stg923beaad-ee59-4abf-8d3b-0dafe99db832/GCF_019430945.1_ASM1943094v1_genomic.fna.gz --refList GCF_019430945.1_ASM1943094v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019430945.1_ASM1943094v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:45:50,724] [INFO] Task succeeded: fastANI
[2024-01-24 11:45:50,737] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 11:45:50,737] [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_003425685.1	s__Neorhizobium sp003425685	83.7693	1402	2258	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900471605.1	s__Neorhizobium sp900471605	83.6452	1357	2258	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	98.26	98.25	0.92	0.92	3	-
GCF_000282095.2	s__Neorhizobium sp000282095	83.5817	1361	2258	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000985895.1	s__Neorhizobium galegae_B	83.4564	1322	2258	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	98.06	98.00	0.96	0.95	4	-
GCF_000732195.1	s__Neorhizobium vignae	83.4442	1322	2258	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017877055.1	s__Neorhizobium galegae_D	83.3968	1344	2258	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000985875.1	s__Neorhizobium galegae_C	83.3651	1282	2258	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	97.95	97.84	0.92	0.90	4	-
GCA_002968845.1	s__Neorhizobium tomejilense	83.3281	1319	2258	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	97.02	95.22	0.90	0.84	9	-
GCF_002968635.1	s__Neorhizobium alkalisoli	81.5931	1096	2258	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003491345.1	s__Neorhizobium sp003491345	81.527	936	2258	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002968575.1	s__Neorhizobium huautlense	81.26	1059	2258	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	98.14	97.99	0.92	0.90	5	-
GCF_003597675.1	s__Neorhizobium sp003597675	81.0111	964	2258	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900466875.1	s__Neorhizobium sp900466875	80.9297	904	2258	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006335145.1	s__Neorhizobium smilacinae	80.855	938	2258	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900472575.1	s__Neorhizobium cellulosilyticum	80.7863	930	2258	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	97.58	97.10	0.87	0.85	7	-
GCA_002376235.1	s__Neorhizobium sp002376235	80.6398	907	2258	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:45:50,739] [INFO] GTDB search result was written to GCF_019430945.1_ASM1943094v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:45:50,739] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:45:50,743] [INFO] DFAST_QC result json was written to GCF_019430945.1_ASM1943094v1_genomic.fna/dqc_result.json
[2024-01-24 11:45:50,743] [INFO] DFAST_QC completed!
[2024-01-24 11:45:50,743] [INFO] Total running time: 0h1m57s